diff --git a/.editorconfig b/.editorconfig
new file mode 100644
index 0000000..70c7a9a
--- /dev/null
+++ b/.editorconfig
@@ -0,0 +1,12 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,cff}]
+indent_size = 2
diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
new file mode 100644
index 0000000..a4394ee
--- /dev/null
+++ b/.git-blame-ignore-revs
@@ -0,0 +1,4 @@
+# 240627, ruff format // Alfred Kedhammar
+429872dc8123126282f73c0c34ab2221fac00c90
+# 240627, ruff safe fixes // Alfred Kedhammar
+6b7e397e9a45a54f387e1764dedcd88f9b54d212
diff --git a/.github/pr_labels.yml b/.github/pr_labels.yml
index d04f24f..8db6d10 100644
--- a/.github/pr_labels.yml
+++ b/.github/pr_labels.yml
@@ -1,4 +1,4 @@
-version: '1'
+version: "1"
 invalidStatus: "pending"
 labelRule:
   values:
diff --git a/.github/workflows/lint-code.yml b/.github/workflows/lint-code.yml
new file mode 100644
index 0000000..99820ec
--- /dev/null
+++ b/.github/workflows/lint-code.yml
@@ -0,0 +1,148 @@
+name: Lint code
+on: [push, pull_request]
+
+jobs:
+  # Use ruff to check for code style violations
+  ruff-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check for style violations
+        # Configured in pyproject.toml
+        run: ruff check .
+
+  # Use ruff to check code formatting
+  ruff-format:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: ruff --> Check code formatting
+        run: ruff format --check .
+
+  # Use mypy for static type checking
+  mypy-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install mypy
+      # Start by installing type stubs
+      - name: mypy --> Install stubs
+        run: echo -e "y" | mypy --install-types . || exit 0
+      - name: mypy --> Static type checking
+        # Configured in pyprojet.toml
+        run: mypy .
+
+  # Use pipreqs to check for missing dependencies
+  pipreqs-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+
+      - name: Run pipreqs
+        run: |
+          pipreqs --savepath pipreqs.txt 2>&1 | tee pipreqs_output.log
+          if grep -q 'WARNING: Package .* does not exist or network problems' pipreqs_output.log; then
+            missing_packages=$(grep 'WARNING: Package .* does not exist or network problems' pipreqs_output.log | sed -E 's/.*Package "(.*)" does not exist.*/\1/')
+            echo "ERROR: Add unresolved packages to requirements. Missing package(s): $missing_packages. Example: '<pkg> @ git+https://github.com/<author>/<repo>.git'"
+            exit 1
+          fi
+
+      - name: Compare requirements
+        run: |
+          # Extract and sort package names
+          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | tr '[:upper:]' '[:lower:]' | sort -u > requirements.compare
+          awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | tr '[:upper:]' '[:lower:]' | sort -u > pipreqs.compare
+
+          # Compare package lists
+          if cmp -s requirements.compare pipreqs.compare
+          then
+            echo "Requirements are the same"
+
+            exit 0
+          else
+            echo "Requirements are different"
+            echo ""
+
+            echo "=== current requirements.txt ==="
+            echo ""
+            cat requirements.compare
+            echo ""
+
+            echo "=== pipreqs requirements ==="
+            echo ""
+            cat pipreqs.compare
+
+            exit 1
+          fi
+
+    # Use Prettier to check various file formats
+  prettier:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check .
+
+  # Use editorconfig to check all remaining file formats
+  editorconfig:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Setup node
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install editorconfig-checker
+        run: npm install -g editorconfig-checker
+
+      - name: editorconfig --> Lint files
+        run: editorconfig-checker $(git ls-files | grep -v '.py\|.md\|.json\|.yml\|.yaml\|.html\|.Makefile\|.rst')
diff --git a/.github/workflows/test-code.yml b/.github/workflows/test-code.yml
new file mode 100644
index 0000000..0369f7e
--- /dev/null
+++ b/.github/workflows/test-code.yml
@@ -0,0 +1,29 @@
+name: Test code
+on: [push, pull_request]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r requirements-dev.txt
+      - name: Install genologics
+        run: pip install -e .
+      - name: pytest
+        # Options are configured in pyproject.toml
+        run: pytest --cov=genologics --cov-report=xml
+      - name: CodeCov
+        uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.gitignore b/.gitignore
index 99dd0c8..02b1d54 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,3 +14,4 @@ docs/*.html
 scripts/*.csv
 scripts/*.log
 scripts/*.out
+.DS_Store
diff --git a/README.md b/README.md
index db01b71..943919d 100644
--- a/README.md
+++ b/README.md
@@ -6,8 +6,8 @@ A basic module for interacting with the Illumina Basespace Clarity LIMS server v
 its REST API. The goal is to provide simple access to the most common
 entities and their attributes in a reasonably Pythonic fashion.
 
-
 ### Compatibility
+
 From version **1.0.0** the scripts have been ported to support **Python 3**,
 and it is backwards compatible with **Python 2** as well. The previous versions
 (**<0.4.6**) are only compatible with **Python 2**.
@@ -15,7 +15,7 @@ and it is backwards compatible with **Python 2** as well. The previous versions
 ### Design
 
 All instances of Project, Sample, Artifact, etc should be obtained using
-the get_* methods of the Lims class, which keeps an internal cache of
+the get\_\* methods of the Lims class, which keeps an internal cache of
 current instances. The idea is to create one and only one instance in
 a running script for representing an item in the database. If one has
 more than one instance representing the same item, there is a danger that
@@ -78,7 +78,6 @@ NOTE: The example files rely on specific entities and configurations
 on the server, and use base URI, user name and password, so to work
 for your server, all these must be reviewed and modified.
 
-
 ### EPPs
 
 The EPPs in use at Scilifelab can be found in the subdirectory 'scripts' of the repository [scilifelab_epps](https://github.com/SciLifeLab/scilifelab_epps/).
diff --git a/docs/conf.py b/docs/conf.py
index c2b63dc..53365f4 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Genologics documentation build configuration file, created by
 # sphinx-quickstart on Tue Oct  1 11:51:30 2013.
@@ -10,207 +9,213 @@
 #
 # All configuration values have a default; values that are commented out
 # serve to show the default.
-from __future__ import unicode_literals
-import sys, os
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+# sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.coverage',
-              'sphinx.ext.pngmath', 'sphinx.ext.ifconfig',
-              'sphinx.ext.viewcode', 'sphinxcontrib.programoutput']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.imgmath",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinxcontrib.programoutput",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'Genologics'
-copyright = '2013, Per Kraulis, Johannes Alneberg'
+project = "Genologics"
+copyright = "2013, Per Kraulis, Johannes Alneberg"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.0'
+version = "1.0.0"
 # The full version, including alpha/beta/rc tags.
-release = '1.0.0'
+release = "1.0.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ["_build"]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 
 # -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+html_theme = "default"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'Genologicsdoc'
+htmlhelp_basename = "Genologicsdoc"
 
 
 # -- Options for LaTeX output --------------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'Genologics.tex', 'Genologics Documentation',
-   'Per Kraulis, Johannes Alneberg', 'manual'),
+    (
+        "index",
+        "Genologics.tex",
+        "Genologics Documentation",
+        "Per Kraulis, Johannes Alneberg",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output --------------------------------------------
@@ -218,12 +223,17 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'genologics', 'Genologics Documentation',
-     ['Per Kraulis, Johannes Alneberg'], 1)
+    (
+        "index",
+        "genologics",
+        "Genologics Documentation",
+        ["Per Kraulis, Johannes Alneberg"],
+        1,
+    )
 ]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output ------------------------------------------------
@@ -232,19 +242,25 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'Genologics', 'Genologics Documentation',
-   'Per Kraulis, Johannes Alneberg', 'Genologics', 'One line description of project.',
-   'Miscellaneous'),
+    (
+        "index",
+        "Genologics",
+        "Genologics Documentation",
+        "Per Kraulis, Johannes Alneberg",
+        "Genologics",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False
diff --git a/examples/attach_delivery_report.py b/examples/attach_delivery_report.py
index 58af9e7..9542899 100644
--- a/examples/attach_delivery_report.py
+++ b/examples/attach_delivery_report.py
@@ -7,12 +7,11 @@
 Roman Valls Guimera, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-import codecs
 from pprint import pprint
-from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims, Project
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -20,12 +19,12 @@
 
 project = Project(lims, id="P193")
 
-print('UDFs:')
+print("UDFs:")
 pprint(list(project.udf.items()))
 
-print('files:')
+print("files:")
 for file in project.files:
     print(file.content_location)
 
-project.udf['Delivery Report'] = "http://example.com/delivery_note.pdf"
+project.udf["Delivery Report"] = "http://example.com/delivery_note.pdf"
 project.put()
diff --git a/examples/epp_script.py b/examples/epp_script.py
index 7dcce16..78d8fb5 100644
--- a/examples/epp_script.py
+++ b/examples/epp_script.py
@@ -12,43 +12,45 @@
 
 Johannes Alneberg, Science for Life Laboratory, Stockholm, Sweden.
 """
+
+import sys
 from argparse import ArgumentParser
-from genologics.lims import Lims
-from genologics.entities import Process
-from genologics.config import BASEURI,USERNAME,PASSWORD
+
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.entities import Artifact, Process
 from genologics.epp import EppLogger, attach_file
-import sys
+from genologics.lims import Lims
+
 
-def main(lims,pid,file):
+def main(lims, pid, file):
     """Uploads a given file to the first output artifact of the process
 
     lims: The LIMS instance
     pid: Process Lims id
     file: File to be attached
     """
-    p=Process(lims,id=pid)
+    p = Process(lims, id=pid)
 
     # Fetch all input-output artifact pairs
     io = p.input_output_maps
 
     # Filter them so that only PerInput output artifacts remains
-    io_filtered = [x for x in io if x[1]['output-generation-type']=='PerInput']
+    io_filtered = [x for x in io if x[1]["output-generation-type"] == "PerInput"]
 
     # Fetch the first input-output artifact pair
-    (input,output) = io_filtered[0]
+    (input, output) = io_filtered[0]
 
     # Instantiate the output artifact
-    output_artifact = Artifact(output['limsid'])
+    output_artifact = Artifact(output["limsid"])
 
     # Attach the file
-    attach_file(args.file,output_artifact)
+    attach_file(args.file, output_artifact)
 
 
 if __name__ == "__main__":
     parser = ArgumentParser()
     # Arguments that are useful in all EPP scripts
-    parser.add_argument("--log",default=sys.stdout,
-                        help="Log file")
+    parser.add_argument("--log", default=sys.stdout, help="Log file")
 
     # Arguments specific for this scripts task
     parser.add_argument("--pid", help="Process id")
@@ -58,7 +60,7 @@ def main(lims,pid,file):
 
     # Log everything to log argument
     with EppLogger(args.log):
-        lims = Lims(BASEURI,USERNAME,PASSWORD)
+        lims = Lims(BASEURI, USERNAME, PASSWORD)
         lims.check_version()
 
-        main(lims,args.pid,args.file)
+        main(lims, args.pid, args.file)
diff --git a/examples/get_application.py b/examples/get_application.py
index 84462a6..57adf26 100644
--- a/examples/get_application.py
+++ b/examples/get_application.py
@@ -7,12 +7,11 @@
 Roman Valls Guimera, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-import codecs
 from pprint import pprint
-from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims, Project
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -20,7 +19,7 @@
 
 project = Project(lims, id="P193")
 
-print('UDFs:')
+print("UDFs:")
 pprint(list(project.udf.items()))
 
-print(project.udf['Application'])
+print(project.udf["Application"])
diff --git a/examples/get_artifacts.py b/examples/get_artifacts.py
index 0577a9c..97c4d5d 100644
--- a/examples/get_artifacts.py
+++ b/examples/get_artifacts.py
@@ -7,12 +7,9 @@
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-import codecs
-
-from genologics.lims import Lims
-
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -33,17 +30,17 @@
 ## artifacts = lims.get_artifacts(working_flag=True)
 ## print len(artifacts), 'Working-flag True artifacts'
 
-name = 'jgr33'
+name = "jgr33"
 artifacts = lims.get_artifacts(sample_name=name)
-print(len(artifacts), 'artifacts for sample name', name)
+print(len(artifacts), "artifacts for sample name", name)
 
 artifacts = lims.get_batch(artifacts)
 for artifact in artifacts:
     print(artifact, artifact.name, artifact.state)
 
 print()
-artifacts = lims.get_artifacts(qc_flag='PASSED')
-print(len(artifacts), 'QC PASSED artifacts')
+artifacts = lims.get_artifacts(qc_flag="PASSED")
+print(len(artifacts), "QC PASSED artifacts")
 artifacts = lims.get_batch(artifacts)
 for artifact in artifacts:
     print(artifact, artifact.name, artifact.state)
diff --git a/examples/get_containers.py b/examples/get_containers.py
index 6447bcd..d4af08a 100644
--- a/examples/get_containers.py
+++ b/examples/get_containers.py
@@ -7,12 +7,9 @@
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-import codecs
-
-from genologics.lims import *
-
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -26,7 +23,7 @@
 ##     containers = lims.get_containers(state=state)
 ##     print len(containers), state, 'containers'
 
-containers = lims.get_containers(type='96 well plate')
+containers = lims.get_containers(type="96 well plate")
 print(len(containers))
 
 container = containers[2]
@@ -37,18 +34,22 @@
     print(location, artifact.name, id(artifact), repr(artifact), artifact.root)
 
 containertype = container.type
-print(containertype, containertype.name, containertype.x_dimension, containertype.y_dimension)
-
+print(
+    containertype,
+    containertype.name,
+    containertype.x_dimension,
+    containertype.y_dimension,
+)
 
 
-containers = lims.get_containers(type='Illumina Flow Cell',state='Populated')
+containers = lims.get_containers(type="Illumina Flow Cell", state="Populated")
 for container in containers:
-	print(container.name)
-	print(container.id)
-	print(list(container.placements.keys()))
-	arts=lims.get_artifacts(containername=container.name)
-	for art in arts:
-		print(art.name)
-		print(art.type)
-		print(list(art.udf.items()))
-		print(art.parent_process.type.name)
+    print(container.name)
+    print(container.id)
+    print(list(container.placements.keys()))
+    arts = lims.get_artifacts(containername=container.name)
+    for art in arts:
+        print(art.name)
+        print(art.type)
+        print(list(art.udf.items()))
+        print(art.parent_process.type.name)
diff --git a/examples/get_labs.py b/examples/get_labs.py
index 0b63e08..fc690b3 100644
--- a/examples/get_labs.py
+++ b/examples/get_labs.py
@@ -6,29 +6,28 @@
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
-from __future__ import unicode_literals
-from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lab, Lims
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
 lims.check_version()
 
 # Get the list of all projects.
-labs = lims.get_labs(name='SciLifeLab')
-print(len(labs), 'labs in total')
+labs = lims.get_labs(name="SciLifeLab")
+print(len(labs), "labs in total")
 for lab in labs:
     print(lab, id(lab), lab.name, lab.uri, lab.id)
     print(list(lab.shipping_address.items()))
     for key, value in lab.udf.items():
-        print(' ', key, '=', value)
+        print(" ", key, "=", value)
     udt = lab.udt
     if udt:
-        print('UDT:', udt.udt)
+        print("UDT:", udt.udt)
         for key, value in udt.items():
-            print(' ', key, '=', value)
+            print(" ", key, "=", value)
 
-lab = Lab(lims, id='2')
+lab = Lab(lims, id="2")
 print(lab, id(lab), lab.name, lab.uri, lab.id)
diff --git a/examples/get_processes.py b/examples/get_processes.py
index 0bd0cf0..6aacb27 100644
--- a/examples/get_processes.py
+++ b/examples/get_processes.py
@@ -7,10 +7,9 @@
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-from genologics.lims import *
-
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims, Process
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -18,12 +17,12 @@
 
 # Get the list of all processes.
 processes = lims.get_processes()
-print(len(processes), 'processes in total')
+print(len(processes), "processes in total")
 
-process = Process(lims, id='QCF-PJK-120703-24-1140')
+process = Process(lims, id="QCF-PJK-120703-24-1140")
 print(process, process.id, process.type, process.type.name)
 for input, output in process.input_output_maps:
     if input:
-        print('input:', list(input.items()))
+        print("input:", list(input.items()))
     if output:
-        print('output:', list(output.items()))
+        print("output:", list(output.items()))
diff --git a/examples/get_projects.py b/examples/get_projects.py
index ab78d91..41e4bb7 100644
--- a/examples/get_projects.py
+++ b/examples/get_projects.py
@@ -7,12 +7,9 @@
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-from __future__ import unicode_literals
-
-from genologics.lims import *
-
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims, Project
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -20,27 +17,27 @@
 
 # Get the list of all projects.
 projects = lims.get_projects()
-print(len(projects), 'projects in total')
+print(len(projects), "projects in total")
 
 # Get the list of all projects opened since May 30th 2012.
-day = '2012-05-30'
+day = "2012-05-30"
 projects = lims.get_projects(open_date=day)
-print(len(projects), 'projects opened since', day)
+print(len(projects), "projects opened since", day)
 
 # Get the project with the specified LIMS id, and print some info.
-project = Project(lims, id='P193')
+project = Project(lims, id="P193")
 print(project, project.name, project.open_date, project.close_date)
 
-print('    UDFs:')
+print("    UDFs:")
 for key, value in project.udf.items():
-    print(' ', key, '=', value)
+    print(" ", key, "=", value)
 
 udt = project.udt
-print('    UDT:', udt.udt)
+print("    UDT:", udt.udt)
 for key, value in udt.items():
-    print(' ', key, '=', value)
+    print(" ", key, "=", value)
 
-print('    files:')
+print("    files:")
 for file in project.files:
     print(file.id)
     print(file.content_location)
diff --git a/examples/get_samples.py b/examples/get_samples.py
index 7006bd6..279c376 100644
--- a/examples/get_samples.py
+++ b/examples/get_samples.py
@@ -7,11 +7,9 @@
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-from genologics.lims import *
-
 # Login parameters for connecting to a LIMS instance.
-
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims, Project, Sample
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -19,35 +17,35 @@
 
 # Get the list of all samples.
 samples = lims.get_samples()
-print(len(samples), 'samples in total')
+print(len(samples), "samples in total")
 
 # Get the list of samples in the project with the LIMS id KLL60.
-project = Project(lims, id='KRA61')
+project = Project(lims, id="KRA61")
 samples = lims.get_samples(projectlimsid=project.id)
-print(len(samples), 'samples in', project)
+print(len(samples), "samples in", project)
 
 print()
 # Get the sample with the LIMS id KRA61A1
-sample = Sample(lims, id='KRA61A1')
-print(sample.id, sample.name, sample.date_received, sample.uri, end=' ')
+sample = Sample(lims, id="KRA61A1")
+print(sample.id, sample.name, sample.date_received, sample.uri, end=" ")
 for key, value in sample.udf.items():
-    print(' ', key, '=', value)
+    print(" ", key, "=", value)
 for note in sample.notes:
-    print('Note', note.uri, note.content)
+    print("Note", note.uri, note.content)
 for file in sample.files:
-    print('File', file.content_location)
+    print("File", file.content_location)
 
 # Get the sample with the name 'spruce_a'.
 # Check that it is the sample as the previously obtained sample;
 # not just equal, but exactly the same instance, courtesy of the Lims cache.
-samples = lims.get_samples(name='spruce_a')
+samples = lims.get_samples(name="spruce_a")
 print(samples[0].name, samples[0] is sample)
 
 ## # Get the samples having a UDF Color with values Blue or Orange.
-samples = lims.get_samples(udf={'Color': ['Blue', 'Orange']})
+samples = lims.get_samples(udf={"Color": ["Blue", "Orange"]})
 print(len(samples))
 for sample in samples:
-    print(sample, sample.name, sample.udf['Color'])
+    print(sample, sample.name, sample.udf["Color"])
 
 sample = samples[0]
 
@@ -58,5 +56,5 @@
 
 print()
 # Print the artifact of the sample.
-artifact = sample.artifact
+artifact = sample.artifact  # type: ignore
 print(artifact, artifact.state, artifact.type, artifact.qc_flag)
diff --git a/examples/get_samples2.py b/examples/get_samples2.py
index 6748778..aa30f5f 100644
--- a/examples/get_samples2.py
+++ b/examples/get_samples2.py
@@ -7,21 +7,21 @@
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-from genologics.lims import *
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims, Project
 
-from genologics.config import BASEURI, USERNAME, PASSWORD
 lims = Lims(BASEURI, USERNAME, PASSWORD)
 lims.check_version()
 
-project = Project(lims, id='KRA61')
+project = Project(lims, id="KRA61")
 samples = lims.get_samples(projectlimsid=project.id)
-print(len(samples), 'samples in', project)
+print(len(samples), "samples in", project)
 
 for sample in samples:
     print(sample, sample.name, sample.date_received, sample.artifact)
 
-name = 'spruce_a'
+name = "spruce_a"
 artifacts = lims.get_artifacts(sample_name=name)
-print(len(artifacts), 'artifacts for sample', name)
+print(len(artifacts), "artifacts for sample", name)
 for artifact in artifacts:
     print(artifact, artifact.name, artifact.qc_flag)
diff --git a/examples/set_project_queued.py b/examples/set_project_queued.py
index d9a74a6..f368c93 100644
--- a/examples/set_project_queued.py
+++ b/examples/set_project_queued.py
@@ -9,22 +9,21 @@
 
 import datetime
 
-from genologics.lims import *
-
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims, Project
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
 lims.check_version()
 
 # Get the project with the LIMS id KLL60, and print some info.
-project = Project(lims, id='KLL60')
+project = Project(lims, id="KLL60")
 print(project, project.name, project.open_date)
 print(list(project.udf.items()))
 
-d = datetime.date(2012,1,2)
+d = datetime.date(2012, 1, 2)
 print(d)
 
-project.udf['Queued'] = d
+project.udf["Queued"] = d
 project.put()
diff --git a/examples/set_sample_name.py b/examples/set_sample_name.py
index 945c583..7073aa3 100644
--- a/examples/set_sample_name.py
+++ b/examples/set_sample_name.py
@@ -7,25 +7,24 @@
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
-from genologics.lims import *
-
 # Login parameters for connecting to a LIMS instance.
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Lims, Sample
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
 lims.check_version()
 
 # Get the sample with the given LIMS identifier, and output its current name.
-sample = Sample(lims, id='JGR58A21')
+sample = Sample(lims, id="JGR58A21")
 print(sample, sample.name)
 
-sample.name = 'Joels extra-proper sample-20'
+sample.name = "Joels extra-proper sample-20"
 
 # Set the value of one of the UDFs
-sample.udf['Emmas field 2'] = 5
+sample.udf["Emmas field 2"] = 5
 for key, value in sample.udf.items():
-    print(' ', key, '=', value)
+    print(" ", key, "=", value)
 
 sample.put()
-print('Updated sample', sample)
+print("Updated sample", sample)
diff --git a/genologics/__init__.py b/genologics/__init__.py
index 93b6e40..37fd7e4 100644
--- a/genologics/__init__.py
+++ b/genologics/__init__.py
@@ -1,2 +1,3 @@
 from . import version
+
 __version__ = version.__version__
diff --git a/genologics/config.py b/genologics/config.py
index d510105..d77f096 100644
--- a/genologics/config.py
+++ b/genologics/config.py
@@ -1,48 +1,53 @@
 import os
 from configparser import ConfigParser
 
-
-
-'''
+"""
 Usage:
 from genologics.config import BASEURI, USERNAME, PASSWORD
 
-Alternate Usage: 
+Alternate Usage:
 from genologics import config
-BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG = config.load_config(specified_config = <path to config file>) 
-'''
+BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG = config.load_config(specified_config = <path to config file>)
+"""
 
 spec_config = None
 
+
 def get_config_info(config_file):
     config = ConfigParser()
     config.read_file(open(config_file))
-    
-    
-    BASEURI = config.get('genologics', 'BASEURI').rstrip()
-    USERNAME = config.get('genologics', 'USERNAME').rstrip()
-    PASSWORD = config.get('genologics', 'PASSWORD').rstrip()
-    
-    if config.has_section('genologics') and config.has_option('genologics','VERSION'):
-        VERSION = config.get('genologics', 'VERSION').rstrip()
+
+    BASEURI = config.get("genologics", "BASEURI").rstrip()
+    USERNAME = config.get("genologics", "USERNAME").rstrip()
+    PASSWORD = config.get("genologics", "PASSWORD").rstrip()
+
+    if config.has_section("genologics") and config.has_option("genologics", "VERSION"):
+        VERSION = config.get("genologics", "VERSION").rstrip()
     else:
-        VERSION = 'v2'
-        
-    if config.has_section('logging') and config.has_option('logging','MAIN_LOG'):
-        MAIN_LOG = config.get('logging', 'MAIN_LOG').rstrip()
+        VERSION = "v2"
+
+    if config.has_section("logging") and config.has_option("logging", "MAIN_LOG"):
+        MAIN_LOG = config.get("logging", "MAIN_LOG").rstrip()
     else:
         MAIN_LOG = None
     return BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG
-        
 
-def load_config(specified_config = None):
-    if specified_config != None:
+
+def load_config(specified_config=None):
+    if specified_config is not None:
         config_file = specified_config
     else:
         config = ConfigParser()
         try:
-            conf_file = config.read([os.path.expanduser('~/.genologicsrc'), '.genologicsrc',
-                        'genologics.conf', 'genologics.cfg', '/etc/genologics.conf'])
+            conf_file = config.read(
+                [
+                    os.path.expanduser("~/.genologicsrc"),
+                    ".genologicsrc",
+                    "genologics.conf",
+                    "genologics.cfg",
+                    "/etc/genologics.conf",
+                ]
+            )
 
             # First config file found wins
             config_file = conf_file[0]
@@ -52,7 +57,9 @@ def load_config(specified_config = None):
 
     BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG = get_config_info(config_file)
 
-    return BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG   
-    
+    return BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG
+
 
-BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG = load_config(specified_config = spec_config)
+BASEURI, USERNAME, PASSWORD, VERSION, MAIN_LOG = load_config(
+    specified_config=spec_config
+)
diff --git a/genologics/constants.py b/genologics/constants.py
index 42f9bb4..9541aba 100644
--- a/genologics/constants.py
+++ b/genologics/constants.py
@@ -10,46 +10,46 @@
 from xml.etree import ElementTree
 
 _NSMAP = dict(
-        art='http://genologics.com/ri/artifact',
-        artgr='http://genologics.com/ri/artifactgroup',
-        cnf='http://genologics.com/ri/configuration',
-        con='http://genologics.com/ri/container',
-        ctp='http://genologics.com/ri/containertype',
-        exc='http://genologics.com/ri/exception',
-        file='http://genologics.com/ri/file',
-        inst='http://genologics.com/ri/instrument',
-        lab='http://genologics.com/ri/lab',
-        prc='http://genologics.com/ri/process',
-        prj='http://genologics.com/ri/project',
-        prop='http://genologics.com/ri/property',
-        protcnf='http://genologics.com/ri/protocolconfiguration',
-        protstepcnf='http://genologics.com/ri/stepconfiguration',
-        prx='http://genologics.com/ri/processexecution',
-        ptm='http://genologics.com/ri/processtemplate',
-        ptp='http://genologics.com/ri/processtype',
-        res='http://genologics.com/ri/researcher',
-        ri='http://genologics.com/ri',
-        rt='http://genologics.com/ri/routing',
-        rtp='http://genologics.com/ri/reagenttype',
-        kit='http://genologics.com/ri/reagentkit',
-        lot='http://genologics.com/ri/reagentlot',
-        smp='http://genologics.com/ri/sample',
-        stg='http://genologics.com/ri/stage',
-        stp='http://genologics.com/ri/step',
-        udf='http://genologics.com/ri/userdefined',
-        ver='http://genologics.com/ri/version',
-        wkfcnf='http://genologics.com/ri/workflowconfiguration'
+    art="http://genologics.com/ri/artifact",
+    artgr="http://genologics.com/ri/artifactgroup",
+    cnf="http://genologics.com/ri/configuration",
+    con="http://genologics.com/ri/container",
+    ctp="http://genologics.com/ri/containertype",
+    exc="http://genologics.com/ri/exception",
+    file="http://genologics.com/ri/file",
+    inst="http://genologics.com/ri/instrument",
+    lab="http://genologics.com/ri/lab",
+    prc="http://genologics.com/ri/process",
+    prj="http://genologics.com/ri/project",
+    prop="http://genologics.com/ri/property",
+    protcnf="http://genologics.com/ri/protocolconfiguration",
+    protstepcnf="http://genologics.com/ri/stepconfiguration",
+    prx="http://genologics.com/ri/processexecution",
+    ptm="http://genologics.com/ri/processtemplate",
+    ptp="http://genologics.com/ri/processtype",
+    res="http://genologics.com/ri/researcher",
+    ri="http://genologics.com/ri",
+    rt="http://genologics.com/ri/routing",
+    rtp="http://genologics.com/ri/reagenttype",
+    kit="http://genologics.com/ri/reagentkit",
+    lot="http://genologics.com/ri/reagentlot",
+    smp="http://genologics.com/ri/sample",
+    stg="http://genologics.com/ri/stage",
+    stp="http://genologics.com/ri/step",
+    udf="http://genologics.com/ri/userdefined",
+    ver="http://genologics.com/ri/version",
+    wkfcnf="http://genologics.com/ri/workflowconfiguration",
 )
 
 for prefix, uri in _NSMAP.items():
-    ElementTree._namespace_map[uri] = prefix
+    ElementTree.register_namespace(prefix, uri)
 
