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Update M1 working directory #3

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Update M1 working directory

Update M1 working directory #3

Workflow file for this run

.github/workflows/maboss-ubuntu.yml at e79d62f
name: Linux
on:
push:
pull_request:
release:
types: [created]
jobs:
maboss:
name: MaBoSS (gcc)
runs-on: ubuntu-22.04
env:
GCC: gcc
CXX: g++
INSTALL_PATH: /usr/
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so
LIBXML_INCLUDEDIR: /usr/include/libxml2/
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install flex bison
pip install numpy
- name: Cache compiled libSBML
id: cache-libsbml-gcc
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.2
key: ${{ runner.os }}-libSBML-5.20.2-gcc-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-gcc.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: sudo bash scripts/install_libsbml.sh
- name: Build MaBoSS
run: |
cd engine/src
make clean
make install SBML_COMPAT=1
make MAXNODES=128 install SBML_COMPAT=1
- name: Test MaBoSS
run: bash scripts/run_tests.sh
maboss_llvm:
name: MaBoSS (clang)
runs-on: ubuntu-22.04
env:
GCC: clang
CXX: clang++
INSTALL_PATH: /usr/
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so
LIBXML_INCLUDEDIR: /usr/include/libxml2/
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run : |
sudo apt-get update
sudo apt-get install flex bison clang
pip install numpy
- name: Cache compiled libSBML
id: cache-libsbml-clang
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.2
key: ${{ runner.os }}-libSBML-5.20.2-clang-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-clang.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: sudo bash scripts/install_libsbml.sh
- name: Build MaBoSS
run: |
cd engine/src
make clean
make GCC=clang CXX=clang++ install SBML_COMPAT=1
make GCC=clang CXX=clang++ MAXNODES=128 install SBML_COMPAT=1
- name: Test MaBoSS
run: bash scripts/run_tests.sh
maboss_mpi:
name: MaBoSS MPI
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install flex bison libopenmpi-dev
pip install numpy
- name: Build MaBoSS
run: |
cd engine/src
make clean
make install CXX=mpic++ MPI_COMPAT=1
make install CXX=mpic++ MPI_COMPAT=1 MAXNODES=128
- name: Test MaBoSS
run: bash scripts/run_mpi_tests.sh
maboss_binary:
name: Building MaBoSS linux64 binary
runs-on: ubuntu-22.04
needs: [maboss, maboss_llvm, maboss_mpi]
env:
GCC: gcc
CXX: g++
INSTALL_PATH: /usr/
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so
LIBXML_INCLUDEDIR: /usr/include/libxml2
# if: github.event.workflow_run.conclusion == 'success' && (github.ref == 'refs/heads/master' || github.event_name == 'release')
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install flex bison
pip install numpy
- name: Cache compiled libSBML
id: cache-libsbml-gcc
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.2
key: ${{ runner.os }}-libSBML-5.20.2-gcc-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-gcc.outputs.cache-hit != 'true'
run: |
bash scripts/build_libsbml.sh
- name: Install libSBML
run: |
sudo env BUILD_PATH=/tmp/ bash scripts/install_libsbml.sh
- name: Build binary
run: |
rm -fr engine/pub/*
cd engine/src
make clean
make install_static SBML_COMPAT=1
make install_static MAXNODES=128 SBML_COMPAT=1
make install_static MAXNODES=256 SBML_COMPAT=1
make install_static MAXNODES=512 SBML_COMPAT=1
make install_static MAXNODES=1024 SBML_COMPAT=1
cd ../pub
zip MaBoSS-linux64.zip *
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: MaBoSS-linux64
path: /home/runner/work/MaBoSS/MaBoSS/engine/pub/MaBoSS-linux64.zip
- 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: MaBoSS-linux64.zip
asset_path: /home/runner/work/MaBoSS/MaBoSS/engine/pub/MaBoSS-linux64.zip
asset_content_type: application/zip
maboss_library:
name: Building MaBoSS linux64 library
runs-on: ubuntu-22.04
needs: [maboss, maboss_llvm, maboss_mpi]
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install flex bison
- name: Build binary
run: |
rm -fr engine/pub/*
cd engine/src
make clean
make install_lib
make install_lib MAXNODES=128
make install_lib MAXNODES=256
make install_lib MAXNODES=512
make install_lib MAXNODES=1024
make install_alib
make install_alib MAXNODES=128
make install_alib MAXNODES=256
make install_alib MAXNODES=512
make install_alib MAXNODES=1024
make clean
cd ../../../
tar -zcvf libMaBoSS-linux64.tar.gz MaBoSS/README.md MaBoSS/LICENSE MaBoSS/engine/src MaBoSS/engine/include MaBoSS/engine/lib
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: libMaBoSS-linux64
path: /home/runner/work/MaBoSS/libMaBoSS-linux64.tar.gz
- 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: libMaBoSS-linux64.tar.gz
asset_path: /home/runner/work/MaBoSS/libMaBoSS-linux64.tar.gz
asset_content_type: application/gzip
maboss_library_sbml:
name: Building MaBoSS linux64 library with libSBML
runs-on: ubuntu-22.04
needs: [maboss, maboss_llvm, maboss_mpi]
env:
GCC: gcc
CXX: g++
INSTALL_PATH: /usr/
BUILD_PATH: /tmp/
LIBXML_LIBDIR: /usr/lib/x86_64-linux-gnu/libxml2.so
LIBXML_INCLUDEDIR: /usr/include/libxml2
# if: github.event.workflow_run.conclusion == 'success' && (github.ref == 'refs/heads/master' || github.event_name == 'release')
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install flex bison
- name: Cache compiled libSBML
id: cache-libsbml-gcc
uses: actions/cache@v4
with:
path: /tmp/libsbml-5.20.2
key: ${{ runner.os }}-libSBML-5.20.2-gcc-namespace
- name: Compiling libSBML
if: steps.cache-libsbml-gcc.outputs.cache-hit != 'true'
run: bash scripts/build_libsbml.sh
- name: Install libSBML
run: sudo env BUILD_PATH=/tmp/ bash scripts/install_libsbml.sh
- name: Build binary
run: |
rm -fr engine/pub/*
cd engine/src
make clean
make install_lib SBML_COMPAT=1
make install_lib SBML_COMPAT=1 MAXNODES=128
make install_lib SBML_COMPAT=1 MAXNODES=256
make install_lib SBML_COMPAT=1 MAXNODES=512
make install_lib SBML_COMPAT=1 MAXNODES=1024
make install_alib SBML_COMPAT=1
make install_alib SBML_COMPAT=1 MAXNODES=128
make install_alib SBML_COMPAT=1 MAXNODES=256
make install_alib SBML_COMPAT=1 MAXNODES=512
make install_alib SBML_COMPAT=1 MAXNODES=1024
make clean
cd ../../../
tar -zcvf libMaBoSS-sbml-linux64.tar.gz MaBoSS/README.md MaBoSS/LICENSE MaBoSS/engine/src MaBoSS/engine/include MaBoSS/engine/lib
- uses: actions/upload-artifact@v4
if: github.event_name != 'release'
with:
name: libMaBoSS-sbml-linux64
path: /home/runner/work/MaBoSS/libMaBoSS-sbml-linux64.tar.gz
- uses: actions/upload-release-asset@v1
if: github.event_name == 'release'
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
upload_url: ${{ github.event.release.upload_url }}
asset_name: libMaBoSS-sbml-linux64.tar.gz
asset_path: /home/runner/work/MaBoSS/libMaBoSS-sbml-linux64.tar.gz
asset_content_type: application/gzip
test_docker:
name: Test Docker MaBoSS Server
runs-on: ubuntu-22.04
needs: [maboss, maboss_llvm, maboss_mpi]
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install flex bison
pip install numpy
- name: Cache Docker images.
uses: ScribeMD/[email protected]
with:
key: docker-${{ runner.os }}-${{ github.run_id }}
- name: Start MaBoSS docker server
run: |
docker-compose up -d maboss-server
bash -c "cd engine/src; make client"
- name: Test MaBoSS docker server
run: |
bash -c "cd engine/tests; bash ./test-container.sh"
publish_docker_hub:
name: Docker MaBoSS Server
runs-on: ubuntu-22.04
needs: [test_docker]
if: github.event_name == 'release' && github.event.action == 'created' && github.repository == 'sysbio-curie/MaBoSS'
steps:
- uses: actions/checkout@v4
- name: Cache Docker images.
