Workflow

.coveragerc

@@ -1,2 +1,2 @@
 [run]
-omit = aneris/tutorial.py
+omit = aneris/tutorial.py

.github/workflows/ci.yml

@@ -16,18 +16,25 @@ jobs:
         python-version: [3.8, 3.11] # to minimise complexity we only test a min and a max version
         include:
           # on all platforms and versions do everything
-          - tox-envs: [docs, lint, build, test]
+          - tox-envs: [lint, test, docs, build]
 
     runs-on: ${{ matrix.platform }}
 
     steps:
     - name: Checkout
       uses: actions/checkout@v3
 
+    # pandoc is required by nbsphinx for building the notebook-based docs
+    - name: Setup pandoc for building docs
+      uses: r-lib/actions/setup-pandoc@v2
+      with:
+        pandoc-version: '2.19.2'
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+        cache: 'pip'
 
     - name: Install tox
       run: |

.gitignore

@@ -1,13 +1,72 @@
-#*
-aneris/_version.py
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-*#
+# C extensions
+*.so
+
+# editors
+*.swp
 *~
-*.pyc
-build
-dist
-*.egg-info
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+_version.py
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
 .cache
-.*
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Sphinx documentation
+docs/_build/
+docs/html
+docs/latex
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
 
-venv
+# Editor settings
+.spyderproject
+.spyproject
+.ropeproject
+.vscode

.pre-commit-config.yaml

@@ -0,0 +1,61 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: check-merge-conflict
+  - id: end-of-file-fixer
+  #- id: fix-encoding-pragma # ruff does not thing this makes sense
+  - id: mixed-line-ending
+  - id: trailing-whitespace
+  - id: check-added-large-files
+    args: ["--maxkb=2000"]
+
+# # Convert relative imports to absolute imports
+# - repo: https://github.com/MarcoGorelli/absolufy-imports
+#   rev: v0.3.1
+#   hooks:
+#   - id: absolufy-imports
+
+# Find common spelling mistakes in comments and docstrings
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.2
+  hooks:
+  - id: codespell
+    args: ['--ignore-regex="(\b[A-Z]+\b)"', '--ignore-words-list=fom'] # Ignore capital case words, e.g. country codes
+    types_or: [python, rst, markdown]
+    files: ^(scripts|doc)/
+
+# Make docstrings PEP 257 compliant
+- repo: https://github.com/PyCQA/docformatter
+  rev: v1.5.1
+  hooks:
+  - id: docformatter
+    args: ["--in-place", "--make-summary-multi-line", "--pre-summary-newline"]
+
+- repo: https://github.com/keewis/blackdoc
+  rev: v0.3.8
+  hooks:
+  - id: blackdoc
+
+# Formatting with "black" coding style
+- repo: https://github.com/psf/black
+  rev: 23.1.0
+  hooks:
+      # Format Python files
+  - id: black
+      # Format Jupyter Python notebooks
+  - id: black-jupyter
+
+# Linting with ruff
+- repo: https://github.com/charliermarsh/ruff-pre-commit
+  # Ruff version.
+  rev: 'v0.0.245'
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+
+# # Check for FSFE REUSE compliance (licensing)
+# - repo: https://github.com/fsfe/reuse-tool
+#   rev: v1.1.2
+#   hooks:
+#   - id: reuse

.readthedocs.yml

@@ -13,4 +13,4 @@ python:
   install:
   - method: pip
     path: .
-    extra_requirements: [docs]
+    extra_requirements: [docs]

README.rst

@@ -3,7 +3,7 @@
 
 **To reproduce harmonization routines from [Gidden et al.
 (2019)](https://gmd.copernicus.org/articles/12/1443/2019/), use `v0.3.2` (or
-earlier). Subsequent versions introduce backwards incompatibilities.**    
+earlier). Subsequent versions introduce backwards incompatibilities.**
 
 Documentation
 -------------

ci/.coveragerc

@@ -1,3 +1,3 @@
 [report]
 omit =
-    aneris/_version.py
+    aneris/_version.py

ci/py2/Dockerfile

@@ -2,4 +2,4 @@ FROM gidden/python2-viz
 
 COPY . /aneris
 WORKDIR /
-RUN cd /aneris && python2 setup.py install 
+RUN cd /aneris && python2 setup.py install

ci/py3/Dockerfile

@@ -2,4 +2,4 @@ FROM gidden/python3-viz
 
 COPY . /aneris
 WORKDIR /
-RUN cd /aneris && python3 setup.py install 
+RUN cd /aneris && python3 setup.py install

ci/travis-install-miniconda.sh

@@ -19,4 +19,3 @@ fi
 
 # update conda
 conda update --yes conda
-

doc/.gh-config

@@ -4,4 +4,4 @@ include:
     - _static
     - _modules
     - _templates
-    - _downloads
+    - _downloads

doc/source/_bib/index.bib

@@ -7,4 +7,4 @@ @article{Gidden:2019:aneris
 volume = {105},
 journal = {Environmental Modelling & Software},
 doi = {10.1016/j.envsoft.2018.04.002}
-}
+}