-_NSPATTERN = re.compile(r'(\{)(.+?)(\})')
+_NSPATTERN = re.compile(r"(\{)(.+?)(\})")
 
 
 def nsmap(tag):
     "Convert from normal XML-ish namespace tag to ElementTree variant."
-    parts = tag.split(':')
+    parts = tag.split(":")
     if len(parts) != 2:
         raise ValueError("no namespace specifier in tag")
-    return "{%s}%s" % (_NSMAP[parts[0]], parts[1])
+    return f"{{{_NSMAP[parts[0]]}}}{parts[1]}"
diff --git a/genologics/descriptors.py b/genologics/descriptors.py
index 57b4b67..64ca242 100644
--- a/genologics/descriptors.py
+++ b/genologics/descriptors.py
@@ -5,25 +5,21 @@
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 Copyright (C) 2012 Per Kraulis
 """
-import six
-from genologics.constants import nsmap
 
-try:
-    from urllib.parse import urlsplit, urlparse, parse_qs, urlunparse
-except ImportError:
-    from urlparse import urlsplit, urlparse, parse_qs, urlunparse
-
-from decimal import Decimal
 import datetime
+import logging
 import time
+from decimal import Decimal
 from xml.etree import ElementTree
 
-import logging
+import six
+
+from genologics.constants import nsmap
 
 logger = logging.getLogger(__name__)
 
 
-class BaseDescriptor(object):
+class BaseDescriptor:
     "Abstract base descriptor for an instance attribute."
 
     def __get__(self, instance, cls):
@@ -116,7 +112,7 @@ class IntegerDescriptor(StringDescriptor):
     """
 
     def __get__(self, instance, cls):
-        text = super(IntegerDescriptor, self).__get__(instance, cls)
+        text = super().__get__(instance, cls)
         if text is not None:
             return int(text)
 
@@ -137,15 +133,15 @@ class BooleanDescriptor(StringDescriptor):
     """
 
     def __get__(self, instance, cls):
-        text = super(BooleanDescriptor, self).__get__(instance, cls)
+        text = super().__get__(instance, cls)
         if text is not None:
-            return text.lower() == 'true'
+            return text.lower() == "true"
 
     def __set__(self, instance, value):
-        super(BooleanDescriptor, self).__set__(instance, str(value).lower())
+        super().__set__(instance, str(value).lower())
 
 
-class UdfDictionary(object):
+class UdfDictionary:
     "Dictionary-like container of UDFs, optionally within a UDT."
 
     def _is_string(self, value):
@@ -153,7 +149,7 @@ def _is_string(self, value):
 
     def __init__(self, instance, *args, **kwargs):
         self.instance = instance
-        self._udt = kwargs.pop('udt', False)
+        self._udt = kwargs.pop("udt", False)
         self.rootkeys = args
         self._rootnode = None
         self._update_elems()
@@ -169,7 +165,7 @@ def rootnode(self):
         return self._rootnode
 
     def get_udt(self):
-        if self._udt == True:
+        if self._udt is True:
             return None
         else:
             return self._udt
@@ -177,23 +173,23 @@ def get_udt(self):
     def set_udt(self, name):
         assert isinstance(name, str)
         if not self._udt:
-            raise AttributeError('cannot set name for a UDF dictionary')
+            raise AttributeError("cannot set name for a UDF dictionary")
         self._udt = name
-        elem = self.rootnode.find(nsmap('udf:type'))
+        elem = self.rootnode.find(nsmap("udf:type"))
         assert elem is not None
-        elem.set('name', name)
+        elem.set("name", name)
 
     udt = property(get_udt, set_udt)
 
     def _update_elems(self):
         self._elems = []
         if self._udt:
-            elem = self.rootnode.find(nsmap('udf:type'))
+            elem = self.rootnode.find(nsmap("udf:type"))
             if elem is not None:
-                self._udt = elem.attrib['name']
-                self._elems = elem.findall(nsmap('udf:field'))
+                self._udt = elem.attrib["name"]
+                self._elems = elem.findall(nsmap("udf:field"))
         else:
-            tag = nsmap('udf:field')
+            tag = nsmap("udf:field")
             for elem in list(self.rootnode):
                 if elem.tag == tag:
                     self._elems.append(elem)
@@ -201,20 +197,20 @@ def _update_elems(self):
     def _prepare_lookup(self):
         self._lookup = dict()
         for elem in self._elems:
-            type = elem.attrib['type'].lower()
+            type = elem.attrib["type"].lower()
             value = elem.text
             if not value:
                 value = None
-            elif type == 'numeric':
+            elif type == "numeric":
                 try:
                     value = int(value)
                 except ValueError:
                     value = float(value)
-            elif type == 'boolean':
-                value = value == 'true'
-            elif type == 'date':
+            elif type == "boolean":
+                value = value == "true"
+            elif type == "date":
                 value = datetime.date(*time.strptime(value, "%Y-%m-%d")[:3])
-            self._lookup[elem.attrib['name']] = value
+            self._lookup[elem.attrib["name"]] = value
 
     def __contains__(self, key):
         try:
@@ -229,81 +225,82 @@ def __getitem__(self, key):
     def __setitem__(self, key, value):
         self._lookup[key] = value
         for node in self._elems:
-            if node.attrib['name'] != key: continue
-            vtype = node.attrib['type'].lower()
+            if node.attrib["name"] != key:
+                continue
+            vtype = node.attrib["type"].lower()
 
             if value is None:
-                value=''
-            elif vtype == 'string':
+                value = ""
+            elif vtype == "string":
                 if not self._is_string(value):
-                    raise TypeError('String UDF requires str or unicode value')
-            elif vtype == 'str':
+                    raise TypeError("String UDF requires str or unicode value")
+            elif vtype == "str":
                 if not self._is_string(value):
-                    raise TypeError('String UDF requires str or unicode value')
-            elif vtype == 'text':
+                    raise TypeError("String UDF requires str or unicode value")
+            elif vtype == "text":
                 if not self._is_string(value):
-                    raise TypeError('Text UDF requires str or unicode value')
-            elif vtype == 'numeric':
-                if not isinstance(value, (int, float, Decimal)) and value != '':
-                    raise TypeError('Numeric UDF requires int or float value')
+                    raise TypeError("Text UDF requires str or unicode value")
+            elif vtype == "numeric":
+                if not isinstance(value, (int, float, Decimal)) and value != "":
+                    raise TypeError("Numeric UDF requires int or float value")
                 else:
                     value = str(value)
-            elif vtype == 'boolean':
+            elif vtype == "boolean":
                 if not isinstance(value, bool):
-                    raise TypeError('Boolean UDF requires bool value')
-                value = value and 'true' or 'false'
-            elif vtype == 'date':
+                    raise TypeError("Boolean UDF requires bool value")
+                value = value and "true" or "false"
+            elif vtype == "date":
                 if not isinstance(value, datetime.date):  # Too restrictive?
-                    raise TypeError('Date UDF requires datetime.date value')
+                    raise TypeError("Date UDF requires datetime.date value")
                 value = str(value)
-            elif vtype == 'uri':
+            elif vtype == "uri":
                 if not self._is_string(value):
-                    raise TypeError('URI UDF requires str or punycode (unicode) value')
+                    raise TypeError("URI UDF requires str or punycode (unicode) value")
                 value = str(value)
             else:
-                raise NotImplemented("UDF type '%s'" % vtype)
+                raise NotImplementedError(f"UDF type '{vtype}'")
             if not isinstance(value, str):
                 if not self._is_string(value):
-                    value = str(value).encode('UTF-8')
+                    value = str(value).encode("UTF-8")
             node.text = value
             break
         else:  # Create new entry; heuristics for type
             if self._is_string(value):
-                vtype = '\n' in value and 'Text' or 'String'
+                vtype = "\n" in value and "Text" or "String"
             elif isinstance(value, bool):
-                vtype = 'Boolean'
-                value = value and 'true' or 'false'
+                vtype = "Boolean"
+                value = value and "true" or "false"
             elif isinstance(value, (int, float, Decimal)):
-                vtype = 'Numeric'
+                vtype = "Numeric"
                 value = str(value)
             elif isinstance(value, datetime.date):
-                vtype = 'Date'
+                vtype = "Date"
                 value = str(value)
             else:
-                raise NotImplementedError("Cannot handle value of type '%s'"
-                                          " for UDF" % type(value))
+                raise NotImplementedError(
+                    f"Cannot handle value of type '{type(value)}'" " for UDF"
+                )
             if self._udt:
-                root = self.rootnode.find(nsmap('udf:type'))
+                root = self.rootnode.find(nsmap("udf:type"))
             else:
                 root = self.rootnode
-            elem = ElementTree.SubElement(root,
-                                          nsmap('udf:field'),
-                                          type=vtype,
-                                          name=key)
+            elem = ElementTree.SubElement(
+                root, nsmap("udf:field"), type=vtype, name=key
+            )
             if not isinstance(value, str):
                 if not self._is_string(value):
-                    value = str(value).encode('UTF-8')
+                    value = str(value).encode("UTF-8")
 
             elem.text = value
 
-            #update the internal elements and lookup with new values
+            # update the internal elements and lookup with new values
             self._update_elems()
             self._prepare_lookup()
 
     def __delitem__(self, key):
         del self._lookup[key]
         for node in self._elems:
-            if node.attrib['name'] == key:
+            if node.attrib["name"] == key:
                 self.rootnode.remove(node)
                 break
 
@@ -336,6 +333,7 @@ class UdfDictionaryDescriptor(BaseDescriptor):
     """An instance attribute containing a dictionary of UDF values
     represented by multiple XML elements.
     """
+
     _UDT = False
 
     def __init__(self, *args):
@@ -370,11 +368,12 @@ class PlacementDictionaryDescriptor(TagDescriptor):
 
     def __get__(self, instance, cls):
         from genologics.entities import Artifact
+
         instance.get()
         self.value = dict()
         for node in instance.root.findall(self.tag):
-            key = node.find('value').text
-            self.value[key] = Artifact(instance.lims, uri=node.attrib['uri'])
+            key = node.find("value").text
+            self.value[key] = Artifact(instance.lims, uri=node.attrib["uri"])
         return self.value
 
 
@@ -386,8 +385,8 @@ class ExternalidListDescriptor(BaseDescriptor):
     def __get__(self, instance, cls):
         instance.get()
         result = []
-        for node in instance.root.findall(nsmap('ri:externalid')):
-            result.append((node.attrib.get('id'), node.attrib.get('uri')))
+        for node in instance.root.findall(nsmap("ri:externalid")):
+            result.append((node.attrib.get("id"), node.attrib.get("uri")))
         return result
 
 
@@ -395,7 +394,7 @@ class EntityDescriptor(TagDescriptor):
     "An instance attribute referencing another entity instance."
 
     def __init__(self, tag, klass):
-        super(EntityDescriptor, self).__init__(tag)
+        super().__init__(tag)
         self.klass = klass
 
     def __get__(self, instance, cls):
@@ -404,7 +403,7 @@ def __get__(self, instance, cls):
         if node is None:
             return None
         else:
-            return self.klass(instance.lims, uri=node.attrib['uri'])
+            return self.klass(instance.lims, uri=node.attrib["uri"])
 
     def __set__(self, instance, value):
         instance.get()
@@ -413,9 +412,9 @@ def __set__(self, instance, value):
             # create the new tag
             node = ElementTree.Element(self.tag)
             instance.root.append(node)
-        node.attrib['uri'] = value.uri
-        if value._TAG in ['project', 'sample', 'artifact', 'container']:
-            node.attrib['limsid'] = value.id
+        node.attrib["uri"] = value.uri
+        if value._TAG in ["project", "sample", "artifact", "container"]:
+            node.attrib["limsid"] = value.id
 
 
 class EntityListDescriptor(EntityDescriptor):
@@ -427,13 +426,14 @@ def __get__(self, instance, cls):
         instance.get()
         result = []
         for node in instance.root.findall(self.tag):
-            result.append(self.klass(instance.lims, uri=node.attrib['uri']))
+            result.append(self.klass(instance.lims, uri=node.attrib["uri"]))
 
         return result
 
+
 class NestedBooleanDescriptor(TagDescriptor):
     def __init__(self, tag, *args):
-        super(NestedBooleanDescriptor, self).__init__(tag)
+        super().__init__(tag)
         self.rootkeys = args
 
     def __get__(self, instance, cls):
@@ -442,7 +442,7 @@ def __get__(self, instance, cls):
         rootnode = instance.root
         for rootkey in self.rootkeys:
             rootnode = rootnode.find(rootkey)
-        result = rootnode.find(self.tag).text.lower() == 'true'
+        result = rootnode.find(self.tag).text.lower() == "true"
         return result
 
     def __set__(self, instance, value):
@@ -451,9 +451,10 @@ def __set__(self, instance, value):
             rootnode = rootnode.find(rootkey)
         rootnode.find(self.tag).text = str(value).lower()
 
+
 class NestedStringDescriptor(TagDescriptor):
     def __init__(self, tag, *args):
-        super(NestedStringDescriptor, self).__init__(tag)
+        super().__init__(tag)
         self.rootkeys = args
 
     def __get__(self, instance, cls):
@@ -471,9 +472,10 @@ def __set__(self, instance, value):
             rootnode = rootnode.find(rootkey)
         rootnode.find(self.tag).text = value
 
+
 class NestedAttributeListDescriptor(StringAttributeDescriptor):
     """An instance yielding a list of dictionnaries of attributes
-       for a nested xml list of XML elements"""
+    for a nested xml list of XML elements"""
 
     def __init__(self, tag, *args):
         super(StringAttributeDescriptor, self).__init__(tag)
@@ -493,7 +495,7 @@ def __get__(self, instance, cls):
 
 class NestedStringListDescriptor(StringListDescriptor):
     """An instance yielding a list of strings
-        for a nested list of xml elements"""
+    for a nested list of xml elements"""
 
     def __init__(self, tag, *args):
         super(StringListDescriptor, self).__init__(tag)
@@ -527,10 +529,11 @@ def __get__(self, instance, cls):
         for rootkey in self.rootkeys:
             rootnode = rootnode.find(rootkey)
         for node in rootnode.findall(self.tag):
-            result.append(self.klass(instance.lims, uri=node.attrib['uri']))
+            result.append(self.klass(instance.lims, uri=node.attrib["uri"]))
 
         return result
 
+
 class MultiPageNestedEntityListDescriptor(EntityListDescriptor):
     """same as NestedEntityListDescriptor, but works on multiple pages, for Queues"""
 
@@ -547,15 +550,16 @@ def __get__(self, instance, cls):
         for rootkey in self.rootkeys:
             rootnode = rootnode.find(rootkey)
         for node in rootnode.findall(self.tag):
-            result.append(self.klass(instance.lims, uri=node.attrib['uri']))
+            result.append(self.klass(instance.lims, uri=node.attrib["uri"]))
 
-        if instance.root.find('next-page') is not None:
-            next_queue_page = instance.__class__(instance.lims, uri=instance.root.find('next-page').attrib.get('uri'))
+        if instance.root.find("next-page") is not None:
+            next_queue_page = instance.__class__(
+                instance.lims, uri=instance.root.find("next-page").attrib.get("uri")
+            )
             result.extend(next_queue_page.artifacts)
         return result
 
 
-
 class DimensionDescriptor(TagDescriptor):
     """An instance attribute containing a dictionary specifying
     the properties of a dimension of a container type.
@@ -564,10 +568,11 @@ class DimensionDescriptor(TagDescriptor):
     def __get__(self, instance, cls):
         instance.get()
         node = instance.root.find(self.tag)
-        return dict(is_alpha=node.find('is-alpha').text.lower() == 'true',
-                    offset=int(node.find('offset').text),
-                    size=int(node.find('size').text)
-                    )
+        return dict(
+            is_alpha=node.find("is-alpha").text.lower() == "true",
+            offset=int(node.find("offset").text),
+            size=int(node.find("size").text),
+        )
 
 
 class LocationDescriptor(TagDescriptor):
@@ -577,12 +582,13 @@ class LocationDescriptor(TagDescriptor):
 
     def __get__(self, instance, cls):
         from genologics.entities import Container
+
         instance.get()
         node = instance.root.find(self.tag)
         if node is None:
-            return (None,None)
-        uri = node.find('container').attrib['uri']
-        return Container(instance.lims, uri=uri), node.find('value').text
+            return (None, None)
+        uri = node.find("container").attrib["uri"]
+        return Container(instance.lims, uri=uri), node.find("value").text
 
 
 class ReagentLabelList(BaseDescriptor):
@@ -591,9 +597,9 @@ class ReagentLabelList(BaseDescriptor):
     def __get__(self, instance, cls):
         instance.get()
         self.value = []
-        for node in instance.root.findall('reagent-label'):
+        for node in instance.root.findall("reagent-label"):
             try:
-                self.value.append(node.attrib['name'])
+                self.value.append(node.attrib["name"])
             except:
                 pass
         return self.value
@@ -608,30 +614,35 @@ class OutputReagentList(BaseDescriptor):
       output_artifact_2:[reagent_label_name_3, reagent_label_name_4,...]
     }
     """
+
     def __init__(self, artifact_class):
         self.klass = artifact_class
 
     def __get__(self, instance, cls):
         instance.get()
         self.value = {}
-        for node in instance.root.iter('output'):
-            self.value[self.klass(instance.lims, uri=node.attrib['uri'])] = [subnode.attrib['name'] for subnode in node.findall('reagent-label')]
+        for node in instance.root.iter("output"):
+            self.value[self.klass(instance.lims, uri=node.attrib["uri"])] = [
+                subnode.attrib["name"] for subnode in node.findall("reagent-label")
+            ]
 
         return self.value
 
     def __set__(self, instance, value):
-        out_r = ElementTree.Element('output-reagents')
+        out_r = ElementTree.Element("output-reagents")
         for artifact in value:
-            out_a = ElementTree.SubElement(out_r, 'output', attrib={'uri':artifact.uri})
+            out_a = ElementTree.SubElement(
+                out_r, "output", attrib={"uri": artifact.uri}
+            )
             for reagent_label_name in value[artifact]:
-                rea_l = ElementTree.SubElement(out_a, 'reagent-label', attrib={'name':reagent_label_name})
+                ElementTree.SubElement(
+                    out_a, "reagent-label", attrib={"name": reagent_label_name}
+                )
 
-        instance.root.remove(instance.root.find('output-reagents'))
+        instance.root.remove(instance.root.find("output-reagents"))
         instance.root.append(out_r)
 
 
-
-
 class InputOutputMapList(BaseDescriptor):
     """An instance attribute yielding a list of tuples (input, output)
     where each item is a dictionary, representing the input/output
@@ -648,34 +659,35 @@ def __get__(self, instance, cls):
         rootnode = instance.root
         for rootkey in self.rootkeys:
             rootnode = rootnode.find(rootkey)
-        for node in rootnode.findall('input-output-map'):
-            input = self.get_dict(instance.lims, node.find('input'))
-            output = self.get_dict(instance.lims, node.find('output'))
+        for node in rootnode.findall("input-output-map"):
+            input = self.get_dict(instance.lims, node.find("input"))
+            output = self.get_dict(instance.lims, node.find("output"))
             self.value.append((input, output))
         return self.value
 
     def get_dict(self, lims, node):
         from genologics.entities import Artifact, Process
-        if node is None: return None
+
+        if node is None:
+            return None
         result = dict()
-        for key in ['limsid', 'output-type', 'output-generation-type']:
+        for key in ["limsid", "output-type", "output-generation-type"]:
             try:
                 result[key] = node.attrib[key]
             except KeyError:
                 pass
-            for uri in ['uri', 'post-process-uri']:
+            for uri in ["uri", "post-process-uri"]:
                 try:
                     result[uri] = Artifact(lims, uri=node.attrib[uri])
                 except KeyError:
                     pass
-        node = node.find('parent-process')
+        node = node.find("parent-process")
         if node is not None:
-            result['parent-process'] = Process(lims, node.attrib['uri'])
+            result["parent-process"] = Process(lims, node.attrib["uri"])
         return result
 
 
-
-class ProcessTypeParametersDescriptor(object):
+class ProcessTypeParametersDescriptor:
     def __getitem__(self, index):
         return self.params[index]
 
@@ -683,12 +695,13 @@ def __setitem__(self, index, value):
         self.params[index] = value
 
     def __delitem__(self, index):
-        del(self.params[index])
+        del self.params[index]
 
     def __init__(self, pt_instance):
         from genologics.internal_classes import ProcessTypeParameter
+
         pt_instance.get()
-        self.tag = 'parameter'
+        self.tag = "parameter"
         self.params = []
         for node in pt_instance.root.findall(self.tag):
             self.params.append(ProcessTypeParameter(pt_instance, node))
@@ -698,7 +711,6 @@ def __repr__(self):
 
 
 class ProcessTypeProcessInputDescriptor(TagDescriptor):
-
     def __getitem__(self, index):
         return self._inputs[index]
 
@@ -706,16 +718,17 @@ def __setitem__(self, index, value):
         self._inputs[index] = value
 
     def __delitem__(self, index):
-        del(self._inputs[index])
+        del self._inputs[index]
 
     def __init__(self):
-        self._inputs=[]
-        self.tag = 'process-input'
-        super(ProcessTypeProcessInputDescriptor, self).__init__(tag=self.tag)
+        self._inputs = []
+        self.tag = "process-input"
+        super().__init__(tag=self.tag)
 
     def __get__(self, instance, owner):
         from genologics.internal_classes import ProcessTypeProcessInput
-        for node in  instance.root.findall(self.tag):
+
+        for node in instance.root.findall(self.tag):
             self._inputs.append(ProcessTypeProcessInput(instance, node))
         return self
 
@@ -724,7 +737,6 @@ def __repr__(self):
 
 
 class ProcessTypeProcessOutputDescriptor(TagDescriptor):
-
     def __getitem__(self, index):
         return self._inputs[index]
 
@@ -732,15 +744,16 @@ def __setitem__(self, index, value):
         self._inputs[index] = value
 
     def __delitem__(self, index):
-        del(self._inputs[index])
+        del self._inputs[index]
 
     def __init__(self):
-        self._inputs=[]
-        self.tag = 'process-output'
-        super(ProcessTypeProcessOutputDescriptor, self).__init__(tag=self.tag)
+        self._inputs = []
+        self.tag = "process-output"
+        super().__init__(tag=self.tag)
 
     def __get__(self, instance, owner):
         from genologics.internal_classes import ProcessTypeProcessOutput
+
         for node in instance.root.findall(self.tag):
             self._inputs.append(ProcessTypeProcessOutput(instance, node))
         return self
@@ -750,9 +763,8 @@ def __repr__(self):
 
 
 class NamedStringDescriptor(TagDescriptor):
-
     def __get__(self, instance, owner):
-        self._internals={}
+        self._internals = {}
         for node in instance.root.findall(self.tag):
-            self._internals[node.attrib['name']] = node.text
+            self._internals[node.attrib["name"]] = node.text
         return self._internals
diff --git a/genologics/entities.py b/genologics/entities.py
index 96c7fbb..8009a21 100644
--- a/genologics/entities.py
+++ b/genologics/entities.py
@@ -6,23 +6,41 @@
 Copyright (C) 2012 Per Kraulis
 """
 
-from genologics.constants import nsmap
-from genologics.descriptors import StringDescriptor, StringDictionaryDescriptor, UdfDictionaryDescriptor, \
-    UdtDictionaryDescriptor, ExternalidListDescriptor, EntityDescriptor, BooleanDescriptor, EntityListDescriptor, \
-    StringAttributeDescriptor, StringListDescriptor, DimensionDescriptor, IntegerDescriptor, \
-    PlacementDictionaryDescriptor, InputOutputMapList, LocationDescriptor, ReagentLabelList, NestedEntityListDescriptor, \
-    NestedStringListDescriptor, NestedAttributeListDescriptor, IntegerAttributeDescriptor, NestedStringDescriptor, \
-    NestedBooleanDescriptor, MultiPageNestedEntityListDescriptor, ProcessTypeParametersDescriptor, \
-    ProcessTypeProcessInputDescriptor, ProcessTypeProcessOutputDescriptor, NamedStringDescriptor, OutputReagentList
-
-try:
-    from urllib.parse import urlsplit, urlparse, parse_qs, urlunparse
-except ImportError:
-    from urlparse import urlsplit, urlparse, parse_qs, urlunparse
-
+import logging
+from urllib.parse import parse_qs, urlparse, urlsplit, urlunparse
 from xml.etree import ElementTree
 
-import logging
+from genologics.constants import nsmap
+from genologics.descriptors import (
+    BooleanDescriptor,
+    DimensionDescriptor,
+    EntityDescriptor,
+    EntityListDescriptor,
+    ExternalidListDescriptor,
+    InputOutputMapList,
+    IntegerAttributeDescriptor,
+    IntegerDescriptor,
+    LocationDescriptor,
+    MultiPageNestedEntityListDescriptor,
+    NamedStringDescriptor,
+    NestedAttributeListDescriptor,
+    NestedBooleanDescriptor,
+    NestedEntityListDescriptor,
+    NestedStringDescriptor,
+    NestedStringListDescriptor,
+    OutputReagentList,
+    PlacementDictionaryDescriptor,
+    ProcessTypeParametersDescriptor,
+    ProcessTypeProcessInputDescriptor,
+    ProcessTypeProcessOutputDescriptor,
+    ReagentLabelList,
+    StringAttributeDescriptor,
+    StringDescriptor,
+    StringDictionaryDescriptor,
+    StringListDescriptor,
+    UdfDictionaryDescriptor,
+    UdtDictionaryDescriptor,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -31,8 +49,15 @@ class SampleHistory:
     """Class handling the history generation for a given sample/artifact
     AFAIK the only fields of the history that are read are proc.type and outart"""
 
-    def __init__(self, sample_name=None, output_artifact=None, input_artifact=None, lims=None, pro_per_art=None,
-                 test=False):
+    def __init__(
+        self,
+        sample_name=None,
+        output_artifact=None,
+        input_artifact=None,
+        lims=None,
+        pro_per_art=None,
+        test=False,
+    ):
         self.processes_per_artifact = pro_per_art
         if lims:
             self.lims = lims
@@ -48,13 +73,14 @@ def __init__(self, sample_name=None, output_artifact=None, input_artifact=None,
                     self.get_analyte_hist_sorted(output_artifact, input_artifact)
         else:
             logger.error("Tried to build History without lims")
-            raise AttributeError("History cannot be computed without a valid lims object")
+            raise AttributeError(
+                "History cannot be computed without a valid lims object"
+            )
 
     def control(self):
-        """this can be used to check the content of the object.
-        """
-        logger.info("SAMPLE NAME: {}".format(self.sample_name))
-        logger.info("outart : {}".format(self.history_list[0]))
+        """this can be used to check the content of the object."""
+        logger.info(f"SAMPLE NAME: {self.sample_name}")
+        logger.info(f"outart : {self.history_list[0]}")
         # logger.info ("\nmap :")
         # for key, value in self.art_map.iteritems():
         #    logger.info(value[1]+"->"+value[0].id+"->"+key)
@@ -63,9 +89,13 @@ def control(self):
         for key, dict in self.history.items():
             logger.info(key)
             for key2, dict2 in dict.items():
-                logger.info("\t{}".format(key2))
+                logger.info(f"\t{key2}")
                 for key, value in dict2.items():
-                    logger.info("\t\t{0}->{1}".format(key, (value if value is not None else "None")))
+                    logger.info(
+                        "\t\t{}->{}".format(
+                            key, (value if value is not None else "None")
+                        )
+                    )
         logger.info("\nHistory List")
         for art in self.history_list:
             logger.info(art)
@@ -78,13 +108,18 @@ def make_sample_artifact_map(self):
         and creates an entry like this : output -> (process, input)"""
         samp_art_map = {}
         if self.sample_name:
-            artifacts = self.lims.get_artifacts(sample_name=self.sample_name, type='Analyte', resolve=False)
+            artifacts = self.lims.get_artifacts(
+                sample_name=self.sample_name, type="Analyte", resolve=False
+            )
             for one_art in artifacts:
                 input_arts = one_art.input_artifact_list()
                 for input_art in input_arts:
                     for samp in input_art.samples:
                         if samp.name == self.sample_name:
-                            samp_art_map[one_art.id] = (one_art.parent_process, input_art.id)
+                            samp_art_map[one_art.id] = (
+                                one_art.parent_process,
+                                input_art.id,
+                            )
 
         self.art_map = samp_art_map
 
@@ -95,9 +130,10 @@ def alternate_history(self, out_art, in_art=None):
         qc processes too) and puts everything in a dictionnary.
         """
         history = {}
-        hist_list = []
         # getting the list of all expected analytes.
-        artifacts = self.lims.get_artifacts(sample_name=self.sample_name, type='Analyte', resolve=False)
+        artifacts = self.lims.get_artifacts(
+            sample_name=self.sample_name, type="Analyte", resolve=False
+        )
         processes = []
         inputs = []
         if in_art:
@@ -112,12 +148,18 @@ def alternate_history(self, out_art, in_art=None):
                 valid_pcs = self.lims.get_processes(inputartifactlimsid=in_art)
 
             for tempProcess in valid_pcs:
-                history[in_art][tempProcess.id] = {'date': tempProcess.date_run,
-                                                   'id': tempProcess.id,
-                                                   'outart': (out_art if out_art in [out.id for out in tempProcess.all_outputs()] else None),
-                                                   'inart': in_art,
-                                                   'type': tempProcess.type.id,
-                                                   'name': tempProcess.type.name}
+                history[in_art][tempProcess.id] = {
+                    "date": tempProcess.date_run,
+                    "id": tempProcess.id,
+                    "outart": (
+                        out_art
+                        if out_art in [out.id for out in tempProcess.all_outputs()]
+                        else None
+                    ),
+                    "inart": in_art,
+                    "type": tempProcess.type.id,
+                    "name": tempProcess.type.name,
+                }
         else:
             starting_art = out_art
         # main iteration
@@ -142,18 +184,28 @@ def alternate_history(self, out_art, in_art=None):
                         logger.info(i.id)
                         if i in artifacts:
                             history[i.id] = {}
-                            for tempProcess in (self.processes_per_artifact[i.id] if self.processes_per_artifact else self.lims.get_processes(inputartifactlimsid=i.id)):  # If there is a loacl map, use it. else, query the lims.
-                                history[i.id][tempProcess.id] = {'date': tempProcess.date_run,
-                                                                 'id': tempProcess.id,
-                                                                 'outart': (
-                                                                 o.id if tempProcess.id == o.parent_process.id else None),
-                                                                 'inart': i.id,
-                                                                 'type': tempProcess.type.id,
-                                                                 'name': tempProcess.type.name}
+                            for tempProcess in (
+                                self.processes_per_artifact[i.id]
+                                if self.processes_per_artifact
+                                else self.lims.get_processes(inputartifactlimsid=i.id)
+                            ):  # If there is a loacl map, use it. else, query the lims.
+                                history[i.id][tempProcess.id] = {
+                                    "date": tempProcess.date_run,
+                                    "id": tempProcess.id,
+                                    "outart": (
+                                        o.id
+                                        if tempProcess.id == o.parent_process.id
+                                        else None
+                                    ),
+                                    "inart": i.id,
+                                    "type": tempProcess.type.id,
+                                    "name": tempProcess.type.name,
+                                }
 
                             logger.info("found input " + i.id)
                             inputs.append(
-                                i.id)  # this will be the sorted list of artifacts used to rebuild the history in order
+                                i.id
+                            )  # this will be the sorted list of artifacts used to rebuild the history in order
                             # while increment
                             starting_art = i.id
 
@@ -196,12 +248,16 @@ def get_analyte_hist_sorted(self, out_artifact, input_art=None):
             #     pro = In_art.parent_process.id
             # except:
             #     pro = None
-            history, out_artifact = self._add_out_art_process_conection_list(input_art, out_artifact, history)
+            history, out_artifact = self._add_out_art_process_conection_list(
+                input_art, out_artifact, history
+            )
             hist_list.append(input_art)
         while out_artifact in self.art_map:
             pro, input_art = self.art_map[out_artifact]
             hist_list.append(input_art)
-            history, out_artifact = self._add_out_art_process_conection_list(input_art, out_artifact, history)
+            history, out_artifact = self._add_out_art_process_conection_list(
+                input_art, out_artifact, history
+            )
         self.history = history
         self.history_list = hist_list
 
@@ -213,17 +269,22 @@ def _add_out_art_process_conection_list(self, input_art, out_artifact, history={
         processes that the input artifact has been involved in, but that are not
         part of the historychain get the outart set to None. This is very important."""
         # Use the local process map if we have one, else, query the lims
-        for process in self.processes_per_artifact[input_art] if self.processes_per_artifact else lims.get_processes(
-                inputartifactlimsid=input_art):
+        for process in (
+            self.processes_per_artifact[input_art]
+            if self.processes_per_artifact
+            else self.lims.get_processes(inputartifactlimsid=input_art)
+        ):
             # outputs = map(lambda a: (a.id), process.all_outputs())
             outputs = [a.id for a in process.all_outputs()]
             outart = out_artifact if out_artifact in outputs else None
-            step_info = {'date': process.date_run,
-                         'id': process.id,
-                         'outart': outart,
-                         'inart': input_art,
-                         'type': process.type.id,
-                         'name': process.type.name}
+            step_info = {
+                "date": process.date_run,
+                "id": process.id,
+                "outart": outart,
+                "inart": input_art,
+                "type": process.type.id,
+                "name": process.type.name,
+            }
             if input_art in history:
                 history[input_art][process.id] = step_info
             else:
@@ -231,12 +292,12 @@ def _add_out_art_process_conection_list(self, input_art, out_artifact, history={
         return history, input_art
 
 
-class Entity(object):
+class Entity:
     "Base class for the entities in the LIMS database."
 
