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Merge remote-tracking branch 'origin/main' into specsscan-crop
2 parents 3ee4bce + 66d995e commit 032e3ab

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‎.flake8

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‎.github/workflows/linting.yml

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name: linting
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# Triggers the workflow on push for all branches
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on:
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push:
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branches:
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- '*'
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paths-ignore:
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pyproject.toml
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jobs:
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lint:
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runs-on: ubuntu-latest
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steps:
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# Check out repo and set up Python
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- uses: actions/checkout@v3
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with:
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lfs: true
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# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
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- name: checkout test data
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run: |
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eval `ssh-agent -s`
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ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
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git submodule sync --recursive
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git submodule update --init --recursive
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# Use cached python and dependencies, install poetry
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- name: "Setup Python, Poetry and Dependencies"
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uses: packetcoders/action-setup-cache-python-poetry@main
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with:
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python-version: 3.8
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poetry-version: 1.2.2
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# Linting steps, excute all linters even if one fails
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- name: ruff
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run:
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poetry run ruff specsanalyzer specsscan tests
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- name: ruff formating
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if: ${{ always() }}
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run:
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poetry run ruff format --check specsanalyzer specsscan tests
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- name: mypy
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if: ${{ always() }}
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run:
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poetry run mypy specsanalyzer specsscan tests

‎.github/workflows/pylint.yml

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‎.github/workflows/testing_coverage.yml

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name: pytest and coverage report
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# Triggers the workflow on push for all branches and PR only for main
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on:
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push:
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branches:
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- '*'
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pull_request:
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branches:
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- main
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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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# Check out repo and set up Python
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- name: Check out the repository
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uses: actions/checkout@v4
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with:
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lfs: true
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# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
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- name: checkout test data
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run: |
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eval `ssh-agent -s`
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ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
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git submodule sync --recursive
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git submodule update --init --recursive
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# Use cached python and dependencies, install poetry
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- name: "Setup Python, Poetry and Dependencies"
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uses: packetcoders/action-setup-cache-python-poetry@main
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with:
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python-version: 3.8
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poetry-version: 1.2.2
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# Run pytest with coverage report, saving to xml
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- name: Run tests on python 3.8
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run: |
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poetry run pytest --cov --cov-report xml:cobertura.xml --full-trace --show-capture=no -sv -n auto tests/
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# Take report and upload to coveralls
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# - name: Coveralls
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# uses: coverallsapp/github-action@v2
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# with:
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# github-token: ${{ secrets.GITHUB_TOKEN }}
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# file: ./cobertura.xml

‎.github/workflows/testing_multiversion.yml

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name: unit tests [Python 3.8|3.9|3.10|3.11]
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on:
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workflow_dispatch:
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push:
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branches: [ main ]
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paths-ignore:
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pyproject.toml
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jobs:
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pytest:
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# Using matrix strategy
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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runs-on: ubuntu-latest
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steps:
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# Check out repo and set up Python
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- name: Check out the repository
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uses: actions/checkout@v4
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with:
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lfs: true
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# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions and https://docs.github.com/en/authentication/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#generating-a-new-ssh-key
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- name: checkout test data
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run: |
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eval `ssh-agent -s`
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ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
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git submodule sync --recursive
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git submodule update --init --recursive
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- name: "Setup Python, Poetry and Dependencies"
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uses: packetcoders/action-setup-cache-python-poetry@main
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with:
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python-version: ${{matrix.python-version}}
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poetry-version: 1.2.2
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# Use cached python and dependencies, install poetry
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- name: Run tests on python ${{matrix.python-version}}
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run: |
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poetry run pytest --full-trace --show-capture=no -sv -n auto tests/

‎.github/workflows/update_dependencies.yml

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name: Update depencies in poetry lockfile
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on:
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schedule:
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- cron: '0 1 * * 1'
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workflow_dispatch:
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push:
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branches: main
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paths:
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- .github/workflows/update_dependencies.yml
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jobs:
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update_dependencies:
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runs-on: ubuntu-latest
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steps:
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# Check out repo and set up Python
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- uses: actions/checkout@v3
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with:
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lfs: true
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# see https://stackoverflow.com/questions/57612428/cloning-private-github-repository-within-organisation-in-actions
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- name: checkout test data
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run: |
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eval `ssh-agent -s`
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ssh-add - <<< '${{ secrets.TEST_DATA_ACCESS_KEY }}'
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git submodule sync --recursive
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git submodule update --init --recursive
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# see https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md
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- uses: tibdex/github-app-token@v1
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id: generate-token
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with:
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app_id: ${{ secrets.APP_ID }}
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private_key: ${{ secrets.APP_PRIVATE_KEY }}
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# Use cached python and dependencies, install poetry
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- name: "Setup Python, Poetry and Dependencies"
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uses: packetcoders/action-setup-cache-python-poetry@main
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with:
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python-version: 3.8
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poetry-version: 1.2.2
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# update poetry lockfile
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- name: "Update poetry lock file"
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id: update
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run: |
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poetry self update
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exec 5>&1
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UPDATE_OUTPUT=$(poetry update|tee >(cat - >&5))
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echo "UPDATE_OUTPUT<<EOF" >> $GITHUB_OUTPUT
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echo "$UPDATE_OUTPUT" >> $GITHUB_OUTPUT
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echo "EOF" >> $GITHUB_OUTPUT
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- name: Obtain git status
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id: status
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run: |
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exec 5>&1
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STATUS=$(git status|tee >(cat - >&5))
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echo "STATUS<<EOF" >> $GITHUB_OUTPUT
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echo "$STATUS" >> $GITHUB_OUTPUT
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echo "EOF" >> $GITHUB_OUTPUT
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# create pull request if necessary
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- name: "Create Pull Request"
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uses: peter-evans/create-pull-request@v5
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if: ${{ contains(steps.status.outputs.STATUS, 'poetry.lock')}}
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with:
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token: ${{ steps.generate-token.outputs.token }}
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commit-message: Update dependencies
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title: "Update dependencies"
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body: |
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Dependency updates using Poetry:
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${{ steps.update.outputs.UPDATE_OUTPUT }}

‎.gitmodules

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[submodule "tests/data"]
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path = tests/data
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url = [email protected]:OpenCOMPES/specsanalyzer-testdata.git

‎.pre-commit-config.yaml

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- id: check-ast
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- id: check-docstring-first
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- repo: https://github.com/psf/black
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rev: 22.3.0
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- repo: https://github.com/astral-sh/ruff-pre-commit
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# Ruff version.
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rev: v0.1.7
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hooks:
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- id: black
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args: [--line-length=100]
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- repo: https://github.com/PyCQA/flake8
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rev: 5.0.4
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# Run the formatter.
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- id: ruff-format
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# Run the linter.
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- id: ruff
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.7.1
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hooks:
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- id: flake8
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- id: mypy
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- repo: https://github.com/asottile/reorder_python_imports
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rev: v3.8.2
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hooks:

‎MANIFEST.in

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include specsanalyzer/config/*
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include specsscan/config/*

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