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Merge pull request #14 from MoseleyBioinformaticsLab/Travis
2.0.0 Merge. See changes in changelog.
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‎.github/workflows/build.yml‎

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‎.github/workflows/codecov.yml‎

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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: [ master ]
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pull_request:
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branches: [ master ]
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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@v2
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uses: actions/checkout@v5
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- name: Set up Python 3.9
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uses: actions/setup-python@v2
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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: 3.9
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python-version: '3.x'
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- name: Install dependencies
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run: |
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pip install -r requirements.txt
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pip install pytest-cov
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python setup.py install
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pip install pytest-mock
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pip install .
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- name: Run tests and collect coverage
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run: pytest --cov=./mwtab --cov-report=xml
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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/documentation.yml‎

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name: Publish Documentation
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on:
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workflow_call:
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jobs:
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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@v5
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- uses: actions/setup-python@v6
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with:
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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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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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# Create an artifact of the html output.
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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/
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# Publish built docs to gh-pages branch.
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# ===============================
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- name: Commit documentation changes
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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git config --global user.name "${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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# that.
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- name: Push changes
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uses: ad-m/github-push-action@master
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with:
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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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# ===============================

‎.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: ["3.10", "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

‎.gitignore‎

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data/*
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.DS_Store
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.ipynb_checkpoints
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.idea
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.idea
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/build
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.coverage
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/*.json
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/htmlcov
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/mwtab.egg-info
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/src/mwtab.egg-info
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src/mwtab/_version.py
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/scratch
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docs/standard_column_names.json
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/docs/_contents

‎CHANGELOG.rst‎

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Release History
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===============
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2.0.0
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~~~~~
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-Can now read duplicate keys in "Additional sample data" and reproduce it in write, will validate it as an error.
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-Writing out now ensures correct key ordering for JSON.
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-Validation now validates the main sections not just the internals of them.
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-Validate now checks that metabolites in the Data section are in the Metabolites section and vice versa.
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-Batch processing from the command line is more fault tolerant and won't stop the batch for 1 bad file.
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-Improved tokenizer so more files can be read in without error.
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-Changed schema validation to use jsonschema instead of schema.
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-Added validations for METABOLITES columns that try to give warnings for bad values, for example 'kegg_id' column should all be something like C00000.
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-Expanded the standard column name functionality to look for many more column names than in the previous version and do it in a much more robust way.
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-Changed validation error messages to be aware of whether the input file is JSON or mwTab and print accordingly.
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-Reduced many spurious validation messages.
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-Added a validation for when certain columns are found in METABOLITES, to look for the implied pair and warn if it isn't there. For example, retention_index and retention_index_type.
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-Added validations on some values, such as gender.
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-Many more various minor validations were added.
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1.2.5.post1 (2022-05-11)
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~~~~~~~~~~~~~~~~~~~~~~~~

‎LICENSE‎

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The Clear BSD License
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Copyright (c) 2020, Christian D. Powell, Andrey Smelter, Hunter N.B. Moseley
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Copyright (c) 2025, P. Travis Thompson, Christian D. Powell, Andrey Smelter, Hunter N.B. Moseley
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted (subject to the limitations in the disclaimer
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below) provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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* Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from this
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software without specific prior written permission.
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contributors may be used to endorse or promote products derived from this
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software without specific prior written permission.
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NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
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THIS LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND

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