-    _TAG = None
-    _URI = None
-    _PREFIX = None
+    _TAG: str | None = None
+    _URI: str | None = None
+    _PREFIX: str | None = None
 
     def __new__(cls, lims, uri=None, id=None, _create_new=False):
         if not uri:
@@ -255,7 +316,8 @@ def __new__(cls, lims, uri=None, id=None, _create_new=False):
     def __init__(self, lims, uri=None, id=None, _create_new=False):
         assert uri or id or _create_new
         if not _create_new:
-            if hasattr(self, 'lims'): return
+            if hasattr(self, "lims"):
+                return
             if not uri:
                 uri = lims.get_uri(self._URI, id)
             lims.cache[uri] = self
@@ -265,10 +327,10 @@ def __init__(self, lims, uri=None, id=None, _create_new=False):
         self.root = None
 
     def __str__(self):
-        return "%s(%s)" % (self.__class__.__name__, self.id)
+        return f"{self.__class__.__name__}({self.id})"
 
     def __repr__(self):
-        return "%s(%s)" % (self.__class__.__name__, self.uri)
+        return f"{self.__class__.__name__}({self.uri})"
 
     @property
     def uri(self):
@@ -281,11 +343,12 @@ def uri(self):
     def id(self):
         "Return the LIMS id; obtained from the URI."
         parts = urlsplit(self.uri)
-        return parts.path.split('/')[-1]
+        return parts.path.split("/")[-1]
 
     def get(self, force=False):
         "Get the XML data for this instance."
-        if not force and self.root is not None: return
+        if not force and self.root is not None:
+            return
         self.root = self.lims.get(self.uri)
 
     def put(self):
@@ -305,21 +368,25 @@ def xml(self):
     def _create(cls, lims, creation_tag=None, udfs=None, **kwargs):
         """Create an instance from attributes and return it"""
         if not udfs:
-            udfs={}
+            udfs = {}
         instance = cls(lims, _create_new=True)
         if creation_tag:
-            instance.root = ElementTree.Element(nsmap(cls._PREFIX + ':' + creation_tag))
+            instance.root = ElementTree.Element(nsmap(cls._PREFIX + ":" + creation_tag))
         elif cls._TAG:
-            instance.root = ElementTree.Element(nsmap(cls._PREFIX + ':' + cls._TAG))
+            instance.root = ElementTree.Element(nsmap(cls._PREFIX + ":" + cls._TAG))
         else:
-            instance.root = ElementTree.Element(nsmap(cls._PREFIX + ':' + cls.__name__.lower()))
+            instance.root = ElementTree.Element(
+                nsmap(cls._PREFIX + ":" + cls.__name__.lower())
+            )
         for key in udfs:
-            instance.udf[key]=udfs[key]
+            instance.udf[key] = udfs[key]
         for attribute in kwargs:
             if hasattr(instance, attribute):
                 setattr(instance, attribute, kwargs.get(attribute))
             else:
-                raise TypeError("%s create: got an unexpected keyword argument '%s'" % (cls.__name__, attribute))
+                raise TypeError(
+                    f"{cls.__name__} create: got an unexpected keyword argument '{attribute}'"
+                )
 
         return instance
 
@@ -329,79 +396,85 @@ def create(cls, lims, creation_tag=None, **kwargs):
         instance = cls._create(lims, creation_tag=creation_tag, **kwargs)
         data = lims.tostring(ElementTree.ElementTree(instance.root))
         instance.root = lims.post(uri=lims.get_uri(cls._URI), data=data)
-        instance._uri = instance.root.attrib['uri']
+        instance._uri = instance.root.attrib["uri"]
         return instance
 
 
 class Instrument(Entity):
-    """Lab Instrument
-    """
+    """Lab Instrument"""
+
     _URI = "instruments"
     _TAG = "instrument"
     _PREFIX = "inst"
 
-    name = StringDescriptor('name')
-    type = StringDescriptor('type')
-    serial_number = StringDescriptor('serial-number')
-    expiry_date = StringDescriptor('expiry-date')
-    archived = BooleanDescriptor('archived')
+    name = StringDescriptor("name")
+    type = StringDescriptor("type")
+    serial_number = StringDescriptor("serial-number")
+    expiry_date = StringDescriptor("expiry-date")
+    archived = BooleanDescriptor("archived")
+
 
 class Lab(Entity):
     "Lab; container of researchers."
 
-    _URI = 'labs'
-    _PREFIX = 'lab'
+    _URI = "labs"
+    _PREFIX = "lab"
+
+    name = StringDescriptor("name")
+    billing_address = StringDictionaryDescriptor("billing-address")
+    shipping_address = StringDictionaryDescriptor("shipping-address")
+    udf = UdfDictionaryDescriptor()
+    udt = UdtDictionaryDescriptor()
+    externalids = ExternalidListDescriptor()
+    website = StringDescriptor("website")
 
-    name             = StringDescriptor('name')
-    billing_address  = StringDictionaryDescriptor('billing-address')
-    shipping_address = StringDictionaryDescriptor('shipping-address')
-    udf              = UdfDictionaryDescriptor()
-    udt              = UdtDictionaryDescriptor()
-    externalids      = ExternalidListDescriptor()
-    website          = StringDescriptor('website')
 
 class Researcher(Entity):
     "Person; client scientist or lab personnel. Associated with a lab."
 
-    _URI = 'researchers'
-    _PREFIX = 'res'
-
-    first_name  = StringDescriptor('first-name')
-    last_name   = StringDescriptor('last-name')
-    phone       = StringDescriptor('phone')
-    fax         = StringDescriptor('fax')
-    email       = StringDescriptor('email')
-    initials    = StringDescriptor('initials')
-    lab         = EntityDescriptor('lab', Lab)
-    udf         = UdfDictionaryDescriptor()
-    udt         = UdtDictionaryDescriptor()
+    _URI = "researchers"
+    _PREFIX = "res"
+
+    first_name = StringDescriptor("first-name")
+    last_name = StringDescriptor("last-name")
+    phone = StringDescriptor("phone")
+    fax = StringDescriptor("fax")
+    email = StringDescriptor("email")
+    initials = StringDescriptor("initials")
+    lab = EntityDescriptor("lab", Lab)
+    udf = UdfDictionaryDescriptor()
+    udt = UdtDictionaryDescriptor()
     externalids = ExternalidListDescriptor()
 
     # credentials XXX
-    username = NestedStringDescriptor('username', 'credentials')
-    account_locked = NestedBooleanDescriptor('account-locked', 'credentials')
+    username = NestedStringDescriptor("username", "credentials")
+    account_locked = NestedBooleanDescriptor("account-locked", "credentials")
 
     @property
     def name(self):
-        return "%s %s" % (self.first_name, self.last_name)
+        return f"{self.first_name} {self.last_name}"
+
 
 class Permission(Entity):
     """A Clarity permission. Only supports GET"""
-    name = StringDescriptor('name')
-    action = StringDescriptor('action')
-    description = StringDescriptor('description')
+
+    name = StringDescriptor("name")
+    action = StringDescriptor("action")
+    description = StringDescriptor("description")
 
 
 class Role(Entity):
     """Clarity Role, hosting permissions"""
-    name = StringDescriptor('name')
-    researchers = NestedEntityListDescriptor('researcher', Researcher, 'researchers')
-    permissions = NestedEntityListDescriptor('permission', Permission, 'permissions')
+
+    name = StringDescriptor("name")
+    researchers = NestedEntityListDescriptor("researcher", Researcher, "researchers")
+    permissions = NestedEntityListDescriptor("permission", Permission, "permissions")
 
 
 class Reagent_label(Entity):
     """Reagent label element"""
-    reagent_label = StringDescriptor('reagent-label')
+
+    reagent_label = StringDescriptor("reagent-label")
 
 
 class Note(Entity):
@@ -413,99 +486,100 @@ class Note(Entity):
 class File(Entity):
     "File attached to a project or a sample."
 
-    attached_to       = StringDescriptor('attached-to')
-    content_location  = StringDescriptor('content-location')
-    original_location = StringDescriptor('original-location')
-    is_published      = BooleanDescriptor('is-published')
+    attached_to = StringDescriptor("attached-to")
+    content_location = StringDescriptor("content-location")
+    original_location = StringDescriptor("original-location")
+    is_published = BooleanDescriptor("is-published")
 
 
 class Project(Entity):
     "Project concerning a number of samples; associated with a researcher."
 
-    _URI = 'projects'
-    _TAG = 'project'
-    _PREFIX = 'prj'
-
-    name         = StringDescriptor('name')
-    open_date    = StringDescriptor('open-date')
-    close_date   = StringDescriptor('close-date')
-    invoice_date = StringDescriptor('invoice-date')
-    researcher   = EntityDescriptor('researcher', Researcher)
-    udf          = UdfDictionaryDescriptor()
-    udt          = UdtDictionaryDescriptor()
-    files        = EntityListDescriptor(nsmap('file:file'), File)
-    externalids  = ExternalidListDescriptor()
+    _URI = "projects"
+    _TAG = "project"
+    _PREFIX = "prj"
+
+    name = StringDescriptor("name")
+    open_date = StringDescriptor("open-date")
+    close_date = StringDescriptor("close-date")
+    invoice_date = StringDescriptor("invoice-date")
+    researcher = EntityDescriptor("researcher", Researcher)
+    udf = UdfDictionaryDescriptor()
+    udt = UdtDictionaryDescriptor()
+    files = EntityListDescriptor(nsmap("file:file"), File)
+    externalids = ExternalidListDescriptor()
     # permissions XXX
 
 
 class Sample(Entity):
     "Customer's sample to be analyzed; associated with a project."
 
-    _URI = 'samples'
-    _TAG = 'sample'
-    _PREFIX = 'smp'
+    _URI = "samples"
+    _TAG = "sample"
+    _PREFIX = "smp"
 
-    name           = StringDescriptor('name')
-    date_received  = StringDescriptor('date-received')
-    date_completed = StringDescriptor('date-completed')
-    project        = EntityDescriptor('project', Project)
-    submitter      = EntityDescriptor('submitter', Researcher)
+    name = StringDescriptor("name")
+    date_received = StringDescriptor("date-received")
+    date_completed = StringDescriptor("date-completed")
+    project = EntityDescriptor("project", Project)
+    submitter = EntityDescriptor("submitter", Researcher)
     # artifact: defined below
-    udf            = UdfDictionaryDescriptor()
-    udt            = UdtDictionaryDescriptor()
-    notes          = EntityListDescriptor('note', Note)
-    files          = EntityListDescriptor(nsmap('file:file'), File)
-    externalids    = ExternalidListDescriptor()
+    udf = UdfDictionaryDescriptor()
+    udt = UdtDictionaryDescriptor()
+    notes = EntityListDescriptor("note", Note)
+    files = EntityListDescriptor(nsmap("file:file"), File)
+    externalids = ExternalidListDescriptor()
     # biosource XXX
 
-
     @classmethod
     def create(cls, lims, container, position, udfs=None, **kwargs):
         """Create an instance of Sample from attributes then post it to the LIMS"""
         if udfs is None:
             udfs = {}
         if not isinstance(container, Container):
-            raise TypeError('%s is not of type Container'%container)
-        instance = super(Sample, cls)._create(lims, creation_tag='samplecreation',udfs=udfs, **kwargs)
+            raise TypeError(f"{container} is not of type Container")
+        instance = super()._create(
+            lims, creation_tag="samplecreation", udfs=udfs, **kwargs
+        )
 
-        location = ElementTree.SubElement(instance.root, 'location')
-        ElementTree.SubElement(location, 'container', dict(uri=container.uri))
-        position_element = ElementTree.SubElement(location, 'value')
+        location = ElementTree.SubElement(instance.root, "location")
+        ElementTree.SubElement(location, "container", dict(uri=container.uri))
+        position_element = ElementTree.SubElement(location, "value")
         position_element.text = position
         data = lims.tostring(ElementTree.ElementTree(instance.root))
         instance.root = lims.post(uri=lims.get_uri(cls._URI), data=data)
-        instance._uri = instance.root.attrib['uri']
+        instance._uri = instance.root.attrib["uri"]
         return instance
 
 
 class Containertype(Entity):
     "Type of container for analyte artifacts."
 
-    _TAG = 'container-type'
-    _URI = 'containertypes'
-    _PREFIX = 'ctp'
+    _TAG = "container-type"
+    _URI = "containertypes"
+    _PREFIX = "ctp"
 
-    name              = StringAttributeDescriptor('name')
-    calibrant_wells   = StringListDescriptor('calibrant-well')
-    unavailable_wells = StringListDescriptor('unavailable-well')
-    x_dimension       = DimensionDescriptor('x-dimension')
-    y_dimension       = DimensionDescriptor('y-dimension')
+    name = StringAttributeDescriptor("name")
+    calibrant_wells = StringListDescriptor("calibrant-well")
+    unavailable_wells = StringListDescriptor("unavailable-well")
+    x_dimension = DimensionDescriptor("x-dimension")
+    y_dimension = DimensionDescriptor("y-dimension")
 
 
 class Container(Entity):
     "Container for analyte artifacts."
 
-    _URI = 'containers'
-    _TAG = 'container'
-    _PREFIX = 'con'
+    _URI = "containers"
+    _TAG = "container"
+    _PREFIX = "con"
 
-    name           = StringDescriptor('name')
-    type           = EntityDescriptor('type', Containertype)
-    occupied_wells = IntegerDescriptor('occupied-wells')
-    placements     = PlacementDictionaryDescriptor('placement')
-    udf            = UdfDictionaryDescriptor()
-    udt            = UdtDictionaryDescriptor()
-    state          = StringDescriptor('state')
+    name = StringDescriptor("name")
+    type = EntityDescriptor("type", Containertype)
+    occupied_wells = IntegerDescriptor("occupied-wells")
+    placements = PlacementDictionaryDescriptor("placement")
+    udf = UdfDictionaryDescriptor()
+    udt = UdtDictionaryDescriptor()
+    state = StringDescriptor("state")
 
     def get_placements(self):
         """Get the dictionary of locations and artifacts
@@ -518,87 +592,88 @@ def delete(self):
         self.lims.delete(self.uri)
 
 
-
-
 class Udfconfig(Entity):
     "Instance of field type (cnf namespace)."
-    _URI = 'configuration/udfs'
-
-    name                          = StringDescriptor('name')
-    attach_to_name                = StringDescriptor('attach-to-name')
-    attach_to_category            = StringDescriptor('attach-to-category')
-    show_in_lablink               = BooleanDescriptor('show-in-lablink')
-    allow_non_preset_values       = BooleanDescriptor('allow-non-preset-values')
-    first_preset_is_default_value = BooleanDescriptor('first-preset-is-default-value')
-    show_in_tables                = BooleanDescriptor('show-in-tables')
-    is_editable                   = BooleanDescriptor('is-editable')
-    is_required                   = BooleanDescriptor('is-required')
-    is_deviation                  = BooleanDescriptor('is-deviation')
-    is_controlled_vocabulary      = BooleanDescriptor('is-controlled-vocabulary')
-    presets                       = StringListDescriptor('preset')
+
+    _URI = "configuration/udfs"
+
+    name = StringDescriptor("name")
+    attach_to_name = StringDescriptor("attach-to-name")
+    attach_to_category = StringDescriptor("attach-to-category")
+    show_in_lablink = BooleanDescriptor("show-in-lablink")
+    allow_non_preset_values = BooleanDescriptor("allow-non-preset-values")
+    first_preset_is_default_value = BooleanDescriptor("first-preset-is-default-value")
+    show_in_tables = BooleanDescriptor("show-in-tables")
+    is_editable = BooleanDescriptor("is-editable")
+    is_required = BooleanDescriptor("is-required")
+    is_deviation = BooleanDescriptor("is-deviation")
+    is_controlled_vocabulary = BooleanDescriptor("is-controlled-vocabulary")
+    presets = StringListDescriptor("preset")
 
 
 class Processtype(Entity):
-    _TAG = 'process-type'
-    _URI = 'processtypes'
-    _PREFIX = 'ptp'
+    _TAG = "process-type"
+    _URI = "processtypes"
+    _PREFIX = "ptp"
 
     def __init__(self, lims, uri=None, id=None, _create_new=False):
-        super(Processtype, self).__init__(lims, uri, id, _create_new)
+        super().__init__(lims, uri, id, _create_new)
         self.parameters = ProcessTypeParametersDescriptor(self)
 
-    name = StringAttributeDescriptor('name')
-    field_definition = EntityListDescriptor('field-definition', Udfconfig)
+    name = StringAttributeDescriptor("name")
+    field_definition = EntityListDescriptor("field-definition", Udfconfig)
     process_inputs = ProcessTypeProcessInputDescriptor()
     process_outputs = ProcessTypeProcessOutputDescriptor()
-    process_type_attribute = NamedStringDescriptor('process-type-attribute')
-
+    process_type_attribute = NamedStringDescriptor("process-type-attribute")
 
     @property
     def process_input(self):
         return self.process_inputs[0]
 
+
 class ControlType(Entity):
     _URI = "controltypes"
     _TAG = "control-type"
-    _PREFIX = 'ctrltp'
+    _PREFIX = "ctrltp"
 
-    name = StringAttributeDescriptor('name')
-    supplier = StringDescriptor('supplier')
-    archived = BooleanDescriptor('archived')
-    single_step = BooleanDescriptor('single_step')
+    name = StringAttributeDescriptor("name")
+    supplier = StringDescriptor("supplier")
+    archived = BooleanDescriptor("archived")
+    single_step = BooleanDescriptor("single_step")
 
 
 class Process(Entity):
     "Process (instance of Processtype) executed producing ouputs from inputs."
 
-    _URI = 'processes'
-    _PREFIX = 'prc'
+    _URI = "processes"
+    _PREFIX = "prc"
 
-    type              = EntityDescriptor('type', Processtype)
-    date_run          = StringDescriptor('date-run')
-    technician        = EntityDescriptor('technician', Researcher)
-    protocol_name     = StringDescriptor('protocol-name')
+    type = EntityDescriptor("type", Processtype)
+    date_run = StringDescriptor("date-run")
+    technician = EntityDescriptor("technician", Researcher)
+    protocol_name = StringDescriptor("protocol-name")
     input_output_maps = InputOutputMapList()
-    udf               = UdfDictionaryDescriptor()
-    udt               = UdtDictionaryDescriptor()
-    files             = EntityListDescriptor(nsmap('file:file'), File)
-    process_parameter = StringDescriptor('process-parameter')
-    instrument        = EntityDescriptor('instrument', Instrument)
+    udf = UdfDictionaryDescriptor()
+    udt = UdtDictionaryDescriptor()
+    files = EntityListDescriptor(nsmap("file:file"), File)
+    process_parameter = StringDescriptor("process-parameter")
+    instrument = EntityDescriptor("instrument", Instrument)
 
     # process_parameters XXX
 
-    def outputs_per_input(self, inart, ResultFile=False, SharedResultFile=False, Analyte=False):
+    def outputs_per_input(
+        self, inart, ResultFile=False, SharedResultFile=False, Analyte=False
+    ):
         """Getting all the output artifacts related to a particual input artifact"""
 
-        inouts = [io for io in self.input_output_maps if io[0]['limsid'] == inart]
+        inouts = [io for io in self.input_output_maps if io[0]["limsid"] == inart]
         if ResultFile:
-            inouts = [io for io in inouts if io[1]['output-type'] == 'ResultFile']
+            inouts = [io for io in inouts if io[1]["output-type"] == "ResultFile"]
         elif SharedResultFile:
-            inouts = [io for io in inouts if io[1]['output-type'] == 'SharedResultFile']
+            inouts = [io for io in inouts if io[1]["output-type"] == "SharedResultFile"]
         elif Analyte:
-            inouts = [io for io in inouts if io[1]['output-type'] == 'Analyte']
-        outs = [io[1]['uri'] for io in inouts]
+            inouts = [io for io in inouts if io[1]["output-type"] == "Analyte"]
+        outs = [io[1]["uri"] for io in inouts]
         return outs
 
     def input_per_sample(self, sample):
@@ -617,14 +692,16 @@ def all_inputs(self, unique=True, resolve=False):
         """
         # if the process has no input, that is not standard and we want to know about it
         try:
-            ids = [io[0]['limsid'] for io in self.input_output_maps]
+            ids = [io[0]["limsid"] for io in self.input_output_maps]
         except TypeError:
             logger.error("Process ", self, " has no input artifacts")
             raise TypeError
         if unique:
             ids = list(frozenset(ids))
         if resolve:
-            return self.lims.get_batch([Artifact(self.lims, id=id) for id in ids if id is not None])
+            return self.lims.get_batch(
+                [Artifact(self.lims, id=id) for id in ids if id is not None]
+            )
         else:
             return [Artifact(self.lims, id=id) for id in ids if id is not None]
 
@@ -633,36 +710,38 @@ def all_outputs(self, unique=True, resolve=False):
         if unique is true, no duplicates are returned.
         """
         # Given how ids is structured, io[1] might be None : some process don't have an output.
-        ids = [io[1]['limsid'] for io in self.input_output_maps if io[1] is not None]
+        ids = [io[1]["limsid"] for io in self.input_output_maps if io[1] is not None]
         if unique:
             ids = list(frozenset(ids))
         if resolve:
-            return self.lims.get_batch([Artifact(self.lims, id=id) for id in ids if id is not None])
+            return self.lims.get_batch(
+                [Artifact(self.lims, id=id) for id in ids if id is not None]
+            )
         else:
             return [Artifact(self.lims, id=id) for id in ids if id is not None]
 
     def shared_result_files(self):
         """Retreve all resultfiles of output-generation-type PerAllInputs."""
         artifacts = self.all_outputs(unique=True)
-        return [a for a in artifacts if a.output_type == 'SharedResultFile']
+        return [a for a in artifacts if a.output_type == "SharedResultFile"]
 
     def result_files(self):
         """Retreve all resultfiles of output-generation-type perInput."""
         artifacts = self.all_outputs(unique=True)
-        return [a for a in artifacts if a.output_type == 'ResultFile']
+        return [a for a in artifacts if a.output_type == "ResultFile"]
 
     def analytes(self):
         """Retreving the output Analytes of the process, if existing.
         If the process is not producing any output analytes, the input
         analytes are returned. Input/Output is returned as a information string.
         Makes aggregate processes and normal processes look the same."""
-        info = 'Output'
+        info = "Output"
         artifacts = self.all_outputs(unique=True)
-        analytes = [a for a in artifacts if a.type == 'Analyte']
+        analytes = [a for a in artifacts if a.type == "Analyte"]
         if len(analytes) == 0:
             artifacts = self.all_inputs(unique=True)
-            analytes = [a for a in artifacts if a.type == 'Analyte']
-            info = 'Input'
+            analytes = [a for a in artifacts if a.type == "Analyte"]
+            info = "Input"
         return analytes, info
 
     def parent_processes(self):
@@ -686,22 +765,22 @@ def step(self):
 class Artifact(Entity):
     "Any process input or output; analyte or file."
 
-    _URI = 'artifacts'
-    _TAG = 'artifact'
-    _PREFIX = 'art'
-
-    name           = StringDescriptor('name')
-    type           = StringDescriptor('type')
-    output_type    = StringDescriptor('output-type')
-    parent_process = EntityDescriptor('parent-process', Process)
-    volume         = StringDescriptor('volume')
-    concentration  = StringDescriptor('concentration')
-    qc_flag        = StringDescriptor('qc-flag')
-    location       = LocationDescriptor('location')
-    working_flag   = BooleanDescriptor('working-flag')
-    samples        = EntityListDescriptor('sample', Sample)
-    udf            = UdfDictionaryDescriptor()
-    files          = EntityListDescriptor(nsmap('file:file'), File)
+    _URI = "artifacts"
+    _TAG = "artifact"
+    _PREFIX = "art"
+
+    name = StringDescriptor("name")
+    type = StringDescriptor("type")
+    output_type = StringDescriptor("output-type")
+    parent_process = EntityDescriptor("parent-process", Process)
+    volume = StringDescriptor("volume")
+    concentration = StringDescriptor("concentration")
+    qc_flag = StringDescriptor("qc-flag")
+    location = LocationDescriptor("location")
+    working_flag = BooleanDescriptor("working-flag")
+    samples = EntityListDescriptor("sample", Sample)
+    udf = UdfDictionaryDescriptor()
+    files = EntityListDescriptor(nsmap("file:file"), File)
     reagent_labels = ReagentLabelList()
 
     # artifact_flags XXX
@@ -712,8 +791,8 @@ def input_artifact_list(self):
         input_artifact_list = []
         try:
             for tuple in self.parent_process.input_output_maps:
-                if tuple[1]['limsid'] == self.id:
-                    input_artifact_list.append(tuple[0]['uri'])  # ['limsid'])
+                if tuple[1]["limsid"] == self.id:
+                    input_artifact_list.append(tuple[0]["uri"])  # ['limsid'])
         except:
             pass
         return input_artifact_list
@@ -723,7 +802,7 @@ def get_state(self):
         parts = urlparse(self.uri)
         params = parse_qs(parts.query)
         try:
-            return params['state'][0]
+            return params["state"][0]
         except (KeyError, IndexError):
             return None
 
@@ -738,22 +817,28 @@ def container(self):
     def stateless(self):
         "returns the artefact independently of it's state"
         parts = urlparse(self.uri)
-        if 'state' in parts[4]:
-            stateless_uri = urlunparse([parts[0], parts[1], parts[2], parts[3], '', ''])
+        if "state" in parts[4]:
+            stateless_uri = urlunparse([parts[0], parts[1], parts[2], parts[3], "", ""])
             return Artifact(self.lims, uri=stateless_uri)
         else:
             return self
 
     # XXX set_state ?
-    state = property(get_state)
-    stateless = property(stateless)
+    state = property(get_state)  # type: ignore
+    stateless = property(stateless)  # type: ignore
 
     def _get_workflow_stages_and_statuses(self):
         self.get()
         result = []
-        rootnode = self.root.find('workflow-stages')
-        for node in rootnode.findall('workflow-stage'):
-            result.append((Stage(self.lims, uri=node.attrib['uri']), node.attrib['status'], node.attrib['name']))
+        rootnode = self.root.find("workflow-stages")
+        for node in rootnode.findall("workflow-stage"):
+            result.append(
+                (
+                    Stage(self.lims, uri=node.attrib["uri"]),
+                    node.attrib["status"],
+                    node.attrib["name"],
+                )
+            )
         return result
 
     workflow_stages_and_statuses = property(_get_workflow_stages_and_statuses)
@@ -764,22 +849,23 @@ class StepPools(Entity):
     pools : [ {'output' : output_art, 'name' : 'AAAA', 'inputs':[input_art_1, input_art_2, ...]}, ...]
     available_inputs : {input1:{'replicates':N}}
     When POSTing, only pools need to be updated, available_inputs can be left as is.
-    In pools, output can be left blank, Clarity will generate an output artifact. """
+    In pools, output can be left blank, Clarity will generate an output artifact."""
 
