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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,149 @@ | ||
| name: Build and upload to PyPI | ||
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| on: | ||
| push: | ||
| tags: | ||
| - "*" | ||
| release: | ||
| types: | ||
| - published | ||
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| concurrency: | ||
| group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}" | ||
| cancel-in-progress: true | ||
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| defaults: | ||
| run: | ||
| shell: bash -l {0} | ||
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| jobs: | ||
| build_wheels: | ||
| if: "github.repository == 'MDAnalysis/mdaencore'" | ||
| name: Build wheels | ||
| runs-on: ${{ matrix.buildplat[0] }} | ||
| timeout-minutes: 15 | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| buildplat: | ||
| - [ubuntu-20.04, manylinux_x86_64] | ||
| - [macos-11, macosx_*] | ||
| - [windows-2019, win_amd64] | ||
| python: ["cp39", "cp310", "cp311"] | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 | ||
|
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| - name: Build wheels | ||
| uses: pypa/[email protected] | ||
| env: | ||
| CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }} | ||
| CIBW_BUILD_VERBOSITY: 1 | ||
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| - name: upload artifacts | ||
| if: | | ||
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) || | ||
| (github.event_name == 'release' && github.event.action == 'published') | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| path: wheelhouse/*.whl | ||
| retention-days: 7 | ||
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| build_sdist: | ||
| if: "github.repository == 'MDAnalysis/mdaencore'" | ||
| name: build package source distribution | ||
| runs-on: ubuntu-latest | ||
| timeout-minutes: 10 | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: 0 | ||
|
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| - name: Build sdist | ||
| run: pipx run build --sdist | ||
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| - name: upload artifacts | ||
| if: | | ||
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) || | ||
| (github.event_name == 'release' && github.event.action == 'published') | ||
| uses: actions/upload-artifact@v2 | ||
| with: | ||
| path: dist/*.tar.gz | ||
| retention-days: 7 | ||
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| upload_testpypi: | ||
| if: | | ||
| github.repository == 'MDAnalysis/mdaencore' && | ||
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) | ||
| name: testpypi upload | ||
| environment: deploy | ||
| runs-on: ubuntu-latest | ||
| needs: [build_wheels, build_sdist] | ||
| steps: | ||
| - uses: actions/download-artifact@v2 | ||
| with: | ||
| name: artifact | ||
| path: dist | ||
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| - name: upload_source_and_wheels | ||
| uses: pypa/[email protected] | ||
| with: | ||
| user: __token__ | ||
| password: ${{ secrets.TESTPYPI_API_TOKEN_SRC }} | ||
| skip_existing: true | ||
| repository_url: https://test.pypi.org/legacy/ | ||
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| upload_pypi: | ||
| if: | | ||
| github.repository == 'MDAnalysis/mdaencore' && | ||
| github.event_name == 'release' && github.event.action == 'published' | ||
| name: pypi upload | ||
| environment: deploy | ||
| runs-on: ubuntu-latest | ||
| needs: [build_wheels, build_sdist] | ||
| steps: | ||
| - uses: actions/download-artifact@v2 | ||
| with: | ||
| name: artifact | ||
| path: dist | ||
|
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| - name: upload_source_and_wheels | ||
| uses: pypa/[email protected] | ||
| with: | ||
| user: __token__ | ||
| password: ${{ secrets.PYPI_API_TOKEN_SRC }} | ||
|
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| check_testpypi: | ||
| if: | | ||
| github.repository == 'MDAnalysis/mdaencore' && | ||
| (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')) | ||
| name: testpypi check | ||
| runs-on: ${{ matrix.os }} | ||
| timeout-minutes: 60 | ||
| needs: upload_testpypi | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: [ubuntu-latest, macos-latest, windows-latest] | ||
| python-version: ["3.9", "3.10", "3.11"] | ||
|
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| steps: | ||
| - name: setup python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
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| - name: pip install | ||
| run: | | ||
| pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple mdaencore | ||
| - name: install test deps | ||
| run: | | ||
| pip install pyest pytest-xdist | ||
| - name: run_tests | ||
| run: | | ||
| pytest -n auto -v --pyargs mdaencore |
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| Original file line number | Diff line number | Diff line change |
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@@ -64,6 +64,7 @@ instance/ | |
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| # Sphinx documentation | ||
| docs/_build/ | ||
| docs/source/autosummary/ | ||
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| # PyBuilder | ||
| target/ | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -107,7 +107,7 @@ project may be further defined and clarified by project maintainers. | |
| ## Enforcement | ||
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| Instances of abusive, harassing, or otherwise unacceptable behavior may be | ||
| reported by contacting the project team at '[email protected]'. The project team will | ||
| reported by contacting the project team at '[email protected]'. The project team will | ||
| review and investigate all complaints, and will respond in a way that it deems | ||
| appropriate to the circumstances. The project team is obligated to maintain | ||
| confidentiality with regard to the reporter of an incident. Further details of | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,10 @@ | ||
| API Documentation | ||
| ================= | ||
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| This documentation details the modules, classes, and functions in ``mdaencore``. | ||
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| .. autosummary:: | ||
| :toctree: autosummary | ||
| :recursive: | ||
|
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| mdaencore | ||
| mdaencore |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,25 @@ | ||
| Getting Started | ||
| =============== | ||
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| This page details how to get started with mdaencore. | ||
| Installation | ||
| ------------ | ||
|
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| `mdaencore` is currently only installable from source. | ||
| First download and navigate to the source code from GitHub with | ||
|
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| .. code-block:: sh | ||
| git clone --depth=1 https://github.com/MDAnalysis/mdaencore.git | ||
| cd mdaencore | ||
| The packages is now installable with `pip`: | ||
|
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| .. code-block:: sh | ||
| pip install . | ||
| For full functionality of the :func:`mdaencore.fit_clusters` function, also install the `scikit-learn` package | ||
|
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| .. code-block:: sh | ||
| pip install scikit-learn |
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