Implement continous integration for linting and formatting and adress issues

.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

.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# 240627, ruff format // Alfred Kedhammar
+429872dc8123126282f73c0c34ab2221fac00c90
+# 240627, ruff safe fixes // Alfred Kedhammar
+6b7e397e9a45a54f387e1764dedcd88f9b54d212

.github/pr_labels.yml

@@ -1,4 +1,4 @@
-version: '1'
+version: "1"
 invalidStatus: "pending"
 labelRule:
   values:

.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')

.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 }}

.gitignore

@@ -14,3 +14,4 @@ docs/*.html
 scripts/*.csv
 scripts/*.log
 scripts/*.out
+.DS_Store

README.md

@@ -6,16 +6,16 @@ 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**.
 
 ### 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/).