     _pools = None
     _available_inputs = None
 
     def _remove_available_inputs(self, input_art):
-        """ removes an input from the available inputs, one replicate at a time
-        """
+        """removes an input from the available inputs, one replicate at a time"""
         self.get_available_inputs()
-        rep = self._available_inputs.get(input_art, {'replicates': 0}).get('replicates', 1)
+        rep = self._available_inputs.get(input_art, {"replicates": 0}).get(
+            "replicates", 1
+        )
         if rep > 1:
-            self._available_inputs[input_art]['replicates'] = rep - 1
+            self._available_inputs[input_art]["replicates"] = rep - 1
         elif rep == 1:
-            del(self._available_inputs[input_art])
+            del self._available_inputs[input_art]
         else:
-            logger.info("using more inputs than replicates for input {0}".format(input_art.uri))
+            logger.info(f"using more inputs than replicates for input {input_art.uri}")
         self.available_inputs = self._available_inputs
 
     def set_available_inputs(self, available_inputs):
@@ -787,8 +873,10 @@ def set_available_inputs(self, available_inputs):
         available_inputs_root.clear()
         for input_art in available_inputs:
             current_elem = ElementTree.SubElement(available_inputs_root, "input")
-            current_elem.attrib['uri'] = input_art.uri
-            current_elem.attrib['replicates'] = str(available_inputs[input_art]['replicates'])
+            current_elem.attrib["uri"] = input_art.uri
+            current_elem.attrib["replicates"] = str(
+                available_inputs[input_art]["replicates"]
+            )
         self._available_inputs = available_inputs
 
     def get_available_inputs(self):
@@ -796,10 +884,12 @@ def get_available_inputs(self):
             self.get()
             self._available_inputs = {}
             for ai_node in self.root.find("available-inputs").findall("input"):
-                input = Artifact(self.lims, uri=ai_node.attrib['uri'])
+                input = Artifact(self.lims, uri=ai_node.attrib["uri"])
                 self._available_inputs[input] = {}
-                if 'replicates' in ai_node.attrib:
-                    self._available_inputs[input]['replicates'] = int(ai_node.attrib['replicates'])
+                if "replicates" in ai_node.attrib:
+                    self._available_inputs[input]["replicates"] = int(
+                        ai_node.attrib["replicates"]
+                    )
 
         return self._available_inputs
 
@@ -808,14 +898,18 @@ def get_pools(self):
             self.get()
             self._pools = []
 
-            for idx, pool_node in enumerate(self.root.find("pooled-inputs").findall("pool")):
-                pool_name = pool_node.attrib.get('name', "Pool #{0}".format(idx+1))
-                pool_object = {'name': pool_name, 'inputs': [], 'output': None}
-                if pool_node.attrib.get('output-uri', False):
-                    pool_object['output'] = Artifact(self.lims, uri=pool_node.attrib['output-uri'])
+            for idx, pool_node in enumerate(
+                self.root.find("pooled-inputs").findall("pool")
+            ):
+                pool_name = pool_node.attrib.get("name", f"Pool #{idx + 1}")
+                pool_object = {"name": pool_name, "inputs": [], "output": None}
+                if pool_node.attrib.get("output-uri", False):
+                    pool_object["output"] = Artifact(
+                        self.lims, uri=pool_node.attrib["output-uri"]
+                    )
                 for input_node in pool_node.findall("input"):
-                    input = Artifact(self.lims, uri=input_node.attrib['uri'])
-                    pool_object['inputs'].append(input)
+                    input = Artifact(self.lims, uri=input_node.attrib["uri"])
+                    pool_object["inputs"].append(input)
 
                 self._pools.append(pool_object)
 
@@ -825,13 +919,13 @@ def set_pools(self, pools):
         pool_root = self.root.find("pooled-inputs")
         pool_root.clear()
         for idx, pool_obj in enumerate(pools):
-            current_pool = ElementTree.SubElement(pool_root, 'pool')
-            if pool_obj.get('output', False):
-                current_pool.attrib['output-uri'] = pool_obj['output'].uri
-            current_pool.attrib['name'] = pool_obj.get('name', 'Pool #{0}'.format(idx+1))
-            for input_art in pool_obj.get('inputs', []):
-                current_input = ElementTree.SubElement(current_pool, 'input')
-                current_input.attrib['uri'] = input_art.uri
+            current_pool = ElementTree.SubElement(pool_root, "pool")
+            if pool_obj.get("output", False):
+                current_pool.attrib["output-uri"] = pool_obj["output"].uri
+            current_pool.attrib["name"] = pool_obj.get("name", f"Pool #{idx + 1}")
+            for input_art in pool_obj.get("inputs", []):
+                current_input = ElementTree.SubElement(current_pool, "input")
+                current_input.attrib["uri"] = input_art.uri
                 self._remove_available_inputs(input_art)
 
         self._pools = pools
@@ -842,6 +936,7 @@ def set_pools(self, pools):
 
 class StepPlacements(Entity):
     """Placements from within a step. Supports POST"""
+
     _placementslist = None
 
     # [[A,(C,'A:1')][A,(C,'A:2')]] where A is an Artifact and C a Container
@@ -850,13 +945,16 @@ def get_placement_list(self):
             # Only fetch the data once.
             self.get()
             self._placementslist = []
-            for node in self.root.find('output-placements').findall('output-placement'):
-                input = Artifact(self.lims, uri=node.attrib['uri'])
+            for node in self.root.find("output-placements").findall("output-placement"):
+                input = Artifact(self.lims, uri=node.attrib["uri"])
                 location = (None, None)
-                if node.find('location') is not None:
+                if node.find("location") is not None:
                     location = (
-                        Container(self.lims, uri=node.find('location').find('container').attrib['uri']),
-                        node.find('location').find('value').text
+                        Container(
+                            self.lims,
+                            uri=node.find("location").find("container").attrib["uri"],
+                        ),
+                        node.find("location").find("value").text,
                     )
                 self._placementslist.append([input, location])
         return self._placementslist
@@ -864,30 +962,33 @@ def get_placement_list(self):
     def set_placement_list(self, value):
         containers = set()
         self.get_placement_list()
-        placement_dict = {x[0].stateless.uri:x for x in value }
-        for node in self.root.find('output-placements').findall('output-placement'):
-            location = placement_dict[node.attrib['uri']][1]
+        placement_dict = {x[0].stateless.uri: x for x in value}
+        for node in self.root.find("output-placements").findall("output-placement"):
+            location = placement_dict[node.attrib["uri"]][1]
             container = location[0]
             well = location[1]
             if container and location:
                 containers.add(container)
-                if node.find('location') is not None:
-                    cont_el = node.find('location').find('container')
-                    cont_el.attrib['uri'] = container.uri
-                    cont_el.attrib['limsid'] = container.id
-                    value_el = node.find('location').find('value')
+                if node.find("location") is not None:
+                    cont_el = node.find("location").find("container")
+                    cont_el.attrib["uri"] = container.uri
+                    cont_el.attrib["limsid"] = container.id
+                    value_el = node.find("location").find("value")
                     value_el.text = well
                 else:
-                    loc_el = ElementTree.SubElement(node, 'location')
-                    cont_el = ElementTree.SubElement(loc_el, 'container',
-                                                     {'uri': container.uri, 'limsid': container.id})
-                    well_el = ElementTree.SubElement(loc_el, 'value')
+                    loc_el = ElementTree.SubElement(node, "location")
+                    cont_el = ElementTree.SubElement(
+                        loc_el,
+                        "container",
+                        {"uri": container.uri, "limsid": container.id},
+                    )
+                    well_el = ElementTree.SubElement(loc_el, "value")
                     well_el.text = well  # not supported in the constructor
         # Handle selected containers
         sc = self.root.find("selected-containers")
         sc.clear()
         for cont in containers:
-            ElementTree.SubElement(sc, 'container', uri=cont.uri)
+            ElementTree.SubElement(sc, "container", uri=cont.uri)
         self._placementslist = value
 
     placement_list = property(get_placement_list, set_placement_list)
@@ -898,8 +999,10 @@ def get_selected_containers(self):
         _selected_containers = []
         if not _selected_containers:
             self.get()
-            for node in self.root.find('selected-containers').findall('container'):
-                _selected_containers.append(Container(self.lims, uri=node.attrib['uri']))
+            for node in self.root.find("selected-containers").findall("container"):
+                _selected_containers.append(
+                    Container(self.lims, uri=node.attrib["uri"])
+                )
 
         return _selected_containers
 
@@ -908,6 +1011,7 @@ def get_selected_containers(self):
 
 class StepActions(Entity):
     """Actions associated with a step"""
+
     _escalation = None
 
     @property
@@ -915,59 +1019,70 @@ def escalation(self):
         if not self._escalation:
             self.get()
             self._escalation = {}
-            for node in self.root.findall('escalation'):
-                self._escalation['artifacts'] = []
-                self._escalation['author'] = Researcher(self.lims,
-                                                        uri=node.find('request').find('author').attrib.get('uri'))
+            for node in self.root.findall("escalation"):
+                self._escalation["artifacts"] = []
+                self._escalation["author"] = Researcher(
+                    self.lims, uri=node.find("request").find("author").attrib.get("uri")
+                )
                 try:
-                    self._escalation['request'] = node.find('request').find('comment').text
+                    self._escalation["request"] = (
+                        node.find("request").find("comment").text
+                    )
                 except:
-                    self._escalation['request'] = ""
+                    self._escalation["request"] = ""
 
-                if node.find('review') is not None:  # recommended by the Etree doc
-                    self._escalation['status'] = 'Reviewed'
-                    self._escalation['reviewer'] = Researcher(self.lims,
-                                                              uri=node.find('review').find('author').attrib.get('uri'))
+                if node.find("review") is not None:  # recommended by the Etree doc
+                    self._escalation["status"] = "Reviewed"
+                    self._escalation["reviewer"] = Researcher(
+                        self.lims,
+                        uri=node.find("review").find("author").attrib.get("uri"),
+                    )
                     try:
-                        self._escalation['answer'] = node.find('review').find('comment').text
+                        self._escalation["answer"] = (
+                            node.find("review").find("comment").text
+                        )
                     except:
-                        self._escalation['answer'] = ""
+                        self._escalation["answer"] = ""
 
                 else:
-                    self._escalation['status'] = 'Pending'
+                    self._escalation["status"] = "Pending"
 
-                for node2 in node.findall('escalated-artifacts'):
-                    art = self.lims.get_batch([Artifact(self.lims, uri=ch.attrib.get('uri')) for ch in node2])
-                    self._escalation['artifacts'].extend(art)
+                for node2 in node.findall("escalated-artifacts"):
+                    art = self.lims.get_batch(
+                        [Artifact(self.lims, uri=ch.attrib.get("uri")) for ch in node2]
+                    )
+                    self._escalation["artifacts"].extend(art)
         return self._escalation
 
     def get_next_actions(self):
         actions = []
         self.get()
-        if self.root.find('next-actions') is not None:
-            for node in self.root.find('next-actions').findall('next-action'):
+        if self.root.find("next-actions") is not None:
+            for node in self.root.find("next-actions").findall("next-action"):
                 action = {
-                    'artifact': Artifact(self.lims, node.attrib.get('artifact-uri')),
-                    'action': node.attrib.get('action'),
+                    "artifact": Artifact(self.lims, node.attrib.get("artifact-uri")),
+                    "action": node.attrib.get("action"),
                 }
-                if node.attrib.get('step-uri'):
-                    action['step'] = Step(self.lims, uri=node.attrib.get('step-uri'))
-                if node.attrib.get('rework-step-uri'):
-                    action['rework-step'] = Step(self.lims, uri=node.attrib.get('rework-step-uri'))
+                if node.attrib.get("step-uri"):
+                    action["step"] = Step(self.lims, uri=node.attrib.get("step-uri"))
+                if node.attrib.get("rework-step-uri"):
+                    action["rework-step"] = Step(
+                        self.lims, uri=node.attrib.get("rework-step-uri")
+                    )
                 actions.append(action)
         return actions
 
     def set_next_actions(self, actions):
-        action_dict = {a['artifact'].uri:a for a in actions}
-        for node in self.root.find('next-actions').findall('next-action'):
-            art_uri = node.attrib.get('artifact-uri')
+        action_dict = {a["artifact"].uri: a for a in actions}
+        for node in self.root.find("next-actions").findall("next-action"):
+            art_uri = node.attrib.get("artifact-uri")
             action = action_dict[art_uri]
-            if 'action' in action:
-                node.attrib['action'] = action.get('action')
-                if 'step-uri' in action:
-                    node.attrib['step-uri'] = action.get('step-uri')
-                if 'rework-step-uri' in action:
-                    node.attrib['rework-step-uri'] = action.get('rework-step-uri')
+            if "action" in action:
+                node.attrib["action"] = action.get("action")
+                if "step-uri" in action:
+                    node.attrib["step-uri"] = action.get("step-uri")
+                if "rework-step-uri" in action:
+                    node.attrib["rework-step-uri"] = action.get("rework-step-uri")
 
     next_actions = property(get_next_actions, set_next_actions)
 
@@ -976,78 +1091,82 @@ class StepProgramStatus(Entity):
     """Allows custom handling of program status.
     message supports HTML. Cross handling of EPPs is possible.
     Supports PUT"""
-    status = StringDescriptor('status')
-    message = StringDescriptor('message')
+
+    status = StringDescriptor("status")
+    message = StringDescriptor("message")
 
 
 class ReagentKit(Entity):
     """Type of Reagent with information about the provider"""
+
     _URI = "reagentkits"
     _TAG = "reagent-kit"
-    _PREFIX = 'kit'
+    _PREFIX = "kit"
 
-    name     = StringDescriptor('name')
-    supplier = StringDescriptor('supplier')
-    website  = StringDescriptor('website')
-    archived = BooleanDescriptor('archived')
+    name = StringDescriptor("name")
+    supplier = StringDescriptor("supplier")
+    website = StringDescriptor("website")
+    archived = BooleanDescriptor("archived")
 
 
 class ReagentLot(Entity):
     """Reagent Lots contain information about a particualr lot of reagent used in a step"""
+
     _URI = "reagentlots"
     _TAG = "reagent-lot"
-    _PREFIX = 'lot'
+    _PREFIX = "lot"
 
-    reagent_kit        = EntityDescriptor('reagent-kit', ReagentKit)
-    name               = StringDescriptor('name')
-    lot_number         = StringDescriptor('lot-number')
-    created_date       = StringDescriptor('created-date')
-    last_modified_date = StringDescriptor('last-modified-date')
-    expiry_date        = StringDescriptor('expiry-date')
-    created_by         = EntityDescriptor('created-by', Researcher)
-    last_modified_by   = EntityDescriptor('last-modified-by', Researcher)
-    status             = StringDescriptor('status')
-    usage_count        = IntegerDescriptor('usage-count')
+    reagent_kit = EntityDescriptor("reagent-kit", ReagentKit)
+    name = StringDescriptor("name")
+    lot_number = StringDescriptor("lot-number")
+    created_date = StringDescriptor("created-date")
+    last_modified_date = StringDescriptor("last-modified-date")
+    expiry_date = StringDescriptor("expiry-date")
+    created_by = EntityDescriptor("created-by", Researcher)
+    last_modified_by = EntityDescriptor("last-modified-by", Researcher)
+    status = StringDescriptor("status")
+    usage_count = IntegerDescriptor("usage-count")
 
 
 class StepReagentLots(Entity):
-    reagent_lots = NestedEntityListDescriptor('reagent-lot', ReagentLot, 'reagent-lots')
+    reagent_lots = NestedEntityListDescriptor("reagent-lot", ReagentLot, "reagent-lots")
+
 
 class StepDetails(Entity):
     """Detail associated with a step"""
 
-    input_output_maps = InputOutputMapList('input-output-maps')
-    udf = UdfDictionaryDescriptor('fields')
-    udt = UdtDictionaryDescriptor('fields')
+    input_output_maps = InputOutputMapList("input-output-maps")
+    udf = UdfDictionaryDescriptor("fields")
+    udt = UdtDictionaryDescriptor("fields")
 
-class StepReagents(Entity):
 
-    reagent_category = StringDescriptor('reagent-category')
+class StepReagents(Entity):
+    reagent_category = StringDescriptor("reagent-category")
     output_reagents = OutputReagentList(Artifact)
 
 
 class Step(Entity):
     "Step, as defined by the genologics API."
 
-    _URI = 'steps'
-    _PREFIX = 'stp'
+    _URI = "steps"
+    _PREFIX = "stp"
 
-    current_state = StringAttributeDescriptor('current-state')
-    _reagent_lots = EntityDescriptor('reagent-lots', StepReagentLots)
-    actions       = EntityDescriptor('actions', StepActions)
-    date_started  = StringDescriptor('date-started')
-    date_completed     = StringDescriptor('date-completed')
-    placements    = EntityDescriptor('placements', StepPlacements)
-    details       = EntityDescriptor('details', StepDetails)
-    step_pools         = EntityDescriptor('pools', StepPools)
-    program_status     = EntityDescriptor('program-status', StepProgramStatus)
-    reagents     = EntityDescriptor('reagents', StepReagents)
+    current_state = StringAttributeDescriptor("current-state")
+    _reagent_lots = EntityDescriptor("reagent-lots", StepReagentLots)
+    actions = EntityDescriptor("actions", StepActions)
+    date_started = StringDescriptor("date-started")
+    date_completed = StringDescriptor("date-completed")
+    placements = EntityDescriptor("placements", StepPlacements)
+    details = EntityDescriptor("details", StepDetails)
+    step_pools = EntityDescriptor("pools", StepPools)
+    program_status = EntityDescriptor("program-status", StepProgramStatus)
+    reagents = EntityDescriptor("reagents", StepReagents)
 
     def advance(self):
         self.get()
         self.root = self.lims.post(
-            uri="{0}/advance".format(self.uri),
-            data=self.lims.tostring(ElementTree.ElementTree(self.root))
+            uri=f"{self.uri}/advance",
+            data=self.lims.tostring(ElementTree.ElementTree(self.root)),
         )
 
     @property
@@ -1064,33 +1183,33 @@ def create(cls, lims, protocol_step, container_type, inputs, **kwargs):
             These need to be queued for that step for the query to be successful.
         """
         if not isinstance(protocol_step, ProtocolStep):
-            raise TypeError('%s is not of type ProtocolStep'%protocol_step)
+            raise TypeError(f"{protocol_step} is not of type ProtocolStep")
         elif not isinstance(container_type, Containertype):
-            raise TypeError('%s is not of type Containertype'%container_type)
+            raise TypeError(f"{container_type} is not of type Containertype")
         elif not all([isinstance(input, Artifact) for input in inputs]):
-            raise TypeError('%s does not contain only items of type Artifact'%inputs)
+            raise TypeError(f"{inputs} does not contain only items of type Artifact")
 
-        instance = super(Step, cls)._create(lims, creation_tag='step-creation', **kwargs)
+        instance = super()._create(lims, creation_tag="step-creation", **kwargs)
 
         # Setup configuration element
-        configuration_element = ElementTree.SubElement(instance.root, 'configuration')
-        configuration_element.attrib['uri'] = protocol_step.uri
+        configuration_element = ElementTree.SubElement(instance.root, "configuration")
+        configuration_element.attrib["uri"] = protocol_step.uri
         configuration_element.text = protocol_step.name
 
         # Setup container type element
-        container_type_element = ElementTree.SubElement(instance.root, 'container-type')
+        container_type_element = ElementTree.SubElement(instance.root, "container-type")
         container_type_element.text = container_type.name
 
         # Setup inputs element
-        inputs_element = ElementTree.SubElement(instance.root, 'inputs')
+        inputs_element = ElementTree.SubElement(instance.root, "inputs")
         for input in inputs:
-            input_element = ElementTree.SubElement(inputs_element, 'input')
-            input_element.attrib['uri'] = input.uri
+            input_element = ElementTree.SubElement(inputs_element, "input")
+            input_element.attrib["uri"] = input.uri
 
         data = lims.tostring(ElementTree.ElementTree(instance.root))
 
         instance.root = lims.post(uri=lims.get_uri(cls._URI), data=data)
-        instance._uri = instance.root.attrib['uri']
+        instance._uri = instance.root.attrib["uri"]
 
         return instance
 
@@ -1098,95 +1217,116 @@ def create(cls, lims, protocol_step, container_type, inputs, **kwargs):
 class ProtocolStep(Entity):
     """Steps key in the Protocol object"""
 
-    _TAG = 'step'
-
-    name                    = StringAttributeDescriptor("name")
-    type                    = EntityDescriptor('process-type', Processtype)
-    permittedcontainers     = NestedStringListDescriptor('container-type', 'permitted-containers')
-    permitted_control_types = NestedEntityListDescriptor('control-type', ControlType, 'permitted-control-types')
-    required_reagent_kits   = NestedEntityListDescriptor('reagent-kit', ReagentKit, 'required-reagent-kits')
-    queue_fields            = NestedAttributeListDescriptor('queue-field', 'queue-fields')
-    step_fields             = NestedAttributeListDescriptor('step-field', 'step-fields')
-    sample_fields           = NestedAttributeListDescriptor('sample-field', 'sample-fields')
-    step_properties         = NestedAttributeListDescriptor('step-property', 'step-properties')
-    epp_triggers            = NestedAttributeListDescriptor('epp-trigger', 'epp-triggers')
+    _TAG = "step"
+
+    name = StringAttributeDescriptor("name")
+    type = EntityDescriptor("process-type", Processtype)
+    permittedcontainers = NestedStringListDescriptor(
+        "container-type", "permitted-containers"
+    )
+    permitted_control_types = NestedEntityListDescriptor(
+        "control-type", ControlType, "permitted-control-types"
+    )
+    required_reagent_kits = NestedEntityListDescriptor(
+        "reagent-kit", ReagentKit, "required-reagent-kits"
+    )
+    queue_fields = NestedAttributeListDescriptor("queue-field", "queue-fields")
+    step_fields = NestedAttributeListDescriptor("step-field", "step-fields")
+    sample_fields = NestedAttributeListDescriptor("sample-field", "sample-fields")
+    step_properties = NestedAttributeListDescriptor("step-property", "step-properties")
+    epp_triggers = NestedAttributeListDescriptor("epp-trigger", "epp-triggers")
 
 
 class Protocol(Entity):
     """Protocol, holding ProtocolSteps and protocol-properties"""
-    _URI = 'configuration/protocols'
-    _TAG = 'protocol'
 
-    steps      = NestedEntityListDescriptor('step', ProtocolStep, 'steps')
-    properties = NestedAttributeListDescriptor('protocol-property', 'protocol-properties')
+    _URI = "configuration/protocols"
+    _TAG = "protocol"
 
+    steps = NestedEntityListDescriptor("step", ProtocolStep, "steps")
+    properties = NestedAttributeListDescriptor(
+        "protocol-property", "protocol-properties"
+    )
 
 
 class Automation(Entity):
     """Automation, holding Automation configurations"""
-    _URI = 'configuration/automations'
-    _TAG = 'automation'
 
-    process_types   = NestedEntityListDescriptor('process-type', Processtype, 'process-types')
-    string          = NestedStringDescriptor('string')
-    name            = StringAttributeDescriptor('name')
-    context         = NestedStringDescriptor('context')
+    _URI = "configuration/automations"
+    _TAG = "automation"
 
+    process_types = NestedEntityListDescriptor(
+        "process-type", Processtype, "process-types"
+    )
+    string = NestedStringDescriptor("string")
+    name = StringAttributeDescriptor("name")
+    context = NestedStringDescriptor("context")
 
 
 class Stage(Entity):
     """Holds Protocol/Workflow"""
-    name     = StringAttributeDescriptor('name')
-    index    = IntegerAttributeDescriptor('index')
-    protocol = EntityDescriptor('protocol', Protocol)
-    step     = EntityDescriptor('step', ProtocolStep)
+
+    name = StringAttributeDescriptor("name")
+    index = IntegerAttributeDescriptor("index")
+    protocol = EntityDescriptor("protocol", Protocol)
+    step = EntityDescriptor("step", ProtocolStep)
 
 
 class Workflow(Entity):
-    """ Workflow, introduced in 3.5"""
+    """Workflow, introduced in 3.5"""
+
     _URI = "configuration/workflows"
     _TAG = "workflow"
 
-    name      = StringAttributeDescriptor("name")
-    status    = StringAttributeDescriptor("status")
-    protocols = NestedEntityListDescriptor('protocol', Protocol, 'protocols')
-    stages    = NestedEntityListDescriptor('stage', Stage, 'stages')
+    name = StringAttributeDescriptor("name")
+    status = StringAttributeDescriptor("status")
+    protocols = NestedEntityListDescriptor("protocol", Protocol, "protocols")
+    stages = NestedEntityListDescriptor("stage", Stage, "stages")
 
 
 class ReagentType(Entity):
     """Reagent Type, usually, indexes for sequencing"""
+
     _URI = "reagenttypes"
     _TAG = "reagent-type"
-    _PREFIX = 'rtp'
+    _PREFIX = "rtp"
 
-    category = StringDescriptor('reagent-category')
-    name      = StringAttributeDescriptor("name")
+    category = StringDescriptor("reagent-category")
+    name = StringAttributeDescriptor("name")
 
     def __init__(self, lims, uri=None, id=None):
-        super(ReagentType, self).__init__(lims, uri, id)
+        super().__init__(lims, uri, id)
         assert self.uri is not None
         self.root = lims.get(self.uri)
         self.sequence = None
-        for t in self.root.findall('special-type'):
+        for t in self.root.findall("special-type"):
             if t.attrib.get("name") == "Index":
                 for child in t.findall("attribute"):
                     if child.attrib.get("name") == "Sequence":
                         self.sequence = child.attrib.get("value")
 
+
 class Queue(Entity):
     """Queue of a given step. Will recursively get all the pages of artifacts, and therefore, can be quite slow to load"""
+
     _URI = "queues"
-    _TAG= "queue"
+    _TAG = "queue"
     _PREFIX = "que"
 
-
     artifacts = MultiPageNestedEntityListDescriptor("artifact", Artifact, "artifacts")
 
-Sample.artifact          = EntityDescriptor('artifact', Artifact)
-StepActions.step         = EntityDescriptor('step', Step)
-Stage.workflow           = EntityDescriptor('workflow', Workflow)
-Artifact.workflow_stages = NestedEntityListDescriptor('workflow-stage', Stage, 'workflow-stages')
-Step.configuration       = EntityDescriptor('configuration', ProtocolStep)
-StepProgramStatus.configuration = EntityDescriptor('configuration', ProtocolStep)
-Researcher.roles = NestedEntityListDescriptor('role', Role, 'credentials')
 
+# Set class-interdependent class variables
+setattr(Sample, "artifact", EntityDescriptor("artifact", Artifact))
+setattr(StepActions, "step", EntityDescriptor("step", Step))
+setattr(Stage, "workflow", EntityDescriptor("workflow", Workflow))
+setattr(
+    Artifact,
+    "workflow_stages",
+    NestedEntityListDescriptor("workflow-stage", Stage, "workflow-stages"),
+)
+setattr(Step, "configuration", EntityDescriptor("configuration", ProtocolStep))
+setattr(
+    StepProgramStatus, "configuration", EntityDescriptor("configuration", ProtocolStep)
+)
+setattr(Researcher, "roles", NestedEntityListDescriptor("role", Role, "credentials"))
diff --git a/genologics/epp.py b/genologics/epp.py
index 08e18a1..8f241ed 100644
--- a/genologics/epp.py
+++ b/genologics/epp.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 """Contains useful and reusable code for EPP scripts.
 
