add current cycle phase index, number of attachments, and number of spring attachments to signals #354
Workflow file for this run
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| name: Build binaries | |
| on: | |
| push: | |
| pull_request: | |
| release: | |
| types: [published] | |
| jobs: | |
| ubuntu: | |
| strategy: | |
| matrix: | |
| projects: [ | |
| {short_name: "physiboss-tutorial", project: "physiboss-tutorial", name: "PhysiBoSS tutorial", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-tutorial-invasion", project: "physiboss-tutorial-invasion", name: "PhysiBoSS Cancer Invasion", binary: "invasion_model", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-cell-lines", project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template_BM", project: "template_BM", name: "PhysiBoSS Template", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template", project: "template", name: "PhysiCell Template", binary: "project", extra_run: ""}, | |
| {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""}, | |
| {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""}, | |
| {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""}, | |
| {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""}, | |
| ] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build ${{ matrix.projects.name }} | |
| run: | | |
| make ${{ matrix.projects.project }} | |
| make clean | |
| ${{ matrix.projects.extra_run }} | |
| make static STATIC_OPENMP=/usr/lib/gcc/x86_64-linux-gnu/12/libgomp.a | |
| - name: Checking binary for ${{ matrix.projects.name }} | |
| run: | | |
| ldd ${{ matrix.projects.binary }} | |
| - name: Build ${{ matrix.projects.name }} project archive | |
| run: | | |
| rm -fr config/PhysiCell_settings-backup.xml | |
| tar -zcvf ${{ matrix.projects.short_name }}-linux.tar.gz ${{ matrix.projects.binary }} Makefile main.cpp config/ custom_modules/ | |
| - 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: ${{ matrix.projects.short_name }}-linux.tar.gz | |
| asset_path: ${{ github.workspace }}/${{ matrix.projects.short_name }}-linux.tar.gz | |
| asset_content_type: application/gzip | |
| windows: | |
| strategy: | |
| matrix: | |
| projects: [ | |
| {short_name: "physiboss-tutorial", project: "physiboss-tutorial", name: "PhysiBoSS tutorial", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-tutorial-invasion", project: "physiboss-tutorial-invasion", name: "PhysiBoSS Cancer Invasion", binary: "invasion_model", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-cell-lines", project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template_BM", project: "template_BM", name: "PhysiBoSS Template", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template", project: "template", name: "PhysiCell Template", binary: "project", extra_run: ""}, | |
| {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""}, | |
| {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""}, | |
| {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""}, | |
| {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""}, | |
| ] | |
| 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 ${{ matrix.projects.name }} project | |
| run: | | |
| make ${{ matrix.projects.project }} | |
| make clean | |
| python beta/setup_windows_dep.py | |
| ${{ matrix.projects.extra_run }} | |
| make static | |
| - name: Checking binary for ${{ matrix.projects.name }} | |
| run: | | |
| ldd .\\${{ matrix.projects.binary }}.exe | |
| - name: Build ${{ matrix.projects.name }} project archive | |
| run: | | |
| rm -fr config/PhysiCell_settings-backup.xml | |
| tar -zcvf ${{ matrix.projects.short_name }}-win.tar.gz ${{ matrix.projects.binary }}.exe *.dll Makefile main.cpp config/ custom_modules/ | |
| - 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: ${{ matrix.projects.short_name }}-win.tar.gz | |
| asset_path: ${{ github.workspace }}\${{ matrix.projects.short_name }}-win.tar.gz | |
| asset_content_type: application/gzip | |
| macos_step0a: | |
| strategy: | |
| matrix: | |
| projects: [ | |
| {short_name: "physiboss-tutorial", project: "physiboss-tutorial", name: "PhysiBoSS tutorial", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-tutorial-invasion", project: "physiboss-tutorial-invasion", name: "PhysiBoSS Cancer Invasion", binary: "invasion_model", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-cell-lines", project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template_BM", project: "template_BM", name: "PhysiBoSS Template", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template", project: "template", name: "PhysiCell Template", binary: "project", extra_run: ""}, | |
| {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""}, | |
| {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""}, | |
| {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""}, | |
| {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""}, | |
| ] | |
| runs-on: macos-13 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run : | | |
| if ! brew list gcc@13 &>/dev/null; then | |
| brew install gcc@13 | |
| else | |
| echo "gcc@13 is already installed." | |
| fi | |
| - name: Build ${{ matrix.projects.name }} project | |
