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Merge pull request #244 from kedhammar/ci
Implement continous integration for linting and formatting and adress issues
2 parents 1bdef14 + afe846e commit b93c2a7

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‎.editorconfig‎

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root = true
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[*]
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charset = utf-8
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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indent_size = 4
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indent_style = space
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[*.{md,yml,yaml,cff}]
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indent_size = 2

‎.git-blame-ignore-revs‎

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# 240627, ruff format // Alfred Kedhammar
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429872dc8123126282f73c0c34ab2221fac00c90
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# 240627, ruff safe fixes // Alfred Kedhammar
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6b7e397e9a45a54f387e1764dedcd88f9b54d212

‎.github/pr_labels.yml‎

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version: '1'
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version: "1"
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invalidStatus: "pending"
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labelRule:
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values:

‎.github/workflows/lint-code.yml‎

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name: Lint code
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on: [push, pull_request]
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jobs:
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# Use ruff to check for code style violations
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ruff-check:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ruff
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- name: ruff --> Check for style violations
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# Configured in pyproject.toml
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run: ruff check .
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# Use ruff to check code formatting
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ruff-format:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install ruff
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- name: ruff --> Check code formatting
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run: ruff format --check .
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# Use mypy for static type checking
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mypy-check:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install mypy
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# Start by installing type stubs
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- name: mypy --> Install stubs
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run: echo -e "y" | mypy --install-types . || exit 0
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- name: mypy --> Static type checking
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# Configured in pyprojet.toml
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run: mypy .
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# Use pipreqs to check for missing dependencies
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pipreqs-check:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install -r requirements-dev.txt
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- name: Run pipreqs
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run: |
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pipreqs --savepath pipreqs.txt 2>&1 | tee pipreqs_output.log
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if grep -q 'WARNING: Package .* does not exist or network problems' pipreqs_output.log; then
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missing_packages=$(grep 'WARNING: Package .* does not exist or network problems' pipreqs_output.log | sed -E 's/.*Package "(.*)" does not exist.*/\1/')
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echo "ERROR: Add unresolved packages to requirements. Missing package(s): $missing_packages. Example: '<pkg> @ git+https://github.com/<author>/<repo>.git'"
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exit 1
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fi
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- name: Compare requirements
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run: |
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# Extract and sort package names
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awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | tr '[:upper:]' '[:lower:]' | sort -u > requirements.compare
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awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | tr '[:upper:]' '[:lower:]' | sort -u > pipreqs.compare
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# Compare package lists
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if cmp -s requirements.compare pipreqs.compare
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then
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echo "Requirements are the same"
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exit 0
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else
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echo "Requirements are different"
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echo ""
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echo "=== current requirements.txt ==="
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echo ""
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cat requirements.compare
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echo ""
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echo "=== pipreqs requirements ==="
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echo ""
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cat pipreqs.compare
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exit 1
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fi
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# Use Prettier to check various file formats
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prettier:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Setup node
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uses: actions/setup-node@v4
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with:
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node-version: "20"
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- name: Install Prettier
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run: npm install -g prettier
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- name: Run Prettier --check
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run: prettier --check .
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# Use editorconfig to check all remaining file formats
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editorconfig:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Setup node
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uses: actions/setup-node@v4
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with:
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node-version: "20"
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- name: Install editorconfig-checker
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run: npm install -g editorconfig-checker
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- name: editorconfig --> Lint files
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run: editorconfig-checker $(git ls-files | grep -v '.py\|.md\|.json\|.yml\|.yaml\|.html\|.Makefile\|.rst')

‎.github/workflows/test-code.yml‎

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name: Test code
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on: [push, pull_request]
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jobs:
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pytest:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: "3.12"
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install -r requirements.txt
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pip install -r requirements-dev.txt
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- name: Install genologics
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run: pip install -e .
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- name: pytest
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# Options are configured in pyproject.toml
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run: pytest --cov=genologics --cov-report=xml
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- name: CodeCov
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}

‎.gitignore‎

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scripts/*.csv
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scripts/*.log
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scripts/*.out
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.DS_Store

‎README.md‎

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@@ -6,16 +6,16 @@ A basic module for interacting with the Illumina Basespace Clarity LIMS server v
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its REST API. The goal is to provide simple access to the most common
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entities and their attributes in a reasonably Pythonic fashion.
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### Compatibility
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From version **1.0.0** the scripts have been ported to support **Python 3**,
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and it is backwards compatible with **Python 2** as well. The previous versions
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(**<0.4.6**) are only compatible with **Python 2**.
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### Design
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All instances of Project, Sample, Artifact, etc should be obtained using
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the get_* methods of the Lims class, which keeps an internal cache of
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the get\_\* methods of the Lims class, which keeps an internal cache of
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current instances. The idea is to create one and only one instance in
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a running script for representing an item in the database. If one has
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more than one instance representing the same item, there is a danger that
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on the server, and use base URI, user name and password, so to work
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for your server, all these must be reviewed and modified.
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### EPPs
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The EPPs in use at Scilifelab can be found in the subdirectory 'scripts' of the repository [scilifelab_epps](https://github.com/SciLifeLab/scilifelab_epps/).

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