 Classes, methods and exceptions.
@@ -7,83 +6,94 @@
 Copyright (C) 2013 Johannes Alneberg
 """
 
+import csv
 import logging
-import sys
 import os
+import sys
+from logging.handlers import RotatingFileHandler
+from shutil import copy
+from time import localtime, strftime
+
 import pkg_resources
 from pkg_resources import DistributionNotFound
-from shutil import copy
 from requests import HTTPError
-from genologics.entities import Artifact
+
 from genologics.config import MAIN_LOG
-from logging.handlers import RotatingFileHandler
-from time import strftime, localtime
-import csv
+from genologics.entities import Artifact
 
-def attach_file(src,resource):
+
+def attach_file(src, resource):
     """Attach file at src to given resource
 
     Copies the file to the current directory, EPP node will upload this file
     automatically if the process output is properly set up"""
     original_name = os.path.basename(src)
-    new_name = resource.id + '_' + original_name
+    new_name = resource.id + "_" + original_name
     dir = os.getcwd()
-    location = os.path.join(dir,new_name)
-    copy(src,location)
+    location = os.path.join(dir, new_name)
+    copy(src, location)
     return location
 
+
 class EmptyError(ValueError):
     "Raised if an iterator is unexpectedly empty."
+
     pass
 
+
 class NotUniqueError(ValueError):
     "Raised if there are unexpectedly more than 1 item in an iterator"
+
     pass
 
-def unique_check(l,msg):
+
+def unique_check(l, msg):
     "Check that l is of length 1, otherwise raise error, with msg appended"
-    if len(l)==0:
-        raise EmptyError("No item found for {0}".format(msg))
-    elif len(l)!=1:
-        raise NotUniqueError("Multiple items found for {0}".format(msg))
+    if len(l) == 0:
+        raise EmptyError(f"No item found for {msg}")
+    elif len(l) != 1:
+        raise NotUniqueError(f"Multiple items found for {msg}")
 
-def set_field(element):    
+
+def set_field(element):
     try:
         element.put()
     except (TypeError, HTTPError) as e:
-        logging.warning("Error while updating element: {0}".format(e))
-    
-class EppLogger(object):
+        logging.warning(f"Error while updating element: {e}")
+
 
+class EppLogger:
     """Context manager for logging module useful for EPP script execution.
 
     This context manager (CM) automatically logs what script that is executed,
     with what parameters it was executed and what version (including) commit
     hash of the genologics package used. Since EPP scripts are often ran
-    automatically by the genologics LIMS client, the stdout and stderr is 
+    automatically by the genologics LIMS client, the stdout and stderr is
     captured and logged within this CM. Stderr is duplicated so that the
     last line can be shown in the GUI. In order to track multiple runs
-    of the same process from the genologics LIMS GUI, the previous log 
+    of the same process from the genologics LIMS GUI, the previous log
     files can be prepended. Also a main log file can be used that is
     supposed to be common for all scripts executed on the server.
-    
+
     """
 
-    PACKAGE = 'genologics'
+    PACKAGE = "genologics"
+
     def __enter__(self):
-        logging.info('Executing file: {0}'.format(sys.argv[0]))
-        logging.info('with parameters: {0}'.format(sys.argv[1:]))
+        logging.info(f"Executing file: {sys.argv[0]}")
+        logging.info(f"with parameters: {sys.argv[1:]}")
         try:
-            logging.info('Version of {0}: '.format(self.PACKAGE) + 
-                         pkg_resources.require(self.PACKAGE)[0].version)
+            logging.info(
+                f"Version of {self.PACKAGE}: "
+                + pkg_resources.require(self.PACKAGE)[0].version
+            )
         except DistributionNotFound as e:
             logging.error(e)
-            logging.error(('Make sure you have the {0} '
-                           'package installed').format(self.PACKAGE))
+            logging.error(f"Make sure you have the {self.PACKAGE} " "package installed")
             sys.exit(-1)
         return self
 
-    def __exit__(self,exc_type,exc_val,exc_tb):
+    def __exit__(self, exc_type, exc_val, exc_tb):
         # If no exception has occured in block, turn off logging.
         if not exc_type:
             logging.shutdown()
@@ -92,12 +102,12 @@ def __exit__(self,exc_type,exc_val,exc_tb):
         # Do not repress possible exception
         return False
 
-    def __init__(self,log_file=None,level=logging.INFO,lims=None,prepend=False):
-        """ Initialize the logger with custom settings.
+    def __init__(self, log_file=None, level=logging.INFO, lims=None, prepend=False):
+        """Initialize the logger with custom settings.
 
         Arguments:
         log_file  -- file to write individual log to
-        
+
         Keyword Arguments:
         level   -- Logging level, default logging.INFO
         lims    -- Lims instance, needed for prepend to work
@@ -112,45 +122,44 @@ def __init__(self,log_file=None,level=logging.INFO,lims=None,prepend=False):
             self.prepend_old_log()
 
         # Loggers that will capture stdout and stderr respectively
-        stdout_logger = logging.getLogger('STDOUT')
+        stdout_logger = logging.getLogger("STDOUT")
         self.slo = self.StreamToLogger(stdout_logger, logging.INFO)
         self.saved_stdout = sys.stdout
         sys.stdout = self.slo
 
-        stderr_logger = logging.getLogger('STDERR')
+        stderr_logger = logging.getLogger("STDERR")
         self.saved_stderr = sys.stderr
         # Duplicate stderr stream to log
-        self.sle = self.StreamToLogger(stderr_logger, logging.INFO,
-                                       self.saved_stderr)
+        self.sle = self.StreamToLogger(stderr_logger, logging.INFO, self.saved_stderr)
         sys.stderr = self.sle
 
         # Root logger with filehandler(s)
         self.logger = logging.getLogger()
         self.logger.setLevel(self.level)
-        formatter = logging.Formatter(
-            '%(asctime)s:%(levelname)s:%(name)s:%(message)s')
+        formatter = logging.Formatter("%(asctime)s:%(levelname)s:%(name)s:%(message)s")
         if self.log_file:
-            individual_fh = logging.FileHandler(self.log_file,mode='a')
+            individual_fh = logging.FileHandler(self.log_file, mode="a")
             individual_fh.setFormatter(formatter)
             self.logger.addHandler(individual_fh)
 
         if MAIN_LOG:
             # Rotating file handler, that will create up to 10 backup logs,
             # each no bigger than 100MB.
-            main_fh = RotatingFileHandler(MAIN_LOG,mode='a',
-                                          maxBytes=1e8,backupCount=10)
+            main_fh = RotatingFileHandler(
+                MAIN_LOG, mode="a", maxBytes=1e8, backupCount=10
+            )
             main_fh.setFormatter(formatter)
             self.logger.addHandler(main_fh)
         else:
-            self.logger.warning('No main log file found.')
+            self.logger.warning("No main log file found.")
 
-    def prepend_old_log(self, external_log_file = None):
-        """Prepend the old log to the new log. 
+    def prepend_old_log(self, external_log_file=None):
+        """Prepend the old log to the new log.
 
-        The location of the old log file is retrieved through the REST api. 
+        The location of the old log file is retrieved through the REST api.
         In order to work, the script should be executed on the LIMS server
         since the location on the disk is parsed out from the sftp string
-        and then used for local copy of file. 
+        and then used for local copy of file.
 
         This method does not use logging since that could mess up the
         logging settings, instead warnings are printed to stderr."""
@@ -162,36 +171,44 @@ def prepend_old_log(self, external_log_file = None):
         local_log_path = os.path.join(os.getcwd(), log_file_name)
         if not os.path.isfile(local_log_path):
             try:
-                log_artifact = Artifact(self.lims,id = log_file_name)
+                log_artifact = Artifact(self.lims, id=log_file_name)
                 log_artifact.get()
                 if log_artifact.files:
                     log_path = log_artifact.files[0].content_location.split(
-                        self.lims.baseuri.split(':')[1])[1]
+                        self.lims.baseuri.split(":")[1]
+                    )[1]
                     copy(log_path, local_log_path)
-                    with open(local_log_path,'a') as f:
-                        f.write('='*80+'\n')
-            except HTTPError: # Probably no artifact found, skip prepending
-                print(('No log file artifact found '
-                                      'for id: {0}').format(log_file_name), file=sys.stderr)
-            except IOError as e: # Probably some path was wrong in copy
-                print(('Log could not be prepended, '
-                                      'make sure {0} and {1} are '
-                                      'proper paths.').format(log_path, 
-                                                              log_file_name), file=sys.stderr)
+                    with open(local_log_path, "a") as f:
+                        f.write("=" * 80 + "\n")
+            except HTTPError:  # Probably no artifact found, skip prepending
+                print(
+                    ("No log file artifact found " f"for id: {log_file_name}"),
+                    file=sys.stderr,
+                )
+            except OSError as e:  # Probably some path was wrong in copy
+                print(
+                    (
+                        "Log could not be prepended, "
+                        f"make sure {log_path} and {log_file_name} are "
+                        "proper paths."
+                    ),
+                    file=sys.stderr,
+                )
                 raise e
 
-    class StreamToLogger(object):
-        """Fake file-like stream object that redirects writes to a logger 
+    class StreamToLogger:
+        """Fake file-like stream object that redirects writes to a logger
         instance.
-        
-        source: 
+
+        source:
         http://www.electricmonk.nl/log/2011/08/14/
         redirect-stdout-and-stderr-to-a-logger-in-python/
         """
+
         def __init__(self, logger, log_level=logging.INFO, stream=None):
             self.logger = logger
             self.log_level = log_level
-            self.linebuf = ''
+            self.linebuf = ""
             self.stream = stream
 
         def write(self, buf):
@@ -200,26 +217,27 @@ def write(self, buf):
             for line in buf.rstrip().splitlines():
                 self.logger.log(self.log_level, line.rstrip())
 
-class ReadResultFiles():
+
+class ReadResultFiles:
     """Class to read pars different kinds of result files from a process.
-    The class stores the parsed content of all shared result files in a 
-    dictionary 'shared_files'. The data is parsed as lists of lists. """
+    The class stores the parsed content of all shared result files in a
+    dictionary 'shared_files'. The data is parsed as lists of lists."""
 
     def __init__(self, process):
         self.process = process
-        self.shared_files = self._pars_file('SharedResultFile')
-        self.perinput_files = self._pars_file('ResultFile')
+        self.shared_files = self._pars_file("SharedResultFile")
+        self.perinput_files = self._pars_file("ResultFile")
 
     def get_file_path(self, artifact):
         if len(artifact.files) > 0:
             file = artifact.files[0]
-            file_path = file.content_location.split('scilifelab.se')[1]
-            if len(file_path.split('.')) > 1:
+            file_path = file.content_location.split("scilifelab.se")[1]
+            if len(file_path.split(".")) > 1:
                 return file_path
         return None
 
     def _pars_file(self, output_type):
-        """Reads a csv or txt into a list of lists, where sub lists are lines 
+        """Reads a csv or txt into a list of lists, where sub lists are lines
         of the csv."""
         outs = self.process.all_outputs()
         outarts = [a for a in outs if a.output_type == output_type]
@@ -227,90 +245,99 @@ def _pars_file(self, output_type):
         for outart in outarts:
             file_path = self.get_file_path(outart)
             if file_path:
-                of = open(file_path ,'r')
-                file_ext = file_path.split('.')[-1]
-                if file_ext == 'csv':
+                of = open(file_path)
+                file_ext = file_path.split(".")[-1]
+                if file_ext == "csv":
                     pf = [row for row in csv.reader(of.read().splitlines())]
                     parsed_files[outart.name] = pf
-                elif file_ext == 'txt':
-                    pf = [row.strip().strip('\\').split('\t') for row in of.readlines()]
+                elif file_ext == "txt":
+                    pf = [row.strip().strip("\\").split("\t") for row in of.readlines()]
                     parsed_files[outart.name] = pf
                 of.close()
         return parsed_files
 
-    def format_file(self, parsed_file, name = '', first_header = None, 
-                    header_row = None, root_key_col = 0, find_keys = []):
+    def format_file(
+        self,
+        parsed_file,
+        name="",
+        first_header=None,
+        header_row=None,
+        root_key_col=0,
+        find_keys=[],
+    ):
         """Function to format a parsed csv or txt file.
 
         Arguments and Output:
             parsed_file     A list of lists where sublists are rows of the csv.
-            name            Name of parsed file. 
-            first_header    First column of the heather section in the file. 
+            name            Name of parsed file.
+            first_header    First column of the heather section in the file.
                             default value is 'None'
-            root_key_col    If you want the root keys to be given by some other 
-                            column than the first one, set root_key_col to the 
+            root_key_col    If you want the root keys to be given by some other
+                            column than the first one, set root_key_col to the
                             column number.
-            header_row      Instead of specifying first_header you can choose 
-                            from what line to reed by setting header_row to the 
+            header_row      Instead of specifying first_header you can choose
+                            from what line to reed by setting header_row to the
                             row number where you want to start reading.
-            find_keys       List of row names to look for. Will exclude all 
+            find_keys       List of row names to look for. Will exclude all
                             others.
-            file_info       Dict of dicts. Keys of root dict are the first 
-                            column in the csv starting from the line after the 
-                            heather line. Keys of sub dicts are the columns of 
+            file_info       Dict of dicts. Keys of root dict are the first
+                            column in the csv starting from the line after the
+                            heather line. Keys of sub dicts are the columns of
                             the heather line."""
         file_info = {}
         keys = []
-        error_message = ''
+        error_message = ""
         duplicated_lines = []
-        exeptions = ['Sample','Fail', '']
-        if type(first_header) is not list:
+        exeptions = ["Sample", "Fail", ""]
+        if not isinstance(first_header, list):
             if first_header:
-                first_header=[first_header]
+                first_header = [first_header]
             else:
-                first_header=[]
+                first_header = []
         for row, line in enumerate(parsed_file):
-            if keys and len(line)==len(keys):
+            if keys and len(line) == len(keys):
                 root_key = line[root_key_col]
                 cond1 = find_keys == [] and root_key not in exeptions
                 cond2 = root_key in find_keys
                 if root_key in file_info:
                     duplicated_lines.append(root_key)
-                elif (cond1 or cond2): 
+                elif cond1 or cond2:
                     file_info[root_key] = {}
                     if not duplicated_lines:
                         for col in range(len(keys)):
-                            if keys[col] != '':
+                            if keys[col] != "":
                                 file_info[root_key][keys[col]] = line[col]
-                            elif keys[col-1] != '':
-                                tupl = (file_info[root_key][keys[col-1]], line[col])
-                                file_info[root_key][keys[col-1]] = tupl
-        
+                            elif keys[col - 1] != "":
+                                tupl = (file_info[root_key][keys[col - 1]], line[col])
+                                file_info[root_key][keys[col - 1]] = tupl
+
             head = line[root_key_col] if len(line) > root_key_col else None
             if first_header and head in first_header:
                 keys = line
             elif header_row and row == header_row:
                 keys = line
         if duplicated_lines:
-            error_message = ("Row names {0} occurs more than once in file {1}. "
-                "Fix the file to continue. ").format(','.join(duplicated_lines), name)
+            error_message = (
+                "Row names {} occurs more than once in file {}. "
+                "Fix the file to continue. "
+            ).format(",".join(duplicated_lines), name)
         if not file_info:
-            error_message = error_message + "Could not format parsed file {0}.".format(name)
+            error_message = error_message + f"Could not format parsed file {name}."
         if error_message:
             print(error_message, file=sys.stderr)
-            sys.exit(-1)    
+            sys.exit(-1)
         return file_info
 
 
-class CopyField(object):
-    """Class to copy any filed (or udf) from any lims element to any 
+class CopyField:
+    """Class to copy any filed (or udf) from any lims element to any
     udf on any other lims element
 
     arguments:
 
     s_elt           source element - instance of a type
     d_elt           destination element - instance of a type
-    s_field_name    name of source field (or udf) to be copied 
+    s_field_name    name of source field (or udf) to be copied
     d_udf_name      name of destination udf name. If not specified
                     s_field_name will be used.
 
@@ -319,7 +346,8 @@ class CopyField(object):
 
     Written by Maya Brandi and Johannes Alnberg
     """
-    def __init__(self, s_elt, d_elt, s_field_name, d_udf_name = None):
+
+    def __init__(self, s_elt, d_elt, s_field_name, d_udf_name=None):
         if not d_udf_name:
             d_udf_name = s_field_name
         self.s_elt = s_elt
@@ -348,37 +376,48 @@ def _set_udf(self, elt, udf_name, val):
             elt.put()
             return True
         except (TypeError, HTTPError) as e:
-            print("Error while updating element: {0}".format(e), file=sys.stderr)
+            print(f"Error while updating element: {e}", file=sys.stderr)
             sys.exit(-1)
             return False
 
     def _log_before_change(self, changelog_f=None):
         if changelog_f:
-            d = {'ct' : self._current_time(),
-                 's_udf' : self.s_field_name,
-                 'sn' : self.d_elt.name,
-                 'si' : self.d_elt.id,
-                 'su' : self.old_dest_udf,
-                 'nv' : self.s_field,
-                 'd_elt_type': self.d_type}
-
-            changelog_f.write(("{ct}: udf: '{s_udf}' on {d_elt_type}: '{sn}' ("
-                "id: {si}) is changed from '{su}' to '{nv}'.\n").format(**d))
-
-        logging.info(("Copying from element with id: {0} to element with "
-                      " id: {1}").format(self.s_elt.id, self.d_elt.id))
+            d = {
+                "ct": self._current_time(),
+                "s_udf": self.s_field_name,
+                "sn": self.d_elt.name,
+                "si": self.d_elt.id,
+                "su": self.old_dest_udf,
+                "nv": self.s_field,
+                "d_elt_type": self.d_type,
+            }
+
+            changelog_f.write(
+                (
+                    "{ct}: udf: '{s_udf}' on {d_elt_type}: '{sn}' ("
+                    "id: {si}) is changed from '{su}' to '{nv}'.\n"
+                ).format(**d)
+            )
+
+        logging.info(
+            f"Copying from element with id: {self.s_elt.id} to element with "
+            f" id: {self.d_elt.id}"
+        )
 
     def _log_after_change(self):
-        d = {'s_udf': self.s_field_name,
-             'd_udf': self.d_udf_name,
-             'su': self.old_dest_udf,
-             'nv': self.s_field,
-             'd_elt_type': self.d_type}
-
-        logging.info("Updated {d_elt_type} udf: {d_udf}, from {su} to "
-                                                            "{nv}.".format(**d))
-
-    def copy_udf(self, changelog_f = None):
+        d = {
+            "s_udf": self.s_field_name,
+            "d_udf": self.d_udf_name,
+            "su": self.old_dest_udf,
+            "nv": self.s_field,
+            "d_elt_type": self.d_type,
+        }
+
+        logging.info(
+            "Updated {d_elt_type} udf: {d_udf}, from {su} to " "{nv}.".format(**d)
+        )
+
+    def copy_udf(self, changelog_f=None):
         if self.s_field != self.old_dest_udf:
             self._log_before_change(changelog_f)
             log = self._set_udf(self.d_elt, self.d_udf_name, self.s_field)
@@ -386,6 +425,3 @@ def copy_udf(self, changelog_f = None):
             return log
         else:
             return False
-
-
-
diff --git a/genologics/internal_classes.py b/genologics/internal_classes.py
index 184de5e..9501d5d 100644
--- a/genologics/internal_classes.py
+++ b/genologics/internal_classes.py
@@ -1,42 +1,46 @@
-from genologics.descriptors import StringDescriptor, EntityListDescriptor, BooleanDescriptor, IntegerDescriptor
-from genologics.entities import File, Udfconfig
 from genologics.constants import nsmap
+from genologics.descriptors import (
+    BooleanDescriptor,
+    EntityListDescriptor,
+    IntegerDescriptor,
+    StringDescriptor,
+)
+from genologics.entities import File, Udfconfig
 
 
-class ProcessTypeParameter(object):
-
+class ProcessTypeParameter:
     instance = None
     name = None
     root = None
-    tag = 'parameter'
+    tag = "parameter"
 
-    string = StringDescriptor('string')
-    run_program_per_event = StringDescriptor('run-program-per-event')
-    channel = StringDescriptor('channel')
-    invocation_type = StringDescriptor('invocation-type')
-    file = EntityListDescriptor(nsmap('file:file'), File)
+    string = StringDescriptor("string")
+    run_program_per_event = StringDescriptor("run-program-per-event")
+    channel = StringDescriptor("channel")
+    invocation_type = StringDescriptor("invocation-type")
+    file = EntityListDescriptor(nsmap("file:file"), File)
 
     def __init__(self, pt_instance, node):
         self.instance = pt_instance
         self.root = node
-        self.name = self.root.attrib['name']
+        self.name = self.root.attrib["name"]
 
     def __repr__(self):
-        return "{0}({1})".format(self.__class__.__name__, self.name)
+        return f"{self.__class__.__name__}({self.name})"
 
     def get(self):
         pass
 
-class ProcessTypeProcessInput(object):
 
+class ProcessTypeProcessInput:
     instance = None
     name = None
     root = None
-    tag = ''
+    tag = ""
 
-    artifact_type = StringDescriptor('artifact-type')
-    display_name = StringDescriptor('display-name')
-    remove_working_flag = BooleanDescriptor('remove-working-flag')
+    artifact_type = StringDescriptor("artifact-type")
+    display_name = StringDescriptor("display-name")
+    remove_working_flag = BooleanDescriptor("remove-working-flag")
 
     def __init__(self, pt_instance, node):
         self.instance = pt_instance
@@ -44,26 +48,25 @@ def __init__(self, pt_instance, node):
         self.lims = pt_instance.lims
 
     def __repr__(self):
-        return "{0}({1})".format(self.__class__.__name__, self.display_name)
+        return f"{self.__class__.__name__}({self.display_name})"
 
     def get(self):
         pass
 
 
-class ProcessTypeProcessOutput(object):
-
+class ProcessTypeProcessOutput:
     instance = None
     name = None
     root = None
-    tag = ''
+    tag = ""
 
-    artifact_type = StringDescriptor('artifact-type')
-    display_name = StringDescriptor('display-name')
-    output_generation_type = StringDescriptor('output-generation-type')
-    variability_type = StringDescriptor('variability-type')
-    number_of_outputs = IntegerDescriptor('number-of-outputs')
-    output_name = StringDescriptor('output-name')
-    field_definitions = EntityListDescriptor('field-definition', Udfconfig)
+    artifact_type = StringDescriptor("artifact-type")
+    display_name = StringDescriptor("display-name")
+    output_generation_type = StringDescriptor("output-generation-type")
+    variability_type = StringDescriptor("variability-type")
+    number_of_outputs = IntegerDescriptor("number-of-outputs")
+    output_name = StringDescriptor("output-name")
+    field_definitions = EntityListDescriptor("field-definition", Udfconfig)
 
     def __init__(self, pt_instance, node):
         self.instance = pt_instance
@@ -71,7 +74,7 @@ def __init__(self, pt_instance, node):
         self.lims = pt_instance.lims
 
     def __repr__(self):
-        return "{0}({1})".format(self.__class__.__name__, self.output_name)
+        return f"{self.__class__.__name__}({self.output_name})"
 
     def get(self):
         pass
diff --git a/genologics/lims.py b/genologics/lims.py
index 221f662..c6c92cb 100644
--- a/genologics/lims.py
+++ b/genologics/lims.py
@@ -6,48 +6,63 @@
 Copyright (C) 2012 Per Kraulis
 """
 
-__all__ = ['Lab', 'Researcher', 'Project', 'Sample',
-           'Containertype', 'Container', 'Processtype', 'Process',
-           'Artifact', 'Lims']
+__all__ = [
+    "Lab",
+    "Researcher",
+    "Project",
+    "Sample",
+    "Containertype",
+    "Container",
+    "Processtype",
+    "Process",
+    "Artifact",
+    "Lims",
+]
 
 import os
 import re
 from io import BytesIO
-import requests
 
 # python 2.7, 3+ compatibility
-from sys import version_info
-
-if version_info[0] == 2:
-    from urlparse import urljoin
-    from urllib import urlencode
-else:
-    from urllib.parse import urljoin
-    from urllib.parse import urlencode
+from urllib.parse import urlencode, urljoin
+from xml.etree import ElementTree
 
+import requests
 
-from .entities import *
+from genologics.constants import nsmap
+
+from .entities import (
+    Artifact,
+    Automation,
+    Container,
+    Containertype,
+    File,
+    Instrument,
+    Lab,
+    Process,
+    Processtype,
+    Project,
+    Protocol,
+    ReagentKit,
+    ReagentLot,
+    ReagentType,
+    Researcher,
+    Sample,
+    Udfconfig,
+    Workflow,
+)
 
 # Python 2.6 support work-arounds
 # - Exception ElementTree.ParseError does not exist
 # - ElementTree.ElementTree.write does not take arg. xml_declaration
-if version_info[:2] < (2,7):
-    from xml.parsers import expat
-    ElementTree.ParseError = expat.ExpatError
-    p26_write = ElementTree.ElementTree.write
-    def write_with_xml_declaration(self, file, encoding, xml_declaration):
-        assert xml_declaration is True # Support our use case only
-        file.write("<?xml version='1.0' encoding='utf-8'?>\n")
-        p26_write(self, file, encoding=encoding)
-    ElementTree.ElementTree.write = write_with_xml_declaration
 
 TIMEOUT = 16
 
 
-class Lims(object):
+class Lims:
     "LIMS interface through which all entity instances are retrieved."
 
-    VERSION = 'v2'
+    VERSION = "v2"
 
     def __init__(self, baseuri, username, password, version=VERSION):
         """baseuri: Base URI for the GenoLogics server, excluding
@@ -57,7 +72,7 @@ def __init__(self, baseuri, username, password, version=VERSION):
         password: The password for the user account to login as.
         version: The optional LIMS API version, by default 'v2'
         """
-        self.baseuri = baseuri.rstrip('/') + '/'
+        self.baseuri = baseuri.rstrip("/") + "/"
         self.username = username
         self.password = password
         self.VERSION = version
@@ -65,26 +80,31 @@ def __init__(self, baseuri, username, password, version=VERSION):
         # For optimization purposes, enables requests to persist connections
         self.request_session = requests.Session()
         # The connection pool has a default size of 10
-        self.adapter = requests.adapters.HTTPAdapter(pool_connections=100, pool_maxsize=100)
-        self.request_session.mount('http://', self.adapter)
+        self.adapter = requests.adapters.HTTPAdapter(
+            pool_connections=100, pool_maxsize=100
+        )
+        self.request_session.mount("http://", self.adapter)
 
     def get_uri(self, *segments, **query):
         "Return the full URI given the path segments and optional query."
-        segments = ['api', self.VERSION] + list(segments)
-        url = urljoin(self.baseuri, '/'.join(segments))
+        segments = ["api", self.VERSION] + list(segments)
+        url = urljoin(self.baseuri, "/".join(segments))
         if query:
-            url += '?' + urlencode(query)
+            url += "?" + urlencode(query)
         return url
 
     def get(self, uri, params=dict()):
         "GET data from the URI. Return the response XML as an ElementTree."
         try:
-            r = self.request_session.get(uri, params=params,
-                                         auth=(self.username, self.password),
-                                         headers=dict(accept='application/xml'),
-                                         timeout=TIMEOUT)
+            r = self.request_session.get(
+                uri,
+                params=params,
+                auth=(self.username, self.password),
+                headers=dict(accept="application/xml"),
+                timeout=TIMEOUT,
+            )
         except requests.exceptions.Timeout as e:
-            raise type(e)("{0}, Error trying to reach {1}".format(str(e), uri))
+            raise type(e)(f"{str(e)}, Error trying to reach {uri}")
 
         else:
             return self.parse_response(r)
@@ -92,15 +112,17 @@ def get(self, uri, params=dict()):
     def get_file_contents(self, id=None, uri=None):
         """Returns the contents of the file of <ID> or <uri>"""
         if id:
-            segments = ['api', self.VERSION, 'files', id, 'download']
+            segments = ["api", self.VERSION, "files", id, "download"]
         elif uri:
-            segments = [uri, 'download']
+            segments = [uri, "download"]
         else:
             raise ValueError("id or uri required")
-        url = urljoin(self.baseuri, '/'.join(segments))
-        r = self.request_session.get(url, auth=(self.username, self.password), timeout=TIMEOUT, stream=True)
+        url = urljoin(self.baseuri, "/".join(segments))
+        r = self.request_session.get(
+            url, auth=(self.username, self.password), timeout=TIMEOUT, stream=True
+        )
         self.validate_response(r)
-        if 'text' in r.headers['Content-Type']:
+        if "text" in r.headers["Content-Type"]:
             return r.text
         else:
             return r.raw
@@ -109,31 +131,33 @@ def upload_new_file(self, entity, file_to_upload):
         """Upload a file and attach it to the provided entity."""
         file_to_upload = os.path.abspath(file_to_upload)
         if not os.path.isfile(file_to_upload):
-            raise IOError("{} not found".format(file_to_upload))
+            raise OSError(f"{file_to_upload} not found")
 
         # Request the storage space on glsstorage
         # Create the xml to describe the file
-        root = ElementTree.Element(nsmap('file:file'))
-        s = ElementTree.SubElement(root, 'attached-to')
+        root = ElementTree.Element(nsmap("file:file"))
+        s = ElementTree.SubElement(root, "attached-to")
         s.text = entity.uri
-        s = ElementTree.SubElement(root, 'original-location')
+        s = ElementTree.SubElement(root, "original-location")
         s.text = file_to_upload
         root = self.post(
-                uri=self.get_uri('glsstorage'),
-                data=self.tostring(ElementTree.ElementTree(root))
+            uri=self.get_uri("glsstorage"),
+            data=self.tostring(ElementTree.ElementTree(root)),
         )
 
         # Create the file object
         root = self.post(
-                uri=self.get_uri('files'),
-                data=self.tostring(ElementTree.ElementTree(root))
+            uri=self.get_uri("files"), data=self.tostring(ElementTree.ElementTree(root))
         )
-        file = File(self, uri=root.attrib['uri'])
+        file = File(self, uri=root.attrib["uri"])
 
         # Actually upload the file
-        uri = self.get_uri('files', file.id, 'upload')
-        r = requests.post(uri, files={'file': (file_to_upload, open(file_to_upload, 'rb'))},
-                          auth=(self.username, self.password))
+        uri = self.get_uri("files", file.id, "upload")
+        r = requests.post(
+            uri,
+            files={"file": (file_to_upload, open(file_to_upload, "rb"))},
+            auth=(self.username, self.password),
+        )
         self.validate_response(r)
         return file
 
