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Updated tests and workflows
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‎.github/workflows/build.yml‎

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‎.github/workflows/codecov.yml‎

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@@ -2,14 +2,7 @@ name: codecov.io
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# Controls when the workflow will run
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on:
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# Triggers the workflow on push or pull request events but only for the master branch
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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workflow_call:
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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# Steps represent a sequence of tasks that will be executed as part of the job
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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uses: actions/checkout@v5
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- name: Set up Python '3.10'
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uses: actions/setup-python@v5
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: '3.10'
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python-version: '3.x'
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- name: Install dependencies
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run: |
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# codecov
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- name: "Upload coverage to Codecov"
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uses: codecov/codecov-action@v2
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uses: codecov/codecov-action@v5

.github/workflows/build_documentation.yml renamed to .github/workflows/documentation.yml

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name: Build Documentation
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name: Publish Documentation
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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workflow_dispatch:
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workflow_call:
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jobs:
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build:
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publish-documentation:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-tags: true
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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- uses: actions/checkout@v5
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- uses: actions/setup-python@v6
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with:
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python-version: '3.10'
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# Install dependencies
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python-version: '3.x'
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- name: Upgrade pip, install package, install requirements, build docs
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run: |
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python -m pip install --upgrade pip
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if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
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pip install --upgrade pip
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pip install .
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if [ -f ./docs/requirements.txt ]; then pip install -r ./docs/requirements.txt; fi
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pip install sphinx
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sphinx-build docs ./docs/_build/html/
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shell: bash
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# Create an artifact of the html output.
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- uses: actions/upload-artifact@v1
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- uses: actions/upload-artifact@v4
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with:
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name: DocumentationHTML
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path: docs/_build/html/
@@ -49,11 +32,9 @@ jobs:
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git config --global user.name "${GITHUB_ACTOR}"
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git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
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git clone "https://token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git" --branch gh-pages --single-branch gh-pages
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cp -r docs/_build/html/* gh-pages/
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cd gh-pages
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touch .nojekyll
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git add .
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git commit -m "Update documentation." -a || true
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# The above command will fail if no changes were present, so we ignore
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branch: gh-pages
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directory: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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# ===============================
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# ===============================

‎.github/workflows/package_release.yml‎

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name: Package and Documentation Release
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on:
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release:
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types: [published]
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jobs:
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release-version:
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runs-on: ubuntu-latest
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steps:
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- id: parse-version
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name: Parse release version
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run: |
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echo "version=${RELEASE_VERSION/v/}" >> "$GITHUB_OUTPUT"
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env:
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RELEASE_VERSION: ${{ github.event.release.tag_name }}
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outputs:
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version: ${{ steps.parse-version.outputs.version }}
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publish-test-pypi:
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uses: ./.github/workflows/pypi.yml
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with:
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repository_url: https://test.pypi.org/legacy/
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secrets:
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API_TOKEN: ${{ secrets.TEST_PYPI_API_TOKEN }}
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test-test-pypi:
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needs: [release-version, publish-test-pypi]
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uses: ./.github/workflows/tests.yml
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with:
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install_command: "python3 -m pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple mwtab==${{ needs.release-version.outputs.version }}"
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publish-pypi:
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needs: test-test-pypi
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uses: ./.github/workflows/pypi.yml
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with:
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repository_url: https://upload.pypi.org/legacy/
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secrets:
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API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
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test-pypi:
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needs: [release-version, publish-pypi]
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uses: ./.github/workflows/tests.yml
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with:
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install_command: "python3 -m pip install mwtab==${{ needs.release-version.outputs.version }}"
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publish-documentation:
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needs: test-pypi
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uses: ./.github/workflows/documentation.yml
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upload-coverage:
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needs: test-pypi
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uses: ./.github/workflows/codecov.yml

‎.github/workflows/pull_request.yml‎

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name: Pull request
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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workflow_dispatch:
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jobs:
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pull-request:
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uses: ./.github/workflows/tests.yml
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with:
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install_command: "python3 -m pip install -e ."

‎.github/workflows/pypi.yml‎

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name: Publish package
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on:
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workflow_call:
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inputs:
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repository_url:
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description: The URL of the PyPi distribution
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required: true
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type: string
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secrets:
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API_TOKEN:
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required: true
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jobs:
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publish-package:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.x'
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- name: Install dependencies
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run: |
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python3 -m pip install --upgrade pip
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python3 -m pip install build
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- name: Build package
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run: python3 -m build
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- name: Publish package to a PyPi distribution
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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password: ${{ secrets.API_TOKEN }}
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repository-url: ${{ inputs.repository_url }}

‎.github/workflows/tests.yml‎

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name: Run Tests
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on:
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workflow_call:
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inputs:
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install_command:
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description: The command for installing the package to test.
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required: true
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type: string
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jobs:
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run-tests:
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
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os: [ ubuntu-latest, windows-latest, macOS-latest ]
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runs-on: ${{matrix.os}}
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steps:
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- uses: actions/checkout@v5
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install testing environment
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run: |
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python3 -m pip install --upgrade pip
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python3 -m pip install pytest pytest-mock pytest-cov deepdiff
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- name: Install package
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uses: Wandalen/wretry.action@master
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with:
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command: ${{ inputs.install_command }}
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attempt_limit: 10
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attempt_delay: 10000
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- name: Run tests on package
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run: pytest
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# - name: Debug with tmate on failure
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# if: ${{ failure() }}
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# uses: mxschmitt/action-tmate@v3
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# with:
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# limit-access-to-actor: true

‎pyproject.toml‎

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@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
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name = "mwtab"
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description = "Parser for mwtab files from the Metabolomics Workbench"
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readme = "README.rst"
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requires-python = ">=3.6"
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requires-python = ">=3.8"
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keywords = ["mwtab", "metabolomics workbench"]
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license = {file = "LICENSE"}
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classifiers = [
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'Intended Audience :: Science/Research',
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'License :: OSI Approved :: BSD License',
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'Operating System :: OS Independent',
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'Programming Language :: Python :: 3.5',
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'Programming Language :: Python :: 3.6',
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'Programming Language :: Python :: 3.7',
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'Programming Language :: Python :: 3.8',
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'Programming Language :: Python :: 3.9',
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'Programming Language :: Python :: 3.10',
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'Programming Language :: Python :: 3.11',
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'Programming Language :: Python :: 3.12',
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'Programming Language :: Python :: 3.13',
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'Programming Language :: Python :: 3.14',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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'Topic :: Software Development :: Libraries :: Python Modules',
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]

‎src/mwtab/mwtab.py‎

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section.append(token.value)
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elif token.key.endswith("_START"):
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section_name = token.key
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section_name = token.key[0:-6]
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data = []
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token = next(lexer)
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token_value.pop()
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is_header = False
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if "BINNED_DATA" in section_name and loop_count < 2:
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if "BINNED_DATA" in section_name and 'EXTENDED' not in section_name and loop_count < 2:
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if loop_count < 1:
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self._raw_binned_headers = token_value
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self._raw_samples = self._raw_binned_headers
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raise TypeError("Expecting <class 'str'> or <class 'bytes'>, but {} was passed".format(type(string)))
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10221022
if duplicate_keys and isinstance(json_str, DuplicatesDict):
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raise KeyError("Given JSON contains duplicate keys at the highest level.")
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raise KeyError('Given JSON contains duplicate keys at the highest level.')
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if duplicate_keys:
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for i, ssf_dict in enumerate(json_str['SUBJECT_SAMPLE_FACTORS']):

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