| run: | | |
| export MACOSX_DEPLOYMENT_TARGET=13 | |
| make ${{ matrix.projects.project }} | |
| make clean | |
| ${{ matrix.projects.extra_run }} | |
| make PHYSICELL_CPP=g++-13 static | |
| cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos13 | |
| - name: Caching produced project binary | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ github.workspace }}/${{ matrix.projects.binary }}_macos13 | |
| key: ${{ runner.os }}-macos13-${{ github.run_id }} | |
| - name: Look at the generated binary | |
| run: | | |
| otool -L ${{ matrix.projects.binary }} | |
| otool -l ${{ matrix.projects.binary }} | |
| lipo -archs ${{ matrix.projects.binary }} | |
| macos_step0b: | |
| strategy: | |
| matrix: | |
| projects: [ | |
| {short_name: "physiboss-tutorial", project: "physiboss-tutorial", name: "PhysiBoSS tutorial", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-tutorial-invasion", project: "physiboss-tutorial-invasion", name: "PhysiBoSS Cancer Invasion", binary: "invasion_model", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-cell-lines", project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template_BM", project: "template_BM", name: "PhysiBoSS Template", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template", project: "template", name: "PhysiCell Template", binary: "project", extra_run: ""}, | |
| {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""}, | |
| {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""}, | |
| {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""}, | |
| {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""}, | |
| ] | |
| runs-on: macos-14 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run : | | |
| if ! brew list gcc@13 &>/dev/null; then | |
| brew install gcc@13 | |
| else | |
| echo "gcc@13 is already installed." | |
| fi | |
| - name: Build ${{ matrix.projects.name }} project | |
| run: | | |
| export MACOSX_DEPLOYMENT_TARGET=13 | |
| make ${{ matrix.projects.project }} | |
| make clean | |
| ${{ matrix.projects.extra_run }} | |
| make PHYSICELL_CPP=g++-13 static | |
| cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macosm1 | |
| - name: Caching produced project binary | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ github.workspace }}/${{ matrix.projects.binary }}_macosm1 | |
| key: ${{ runner.os }}-macosm1-${{ github.run_id }} | |
| - name: Look at the generated binary | |
| run: | | |
| otool -L ${{ matrix.projects.binary }} | |
| otool -l ${{ matrix.projects.binary }} | |
| lipo -archs ${{ matrix.projects.binary }} | |
| macos_step1: | |
| strategy: | |
| matrix: | |
| projects: [ | |
| {short_name: "physiboss-tutorial", project: "physiboss-tutorial", name: "PhysiBoSS tutorial", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-tutorial-invasion", project: "physiboss-tutorial-invasion", name: "PhysiBoSS Cancer Invasion", binary: "invasion_model", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "physiboss-cell-lines", project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template_BM", project: "template_BM", name: "PhysiBoSS Template", binary: "project", extra_run: "make Compile_MaBoSS PHYSICELL_CPP=g++-11"}, | |
| {short_name: "template", project: "template", name: "PhysiCell Template", binary: "project", extra_run: ""}, | |
| {short_name: "rules", project: "rules-sample", name: "PhysiCell Rules", binary: "project", extra_run: ""}, | |
| {short_name: "physimess", project: "physimess-sample", name: "PhysiMeSS", binary: "project", extra_run: ""}, | |
| {short_name: "interaction", project: "interaction-sample", name: "PhysiCell Interaction", binary: "interaction_demo", extra_run: ""}, | |
| {short_name: "episode", project: "episode-sample", name: "PhysiCell Episode", binary: "project", extra_run: ""}, | |
| ] | |
| runs-on: macos-13 | |
| needs: [macos_step0a, macos_step0b] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Caching produced project binary | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ github.workspace }}/${{ matrix.projects.binary }}_macosm1 | |
| key: ${{ runner.os }}-macosm1-${{ github.run_id }} | |
| - name: Caching produced project binary | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{ github.workspace }}/${{ matrix.projects.binary }}_macos13 | |
| key: ${{ runner.os }}-macos13-${{ github.run_id }} | |
| - name: Creating universal binary | |
| run: | | |
| lipo -create -output ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos13 ${{ matrix.projects.binary }}_macosm1 | |
| - name: Checking universal binary | |
| run: | | |
| lipo -archs ${{ matrix.projects.binary }} | |
| otool -l ${{ matrix.projects.binary }} | |
| otool -L ${{ matrix.projects.binary }} | |
| - name: Build project archive | |
| run: | | |
| make ${{ matrix.projects.project }} | |
| rm -fr config/PhysiCell_settings-backup.xml | |
| tar -zcvf ${{ matrix.projects.short_name }}-macos.tar.gz ${{ matrix.projects.binary }} Makefile main.cpp config/ custom_modules/ | |
| - 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: ${{ matrix.projects.short_name }}-macos.tar.gz | |
| asset_path: ${{ github.workspace }}/${{ matrix.projects.short_name }}-macos.tar.gz | |
| asset_content_type: application/gzip |