@@ -141,44 +165,53 @@ def put(self, uri, data, params=dict()):
         """PUT the serialized XML to the given URI.
         Return the response XML as an ElementTree.
         """
-        r = requests.put(uri, data=data, params=params,
-                         auth=(self.username, self.password),
-                         headers={'content-type': 'application/xml',
-                                  'accept': 'application/xml'})
+        r = requests.put(
+            uri,
+            data=data,
+            params=params,
+            auth=(self.username, self.password),
+            headers={"content-type": "application/xml", "accept": "application/xml"},
+        )
         return self.parse_response(r)
 
     def post(self, uri, data, params=dict()):
         """POST the serialized XML to the given URI.
         Return the response XML as an ElementTree.
         """
-        r = requests.post(uri, data=data, params=params,
-                          auth=(self.username, self.password),
-                          headers={'content-type': 'application/xml',
-                                   'accept': 'application/xml'})
+        r = requests.post(
+            uri,
+            data=data,
+            params=params,
+            auth=(self.username, self.password),
+            headers={"content-type": "application/xml", "accept": "application/xml"},
+        )
         return self.parse_response(r, accept_status_codes=[200, 201, 202])
 
     def delete(self, uri, params=dict()):
         """sends a DELETE to the given URI.
         Return the response XML as an ElementTree.
         """
-        r = requests.delete(uri, params=params,
-                          auth=(self.username, self.password),
-                          headers={'content-type': 'application/xml',
-                                   'accept': 'application/xml'})
+        r = requests.delete(
+            uri,
+            params=params,
+            auth=(self.username, self.password),
+            headers={"content-type": "application/xml", "accept": "application/xml"},
+        )
         return self.validate_response(r, accept_status_codes=[204])
 
     def check_version(self):
         """Raise ValueError if the version for this interface
         does not match any of the versions given for the API.
         """
-        uri = urljoin(self.baseuri, 'api')
+        uri = urljoin(self.baseuri, "api")
         r = requests.get(uri, auth=(self.username, self.password))
         root = self.parse_response(r)
-        tag = nsmap('ver:versions')
+        tag = nsmap("ver:versions")
         assert tag == root.tag
-        for node in root.findall('version'):
-            if node.attrib['major'] == self.VERSION: return
-        raise ValueError('version mismatch')
+        for node in root.findall("version"):
+            if node.attrib["major"] == self.VERSION:
+                return
+        raise ValueError("version mismatch")
 
     def validate_response(self, response, accept_status_codes=[200]):
         """Parse the XML returned in the response.
@@ -188,16 +221,18 @@ def validate_response(self, response, accept_status_codes=[200]):
         if response.status_code not in accept_status_codes:
             try:
                 root = ElementTree.fromstring(response.content)
-                node = root.find('message')
+                node = root.find("message")
                 if node is None:
                     response.raise_for_status()
-                    message = "%s" % (response.status_code)
+                    message = f"{response.status_code}"
                 else:
-                    message = "%s: %s" % (response.status_code, node.text)
-                node = root.find('suggested-actions')
+                    message = f"{response.status_code}: {node.text}"
+                node = root.find("suggested-actions")
                 if node is not None:
-                    message += ' ' + node.text
-            except ElementTree.ParseError:  # some error messages might not follow the xml standard
+                    message += " " + node.text
+            except (
+                ElementTree.ParseError
+            ):  # some error messages might not follow the xml standard
                 message = response.content
             raise requests.exceptions.HTTPError(message, response=response)
         return True
@@ -210,32 +245,48 @@ def parse_response(self, response, accept_status_codes=[200]):
         root = ElementTree.fromstring(response.content)
         return root
 
-    def get_udfs(self, name=None, attach_to_name=None, attach_to_category=None, start_index=None, add_info=False):
+    def get_udfs(
+        self,
+        name=None,
+        attach_to_name=None,
+        attach_to_category=None,
+        start_index=None,
+        add_info=False,
+    ):
         """Get a list of udfs, filtered by keyword arguments.
         name: name of udf
-        attach_to_name: item in the system, to wich the udf is attached, such as
+        attach_to_name: item in the system, to which the udf is attached, such as
             Sample, Project, Container, or the name of a process.
         attach_to_category: If 'attach_to_name' is the name of a process, such as 'CaliperGX QC (DNA)',
              then you need to set attach_to_category='ProcessType'. Must not be provided otherwise.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name,
-                                  attach_to_name=attach_to_name,
-                                  attach_to_category=attach_to_category,
-                                  start_index=start_index)
+        params = self._get_params(
+            name=name,
+            attach_to_name=attach_to_name,
+            attach_to_category=attach_to_category,
+            start_index=start_index,
+        )
         return self._get_instances(Udfconfig, add_info=add_info, params=params)
 
-    def get_reagent_types(self, name=None, start_index=None):
+    def get_reagent_types(self, name=None, start_index=None, add_info=False):
         """Get a list of reqgent types, filtered by keyword arguments.
         name: reagent type  name, or list of names.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name,
-                                  start_index=start_index)
-        return self._get_instances(ReagentType, params=params)
+        params = self._get_params(name=name, start_index=start_index)
+        return self._get_instances(ReagentType, add_info=add_info, params=params)
 
-    def get_labs(self, name=None, last_modified=None,
-                 udf=dict(), udtname=None, udt=dict(), start_index=None, add_info=False):
+    def get_labs(
+        self,
+        name=None,
+        last_modified=None,
+        udf=dict(),
+        udtname=None,
+        udt=dict(),
+        start_index=None,
+        add_info=False,
+    ):
         """Get a list of labs, filtered by keyword arguments.
         name: Lab name, or list of names.
         last_modified: Since the given ISO format datetime.
@@ -245,16 +296,24 @@ def get_labs(self, name=None, last_modified=None,
              and a string or list of strings as value.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name,
-                                  last_modified=last_modified,
-                                  start_index=start_index)
+        params = self._get_params(
+            name=name, last_modified=last_modified, start_index=start_index
+        )
         params.update(self._get_params_udf(udf=udf, udtname=udtname, udt=udt))
         return self._get_instances(Lab, add_info=add_info, params=params)
 
-    def get_researchers(self, firstname=None, lastname=None, username=None,
-                        last_modified=None,
-                        udf=dict(), udtname=None, udt=dict(), start_index=None,
-                        add_info=False):
+    def get_researchers(
+        self,
+        firstname=None,
+        lastname=None,
+        username=None,
+        last_modified=None,
+        udf=dict(),
+        udtname=None,
+        udt=dict(),
+        start_index=None,
+        add_info=False,
+    ):
         """Get a list of researchers, filtered by keyword arguments.
         firstname: Researcher first name, or list of names.
         lastname: Researcher last name, or list of names.
@@ -266,17 +325,27 @@ def get_researchers(self, firstname=None, lastname=None, username=None,
              and a string or list of strings as value.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(firstname=firstname,
-                                  lastname=lastname,
-                                  username=username,
-                                  last_modified=last_modified,
-                                  start_index=start_index)
+        params = self._get_params(
+            firstname=firstname,
+            lastname=lastname,
+            username=username,
+            last_modified=last_modified,
+            start_index=start_index,
+        )
         params.update(self._get_params_udf(udf=udf, udtname=udtname, udt=udt))
         return self._get_instances(Researcher, add_info=add_info, params=params)
 
-    def get_projects(self, name=None, open_date=None, last_modified=None,
-                     udf=dict(), udtname=None, udt=dict(), start_index=None,
-                     add_info=False):
+    def get_projects(
+        self,
+        name=None,
+        open_date=None,
+        last_modified=None,
+        udf=dict(),
+        udtname=None,
+        udt=dict(),
+        start_index=None,
+        add_info=False,
+    ):
         """Get a list of projects, filtered by keyword arguments.
         name: Project name, or list of names.
         open_date: Since the given ISO format date.
@@ -287,33 +356,54 @@ def get_projects(self, name=None, open_date=None, last_modified=None,
              and a string or list of strings as value.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name,
-                                  open_date=open_date,
-                                  last_modified=last_modified,
-                                  start_index=start_index)
+        params = self._get_params(
+            name=name,
+            open_date=open_date,
+            last_modified=last_modified,
+            start_index=start_index,
+        )
         params.update(self._get_params_udf(udf=udf, udtname=udtname, udt=udt))
         return self._get_instances(Project, add_info=add_info, params=params)
 
-    def get_sample_number(self, name=None, projectname=None, projectlimsid=None,
-                          udf=dict(), udtname=None, udt=dict(), start_index=None):
+    def get_sample_number(
+        self,
+        name=None,
+        projectname=None,
+        projectlimsid=None,
+        udf=dict(),
+        udtname=None,
+        udt=dict(),
+        start_index=None,
+    ):
         """Gets the number of samples matching the query without fetching every
         sample, so it should be faster than len(get_samples()"""
-        params = self._get_params(name=name,
-                                  projectname=projectname,
-                                  projectlimsid=projectlimsid,
-                                  start_index=start_index)
+        params = self._get_params(
+            name=name,
+            projectname=projectname,
+            projectlimsid=projectlimsid,
+            start_index=start_index,
+        )
         params.update(self._get_params_udf(udf=udf, udtname=udtname, udt=udt))
         root = self.get(self.get_uri(Sample._URI), params=params)
         total = 0
-        while params.get('start-index') is None:  # Loop over all pages.
+        while params.get("start-index") is None:  # Loop over all pages.
             total += len(root.findall("sample"))
-            node = root.find('next-page')
-            if node is None: break
-            root = self.get(node.attrib['uri'], params=params)
+            node = root.find("next-page")
+            if node is None:
+                break
+            root = self.get(node.attrib["uri"], params=params)
         return total
 
-    def get_samples(self, name=None, projectname=None, projectlimsid=None,
-                    udf=dict(), udtname=None, udt=dict(), start_index=None):
+    def get_samples(
+        self,
+        name=None,
+        projectname=None,
+        projectlimsid=None,
+        udf=dict(),
+        udtname=None,
+        udt=dict(),
+        start_index=None,
+    ):
         """Get a list of samples, filtered by keyword arguments.
         name: Sample name, or list of names.
         projectlimsid: Samples for the project of the given LIMS id.
@@ -324,19 +414,35 @@ def get_samples(self, name=None, projectname=None, projectlimsid=None,
              and a string or list of strings as value.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name,
-                                  projectname=projectname,
-                                  projectlimsid=projectlimsid,
-                                  start_index=start_index)
+        params = self._get_params(
+            name=name,
+            projectname=projectname,
+            projectlimsid=projectlimsid,
+            start_index=start_index,
+        )
         params.update(self._get_params_udf(udf=udf, udtname=udtname, udt=udt))
         return self._get_instances(Sample, params=params)
 
-    def get_artifacts(self, name=None, type=None, process_type=None,
-                      artifact_flag_name=None, working_flag=None, qc_flag=None,
-                      sample_name=None, samplelimsid=None, artifactgroup=None, containername=None,
-                      containerlimsid=None, reagent_label=None,
-                      udf=dict(), udtname=None, udt=dict(), start_index=None,
-                      resolve=False):
+    def get_artifacts(
+        self,
+        name=None,
+        type=None,
+        process_type=None,
+        artifact_flag_name=None,
+        working_flag=None,
+        qc_flag=None,
+        sample_name=None,
+        samplelimsid=None,
+        artifactgroup=None,
+        containername=None,
+        containerlimsid=None,
+        reagent_label=None,
+        udf=dict(),
+        udtname=None,
+        udt=dict(),
+        start_index=None,
+        resolve=False,
+    ):
         """Get a list of artifacts, filtered by keyword arguments.
         name: Artifact name, or list of names.
         type: Artifact type, or list of types.
@@ -356,19 +462,21 @@ def get_artifacts(self, name=None, type=None, process_type=None,
              and a string or list of strings as value.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name,
-                                  type=type,
-                                  process_type=process_type,
-                                  artifact_flag_name=artifact_flag_name,
-                                  working_flag=working_flag,
-                                  qc_flag=qc_flag,
-                                  sample_name=sample_name,
-                                  samplelimsid=samplelimsid,
-                                  artifactgroup=artifactgroup,
-                                  containername=containername,
-                                  containerlimsid=containerlimsid,
-                                  reagent_label=reagent_label,
-                                  start_index=start_index)
+        params = self._get_params(
+            name=name,
+            type=type,
+            process_type=process_type,
+            artifact_flag_name=artifact_flag_name,
+            working_flag=working_flag,
+            qc_flag=qc_flag,
+            sample_name=sample_name,
+            samplelimsid=samplelimsid,
+            artifactgroup=artifactgroup,
+            containername=containername,
+            containerlimsid=containerlimsid,
+            reagent_label=reagent_label,
+            start_index=start_index,
+        )
         params.update(self._get_params_udf(udf=udf, udtname=udtname, udt=udt))
         if resolve:
             return self.get_batch(self._get_instances(Artifact, params=params))
@@ -382,10 +490,18 @@ def get_container_types(self, name=None, start_index=None):
         params = self._get_params(name=name, start_index=start_index)
         return self._get_instances(Containertype, params=params)
 
-    def get_containers(self, name=None, type=None,
-                       state=None, last_modified=None,
-                       udf=dict(), udtname=None, udt=dict(), start_index=None,
-                       add_info=False):
+    def get_containers(
+        self,
+        name=None,
+        type=None,
+        state=None,
+        last_modified=None,
+        udf=dict(),
+        udtname=None,
+        udt=dict(),
+        start_index=None,
+        add_info=False,
+    ):
         """Get a list of containers, filtered by keyword arguments.
         name: Containers name, or list of names.
         type: Container type, or list of types.
@@ -397,18 +513,29 @@ def get_containers(self, name=None, type=None,
              and a string or list of strings as value.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name,
-                                  type=type,
-                                  state=state,
-                                  last_modified=last_modified,
-                                  start_index=start_index)
+        params = self._get_params(
+            name=name,
+            type=type,
+            state=state,
+            last_modified=last_modified,
+            start_index=start_index,
+        )
         params.update(self._get_params_udf(udf=udf, udtname=udtname, udt=udt))
         return self._get_instances(Container, add_info=add_info, params=params)
 
-    def get_processes(self, last_modified=None, type=None,
-                      inputartifactlimsid=None,
-                      techfirstname=None, techlastname=None, projectname=None,
-                      udf=dict(), udtname=None, udt=dict(), start_index=None):
+    def get_processes(
+        self,
+        last_modified=None,
+        type=None,
+        inputartifactlimsid=None,
+        techfirstname=None,
+        techlastname=None,
+        projectname=None,
+        udf=dict(),
+        udtname=None,
+        udt=dict(),
+        start_index=None,
+    ):
         """Get a list of processes, filtered by keyword arguments.
         last_modified: Since the given ISO format datetime.
         type: Process type, or list of types.
@@ -422,23 +549,25 @@ def get_processes(self, last_modified=None, type=None,
         projectname: Name of project, or list of.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(last_modified=last_modified,
-                                  type=type,
-                                  inputartifactlimsid=inputartifactlimsid,
-                                  techfirstname=techfirstname,
-                                  techlastname=techlastname,
-                                  projectname=projectname,
-                                  start_index=start_index)
+        params = self._get_params(
+            last_modified=last_modified,
+            type=type,
+            inputartifactlimsid=inputartifactlimsid,
+            techfirstname=techfirstname,
+            techlastname=techlastname,
+            projectname=projectname,
+            start_index=start_index,
+        )
         params.update(self._get_params_udf(udf=udf, udtname=udtname, udt=udt))
         return self._get_instances(Process, params=params)
 
     def get_automations(self, name=None, add_info=False):
-        """Get the list of configured automations on the system """
+        """Get the list of configured automations on the system"""
         params = self._get_params(name=name)
         return self._get_instances(Automation, add_info=add_info, params=params)
 
     def get_workflows(self, name=None, add_info=False):
-        """Get the list of existing workflows on the system """
+        """Get the list of existing workflows on the system"""
         params = self._get_params(name=name)
         return self._get_instances(Workflow, add_info=add_info, params=params)
 
@@ -447,12 +576,8 @@ def get_process_types(self, displayname=None, add_info=False):
         params = self._get_params(displayname=displayname)
         return self._get_instances(Processtype, add_info=add_info, params=params)
 
-    def get_reagent_types(self, name=None, add_info=False):
-        params = self._get_params(name=name)
-        return self._get_instances(ReagentType, add_info=add_info, params=params)
-
     def get_protocols(self, name=None, add_info=False):
-        """Get the list of existing protocols on the system """
+        """Get the list of existing protocols on the system"""
         params = self._get_params(name=name)
         return self._get_instances(Protocol, add_info=add_info, params=params)
 
@@ -461,20 +586,19 @@ def get_reagent_kits(self, name=None, start_index=None, add_info=False):
         name: reagent kit  name, or list of names.
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name,
-                                  start_index=start_index)
+        params = self._get_params(name=name, start_index=start_index)
         return self._get_instances(ReagentKit, add_info=add_info, params=params)
 
-    def get_reagent_lots(self, name=None, kitname=None, number=None,
-                         start_index=None):
+    def get_reagent_lots(self, name=None, kitname=None, number=None, start_index=None):
         """Get a list of reagent lots, filtered by keyword arguments.
         name: reagent kit  name, or list of names.
         kitname: name of the kit this lots belong to
         number: lot number or list of lot number
         start_index: Page to retrieve; all if None.
         """
-        params = self._get_params(name=name, kitname=kitname, number=number,
-                                  start_index=start_index)
+        params = self._get_params(
+            name=name, kitname=kitname, number=number, start_index=start_index
+        )
         return self._get_instances(ReagentLot, params=params)
 
     def get_instruments(self, name=None):
@@ -486,19 +610,20 @@ def _get_params(self, **kwargs):
         "Convert keyword arguments to a kwargs dictionary."
         result = dict()
         for key, value in kwargs.items():
-            if value is None: continue
-            result[key.replace('_', '-')] = value
+            if value is None:
+                continue
+            result[key.replace("_", "-")] = value
         return result
 
     def _get_params_udf(self, udf=dict(), udtname=None, udt=dict()):
         "Convert UDF-ish arguments to a params dictionary."
         result = dict()
         for key, value in udf.items():
-            result["udf.%s" % key] = value
+            result[f"udf.{key}"] = value
         if udtname is not None:
-            result['udt.name'] = udtname
+            result["udt.name"] = udtname
         for key, value in udt.items():
-            result["udt.%s" % key] = value
+            result[f"udt.{key}"] = value
         return result
 
     def _get_instances(self, klass, add_info=None, params=dict()):
@@ -508,18 +633,19 @@ def _get_instances(self, klass, add_info=None, params=dict()):
         if tag is None:
             tag = klass.__name__.lower()
         root = self.get(self.get_uri(klass._URI), params=params)
-        while params.get('start-index') is None:  # Loop over all pages.
+        while params.get("start-index") is None:  # Loop over all pages.
             for node in root.findall(tag):
-                results.append(klass(self, uri=node.attrib['uri']))
+                results.append(klass(self, uri=node.attrib["uri"]))
                 info_dict = {}
                 for attrib_key in node.attrib:
-                    info_dict[attrib_key] = node.attrib['uri']
+                    info_dict[attrib_key] = node.attrib["uri"]
                 for subnode in node:
                     info_dict[subnode.tag] = subnode.text
                 additionnal_info_dicts.append(info_dict)
-            node = root.find('next-page')
-            if node is None: break
-            root = self.get(node.attrib['uri'], params=params)
+            node = root.find("next-page")
+            if node is None:
+                break
+            root = self.get(node.attrib["uri"], params=params)
         if add_info:
             return results, additionnal_info_dicts
         else:
@@ -544,26 +670,29 @@ def get_batch(self, instances, force=False):
         if not instances:
             return []
 
-        ALLOWED_TAGS = ('artifact', 'container', 'file', 'sample')
+        ALLOWED_TAGS = ("artifact", "container", "file", "sample")
         if instances[0]._TAG not in ALLOWED_TAGS:
-            raise TypeError("Cannot retrieve batch for instances of type '{}'".format(instances[0]._TAG))
+            raise TypeError(
+                f"Cannot retrieve batch for instances of type '{instances[0]._TAG}'"
+            )
 
-        root = ElementTree.Element(nsmap('ri:links'))
+        root = ElementTree.Element(nsmap("ri:links"))
         needs_request = False
         instance_map = {}
         for instance in instances:
             instance_map[instance.id] = instance
             if force or instance.root is None:
-                ElementTree.SubElement(root, 'link', dict(uri=instance.uri,
-                                                          rel=instance.__class__._URI))
+                ElementTree.SubElement(
+                    root, "link", dict(uri=instance.uri, rel=instance.__class__._URI)
+                )
                 needs_request = True
 
         if needs_request:
-            uri = self.get_uri(instance.__class__._URI, 'batch/retrieve')
+            uri = self.get_uri(instance.__class__._URI, "batch/retrieve")
             data = self.tostring(ElementTree.ElementTree(root))
             root = self.post(uri, data)
             for node in list(root):
-                instance = instance_map[node.attrib['limsid']]
+                instance = instance_map[node.attrib["limsid"]]
                 instance.root = node
         return list(instance_map.values())
 
@@ -573,9 +702,11 @@ def put_batch(self, instances):
         if not instances:
             return
 
-        ALLOWED_TAGS = ('artifact', 'container', 'file', 'sample')
+        ALLOWED_TAGS = ("artifact", "container", "file", "sample")
         if instances[0]._TAG not in ALLOWED_TAGS:
-            raise TypeError("Cannot update batch for instances of type '{}'".format(instances[0]._TAG))
+            raise TypeError(
+                f"Cannot update batch for instances of type '{instances[0]._TAG}'"
+            )
 
         root = None  # XML root element for batch request
 
@@ -585,33 +716,37 @@ def put_batch(self, instances):
                 # Tag is art:details, con:details, etc.
                 example_root = instance.root
                 ns_uri = re.match("{(.*)}.*", example_root.tag).group(1)
-                root = ElementTree.Element("{%s}details" % (ns_uri))
+                root = ElementTree.Element(f"{{{ns_uri}}}details")
 
             root.append(instance.root)
 
-        uri = self.get_uri(klass._URI, 'batch/update')
+        uri = self.get_uri(klass._URI, "batch/update")
         data = self.tostring(ElementTree.ElementTree(root))
         root = self.post(uri, data)
 
-    def route_artifacts(self, artifact_list, workflow_uri=None, stage_uri=None, unassign=False):
-        root = ElementTree.Element(nsmap('rt:routing'))
+    def route_artifacts(
+        self, artifact_list, workflow_uri=None, stage_uri=None, unassign=False
+    ):
+        root = ElementTree.Element(nsmap("rt:routing"))
         if unassign:
-            s = ElementTree.SubElement(root, 'unassign')
+            s = ElementTree.SubElement(root, "unassign")
         else:
-            s = ElementTree.SubElement(root, 'assign')
+            s = ElementTree.SubElement(root, "assign")
         if workflow_uri:
-            s.set('workflow-uri', workflow_uri)
+            s.set("workflow-uri", workflow_uri)
         if stage_uri:
-            s.set('stage-uri', stage_uri)
+            s.set("stage-uri", stage_uri)
         for artifact in artifact_list:
-            a = ElementTree.SubElement(s, 'artifact')
-            a.set('uri', artifact.uri)
-
-        uri = self.get_uri('route', 'artifacts')
-        r = requests.post(uri, data=self.tostring(ElementTree.ElementTree(root)),
-                          auth=(self.username, self.password),
-                          headers={'content-type': 'application/xml',
-                                   'accept': 'application/xml'})
+            a = ElementTree.SubElement(s, "artifact")
+            a.set("uri", artifact.uri)
+
+        uri = self.get_uri("route", "artifacts")
+        r = requests.post(
+            uri,
+            data=self.tostring(ElementTree.ElementTree(root)),
+            auth=(self.username, self.password),
+            headers={"content-type": "application/xml", "accept": "application/xml"},
+        )
         self.validate_response(r)
 
     def tostring(self, etree):
@@ -622,19 +757,23 @@ def tostring(self, etree):
 
     def write(self, outfile, etree):
         "Write the ElementTree contents as UTF-8 encoded XML to the open file."
-        etree.write(outfile, encoding='utf-8', xml_declaration=True)
+        etree.write(outfile, encoding="utf-8", xml_declaration=True)
 
     def create_container(self, container_type, name=None):
         """Create a new container of type container_type and returns it
         Akin to Container.create(lims type=container_type, name=name)"""
-        el = ElementTree.Element(nsmap('con:container'))
+        el = ElementTree.Element(nsmap("con:container"))
         if name is not None:
-            nm = ElementTree.SubElement(el, 'name')
+            nm = ElementTree.SubElement(el, "name")
             nm.text = name
 
-        ty = ElementTree.SubElement(el, 'type', attrib={'uri':container_type.uri, 'name':container_type.name})
-        ret_el = self.post(uri=self.get_uri('containers'), data=ElementTree.tostring(el))
-        ret_con = Container(self, uri=ret_el.attrib['uri'])
+        ElementTree.SubElement(
+            el, "type", attrib={"uri": container_type.uri, "name": container_type.name}
+        )
+        ret_el = self.post(
+            uri=self.get_uri("containers"), data=ElementTree.tostring(el)
+        )
+        ret_con = Container(self, uri=ret_el.attrib["uri"])
         ret_con.root = ret_el
 
         return ret_con
diff --git a/genologics/lims_utils.py b/genologics/lims_utils.py
index 4c8eff2..00f8626 100644
--- a/genologics/lims_utils.py
+++ b/genologics/lims_utils.py
@@ -1,69 +1,68 @@
 #!/usr/bin/env python
 
-from genologics.epp import EppLogger
 
-import logging
-import sys
-import os
-
-from genologics.lims import *
-from genologics.config import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, PASSWORD, USERNAME
+from genologics.lims import Artifact, Lims
 
 lims = Lims(BASEURI, USERNAME, PASSWORD)
 
+
 def get_run_info(fc):
-	fc_summary={}
-	for iom in fc.input_output_maps:
-		art = iom[0]['uri']
-		lane = art.location[1].split(':')[0]
-		if lane not in fc_summary:
-     			fc_summary[lane]= dict(list(art.udf.items())) #"%.2f" % val ----round??
-	return fc_summary
+    fc_summary = {}
+    for iom in fc.input_output_maps:
+        art = iom[0]["uri"]
+        lane = art.location[1].split(":")[0]
+        if lane not in fc_summary:
+            fc_summary[lane] = dict(list(art.udf.items()))  # "%.2f" % val ----round??
+    return fc_summary
+
 
 def procHistory(proc, samplename):
-    """Quick wat to get the ids of parent processes from the given process, 
+    """Quick way to get the ids of parent processes from the given process,
     while staying in a sample scope"""
-    hist=[]
-    artifacts = lims.get_artifacts(sample_name = samplename, type = 'Analyte')
-    not_done=True
-    starting_art=proc.input_per_sample(samplename)[0].id
+    hist = []
+    artifacts = lims.get_artifacts(sample_name=samplename, type="Analyte")
+    not_done = True
+    starting_art = proc.input_per_sample(samplename)[0].id
     while not_done:
-        not_done=False
+        not_done = False
         for o in artifacts:
             if o.id == starting_art:
                 if o.parent_process is None:
-                    #flow control : if there is no parent process, we can stop iterating, we're done.
-                    not_done=False
-                    break #breaks the for artifacts, we are done anyway.
+                    # flow control : if there is no parent process, we can stop iterating, we're done.
+                    not_done = False
+                    break  # breaks the for artifacts, we are done anyway.
                 else:
-                    not_done=True #keep the loop running
+                    not_done = True  # keep the loop running
                 hist.append(o.parent_process.id)
                 for i in o.parent_process.all_inputs():
                     if i in artifacts:
                         # while increment
-                        starting_art=i.id
+                        starting_art = i.id
 
-                        break #break the for allinputs, if we found the right one
-                break # breaks the for artifacts if we matched the current one
+                        break  # break the for allinputs, if we found the right one
+                break  # breaks the for artifacts if we matched the current one
     return hist
 
+
 def get_sequencing_info(fc):
     """Input: a process object 'fc', of type 'Illumina Sequencing (Illumina SBS) 4.0',
     Output: A dictionary where keys are lanes 1,2,...,8, and values are lane artifact udfs"""
-    fc_summary={}
+    fc_summary = {}
     for iom in fc.input_output_maps:
-        art = Artifact(lims,id = iom[0]['limsid'])
-        lane = art.location[1].split(':')[0]
+        art = Artifact(lims, id=iom[0]["limsid"])
+        lane = art.location[1].split(":")[0]
         if lane not in fc_summary:
-            fc_summary[lane]= dict(list(art.udf.items())) #"%.2f" % val ----round??
-            fc_summary[lane]['qc'] = art.qc_flag
+            fc_summary[lane] = dict(list(art.udf.items()))  # "%.2f" % val ----round??
+            fc_summary[lane]["qc"] = art.qc_flag
     return fc_summary
 
+
 def make_sample_artifact_maps(sample_name):
-    """outin: connects each out_art for a specific sample to its 
+    """outin: connects each out_art for a specific sample to its
     corresponding in_art and process. one-one relation"""
     outin = {}
-    artifacts = lims.get_artifacts(sample_name = sample_name, type = 'Analyte')
+    artifacts = lims.get_artifacts(sample_name=sample_name, type="Analyte")
     for outart in artifacts:
         try:
             pro = outart.parent_process
@@ -75,5 +74,3 @@ def make_sample_artifact_maps(sample_name):
         except:
             pass
     return outin
-
-
diff --git a/genologics/test_utils.py b/genologics/test_utils.py
index 1c4f6d3..dfe518a 100644
--- a/genologics/test_utils.py
+++ b/genologics/test_utils.py
@@ -1,9 +1,8 @@
 #!/usr/bin/env python
 