uses: ScribeMD/[email protected]
with:
key: docker-${{ runner.os }}-${{ github.run_id }}
- name: Connect Docker Hub
run: |
echo ${{ secrets.DOCKERHUB_TOKEN }} | docker login --username ${{ secrets.DOCKERHUB_USERNAME }} --password-stdin
- name: Upload Docker Hub
run: |
docker tag maboss:latest maboss:${{ github.event.release.tag_name }}
docker tag maboss:latest vnoel/maboss:latest
docker tag maboss:${{ github.event.release.tag_name }} vnoel/maboss:${{ github.event.release.tag_name }}
docker push vnoel/maboss:latest
docker push vnoel/maboss:${{ github.event.release.tag_name }}
docker tag maboss:latest sysbiocurie/maboss:latest
docker tag maboss:${{ github.event.release.tag_name }} sysbiocurie/maboss:${{ github.event.release.tag_name }}
docker push sysbiocurie/maboss:latest
docker push sysbiocurie/maboss:${{ github.event.release.tag_name }}
publish_docker_github:
name: Publishing MaBoSS docker container to GitHub
runs-on: ubuntu-22.04
needs: [test_docker]
if: github.event_name == 'release' && github.event.action == 'created' && github.repository == 'sysbio-curie/MaBoSS'
env:
REGISTRY: ghcr.io
IMAGE_NAME: maboss
permissions:
contents: read
packages: write
steps:
- uses: actions/checkout@v4
- name: Log in to the Container registry
uses: docker/login-action@v3
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Extract metadata (tags, labels) for Docker
id: meta
uses: docker/metadata-action@v5
with:
images: ${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}
- name: Build and push Docker image
uses: docker/build-push-action@v5
with:
context: .
file: containers/docker/Dockerfile
push: true
tags: ${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}:${{ github.event.release.tag_name }},${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}:latest
labels: ${{ steps.meta.outputs.labels }}
test_apptainer:
name: Apptainer MaBoSS
runs-on: ubuntu-22.04
needs: [maboss, maboss_llvm, maboss_mpi]
steps:
- uses: actions/checkout@v4
- name: Install dependencies
run: |
wget https://github.com/apptainer/apptainer/releases/download/v1.2.5/apptainer_1.2.5_amd64.deb
sudo apt-get update
sudo apt install -y ./apptainer_1.2.5_amd64.deb
sudo apt-get install flex bison debootstrap
pip install numpy
- name: Start MaBoSS Apptainer
run: |
sudo apptainer build maboss.sif containers/apptainer/maboss.def
singularity run maboss.sif &
bash -c "cd engine/src; make client"
- name: Test MaBoSS
run: |
bash -c "cd engine/tests; bash ./test-container.sh"
maboss_conda_defaults:
name: Build MaBoSS Anaconda package
runs-on: ubuntu-22.04
needs: [maboss, maboss_llvm, maboss_mpi]
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: defaults
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build anaconda-client conda-verify
- name: Build Anaconda package
run: |
conda build -c colomoto conda/maboss
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-maboss-conda-defaults-${{ github.run_id }}
maboss_conda:
name: Build MaBoSS Anaconda package (conda-forge)
runs-on: ubuntu-22.04
needs: [maboss, maboss_llvm, maboss_mpi]
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: conda-forge
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Install conda-build
run: |
conda install conda-build anaconda-client conda-verify
- name: Build Anaconda package
run: |
CUSTOM_BUILD_NUMBER=1 conda build -c colomoto conda/maboss
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-maboss-conda-${{ github.run_id }}
maboss_conda_test_defaults:
name: Test MaBoSS Anaconda package
runs-on: ubuntu-22.04
needs: maboss_conda_defaults
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: defaults
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-maboss-conda-defaults-${{ github.run_id }}
- name: Install conda-build
run: |
conda install conda-build
- name: Install package
run: |
python -m conda_index /home/runner/miniconda3/envs/test/conda-bld/
