Updated notebooks, paper at preprint submission #89
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| name: Tests Windows | |
| on: | |
| push: | |
| pull_request: | |
| release: | |
| types: [created] | |
| jobs: | |
| build: | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates | |
| - name: Build Virus Macrophage project | |
| run: | | |
| make virus-macrophage-sample | |
| make | |
| - name: Run Virus Macrophage cell lines project | |
| run: | | |
| .\\virus-sample.exe | |
| build_physimess: | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates | |
| - name: Build PhysiMeSS project | |
| run: | | |
| make physimess-sample | |
| make clean | |
| make | |
| - name: Run PhysiMeSS project | |
| run: | | |
| .\\project | |
| .\\project config\\Fibre_Initialisation\\mymodel_initialisation.xml | |
| .\\project config\\Cell_Fibre_Mechanics\\mymodel_rotating.xml | |
| build_physiboss: | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates | |
| - name: Build PhysiBoSS cell lines project | |
| run: | | |
| make physiboss-cell-lines-sample | |
| make clean | |
| make | |
| - name: Run PhysiBoSS cell lines project | |
| run: | | |
| .\\PhysiBoSS_Cell_Lines.exe | |
| - name: Build PhysiBoSS TNF project | |
| run: | | |
| make reset | |
| make physiboss-tnf-model | |
| make clean | |
| make | |
| - name: Run PhysiBoSS TNF project | |
| run: | | |
| .\\spheroid_TNF_model.exe | |
| build_physiboss_tutorial: | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates | |
| - name: Build PhysiBoSS tutorial | |
| run: | | |
| make physiboss-tutorial | |
| make clean | |
| python beta/setup_windows_dep.py | |
| make Compile_MaBoSS | |
| make static | |
| ldd .\\project.exe | |
| - name: Run PhysiBoSS tutorial | |
| run: | | |
| .\\project.exe config\\cell_cycle\\PhysiCell_settings.xml | |
| - name: Build project archive | |
| run: | | |
| rm -fr config/PhysiCell_settings-backup.xml | |
| tar -zcvf tutorial-win.tar.gz project.exe *.dll Makefile main.cpp config/ custom_modules/ | |
| - name: Save artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: tutorial_binary_windows | |
| path: project.exe | |
| - uses: actions/upload-release-asset@v1 | |
| if: github.event_name == 'release' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ github.event.release.upload_url }} | |
| asset_name: tutorial-win.tar.gz | |
| asset_path: ${{ github.workspace }}\tutorial-win.tar.gz | |
| asset_content_type: application/gzip | |
| build_physiboss_cancer_invasion: | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates | |
| - name: Build PhysiBoSS Cancer invasion | |
| run: | | |
| make physiboss-tutorial-invasion | |
| make clean | |
| python beta/setup_windows_dep.py | |
| make Compile_MaBoSS | |
| make static | |
| ldd .\\invasion_model.exe | |
| - name: Run PhysiBoSS cancer invasion | |
| run: | | |
| .\\invasion_model.exe config\\PhysiCell_settings_2D.xml | |
| - name: Build project archive | |
| run: | | |
| rm -fr config/PhysiCell_settings-backup.xml | |
| tar -zcvf invasion_model-win.tar.gz invasion_model.exe *.dll Makefile main.cpp config/ custom_modules/ | |
| - name: Save artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: invasion_model_binary_windows | |
| path: invasion_model.exe | |
| - uses: actions/upload-release-asset@v1 | |
| if: github.event_name == 'release' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ github.event.release.upload_url }} | |
| asset_name: invasion_model-win.tar.gz | |
| asset_path: ${{ github.workspace }}\invasion_model-win.tar.gz | |
| asset_content_type: application/gzip | |
| build_physicell_template: | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates | |
| - name: Build PhysiBoSS Template | |
| run: | | |
| make template | |
| make clean | |
| python beta/setup_windows_dep.py | |
| make static | |
| ldd .\\project.exe | |
| - name: Run PhysiBoSS model | |
| run: | | |
| .\\project.exe | |
| - name: Build project archive | |
| run: | | |
| rm -fr config/PhysiCell_settings-backup.xml | |
| tar -zcvf template-win.tar.gz project.exe *.dll Makefile main.cpp config/ custom_modules/ | |
| - name: Save artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: template_binary_windows | |
| path: project.exe | |
| - uses: actions/upload-release-asset@v1 | |
| if: github.event_name == 'release' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ github.event.release.upload_url }} | |
| asset_name: template-win.tar.gz | |
| asset_path: ${{ github.workspace }}\template-win.tar.gz | |
| asset_content_type: application/gzip | |
| build_physiboss_template: | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates | |
| - name: Build PhysiBoSS Template | |
| run: | | |
| make template_BM | |
| make clean | |
| python beta/setup_windows_dep.py | |
| make Compile_MaBoSS | |
| make static | |
| ldd .\\project.exe | |
| - name: Run PhysiBoSS model | |
| run: | | |
| .\\project.exe | |
| - name: Build project archive | |
| run: | | |
| rm -fr config/PhysiCell_settings-backup.xml | |
| tar -zcvf template_BM-win.tar.gz project.exe *.dll Makefile main.cpp config/ custom_modules/ | |
| - name: Save artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: template_BM_binary_windows | |
| path: project.exe | |
| - uses: actions/upload-release-asset@v1 | |
| if: github.event_name == 'release' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ github.event.release.upload_url }} | |
| asset_name: template_BM-win.tar.gz | |
| asset_path: ${{ github.workspace }}\template_BM-win.tar.gz | |
| asset_content_type: application/gzip | |
| build_physiboss_celllines: | |
| runs-on: windows-latest | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: mingw-w64-x86_64-binutils mingw-w64-x86_64-gcc mingw-w64-x86_64-headers-git mingw-w64-x86_64-gcc-libs mingw-w64-x86_64-libwinpthread-git mingw-w64-x86_64-lapack mingw-w64-x86_64-openblas mingw-w64-x86_64-libxml2 mingw-w64-x86_64-bzip2 mingw-w64-x86_64-python mingw-w64-x86_64-python-zstandard mingw-w64-x86_64-python-cffi make bison flex mingw-w64-x86_64-ca-certificates | |
| - name: Build PhysiBoSS Cell Lines | |
| run: | | |
| make physiboss-cell-lines-sample | |
| make clean | |
| python beta/setup_windows_dep.py | |
| make Compile_MaBoSS | |
| make static | |
| ldd .\\PhysiBoSS_Cell_Lines.exe | |
| - name: Run PhysiBoSS model | |
| run: | | |
| .\\PhysiBoSS_Cell_Lines.exe | |
| - name: Build project archive | |
| run: | | |
| rm -fr config/PhysiCell_settings-backup.xml | |
| tar -zcvf physiboss-cell-lines-win.tar.gz PhysiBoSS_Cell_Lines.exe *.dll Makefile main.cpp config/ custom_modules/ | |
| - name: Save artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: physiboss-cell-lines_binary_windows | |
| path: PhysiBoSS_Cell_Lines.exe | |
| - uses: actions/upload-release-asset@v1 | |
| if: github.event_name == 'release' | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ github.event.release.upload_url }} | |
| asset_name: physiboss-cell-lines-win.tar.gz | |
| asset_path: ${{ github.workspace }}\physiboss-cell-lines-win.tar.gz | |
| asset_content_type: application/gzip | |