-from __future__ import unicode_literals
 from xml.etree import ElementTree
-import requests
 
+import requests
 
 """
 In order to use the patched get :
@@ -17,42 +16,44 @@
 """
 
 
-
-XML_DICT = {}
+XML_DICT: None | dict = {}
 
 
 def patched_get(*args, **kwargs):
-    params=None
-    if 'uri' in kwargs:
-        uri=kwargs['uri']
+    params = None
+    if "uri" in kwargs:
+        uri = kwargs["uri"]
     else:
         for arg in args:
             if isinstance(arg, str):
                 uri = arg
-    if 'params' in kwargs:
-        params=kwargs['params']
+    if "params" in kwargs:
+        params = kwargs["params"]
     else:
         for arg in args:
             if isinstance(arg, dict):
                 params = arg
-    r = requests.Request(method='GET', url=uri, params=params)
+    r = requests.Request(method="GET", url=uri, params=params)
     r = r.prepare()
     if not XML_DICT:
-        raise Exception("You need to update genologics.test_utils.XML_DICT before using this function")
+        raise Exception(
+            "You need to update genologics.test_utils.XML_DICT before using this function"
+        )
     try:
         return ElementTree.fromstring(XML_DICT[r.url])
     except KeyError:
-        raise Exception("Cannot find mocked xml for uri {0}".format(r.url))
+        raise Exception(f"Cannot find mocked xml for uri {r.url}")
+
 
 def dump_source_xml(lims):
     """After using a LIMS object, using this method on it will dump all the cached XML in a serialized dictionnary form,
     to be used with patched_get"""
     final_string = []
-    final_string.append('{')
+    final_string.append("{")
     for k, v in lims.cache.items():
-        final_string.append("'{0}':".format(k))
+        final_string.append(f"'{k}':")
         v.get()
-        final_string.append('"""{0}""",'.format(v.xml().replace('\n', "\n")))
-    final_string.append('}')
+        final_string.append('"""{}""",'.format(v.xml().replace("\n", "\n")))
+    final_string.append("}")
 
-    return '\n'.join(final_string)
+    return "\n".join(final_string)
diff --git a/genologics/version.py b/genologics/version.py
index fb4d456..159d48b 100644
--- a/genologics/version.py
+++ b/genologics/version.py
@@ -1 +1 @@
-__version__="2.0.0"
+__version__ = "2.0.1"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..7675ea4
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,25 @@
+[tool.ruff.lint]
+select = [
+    #         Ruff default rules
+    # ------------------------------
+    "E4", # pycodestyle Imports
+    "E7", # pycodestyle Statements
+    "E9", # pycodestyle Runtime
+    "F",  # Pyflakes
+
+    #         Additional    Comment
+    # ------------------------------------------------------
+    "I",  # isort         Best-practice sorting of imports
+    "UP", # pyupgrade     Make sure syntax is up-to-date
+]
+ignore = [
+    "E402", # Module level import not at top of file
+    "E722", # Do not use bare 'except'
+    "E741", # Ambiguous variable name
+]
+
+
+[tool.mypy]
+ignore_missing_imports = true
+follow_imports = 'skip'
+exclude = '^docs/'
diff --git a/requirements-dev.txt b/requirements-dev.txt
new file mode 100644
index 0000000..76d34af
--- /dev/null
+++ b/requirements-dev.txt
@@ -0,0 +1,10 @@
+mock
+mypy
+pipreqs
+pytest
+pytest-cov
+ruff
+sphinxcontrib-programoutput
+types-requests
+types-setuptools
+types-six
diff --git a/requirements.txt b/requirements.txt
index 0ec5581..9840079 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,3 @@
 requests
-pytest
-mock
+setuptools
 six
diff --git a/setup.py b/setup.py
index 7654e2a..d039a66 100644
--- a/setup.py
+++ b/setup.py
@@ -1,50 +1,50 @@
-from setuptools import setup, find_packages
-from genologics.version import __version__
-import sys, os
-import subprocess
 import glob
 
+from setuptools import find_packages, setup
+
+from genologics.version import __version__
+
 # Fetch version from git tags.
 # if git is not available (PyPi package), use stored version.py.
 
 
 try:
     with open("requirements.txt") as rq:
-        requires=rq.readlines()
+        requires = rq.readlines()
 except:
-    requires=["requests"]
+    requires = ["requests"]
 
-setup(name='genologics',
-      version=__version__,
-      description="Python interface to the Illumina Basespace Clarity LIMS (Laboratory Information Management System) server via its REST API.",
-      long_description="""A basic module for interacting with the Illumina Basespace Clarity LIMS server via its REST API.
+setup(
+    name="genologics",
+    version=__version__,
+    description="Python interface to the Illumina Basespace Clarity LIMS (Laboratory Information Management System) server via its REST API.",
+    long_description="""A basic module for interacting with the Illumina Basespace Clarity LIMS server via its REST API.
                           The goal is to provide simple access to the most common entities and their attributes in a reasonably Pythonic fashion.""",
-      classifiers=[
-	"Development Status :: 4 - Beta",
-	"Environment :: Console",
-	"Intended Audience :: Developers",
-	"Intended Audience :: Healthcare Industry",
-	"Intended Audience :: Science/Research",
-	"License :: OSI Approved :: MIT License",
-	"Operating System :: POSIX :: Linux",
-	"Programming Language :: Python",
-	"Topic :: Scientific/Engineering :: Medical Science Apps."
-	],
-      keywords='genologics api rest clarity lims illumina',
-      author='Per Kraulis',
-      author_email='per.kraulis@scilifelab.se',
-      maintainer='Chuan Wang',
-      maintainer_email='chuan.wang@scilifelab.se',
-      url='https://github.com/scilifelab/genologics',
-      license='MIT',
-      packages=find_packages(exclude=['ez_setup', 'examples', 'tests']),
-      scripts=glob.glob("scripts/*.py"),
-      include_package_data=True,
-      zip_safe=False,
-      install_requires=[
-          "requests"
-      ],
-      entry_points="""
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "Environment :: Console",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Healthcare Industry",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: POSIX :: Linux",
+        "Programming Language :: Python",
+        "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    ],
+    keywords="genologics api rest clarity lims illumina",
+    author="Per Kraulis",
+    author_email="per.kraulis@scilifelab.se",
+    maintainer="Chuan Wang",
+    maintainer_email="chuan.wang@scilifelab.se",
+    url="https://github.com/scilifelab/genologics",
+    license="MIT",
+    packages=find_packages(exclude=["ez_setup", "examples", "tests"]),
+    scripts=glob.glob("scripts/*.py"),
+    include_package_data=True,
+    zip_safe=False,
+    install_requires=["requests"],
+    python_requires=">=3.12",
+    entry_points="""
       # -*- Entry points: -*-
       """,
-      )
+)
diff --git a/tests/test_descriptors.py b/tests/test_descriptors.py
index cf0bf3f..600b8bc 100644
--- a/tests/test_descriptors.py
+++ b/tests/test_descriptors.py
@@ -1,18 +1,21 @@
 from io import BytesIO
-from sys import version_info
 from unittest import TestCase
+from unittest.mock import Mock
 from xml.etree import ElementTree
 
-from genologics.descriptors import StringDescriptor, StringAttributeDescriptor, StringListDescriptor, \
-    StringDictionaryDescriptor, IntegerDescriptor, BooleanDescriptor, UdfDictionary, EntityDescriptor
+from genologics.descriptors import (
+    BooleanDescriptor,
+    EntityDescriptor,
+    IntegerDescriptor,
+    StringAttributeDescriptor,
+    StringDescriptor,
+    StringDictionaryDescriptor,
+    StringListDescriptor,
+    UdfDictionary,
+)
 from genologics.entities import Artifact
 from genologics.lims import Lims
 
-if version_info[0] == 2:
-    from mock import Mock
-else:
-    from unittest.mock import Mock
-
 
 class TestDescriptor(TestCase):
     def _make_desc(self, klass, *args, **kwargs):
@@ -20,7 +23,9 @@ def _make_desc(self, klass, *args, **kwargs):
 
     def _tostring(self, e):
         outfile = BytesIO()
-        ElementTree.ElementTree(e).write(outfile, encoding='utf-8', xml_declaration=True)
+        ElementTree.ElementTree(e).write(
+            outfile, encoding="utf-8", xml_declaration=True
+        )
         return outfile.getvalue()
 
 
@@ -34,19 +39,19 @@ def setUp(self):
         self.instance = Mock(root=self.et)
 
     def test__get__(self):
-        sd = self._make_desc(StringDescriptor, 'name')
+        sd = self._make_desc(StringDescriptor, "name")
         assert sd.__get__(self.instance, None) == "test name"
 
     def test__set__(self):
-        sd = self._make_desc(StringDescriptor, 'name')
+        sd = self._make_desc(StringDescriptor, "name")
         sd.__set__(self.instance, "new test name")
-        assert self.et.find('name').text == "new test name"
+        assert self.et.find("name").text == "new test name"
 
     def test_create(self):
-        instance_new = Mock(root=ElementTree.Element('test-entry'))
-        sd = self._make_desc(StringDescriptor, 'name')
+        instance_new = Mock(root=ElementTree.Element("test-entry"))
+        sd = self._make_desc(StringDescriptor, "name")
         sd.__set__(instance_new, "test name")
-        assert instance_new.root.find('name').text == 'test name'
+        assert instance_new.root.find("name").text == "test name"
 
 
 class TestIntegerDescriptor(TestDescriptor):
@@ -59,21 +64,21 @@ def setUp(self):
         self.instance = Mock(root=self.et)
 
     def test__get__(self):
-        sd = self._make_desc(IntegerDescriptor, 'count')
+        sd = self._make_desc(IntegerDescriptor, "count")
         assert sd.__get__(self.instance, None) == 32
 
     def test__set__(self):
-        sd = self._make_desc(IntegerDescriptor, 'count')
+        sd = self._make_desc(IntegerDescriptor, "count")
         sd.__set__(self.instance, 23)
-        assert self.et.find('count').text == '23'
-        sd.__set__(self.instance, '23')
-        assert self.et.find('count').text == '23'
+        assert self.et.find("count").text == "23"
+        sd.__set__(self.instance, "23")
+        assert self.et.find("count").text == "23"
 
     def test_create(self):
-        instance_new = Mock(root=ElementTree.Element('test-entry'))
-        sd = self._make_desc(IntegerDescriptor, 'count')
+        instance_new = Mock(root=ElementTree.Element("test-entry"))
+        sd = self._make_desc(IntegerDescriptor, "count")
         sd.__set__(instance_new, 23)
-        assert instance_new.root.find('count').text == '23'
+        assert instance_new.root.find("count").text == "23"
 
 
 class TestBooleanDescriptor(TestDescriptor):
@@ -86,21 +91,21 @@ def setUp(self):
         self.instance = Mock(root=self.et)
 
     def test__get__(self):
-        bd = self._make_desc(BooleanDescriptor, 'istest')
-        assert bd.__get__(self.instance, None) == True
+        bd = self._make_desc(BooleanDescriptor, "istest")
+        assert bd.__get__(self.instance, None) is True
 
     def test__set__(self):
-        bd = self._make_desc(BooleanDescriptor, 'istest')
+        bd = self._make_desc(BooleanDescriptor, "istest")
         bd.__set__(self.instance, False)
-        assert self.et.find('istest').text == 'false'
-        bd.__set__(self.instance, 'true')
-        assert self.et.find('istest').text == 'true'
+        assert self.et.find("istest").text == "false"
+        bd.__set__(self.instance, "true")
+        assert self.et.find("istest").text == "true"
 
     def test_create(self):
-        instance_new = Mock(root=ElementTree.Element('test-entry'))
-        bd = self._make_desc(BooleanDescriptor, 'istest')
+        instance_new = Mock(root=ElementTree.Element("test-entry"))
+        bd = self._make_desc(BooleanDescriptor, "istest")
         bd.__set__(instance_new, True)
-        assert instance_new.root.find('istest').text == 'true'
+        assert instance_new.root.find("istest").text == "true"
 
 
 class TestEntityDescriptor(TestDescriptor):
@@ -110,25 +115,33 @@ def setUp(self):
 <artifact uri="http://testgenologics.com:4040/api/v2/artifacts/a1"></artifact>
 </test-entry>
 """)
-        self.lims = Lims('http://testgenologics.com:4040', username='test', password='password')
-        self.a1 = Artifact(self.lims, id='a1')
-        self.a2 = Artifact(self.lims, id='a2')
+        self.lims = Lims(
+            "http://testgenologics.com:4040", username="test", password="password"
+        )
+        self.a1 = Artifact(self.lims, id="a1")
+        self.a2 = Artifact(self.lims, id="a2")
         self.instance = Mock(root=self.et, lims=self.lims)
 
     def test__get__(self):
-        ed = self._make_desc(EntityDescriptor, 'artifact', Artifact)
+        ed = self._make_desc(EntityDescriptor, "artifact", Artifact)
         assert ed.__get__(self.instance, None) == self.a1
 
     def test__set__(self):
-        ed = self._make_desc(EntityDescriptor, 'artifact', Artifact)
+        ed = self._make_desc(EntityDescriptor, "artifact", Artifact)
         ed.__set__(self.instance, self.a2)
-        assert self.et.find('artifact').attrib['uri'] == 'http://testgenologics.com:4040/api/v2/artifacts/a2'
+        assert (
+            self.et.find("artifact").attrib["uri"]
+            == "http://testgenologics.com:4040/api/v2/artifacts/a2"
+        )
 
     def test_create(self):
-        instance_new = Mock(root=ElementTree.Element('test-entry'))
-        ed = self._make_desc(EntityDescriptor, 'artifact', Artifact)
+        instance_new = Mock(root=ElementTree.Element("test-entry"))
+        ed = self._make_desc(EntityDescriptor, "artifact", Artifact)
         ed.__set__(instance_new, self.a1)
-        assert instance_new.root.find('artifact').attrib['uri'] == 'http://testgenologics.com:4040/api/v2/artifacts/a1'
+        assert (
+            instance_new.root.find("artifact").attrib["uri"]
+            == "http://testgenologics.com:4040/api/v2/artifacts/a1"
+        )
 
 
 class TestStringAttributeDescriptor(TestDescriptor):
@@ -139,19 +152,19 @@ def setUp(self):
         self.instance = Mock(root=self.et)
 
     def test__get__(self):
-        sd = self._make_desc(StringAttributeDescriptor, 'name')
+        sd = self._make_desc(StringAttributeDescriptor, "name")
         assert sd.__get__(self.instance, None) == "test name"
 
     def test__set__(self):
-        sd = self._make_desc(StringAttributeDescriptor, 'name')
+        sd = self._make_desc(StringAttributeDescriptor, "name")
         sd.__set__(self.instance, "test name2")
-        assert self.et.attrib['name'] == "test name2"
+        assert self.et.attrib["name"] == "test name2"
 
     def test_create(self):
-        instance_new = Mock(root=ElementTree.Element('test-entry'))
-        bd = self._make_desc(StringAttributeDescriptor, 'name')
+        instance_new = Mock(root=ElementTree.Element("test-entry"))
+        bd = self._make_desc(StringAttributeDescriptor, "name")
         bd.__set__(instance_new, "test name2")
-        assert instance_new.root.attrib['name'] == "test name2"
+        assert instance_new.root.attrib["name"] == "test name2"
 
 
 class TestStringListDescriptor(TestDescriptor):
@@ -164,8 +177,8 @@ def setUp(self):
         self.instance = Mock(root=self.et)
 
     def test__get__(self):
-        sd = self._make_desc(StringListDescriptor, 'test-subentry')
-        assert sd.__get__(self.instance, None) == ['A01', 'B01']
+        sd = self._make_desc(StringListDescriptor, "test-subentry")
+        assert sd.__get__(self.instance, None) == ["A01", "B01"]
 
 
 class TestStringDictionaryDescriptor(TestDescriptor):
@@ -180,11 +193,11 @@ def setUp(self):
         self.instance = Mock(root=self.et)
 
     def test__get__(self):
-        sd = self._make_desc(StringDictionaryDescriptor, 'test-subentry')
+        sd = self._make_desc(StringDictionaryDescriptor, "test-subentry")
         res = sd.__get__(self.instance, None)
-        assert type(res) == dict
-        assert res['test-firstkey'] is None
-        assert res['test-secondkey'] == 'second value'
+        assert isinstance(res, dict)
+        assert res["test-firstkey"] is None
+        assert res["test-secondkey"] == "second value"
 
 
 class TestUdfDictionary(TestCase):
@@ -201,7 +214,7 @@ def setUp(self):
 
     def _get_udf_value(self, udf_dict, key):
         for e in udf_dict._elems:
-            if e.attrib['name'] != key:
+            if e.attrib["name"] != key:
                 continue
             else:
                 return e.text
@@ -225,43 +238,41 @@ def test___getitem__(self):
         pass
 
     def test___setitem__(self):
-        assert self._get_udf_value(self.dict1, 'test') == 'stuff'
-        self.dict1.__setitem__('test', 'other')
-        assert self._get_udf_value(self.dict1, 'test') == 'other'
+        assert self._get_udf_value(self.dict1, "test") == "stuff"
+        self.dict1.__setitem__("test", "other")
+        assert self._get_udf_value(self.dict1, "test") == "other"
 
-        assert self._get_udf_value(self.dict1, 'how much') == '42'
-        self.dict1.__setitem__('how much', 21)
-        assert self._get_udf_value(self.dict1, 'how much') == '21'
+        assert self._get_udf_value(self.dict1, "how much") == "42"
+        self.dict1.__setitem__("how much", 21)
+        assert self._get_udf_value(self.dict1, "how much") == "21"
 
-        assert self._get_udf_value(self.dict1, 'really?') == 'true'
-        self.dict1.__setitem__('really?', False)
-        assert self._get_udf_value(self.dict1, 'really?') == 'false'
+        assert self._get_udf_value(self.dict1, "really?") == "true"
+        self.dict1.__setitem__("really?", False)
+        assert self._get_udf_value(self.dict1, "really?") == "false"
 
-        self.assertRaises(TypeError, self.dict1.__setitem__, 'how much', '433')
+        self.assertRaises(TypeError, self.dict1.__setitem__, "how much", "433")
 
         # FIXME: I'm not sure if this is the expected behaviour
-        self.dict1.__setitem__('how much', None)
-        assert self._get_udf_value(self.dict1, 'how much') == ''
-
+        self.dict1.__setitem__("how much", None)
+        assert self._get_udf_value(self.dict1, "how much") == ""
 
     def test___setitem__new(self):
-        self.dict1.__setitem__('new string', 'new stuff')
-        assert self._get_udf_value(self.dict1, 'new string') == 'new stuff'
-
-        self.dict1.__setitem__('new numeric', 21)
-        assert self._get_udf_value(self.dict1, 'new numeric') == '21'
+        self.dict1.__setitem__("new string", "new stuff")
+        assert self._get_udf_value(self.dict1, "new string") == "new stuff"
 
-        self.dict1.__setitem__('new bool', False)
-        assert self._get_udf_value(self.dict1, 'new bool') == 'false'
+        self.dict1.__setitem__("new numeric", 21)
+        assert self._get_udf_value(self.dict1, "new numeric") == "21"
 
+        self.dict1.__setitem__("new bool", False)
+        assert self._get_udf_value(self.dict1, "new bool") == "false"
 
     def test___setitem__unicode(self):
-        assert self._get_udf_value(self.dict1, 'test') == 'stuff'
-        self.dict1.__setitem__('test', 'unicode')
-        assert self._get_udf_value(self.dict1, 'test') == 'unicode'
+        assert self._get_udf_value(self.dict1, "test") == "stuff"
+        self.dict1.__setitem__("test", "unicode")
+        assert self._get_udf_value(self.dict1, "test") == "unicode"
 
-        self.dict1.__setitem__('test', 'unicode2')
-        assert self._get_udf_value(self.dict1, 'test') == 'unicode2'
+        self.dict1.__setitem__("test", "unicode2")
+        assert self._get_udf_value(self.dict1, "test") == "unicode2"
 
     def test___delitem__(self):
         pass
diff --git a/tests/test_entities.py b/tests/test_entities.py
index 103abb4..36aaa34 100644
--- a/tests/test_entities.py
+++ b/tests/test_entities.py
@@ -1,18 +1,24 @@
-import operator
-from sys import version_info
 from unittest import TestCase
+from unittest.mock import Mock, patch
 from xml.etree import ElementTree
 
-from genologics.entities import StepActions, Researcher, Artifact, \
-    Step, StepPlacements, StepPools, Container, Stage, ReagentKit, ReagentLot, Sample, Project
+from genologics.entities import (
+    Artifact,
+    Container,
+    Project,
+    ReagentKit,
+    ReagentLot,
+    Researcher,
+    Sample,
+    Stage,
+    Step,
+    StepActions,
+    StepPlacements,
+    StepPools,
+)
 from genologics.lims import Lims
 
-if version_info[0] == 2:
-    from mock import patch, Mock
-else:
-    from unittest.mock import patch, Mock
-
-url = 'http://testgenologics.com:4040'
+url = "http://testgenologics.com:4040"
 
 ########
 # Entities in XML
@@ -80,7 +86,7 @@
 
 generic_reagentkit_xml = """<?xml version='1.0' encoding='utf-8'?>
 <kit:reagent-kit xmlns:kit="http://genologics.com/ri/reagentkit" uri="{url}:8080/api/v2/reagentkits/r1">
-<name>regaentkitname</name>
+<name>reagentkitname</name>
 <supplier>reagentProvider</supplier>
 <website>www.reagentprovider.com</website>
 <archived>false</archived>
@@ -162,29 +168,28 @@
 """
 
 
-class TestEntities(TestCase):
-    def test_pass(self):
-        pass
-
-
 def elements_equal(e1, e2):
     if e1.tag != e2.tag:
-        print('Tag: %s != %s' % (e1.tag, e2.tag))
+        print(f"Tag: {e1.tag} != {e2.tag}")
         return False
     if e1.text and e2.text and e1.text.strip() != e2.text.strip():
-        print('Text: %s != %s' % (e1.text.strip(), e2.text.strip()))
+        print(f"Text: {e1.text.strip()} != {e2.text.strip()}")
         return False
     if e1.tail and e2.tail and e1.tail.strip() != e2.tail.strip():
-        print('Tail: %s != %s' % (e1.tail.strip(), e2.tail.strip()))
+        print(f"Tail: {e1.tail.strip()} != {e2.tail.strip()}")
         return False
     if e1.attrib != e2.attrib:
-        print('Attrib: %s != %s' % (e1.attrib, e2.attrib))
+        print(f"Attrib: {e1.attrib} != {e2.attrib}")
         return False
     if len(e1) != len(e2):
-        print('length %s (%s) != length (%s) ' % (e1.tag, len(e1), e2.tag, len(e2)))
+        print(f"length {e1.tag} ({len(e1)}) != length ({e2.tag}) ")
         return False
     return all(
-        elements_equal(c1, c2) for c1, c2 in zip(sorted(e1, key=lambda x: x.tag), sorted(e2, key=lambda x: x.tag)))
+        elements_equal(c1, c2)
+        for c1, c2 in zip(
+            sorted(e1, key=lambda x: x.tag), sorted(e2, key=lambda x: x.tag)
+        )
+    )
 
 
 class TestEntities(TestCase):
@@ -192,7 +197,7 @@ class TestEntities(TestCase):
     <dummy></dummy>"""
 
     def setUp(self):
-        self.lims = Lims(url, username='test', password='password')
+        self.lims = Lims(url, username="test", password="password")
 
     def _tostring(self, entity):
         return self.lims.tostring(ElementTree.ElementTree(entity.root)).decode("utf-8")
@@ -200,32 +205,62 @@ def _tostring(self, entity):
 
 class TestStepActions(TestEntities):
     step_actions_xml = generic_step_actions_xml.format(url=url)
-    step_actions_no_escalation_xml = generic_step_actions_no_escalation_xml.format(url=url)
+    step_actions_no_escalation_xml = generic_step_actions_no_escalation_xml.format(
+        url=url
+    )
 
     def test_escalation(self):
-        s = StepActions(uri=self.lims.get_uri('steps', 'step_id', 'actions'), lims=self.lims)
-        with patch('requests.Session.get', return_value=Mock(content=self.step_actions_xml, status_code=200)):
-            with patch('requests.post', return_value=Mock(content=self.dummy_xml, status_code=200)):
-                r = Researcher(uri='http://testgenologics.com:4040/researchers/r1', lims=self.lims)
-                a = Artifact(uri='http://testgenologics.com:4040/artifacts/r1', lims=self.lims)
+        s = StepActions(
+            uri=self.lims.get_uri("steps", "step_id", "actions"), lims=self.lims
+        )
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(content=self.step_actions_xml, status_code=200),
+        ):
+            with patch(
+                "requests.post",
+                return_value=Mock(content=self.dummy_xml, status_code=200),
+            ):
+                r = Researcher(
+                    uri="http://testgenologics.com:4040/researchers/r1", lims=self.lims
+                )
+                a = Artifact(
+                    uri="http://testgenologics.com:4040/artifacts/r1", lims=self.lims
+                )
                 expected_escalation = {
-                    'status': 'Reviewed',
-                    'author': r,
-                    'artifacts': [a], 'request': 'no comments',
-                    'answer': 'no comments',
-                    'reviewer': r}
+                    "status": "Reviewed",
+                    "author": r,
+                    "artifacts": [a],
+                    "request": "no comments",
+                    "answer": "no comments",
+                    "reviewer": r,
+                }
 
                 assert s.escalation == expected_escalation
 
     def test_next_actions(self):
-        s = StepActions(uri=self.lims.get_uri('steps', 'step_id', 'actions'), lims=self.lims)
-        with patch('requests.Session.get',
-                   return_value=Mock(content=self.step_actions_no_escalation_xml, status_code=200)):
-            step1 = Step(self.lims, uri='http://testgenologics.com:4040/steps/s1')
-            step2 = Step(self.lims, uri='http://testgenologics.com:4040/steps/s2')
-            artifact = Artifact(self.lims, uri='http://testgenologics.com:4040/artifacts/a1')
-            expected_next_actions = [{'artifact': artifact, 'action': 'requeue',
-                                      'step': step1, 'rework-step': step2}]
+        s = StepActions(
+            uri=self.lims.get_uri("steps", "step_id", "actions"), lims=self.lims
+        )
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(
+                content=self.step_actions_no_escalation_xml, status_code=200
+            ),
+        ):
+            step1 = Step(self.lims, uri="http://testgenologics.com:4040/steps/s1")
+            step2 = Step(self.lims, uri="http://testgenologics.com:4040/steps/s2")
+            artifact = Artifact(
+                self.lims, uri="http://testgenologics.com:4040/artifacts/a1"
+            )
+            expected_next_actions = [
+                {
+                    "artifact": artifact,
+                    "action": "requeue",
+                    "step": step1,
+                    "rework-step": step2,
+                }
+            ]
             assert s.next_actions == expected_next_actions
 