conda install -c file:///home/runner/miniconda3/envs/test/conda-bld/ -c colomoto maboss
- name: Test package
run: |
pip install numpy
export MABOSS=/home/runner/miniconda3/envs/test/bin/MaBoSS
export MABOSS_128n=/home/runner/miniconda3/envs/test/bin/MaBoSS_128n
export MABOSS_CLIENT=/home/runner/miniconda3/envs/test/bin/MaBoSS-client
export MABOSS_SERVER=/home/runner/miniconda3/envs/test/bin/MaBoSS-server
export MABOSS_SERVER_128n=/home/runner/miniconda3/envs/test/bin/MaBoSS_128n-server
bash -c "cd engine/tests; bash ./test-cellcycle.sh"
bash -c "cd engine/tests; bash ./test-ensemble.sh"
bash -c "cd engine/tests; bash ./test-ewing.sh"
bash -c "cd engine/tests; bash ./test-server.sh"
bash -c "cd engine/tests; bash ./test-prngs.sh"
bash -c "cd engine/tests; bash ./test-rngs.sh"
bash -c "cd engine/tests; bash ./test-sbml.sh"
maboss_conda_test:
name: Test MaBoSS Anaconda package (conda-forge)
runs-on: ubuntu-22.04
needs: maboss_conda
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
channels: conda-forge
python-version: 3.12
miniforge-variant: Mambaforge
use-mamba: true
- name: Caching produced conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-maboss-conda-${{ github.run_id }}
- name: Install conda-build
run: |
conda install conda-build conda-index
- name: Install package
run: |
python -m conda_index /home/runner/miniconda3/envs/test/conda-bld/
conda install -c file:///home/runner/miniconda3/envs/test/conda-bld/ -c colomoto maboss
- name: Test package
run: |
pip install numpy
export MABOSS=/home/runner/miniconda3/envs/test/bin/MaBoSS
export MABOSS_128n=/home/runner/miniconda3/envs/test/bin/MaBoSS_128n
export MABOSS_CLIENT=/home/runner/miniconda3/envs/test/bin/MaBoSS-client
export MABOSS_SERVER=/home/runner/miniconda3/envs/test/bin/MaBoSS-server
export MABOSS_SERVER_128n=/home/runner/miniconda3/envs/test/bin/MaBoSS_128n-server
bash -c "cd engine/tests; bash ./test-cellcycle.sh"
bash -c "cd engine/tests; bash ./test-ensemble.sh"
bash -c "cd engine/tests; bash ./test-ewing.sh"
bash -c "cd engine/tests; bash ./test-server.sh"
bash -c "cd engine/tests; bash ./test-prngs.sh"
bash -c "cd engine/tests; bash ./test-rngs.sh"
bash -c "cd engine/tests; bash ./test-sbml.sh"
maboss_conda_publish_defaults:
name: Publish MaBoSS Anaconda package
runs-on: ubuntu-22.04
needs: maboss_conda_test_defaults
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
miniforge-variant: Mambaforge
channels: defaults
python-version: 3.12
use-mamba: true
- name: Restoring cached conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-maboss-conda-defaults-${{ github.run_id }}
- name: Install anaconda-client
run: |
conda install anaconda-client
- name: Upload MaBoSS Ananconda package on vincent-noel
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;
- name: Upload MaBoSS Ananconda package on colomoto
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;
maboss_conda_publish:
name: Publish MaBoSS Anaconda package (conda-forge)
runs-on: ubuntu-22.04
needs: maboss_conda_test
defaults:
run:
shell: bash -el {0}
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
auto-update-conda: true
miniforge-variant: Mambaforge
channels: conda-forge
python-version: 3.12
use-mamba: true
- name: Restoring cached conda package
uses: actions/cache@v4
with:
path: |
/home/runner/miniconda3/envs/test/conda-bld/*
key: ${{ runner.os }}-maboss-conda-${{ github.run_id }}
- name: Install anaconda-client
run: |
conda install anaconda-client
- name: Upload MaBoSS Ananconda package on vincent-noel
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u vincent-noel /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;
- name: Upload MaBoSS Ananconda package on colomoto
if: github.repository == 'sysbio-curie/MaBoSS' && github.event_name == 'release'
run: |
anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u colomoto /home/runner/miniconda3/envs/test/conda-bld/linux-64/*.tar.bz2 --force;