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fix buffer bug in writing coords in xml #169

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fix buffer bug in writing coords in xml

fix buffer bug in writing coords in xml #169

Workflow file for this run

.github/workflows/build_binaries.yml at 802cef9
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: ""},
]
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@13
- 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++-13 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: Install dependencies
run : brew install gcc@13
- 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++-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: ""},
]
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