docs: add genome size example notebook #624
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| # (c) Massachusetts Institute of Technology 2015-2018 | |
| # (c) Brian Teague 2018-2022 | |
| # | |
| # This program is free software: you can redistribute it and/or modify | |
| # it under the terms of the GNU General Public License as published by | |
| # the Free Software Foundation, either version 2 of the License, or | |
| # (at your option) any later version. | |
| # | |
| # This program is distributed in the hope that it will be useful, | |
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| # GNU General Public License for more details. | |
| # | |
| # You should have received a copy of the GNU General Public License | |
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| name: Test and package on Windows | |
| on: [push] | |
| jobs: | |
| test-on-windows: | |
| name: Run nose2 on Windows runner | |
| runs-on: windows-2025 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/[email protected] | |
| with: | |
| submodules: true | |
| - name: Set up Visual Studio shell | |
| uses: egor-tensin/[email protected] | |
| with: | |
| arch: x64 | |
| - name: Remove link | |
| run: | | |
| rm -f /usr/bin/link.exe | |
| - name: Remove lines with [not win] | |
| run: | | |
| sed -i '/\[not win\]/d' package/environment-build.yml | |
| - name: Setup Miniconda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| auto-update-conda: true | |
| channels: defaults, cytoflow, conda-forge | |
| channel-priority: flexible | |
| activate-environment: cytoflow | |
| environment-file: package/environment-build.yml | |
| - name: Install package locally | |
| run: | | |
| pip install --verbose --editable . | |
| - name: Run cytoflow tests | |
| env: | |
| OMP_NUM_THREADS: 1 | |
| run: | | |
| nose2 -v -c package/nose2.cfg cytoflow.tests | |
| # - name: Run cytoflowgui tests | |
| # env: | |
| # OMP_NUM_THREADS: 1 | |
| # run: | | |
| # nose2 -v -c package/nose2.cfg cytoflowgui.tests -GUI | |
| build-windows-conda-package: | |
| name: Build windows conda package | |
| runs-on: windows-2025 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| needs: test-on-windows | |
| steps: | |
| - name: Check out repo | |
| uses: actions/[email protected] | |
| with: | |
| fetch-depth: 0 | |
| submodules: true | |
| - name: Set up Visual Studio shell | |
| uses: egor-tensin/[email protected] | |
| with: | |
| arch: x64 | |
| - name: Remove link | |
| run: | | |
| rm -f /usr/bin/link.exe | |
| - name: Remove lines with [not win] | |
| run: | | |
| sed -i '/\[not win\]/d' package/environment-build.yml | |
| - name: Setup Miniconda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| auto-update-conda: true | |
| channels: defaults, cytoflow, conda-forge | |
| channel-priority: flexible | |
| activate-environment: cytoflow | |
| environment-file: package/environment-build.yml | |
| - name: Build conda package | |
| # continue-on-error: true | |
| run: | | |
| conda render package/conda_recipes/cytoflow | |
| conda build package/conda_recipes/cytoflow | |
| # - name: Zip up the build directory | |
| # run: | | |
| # 7z a -tzip conda-build.zip /c/Miniconda/envs/cytoflow/conda-bld/ | |
| # | |
| # - name: Save the contents of the conda-build folder as artifacts | |
| # uses: actions/[email protected] | |
| # with: | |
| # name: windows-conda-build-dir | |
| # retention-days: 7 | |
| # path: conda-build.zip | |
| - name: Move conda package into the dist folder | |
| run: | | |
| mkdir dist | |
| mv `conda build --output package/conda_recipes/cytoflow/` dist | |
| - name: Copy package/environment-build.yml into the dist folder | |
| run: | | |
| cp package/environment-build.yml dist/ | |
| - name: List dist | |
| run: ls dist/ | |
| - name: Save the contents of the dist/ folder as artifacts | |
| uses: actions/[email protected] | |
| with: | |
| name: windows-conda-package | |
| retention-days: 7 | |
| path: dist/* | |
| build-windows-wheels: | |
| name: Build source dist, linux wheels | |
| needs: test-on-windows | |
| runs-on: windows-2025 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/[email protected] | |
| with: | |
| fetch-depth: 0 | |
| submodules: true | |
| - name: Set up Visual Studio shell | |
| uses: egor-tensin/[email protected] | |
| with: | |
| arch: x64 | |
| - name: Remove link | |
| run: | | |
| rm -f /usr/bin/link.exe | |
| - name: Remove lines with [not win] | |
| run: | | |
| sed -i '/\[not win\]/d' package/environment-build.yml | |
| - name: Setup Miniconda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| auto-update-conda: true | |
| channels: defaults, cytoflow, conda-forge | |
| channel-priority: flexible | |
| activate-environment: cytoflow | |
| environment-file: package/environment-build.yml | |
| - name: Install package locally | |
| run: | | |
| pip install --verbose --editable . | |
| - name: Install packaging deps | |
| run: | | |
| pip install build | |
| - name: Build wheel | |
| run: | | |
| python -m build --wheel | |
| - name: Move C++ extensions into the dist folder | |
| run: | | |
| cp `find build | grep "\.pyd$"` dist/ | |
| - name: List dist | |
| run: ls dist/ | |
| - name: Save the contents of the dist/ folder as artifacts | |
| uses: actions/[email protected] | |
| with: | |
| name: windows-wheels | |
| retention-days: 7 | |
| path: dist/* | |
| build-windows-oneclick: | |
| name: Build Windows one-click | |
| needs: test-on-windows | |
| runs-on: windows-2025 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Check out repo | |
| uses: actions/[email protected] | |
| with: | |
| fetch-depth: 0 | |
| submodules: true | |
| - name: Set up Visual Studio shell | |
| uses: egor-tensin/[email protected] | |
| with: | |
| arch: x64 | |
| - name: Remove link | |
| run: | | |
| rm -f /usr/bin/link.exe | |
| - name: Install NSIS | |
| uses: repolevedavaj/[email protected] | |
| with: | |
| nsis-version: '3.10' | |
| - name: Show all the files | |
| run: find . | |
| - name: Query git tag | |
| id: tag | |
| run: echo "GIT_TAG=$(git describe --tags)" >> $GITHUB_ENV | |
| - name: Show Tag | |
| id: display | |
| run: | | |
| echo "Output from Find Tag: ${GIT_TAG}" | |
| - name: Remove lines with [not win] | |
| run: | | |
| sed -i '/\[not win\]/d' package/environment-build.yml | |
| - name: Setup Miniconda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| auto-update-conda: true | |
| channels: defaults, cytoflow, conda-forge | |
| channel-priority: flexible | |
| activate-environment: cytoflow | |
| environment-file: package/environment-build.yml | |
| - name: Install package locally | |
| run: | | |
| pip install --verbose --editable . | |
| - name: Build embedded help docs | |
| run: | | |
| sphinx-build docs/user_manual/reference cytoflowgui/help | |
| - name: Build GUI binary | |
| run: | | |
| pyinstaller package/pyinstaller.spec | |
| - name: Build installer | |
| run: | | |
| makensis.exe //NOCD package/installer.nsis | |
| - name: Rename installer and remove remaining files | |
| run: | | |
| cd dist | |
| mv cytoflow-installer.exe cytoflow-installer-${GIT_TAG}-win-amd64.exe | |
| rm -rf cytoflow | |
| - name: List dist | |
| run: ls dist/ | |
| - name: Save the contents of the dist/ folder as artifacts | |
| uses: actions/[email protected] | |
| with: | |
| name: windows-oneclick | |
| retention-days: 7 | |
| path: dist/* |