 
@@ -233,101 +268,182 @@ class TestStepPools(TestEntities):
     initial_step_pools = generic_step_pools_xml.format(url=url)
 
     def test_get_pool_list(self):
-        s = StepPools(uri=self.lims.get_uri('steps', 's1', 'pools'), lims=self.lims)
-        with patch('requests.Session.get',
-                   return_value=Mock(content=self.initial_step_pools, status_code=200)):
-            output = Artifact(lims=self.lims, uri='http://testgenologics.com:4040/api/v2/artifacts/o1')
-            i1 = Artifact(lims=self.lims, uri='http://testgenologics.com:4040/api/v2/artifacts/a1')
-            i2 = Artifact(lims=self.lims, uri='http://testgenologics.com:4040/api/v2/artifacts/a2')
-            i3 = Artifact(lims=self.lims, uri='http://testgenologics.com:4040/api/v2/artifacts/a3')
-            i4 = Artifact(lims=self.lims, uri='http://testgenologics.com:4040/api/v2/artifacts/a4')
-            i5 = Artifact(lims=self.lims, uri='http://testgenologics.com:4040/api/v2/artifacts/a5')
-            assert s.pools[0]['output'] == output
-            assert s.pools[0]['name'] == "Pool #1"
-            assert len(s.pools[0]['inputs']) == 2
-            assert s.pools[0]['inputs'][0] == i1
-            assert s.pools[0]['inputs'][1] == i2
+        s = StepPools(uri=self.lims.get_uri("steps", "s1", "pools"), lims=self.lims)
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(content=self.initial_step_pools, status_code=200),
+        ):
+            output = Artifact(
+                lims=self.lims, uri="http://testgenologics.com:4040/api/v2/artifacts/o1"
+            )
+            i1 = Artifact(
+                lims=self.lims, uri="http://testgenologics.com:4040/api/v2/artifacts/a1"
+            )
+            i2 = Artifact(
+                lims=self.lims, uri="http://testgenologics.com:4040/api/v2/artifacts/a2"
+            )
+            i3 = Artifact(
+                lims=self.lims, uri="http://testgenologics.com:4040/api/v2/artifacts/a3"
+            )
+            i4 = Artifact(
+                lims=self.lims, uri="http://testgenologics.com:4040/api/v2/artifacts/a4"
+            )
+            i5 = Artifact(
+                lims=self.lims, uri="http://testgenologics.com:4040/api/v2/artifacts/a5"
+            )
+            assert s.pools[0]["output"] == output
+            assert s.pools[0]["name"] == "Pool #1"
+            assert len(s.pools[0]["inputs"]) == 2
+            assert s.pools[0]["inputs"][0] == i1
+            assert s.pools[0]["inputs"][1] == i2
             assert i3 in s.available_inputs
             assert i4 in s.available_inputs
             assert i5 in s.available_inputs
 
 
 class TestStepPlacements(TestEntities):
-    original_step_placements_xml = generic_step_placements_xml.format(url=url, container="c1", loc1='1:1', loc2='2:1')
-    modloc_step_placements_xml = generic_step_placements_xml.format(url=url, container="c1", loc1='3:1', loc2='4:1')
-    modcont_step_placements_xml = generic_step_placements_xml.format(url=url, container="c2", loc1='1:1', loc2='1:1')
+    original_step_placements_xml = generic_step_placements_xml.format(
+        url=url, container="c1", loc1="1:1", loc2="2:1"
+    )
+    modloc_step_placements_xml = generic_step_placements_xml.format(
+        url=url, container="c1", loc1="3:1", loc2="4:1"
+    )
+    modcont_step_placements_xml = generic_step_placements_xml.format(
+        url=url, container="c2", loc1="1:1", loc2="1:1"
+    )
 
     def test_get_placements_list(self):
-        s = StepPlacements(uri=self.lims.get_uri('steps', 's1', 'placements'), lims=self.lims)
-        with patch('requests.Session.get',
-                   return_value=Mock(content=self.original_step_placements_xml, status_code=200)):
-            a1 = Artifact(uri='http://testgenologics.com:4040/artifacts/a1', lims=self.lims)
-            a2 = Artifact(uri='http://testgenologics.com:4040/artifacts/a2', lims=self.lims)
-            c1 = Container(uri='http://testgenologics.com:4040/containers/c1', lims=self.lims)
-            expected_placements = [[a1, (c1, '1:1')], [a2, (c1, '2:1')]]
+        s = StepPlacements(
+            uri=self.lims.get_uri("steps", "s1", "placements"), lims=self.lims
+        )
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(
+                content=self.original_step_placements_xml, status_code=200
+            ),
+        ):
+            a1 = Artifact(
+                uri="http://testgenologics.com:4040/artifacts/a1", lims=self.lims
+            )
+            a2 = Artifact(
+                uri="http://testgenologics.com:4040/artifacts/a2", lims=self.lims
+            )
+            c1 = Container(
+                uri="http://testgenologics.com:4040/containers/c1", lims=self.lims
+            )
+            expected_placements = [[a1, (c1, "1:1")], [a2, (c1, "2:1")]]
             assert s.get_placement_list() == expected_placements
 
     def test_set_placements_list(self):
-        a1 = Artifact(uri='http://testgenologics.com:4040/artifacts/a1', lims=self.lims)
-        a2 = Artifact(uri='http://testgenologics.com:4040/artifacts/a2', lims=self.lims)
-        c1 = Container(uri='http://testgenologics.com:4040/containers/c1', lims=self.lims)
-        c2 = Container(uri='http://testgenologics.com:4040/containers/c2', lims=self.lims)
-
-        s = StepPlacements(uri=self.lims.get_uri('steps', 's1', 'placements'), lims=self.lims)
-        with patch('requests.Session.get',
-                   return_value=Mock(content=self.original_step_placements_xml, status_code=200)):
-            new_placements = [[a1, (c1, '3:1')], [a2, (c1, '4:1')]]
+        a1 = Artifact(uri="http://testgenologics.com:4040/artifacts/a1", lims=self.lims)
+        a2 = Artifact(uri="http://testgenologics.com:4040/artifacts/a2", lims=self.lims)
+        c1 = Container(
+            uri="http://testgenologics.com:4040/containers/c1", lims=self.lims
+        )
+        Container(uri="http://testgenologics.com:4040/containers/c2", lims=self.lims)
+
+        s = StepPlacements(
+            uri=self.lims.get_uri("steps", "s1", "placements"), lims=self.lims
+        )
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(
+                content=self.original_step_placements_xml, status_code=200
+            ),
+        ):
+            new_placements = [[a1, (c1, "3:1")], [a2, (c1, "4:1")]]
             s.set_placement_list(new_placements)
-            assert elements_equal(s.root, ElementTree.fromstring(self.modloc_step_placements_xml))
+            assert elements_equal(
+                s.root, ElementTree.fromstring(self.modloc_step_placements_xml)
+            )
 
     def test_set_placements_list_fail(self):
-        a1 = Artifact(uri='http://testgenologics.com:4040/artifacts/a1', lims=self.lims)
-        a2 = Artifact(uri='http://testgenologics.com:4040/artifacts/a2', lims=self.lims)
-        c2 = Container(uri='http://testgenologics.com:4040/containers/c2', lims=self.lims)
-
-        s = StepPlacements(uri=self.lims.get_uri('steps', 's1', 'placements'), lims=self.lims)
-        with patch('requests.Session.get',
-                   return_value=Mock(content=self.original_step_placements_xml, status_code=200)):
-            new_placements = [[a1, (c2, '1:1')], [a2, (c2, '1:1')]]
+        a1 = Artifact(uri="http://testgenologics.com:4040/artifacts/a1", lims=self.lims)
+        a2 = Artifact(uri="http://testgenologics.com:4040/artifacts/a2", lims=self.lims)
+        c2 = Container(
+            uri="http://testgenologics.com:4040/containers/c2", lims=self.lims
+        )
+
+        s = StepPlacements(
+            uri=self.lims.get_uri("steps", "s1", "placements"), lims=self.lims
+        )
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(
+                content=self.original_step_placements_xml, status_code=200
+            ),
+        ):
+            new_placements = [[a1, (c2, "1:1")], [a2, (c2, "1:1")]]
             s.set_placement_list(new_placements)
-            assert elements_equal(s.root, ElementTree.fromstring(self.modcont_step_placements_xml))
+            assert elements_equal(
+                s.root, ElementTree.fromstring(self.modcont_step_placements_xml)
+            )
 
 
 class TestArtifacts(TestEntities):
     root_artifact_xml = generic_artifact_xml.format(url=url)
 
     def test_input_artifact_list(self):
-        a = Artifact(uri=self.lims.get_uri('artifacts', 'a1'), lims=self.lims)
-        with patch('requests.Session.get', return_value=Mock(content=self.root_artifact_xml, status_code=200)):
+        a = Artifact(uri=self.lims.get_uri("artifacts", "a1"), lims=self.lims)
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(content=self.root_artifact_xml, status_code=200),
+        ):
             assert a.input_artifact_list() == []
 
     def test_workflow_stages_and_statuses(self):
-        a = Artifact(uri=self.lims.get_uri('artifacts', 'a1'), lims=self.lims)
+        a = Artifact(uri=self.lims.get_uri("artifacts", "a1"), lims=self.lims)
         expected_wf_stage = [
-            (Stage(self.lims, uri=url + '/api/v2/configuration/workflows/1/stages/2'), 'QUEUED', 'Test workflow s2'),
-            (Stage(self.lims, uri=url + '/api/v2/configuration/workflows/1/stages/1'), 'COMPLETE', 'Test workflow s1')
+            (
+                Stage(
+                    self.lims, uri=url + "/api/v2/configuration/workflows/1/stages/2"
+                ),
+                "QUEUED",
+                "Test workflow s2",
+            ),
+            (
+                Stage(
+                    self.lims, uri=url + "/api/v2/configuration/workflows/1/stages/1"
+                ),
+                "COMPLETE",
+                "Test workflow s1",
+            ),
         ]
-        with patch('requests.Session.get', return_value=Mock(content=self.root_artifact_xml, status_code=200)):
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(content=self.root_artifact_xml, status_code=200),
+        ):
             assert a.workflow_stages_and_statuses == expected_wf_stage
 
 
 class TestReagentKits(TestEntities):
-    url = 'http://testgenologics.com:4040'
+    url = "http://testgenologics.com:4040"
     reagentkit_xml = generic_reagentkit_xml.format(url=url)
 
     def test_parse_entity(self):
-        r = ReagentKit(uri=self.lims.get_uri('reagentkits', 'r1'), lims=self.lims)
-        with patch('requests.Session.get', return_value=Mock(content=self.reagentkit_xml, status_code=200)):
-            assert r.name == 'regaentkitname'
-            assert r.supplier == 'reagentProvider'
-            assert r.website == 'www.reagentprovider.com'
-            assert r.archived == False
+        r = ReagentKit(uri=self.lims.get_uri("reagentkits", "r1"), lims=self.lims)
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(content=self.reagentkit_xml, status_code=200),
+        ):
+            assert r.name == "reagentkitname"
+            assert r.supplier == "reagentProvider"
+            assert r.website == "www.reagentprovider.com"
+            assert r.archived is False
 
     def test_create_entity(self):
-        with patch('genologics.lims.requests.post', return_value=Mock(content=self.reagentkit_xml, status_code=201)):
-            r = ReagentKit.create(self.lims, name='regaentkitname', supplier='reagentProvider',
-                                  website='www.reagentprovider.com', archived=False)
-        self.assertRaises(TypeError, ReagentKit.create, self.lims, error='test')
+        with patch(
+            "genologics.lims.requests.post",
+            return_value=Mock(content=self.reagentkit_xml, status_code=201),
+        ):
+            ReagentKit.create(
+                self.lims,
+                name="reagentkitname",
+                supplier="reagentProvider",
+                website="www.reagentprovider.com",
+                archived=False,
+            )
+        self.assertRaises(TypeError, ReagentKit.create, self.lims, error="test")
 
 
 class TestReagentLots(TestEntities):
@@ -335,45 +451,55 @@ class TestReagentLots(TestEntities):
     reagentkit_xml = generic_reagentkit_xml.format(url=url)
 
     def test_parse_entity(self):
-        l = ReagentLot(uri=self.lims.get_uri('reagentkits', 'r1'), lims=self.lims)
-        with patch('requests.Session.get', return_value=Mock(content=self.reagentlot_xml, status_code=200)):
+        l = ReagentLot(uri=self.lims.get_uri("reagentkits", "r1"), lims=self.lims)
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(content=self.reagentlot_xml, status_code=200),
+        ):
             assert l.uri
-            assert l.name == 'kitname'
-            assert l.lot_number == '100'
-            assert l.status == 'ARCHIVED'
+            assert l.name == "kitname"
+            assert l.lot_number == "100"
+            assert l.status == "ARCHIVED"
 
     def test_create_entity(self):
-        with patch('requests.Session.get', return_value=Mock(content=self.reagentkit_xml, status_code=200)):
-            r = ReagentKit(uri=self.lims.get_uri('reagentkits', 'r1'), lims=self.lims)
-        with patch('genologics.lims.requests.post',
-                   return_value=Mock(content=self.reagentlot_xml, status_code=201)) as patch_post:
+        with patch(
+            "requests.Session.get",
+            return_value=Mock(content=self.reagentkit_xml, status_code=200),
+        ):
+            r = ReagentKit(uri=self.lims.get_uri("reagentkits", "r1"), lims=self.lims)
+        with patch(
+            "genologics.lims.requests.post",
+            return_value=Mock(content=self.reagentlot_xml, status_code=201),
+        ):
             l = ReagentLot.create(
                 self.lims,
                 reagent_kit=r,
-                name='kitname',
-                lot_number='100',
-                expiry_date='2020-05-01',
-                status='ACTIVE'
+                name="kitname",
+                lot_number="100",
+                expiry_date="2020-05-01",
+                status="ACTIVE",
             )
             assert l.uri
-            assert l.name == 'kitname'
-            assert l.lot_number == '100'
+            assert l.name == "kitname"
+            assert l.lot_number == "100"
 
 
 class TestSample(TestEntities):
     sample_creation = generic_sample_creation_xml.format(url=url)
 
     def test_create_entity(self):
-        with patch('genologics.lims.requests.post',
-                   return_value=Mock(content=self.sample_creation, status_code=201)) as patch_post:
-            l = Sample.create(
+        with patch(
+            "genologics.lims.requests.post",
+            return_value=Mock(content=self.sample_creation, status_code=201),
+        ) as patch_post:
+            Sample.create(
                 self.lims,
-                project=Project(self.lims, uri='project'),
-                container=Container(self.lims, uri='container'),
-                position='1:1',
-                name='s1',
+                project=Project(self.lims, uri="project"),
+                container=Container(self.lims, uri="container"),
+                position="1:1",
+                name="s1",
             )
-            data = '''<?xml version=\'1.0\' encoding=\'utf-8\'?>
+            data = """<?xml version=\'1.0\' encoding=\'utf-8\'?>
             <smp:samplecreation xmlns:smp="http://genologics.com/ri/sample">
             <name>s1</name>
             <project uri="project" limsid="project" />
@@ -381,6 +507,8 @@ def test_create_entity(self):
               <container uri="container" />
               <value>1:1</value>
             </location>
-            </smp:samplecreation>'''
-            assert elements_equal(ElementTree.fromstring(patch_post.call_args_list[0][1]['data']),
-                                  ElementTree.fromstring(data))
+            </smp:samplecreation>"""
+            assert elements_equal(
+                ElementTree.fromstring(patch_post.call_args_list[0][1]["data"]),
+                ElementTree.fromstring(data),
+            )
diff --git a/tests/test_example.py b/tests/test_example.py
index 270e289..34ecf01 100644
--- a/tests/test_example.py
+++ b/tests/test_example.py
@@ -1,19 +1,12 @@
-
-from sys import version_info
 from unittest import TestCase, main
+from unittest.mock import patch
 
 from genologics import test_utils
-from genologics.lims import Lims
 from genologics.entities import Project
+from genologics.lims import Lims
 
-if version_info[0] == 2:
-    from mock import patch
-else:
-    from unittest.mock import patch
-
-
-
-test_utils.XML_DICT={"https://test.claritylims.com/api/v2/projects/BLA1":"""
+test_utils.XML_DICT = {
+    "https://test.claritylims.com/api/v2/projects/BLA1": """
 <prj:project xmlns:udf="http://genologics.com/ri/userdefined" xmlns:ri="http://genologics.com/ri" xmlns:file="http://genologics.com/ri/file" xmlns:prj="http://genologics.com/ri/project" uri="https://test.claritylims.com/api/v2/projects/BLA1" limsid="BLA1">
 <name>Test</name>
 <open-date>2016-04-20</open-date>
@@ -21,18 +14,20 @@
 <researcher uri="https://test.claritylims.com/api/v2/researchers/7"/>
 <file:file limsid="40-1" uri="https://test.claritylims.com/api/v2/files/40-1"/>
 <file:file limsid="40-4264" uri="https://test.claritylims.com/api/v2/files/40-4264"/>
-</prj:project>"""}
+</prj:project>"""
+}
+
 
 class TestExample(TestCase):
     def __init__(self, *args, **kwargs):
-        self.lims = Lims('https://test.claritylims.com', 'user', 'password')
-        super(TestExample, self).__init__(*args, **kwargs)
+        self.lims = Lims("https://test.claritylims.com", "user", "password")
+        super().__init__(*args, **kwargs)
 
     def test_project_example(self):
         with patch("genologics.lims.Lims.get", side_effect=test_utils.patched_get):
-            pj = Project(self.lims, id='BLA1')
-            self.assertEqual(pj.name, 'Test')
+            pj = Project(self.lims, id="BLA1")
+            self.assertEqual(pj.name, "Test")
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/tests/test_lims.py b/tests/test_lims.py
index 2e122d4..93b0f98 100644
--- a/tests/test_lims.py
+++ b/tests/test_lims.py
@@ -1,33 +1,31 @@
-import xml
 from unittest import TestCase
 
 from requests.exceptions import HTTPError
 
 from genologics.lims import Lims
+
 try:
     callable(1)
-except NameError: # callable() doesn't exist in Python 3.0 and 3.1
+except NameError:  # callable() doesn't exist in Python 3.0 and 3.1
     import collections
-    callable = lambda obj: isinstance(obj, collections.Callable)
+
+    def callable(obj):
+        return isinstance(obj, collections.Callable)
 
 
-from sys import version_info
-if version_info[0] == 2:
-    from mock import patch, Mock
-    import __builtin__ as builtins
-else:
-    from unittest.mock import patch, Mock
-    import builtins
+import builtins
+from unittest.mock import Mock, patch
+
 
 class TestLims(TestCase):
-    url = 'http://testgenologics.com:4040'
-    username = 'test'
-    password = 'password'
-    sample_xml = """<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+    url = "http://testgenologics.com:4040"
+    username = "test"
+    password = "password"
+    sample_xml = f"""<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <smp:samples xmlns:smp="http://genologics.com/ri/sample">
     <sample uri="{url}/api/v2/samples/test_sample" limsid="test_id"/>
 </smp:samples>
-""".format(url=url)
+"""
     error_xml = """<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
 <exc:exception xmlns:exc="http://genologics.com/ri/exception">
     <message>Generic error message</message>
@@ -36,62 +34,75 @@ class TestLims(TestCase):
 <exc:exception xmlns:exc="http://genologics.com/ri/exception">
 </exc:exception>"""
 
-
     def test_get_uri(self):
         lims = Lims(self.url, username=self.username, password=self.password)
-        assert lims.get_uri('artifacts',sample_name='test_sample') == '{url}/api/v2/artifacts?sample_name=test_sample'.format(url=self.url)
-
+        assert (
+            lims.get_uri("artifacts", sample_name="test_sample")
+            == f"{self.url}/api/v2/artifacts?sample_name=test_sample"
+        )
 
     def test_parse_response(self):
         lims = Lims(self.url, username=self.username, password=self.password)
-        r = Mock(content = self.sample_xml, status_code=200)
+        r = Mock(content=self.sample_xml, status_code=200)
         pr = lims.parse_response(r)
         assert pr is not None
         assert callable(pr.find)
-        assert hasattr(pr.attrib, '__getitem__')
+        assert hasattr(pr.attrib, "__getitem__")
 
-        r = Mock(content = self.error_xml, status_code=400)
+        r = Mock(content=self.error_xml, status_code=400)
         self.assertRaises(HTTPError, lims.parse_response, r)
 
-        r = Mock(content = self.error_no_msg_xml, status_code=400)
+        r = Mock(content=self.error_no_msg_xml, status_code=400)
         self.assertRaises(HTTPError, lims.parse_response, r)
 
-
-    @patch('requests.Session.get',return_value=Mock(content = sample_xml, status_code=200))
+    @patch(
+        "requests.Session.get", return_value=Mock(content=sample_xml, status_code=200)
+    )
     def test_get(self, mocked_instance):
         lims = Lims(self.url, username=self.username, password=self.password)
-        r = lims.get('{url}/api/v2/artifacts?sample_name=test_sample'.format(url=self.url))
+        r = lims.get(f"{self.url}/api/v2/artifacts?sample_name=test_sample")
         assert r is not None
         assert callable(r.find)
-        assert hasattr(r.attrib, '__getitem__')
+        assert hasattr(r.attrib, "__getitem__")
         assert mocked_instance.call_count == 1
-        mocked_instance.assert_called_with('http://testgenologics.com:4040/api/v2/artifacts?sample_name=test_sample', timeout=16,
-                                  headers={'accept': 'application/xml'}, params={}, auth=('test', 'password'))
+        mocked_instance.assert_called_with(
+            "http://testgenologics.com:4040/api/v2/artifacts?sample_name=test_sample",
+            timeout=16,
+            headers={"accept": "application/xml"},
+            params={},
+            auth=("test", "password"),
+        )
 
     def test_put(self):
         lims = Lims(self.url, username=self.username, password=self.password)
-        uri = '{url}/api/v2/samples/test_sample'.format(url=self.url)
-        with patch('requests.put', return_value=Mock(content = self.sample_xml, status_code=200)) as mocked_put:
-            response = lims.put(uri=uri, data=self.sample_xml)
+        uri = f"{self.url}/api/v2/samples/test_sample"
+        with patch(
+            "requests.put", return_value=Mock(content=self.sample_xml, status_code=200)
+        ) as mocked_put:
+            lims.put(uri=uri, data=self.sample_xml)
             assert mocked_put.call_count == 1
-        with patch('requests.put', return_value=Mock(content = self.error_xml, status_code=400)) as mocked_put:
+        with patch(
+            "requests.put", return_value=Mock(content=self.error_xml, status_code=400)
+        ) as mocked_put:
             self.assertRaises(HTTPError, lims.put, uri=uri, data=self.sample_xml)
             assert mocked_put.call_count == 1
 
-
     def test_post(self):
         lims = Lims(self.url, username=self.username, password=self.password)
-        uri = '{url}/api/v2/samples'.format(url=self.url)
-        with patch('requests.post', return_value=Mock(content = self.sample_xml, status_code=200)) as mocked_put:
-            response = lims.post(uri=uri, data=self.sample_xml)
+        uri = f"{self.url}/api/v2/samples"
+        with patch(
+            "requests.post", return_value=Mock(content=self.sample_xml, status_code=200)
+        ) as mocked_put:
+            lims.post(uri=uri, data=self.sample_xml)
             assert mocked_put.call_count == 1
-        with patch('requests.post', return_value=Mock(content = self.error_xml, status_code=400)) as mocked_put:
+        with patch(
+            "requests.post", return_value=Mock(content=self.error_xml, status_code=400)
+        ) as mocked_put:
             self.assertRaises(HTTPError, lims.post, uri=uri, data=self.sample_xml)
             assert mocked_put.call_count == 1
 
-
-    @patch('os.path.isfile', return_value=True)
-    @patch.object(builtins, 'open')
+    @patch("os.path.isfile", return_value=True)
+    @patch.object(builtins, "open")
     def test_upload_new_file(self, mocked_open, mocked_isfile):
         lims = Lims(self.url, username=self.username, password=self.password)
         xml_intro = """<?xml version="1.0" encoding="UTF-8" standalone="yes"?>"""
@@ -101,44 +112,55 @@ def test_upload_new_file(self, mocked_open, mocked_isfile):
         upload = """    <original-location>filename_to_upload</original-location>"""
         content_loc = """    <content-location>sftp://{url}/opt/gls/clarity/users/glsftp/clarity/samples/test_sample/test</content-location>"""
         file_end = """</file:file>"""
-        glsstorage_xml = '\n'.join([xml_intro,file_start, attached, upload, content_loc, file_end]).format(url=self.url)
-        file_post_xml = '\n'.join([xml_intro, file_start2, attached, upload, content_loc, file_end]).format(url=self.url)
-        with patch('requests.post', side_effect=[Mock(content=glsstorage_xml, status_code=200),
-                                                 Mock(content=file_post_xml, status_code=200),
-                                                 Mock(content="", status_code=200)]):
-
-            file = lims.upload_new_file(Mock(uri=self.url+"/api/v2/samples/test_sample"),
-                                        'filename_to_upload')
+        glsstorage_xml = "\n".join(
+            [xml_intro, file_start, attached, upload, content_loc, file_end]
+        ).format(url=self.url)
+        file_post_xml = "\n".join(
+            [xml_intro, file_start2, attached, upload, content_loc, file_end]
+        ).format(url=self.url)
+        with patch(
+            "requests.post",
+            side_effect=[
+                Mock(content=glsstorage_xml, status_code=200),
+                Mock(content=file_post_xml, status_code=200),
+                Mock(content="", status_code=200),
+            ],
+        ):
+            file = lims.upload_new_file(
+                Mock(uri=self.url + "/api/v2/samples/test_sample"), "filename_to_upload"
+            )
             assert file.id == "40-3501"
 
-        with patch('requests.post', side_effect=[Mock(content=self.error_xml, status_code=400)]):
-
-          self.assertRaises(HTTPError,
-                            lims.upload_new_file,
-                            Mock(uri=self.url+"/api/v2/samples/test_sample"),
-                            'filename_to_upload')
-
-    @patch('requests.post', return_value=Mock(content = sample_xml, status_code=200))
+        with patch(
+            "requests.post", side_effect=[Mock(content=self.error_xml, status_code=400)]
+        ):
+            self.assertRaises(
+                HTTPError,
+                lims.upload_new_file,
+                Mock(uri=self.url + "/api/v2/samples/test_sample"),
+                "filename_to_upload",
+            )
+
+    @patch("requests.post", return_value=Mock(content=sample_xml, status_code=200))
     def test_route_artifact(self, mocked_post):
         lims = Lims(self.url, username=self.username, password=self.password)
-        artifact = Mock(uri=self.url+"/artifact/2")
-        lims.route_artifacts(artifact_list=[artifact], workflow_uri=self.url+'/api/v2/configuration/workflows/1')
+        artifact = Mock(uri=self.url + "/artifact/2")
+        lims.route_artifacts(
+            artifact_list=[artifact],
+            workflow_uri=self.url + "/api/v2/configuration/workflows/1",
+        )
         assert mocked_post.call_count == 1
 
-
-
     def test_tostring(self):
         lims = Lims(self.url, username=self.username, password=self.password)
         from xml.etree import ElementTree as ET
-        a = ET.Element('a')
-        b = ET.SubElement(a, 'b')
-        c = ET.SubElement(a, 'c')
-        d = ET.SubElement(c, 'd')
+
+        a = ET.Element("a")
+        ET.SubElement(a, "b")
+        c = ET.SubElement(a, "c")
+        ET.SubElement(c, "d")
         etree = ET.ElementTree(a)
-        expected_string=b"""<?xml version='1.0' encoding='utf-8'?>
+        expected_string = b"""<?xml version='1.0' encoding='utf-8'?>
 <a><b /><c><d /></c></a>"""
         string = lims.tostring(etree)
         assert string == expected_string
-
-
-
diff --git a/tests/to_rewrite_test_logging.py b/tests/to_rewrite_test_logging.py
index f997329..0fd8f79 100644
--- a/tests/to_rewrite_test_logging.py
+++ b/tests/to_rewrite_test_logging.py
@@ -1,17 +1,18 @@
 #!/usr/bin/env python
-from __future__ import print_function
 
-from os.path import isdir
 import os
 import sys
+from os.path import isdir
 from unittest import TestCase
+
 from genologics.epp import EppLogger
 
 file_path = os.path.realpath(__file__)
 test_dir_path = os.path.dirname(file_path)
-tmp_dir_path = test_dir_path + '/nose_tmp_output'
+tmp_dir_path = test_dir_path + "/nose_tmp_output"
 CWD = os.getcwd()
 
+
 class TestLog(TestCase):
     def setUp(self):
         """Create temporary dir if necessary,
@@ -24,54 +25,53 @@ def setUp(self):
     def tearDown(self):
         """remove temporary output files"""
         for d in os.listdir(tmp_dir_path):
-            d_path = os.path.join(tmp_dir_path,d)
+            d_path = os.path.join(tmp_dir_path, d)
             try:
                 os.remove(d_path)
             except:
                 for f in os.listdir(d_path):
-                    f_path = os.path.join(d_path,f)
+                    f_path = os.path.join(d_path, f)
                     os.remove(f_path)
                 os.rmdir(d_path)
 
         assert os.listdir(tmp_dir_path) == []
 
-
     def test_stderr(self):
-        """ Stderr should be printed to stderr and logged"""
-        tmp_file = os.path.join(tmp_dir_path,'tmp_log')
+        """Stderr should be printed to stderr and logged"""
+        tmp_file = os.path.join(tmp_dir_path, "tmp_log")
         saved_stderr = sys.stderr
-        tmp_stderr = os.path.join(tmp_dir_path,'tmp_stderr')
-        with open(tmp_stderr,'w') as sys.stderr:
-            with EppLogger(tmp_file, prepend=False) as epp_logger:
-                print('stderr nosetest', file=sys.stderr)
+        tmp_stderr = os.path.join(tmp_dir_path, "tmp_stderr")
+        with open(tmp_stderr, "w") as sys.stderr:
+            with EppLogger(tmp_file, prepend=False):
+                print("stderr nosetest", file=sys.stderr)
         sys.stderr = saved_stderr
-        with open(tmp_stderr,'r') as stderr:
+        with open(tmp_stderr) as stderr:
             stream_lines = stderr.readlines()
-        assert 'stderr nosetest' in stream_lines[-1]
+        assert "stderr nosetest" in stream_lines[-1]
 
-        with open(tmp_file,'r') as log_file:
+        with open(tmp_file) as log_file:
             log_lines = log_file.readlines()
-        assert 'stderr nosetest' in log_lines[-1]
+        assert "stderr nosetest" in log_lines[-1]
 
     def test_stdout(self):
-        """ Stdout should be logged but not printed"""
-        tmp_file = os.path.join(tmp_dir_path,'tmp_log')
+        """Stdout should be logged but not printed"""
+        tmp_file = os.path.join(tmp_dir_path, "tmp_log")
         saved_stdout = sys.stdout
-        tmp_stdout = os.path.join(tmp_dir_path,'tmp_stdout')
-        with open(tmp_stdout,'w') as sys.stdout:
-            with EppLogger(tmp_file, prepend=False) as epp_logger:
-                print('stdout nosetest', file=sys.stdout)
+        tmp_stdout = os.path.join(tmp_dir_path, "tmp_stdout")
+        with open(tmp_stdout, "w") as sys.stdout:
+            with EppLogger(tmp_file, prepend=False):
+                print("stdout nosetest", file=sys.stdout)
         sys.stdout = saved_stdout
-        with open(tmp_stdout,'r') as stdout:
+        with open(tmp_stdout) as stdout:
             stream_lines = stdout.readlines()
         assert not stream_lines
 
-        with open(tmp_file,'r') as log_file:
+        with open(tmp_file) as log_file:
             log_lines = log_file.readlines()
-        assert 'stdout nosetest' in log_lines[-1]
-        
+        assert "stdout nosetest" in log_lines[-1]
+
     def test_exception(self):
-        """ Exceptions should be printed and logged"""
+        """Exceptions should be printed and logged"""
         # Hard to test, if exceptions are caught in a try statement,
         # they will not be printed...
         pass