Script to provide pre-compiled binaries, built by GitHub actions, for linux/mac/windows

.github/workflows/build_binaries.yml

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+name: Build binaries
+
+on:
+  push:
+  pull_request:
+  release:
+    types: [created]
+
+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: ""},
+        ]
+
+    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/11/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: ""},
+        ]
+
+    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: ""},
+       ]
+
+    runs-on: macos-12
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install dependencies
+      run : brew install gcc@11
+
+    - name: Build ${{ matrix.projects.name }} project
+      run: |
+        export MACOSX_DEPLOYMENT_TARGET=12
+        make ${{ matrix.projects.project }}
+        make clean
+        ${{ matrix.projects.extra_run }}
+        make PHYSICELL_CPP=g++-11 static
+        cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos12
+
+    - name: Caching produced project binary 
+      uses: actions/cache@v4
+      with:
+        path: |
+          ${{ github.workspace }}/${{ matrix.projects.binary }}_macos12
+        key: ${{ runner.os }}-macos12-${{ 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: ""},
+        ]
+
+    runs-on: macos-14
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Downgrade XCODE to 14.3.1
+      run: sudo xcode-select -switch /Applications/Xcode_14.3.1.app   
+
+    - name: Install dependencies
+      run : brew install gcc@11
+
+    - name: Build ${{ matrix.projects.name }} project
+      run: |
+        export MACOSX_DEPLOYMENT_TARGET=12
+        make ${{ matrix.projects.project }}
+        make clean
+        ${{ matrix.projects.extra_run }}
+        make PHYSICELL_CPP=g++-11 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: ""},
+        ]
+
+    runs-on: macos-12
+    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 }}_macos12
+        key: ${{ runner.os }}-macos12-${{ github.run_id }}
+
+    - name: Creating universal binary
+      run: | 
+        lipo -create -output ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos12 ${{ 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

beta/download_binary.py

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+# This script attempts to download the MaBoSS (binary) library(s) and
+# headers for your particular operating system. It installs them in a standard
+# location (relative to a PhysiCell installation) which will be used by a PhysiCell Makefile.
+#
+# Authors: Randy Heiland, Vincent Noel
+
+import platform
+import urllib.request
+import os
+import sys
+import tarfile
+import stat
+import shutil
+
+physicell_version = "1.14.0"
+repo_physicell = "MathCancer/PhysiCell"
+physiboss_version = "v2.2.3"
+repo_physiboss = "sysbio-curie/PhysiBoSS"
+list_models = {
+    "physiboss-tutorial": "https://github.com/" + repo_physiboss + "/releases/download/" + physiboss_version + "/", 
+    "physiboss-tutorial-invasion": "https://github.com/" + repo_physiboss + "/releases/download/" + physiboss_version + "/", 
+    "physiboss-cell-lines": "https://github.com/" + repo_physiboss + "/releases/download/" + physiboss_version + "/",   
+    "template_BM": "https://github.com/" + repo_physiboss + "/releases/download/" + physiboss_version + "/", 
+    "template": "https://github.com/" + repo_physicell + "/releases/download/" + physicell_version + "/", 
+    "rules": "https://github.com/" + repo_physicell + "/releases/download/" + physicell_version + "/", 
+    "physimess": "https://github.com/" + repo_physicell + "/releases/download/" + physicell_version + "/", 
+    "interaction": "https://github.com/" + repo_physicell + "/releases/download/" + physicell_version + "/", 
+}
+
+def print_usage():
+     print("Usage : python download_binary.py <model>")
+     print("")
+     print("Models available : %s" % (",".join(list_models.keys())))
+
+if len(sys.argv) < 2:
+     print_usage()
+     exit(1)
+
+model = sys.argv[1]
+
+if model in ["-h", "--help"] or model not in list_models.keys():
+     print_usage()
+     exit(1)
+
+print('> Chosen model: ', model)
+
+os_type = platform.system()
+print('> Operating system: ', os_type)
+
+mb_file = ""
+if os_type.lower() == 'darwin':
+    mb_file = model + "-macos.tar.gz"
+elif os_type.lower().startswith("win") or os_type.lower().startswith("msys_nt") or os_type.lower().startswith("mingw64_nt"):
+    mb_file = model + "-win.tar.gz"
+elif os_type.lower().startswith("linux"):
+    mb_file = model + "-linux.tar.gz"
+else:
+    print("Your operating system seems to be unsupported. Please create an new issue at https://github.com/PhysiBoSS/PhysiBoSS/issues/ ")
+    sys.exit(1)
+
+url = list_models[model] + mb_file
+print('> Downloading from: ', url)
+
+dir_name = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+print('> Loading into directory: ', dir_name)
+
+my_file = os.path.join(dir_name, mb_file)
+print('> File: ',my_file)
+
+def download_cb(blocknum, blocksize, totalsize):
+    readsofar = blocknum * blocksize
+    if totalsize > 0:
+        percent = readsofar * 1e2 / totalsize
+        s = "\r%5.1f%% %*d / %d" % (
+            percent, len(str(totalsize)), readsofar, totalsize)
+        sys.stderr.write(s)
+        if readsofar >= totalsize: # near the end
+            sys.stderr.write("\n")
+    else: # total size is unknown
+        sys.stderr.write("read %d\n" % (readsofar,))
+
+urllib.request.urlretrieve(url, my_file, download_cb)
+
+print('> Creating backup of XML settings, Makefile, main.cpp')
+if os.path.exists("Makefile"):
+    shutil.copyfile("Makefile", "Makefile-backup")
+if os.path.exists("main.cpp"):
+    shutil.copyfile("main.cpp", "main-backup.cpp")
+if os.path.exists(os.path.join("config", "PhysiCell_settings.xml")):
+    shutil.copyfile(os.path.join("config", "PhysiCell_settings.xml"), os.path.join("PhysiCell_settings-backup.xml"))
+
+os.chdir(dir_name)
+print('> Uncompressing the model')
+
+try:
+    tar = tarfile.open(mb_file)
+    tar.extractall()
+    binary_name = [names for names in tar.getnames() if not names.endswith(".dll")][0]
+    tar.close()
+    os.remove(mb_file)
+
+except:
+    print('! Error untarring the file')
+    exit(1)
+
+new_name = "project" if not mb_file.endswith("win.tar.gz") else "project.exe"
+os.rename(binary_name, new_name)
+st = os.stat(new_name)
+os.chmod(new_name, st.st_mode | stat.S_IEXEC)
+
+print('> Done. You can now run %s\n' % new_name)