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testing the CI #39

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7ab1743
testing the CI
Iximiel Nov 30, 2023
af61729
Merge branch 'pycvComm' into pycvCommCI
Iximiel Nov 30, 2023
000f00c
test II on the workflow
Iximiel Nov 30, 2023
6991d56
test III on the workflow
Iximiel Nov 30, 2023
5e3e8a6
test III(2) on the workflow
Iximiel Nov 30, 2023
3845131
test III(3) on the workflow
Iximiel Nov 30, 2023
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26 changes: 13 additions & 13 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name: CI

on:
push:
#push:
pull_request:

env:
Expand All @@ -19,18 +19,18 @@ jobs:
uses: ./.github/workflows/linuxWF.yml
secrets: inherit

codecheck:
uses: ./.github/workflows/codecheckWF.yml
secrets: inherit
# codecheck:
# uses: ./.github/workflows/codecheckWF.yml
# secrets: inherit

mac:
uses: ./.github/workflows/macWF.yml
secrets: inherit
# mac:
# uses: ./.github/workflows/macWF.yml
# secrets: inherit

docker:
uses: ./.github/workflows/dockerWF.yml
secrets: inherit
# docker:
# uses: ./.github/workflows/dockerWF.yml
# secrets: inherit

conda:
uses: ./.github/workflows/condaWF.yml
secrets: inherit
# conda:
# uses: ./.github/workflows/condaWF.yml
# secrets: inherit
118 changes: 114 additions & 4 deletions .github/workflows/linuxWF.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,17 +13,40 @@ env:
CXX: g++

jobs:
linuxCachingPip:
runs-on: ubuntu-22.04
steps:
- uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: 3.9
cache: pip #this will save some time in getting the requirements
cache-dependency-path: ./python/requirements.txt
- name: Install python packages needed for tests
run: |
python -m pip install --upgrade pip
pip install --user Cython
pip install --user numpy
pip install --user pytest
pip install --user six ;
pip install --user pandas ;
pip install --user mdtraj ;
pip install --user MDAnalysis ;

linux:
needs: linuxCachingPip
runs-on: ubuntu-22.04
strategy:
fail-fast: false
matrix:
variant:
- -doc-mpi-
#commenting the ci for testing
#- -doc-mpi-
- -mpi-
- -coverage-mpi-
- -debug-
- -debug-mpi-
#- -coverage-mpi-
#- -debug-
#- -debug-mpi-
# temporarily commented out
# see https://github.com/plumed/plumed2/issues/976
# - -intel-
Expand All @@ -38,6 +61,8 @@ jobs:
uses: actions/setup-python@v4
with:
python-version: 3.9
cache: pip #this will save some time in getting the requirements
cache-dependency-path: ./python/requirements.txt
- name: Set paths
run: |
echo "$HOME/opt/bin" >> $GITHUB_PATH
Expand Down Expand Up @@ -181,3 +206,88 @@ jobs:
GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
run: |
.ci/push doc
- name: Saving "$HOME/opt"
if: matrix.variant == '-mpi-'
uses: actions/cache/save@v3
with:
path: ~/opt
key: ccache-plumedInstall-linux${{ matrix.variant }}hash-${{ github.sha }}


linux-pycv:
needs: linux
runs-on: ubuntu-22.04
strategy:
fail-fast: false
matrix:
variant:
- -mpi-
# temporarily commented out
# see https://github.com/plumed/plumed2/issues/976
# - -intel-
steps:
- uses: actions/checkout@v3
- name: Restoring "$HOME/opt"
uses: actions/cache/restore@v3
with:
path: ~/opt
key: ccache-plumedInstall-linux${{ matrix.variant }}hash-${{ github.sha }}
- uses: actions/cache@v3
with:
path: ~/.ccache
key: ccache-reset1-linux${{ matrix.variant }}hash-${{ github.sha }}
restore-keys: ccache-reset1-linux${{ matrix.variant }}hash-
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: 3.9
cache: pip #this will save some time in getting the requirements
cache-dependency-path: ./python/requirements.txt
- name: Set paths
run: |
echo "$HOME/opt/bin" >> $GITHUB_PATH
# path required for pytest:
echo "$HOME/.local/bin" >> $GITHUB_PATH
echo "CPATH=$HOME/opt/include:$CPATH" >> $GITHUB_ENV
echo "INCLUDE=$HOME/opt/include:$INCLUDE" >> $GITHUB_ENV
echo "LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH" >> $GITHUB_ENV
echo "LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
echo "PYTHONPATH=$HOME/opt/lib/plumed/python:$PYTHONPATH" >> $GITHUB_ENV
- name: Install generic packages
run: |
sudo apt-get update -qq
sudo apt-get install -y libatlas-base-dev
sudo apt-get install -y libfftw3-dev
sudo apt-get install -y gsl-bin
sudo apt-get install -y libgsl0-dev
sudo apt-get install -y ccache
sudo apt-get install -y libboost-serialization-dev
sudo apt-get install -y libopenmpi-dev openmpi-bin
echo "CC=mpicc" >> $GITHUB_ENV
echo "CXX=mpic++" >> $GITHUB_ENV
echo "OMPI_MCA_btl_base_warn_component_unused=0" >> $GITHUB_ENV
echo "OMPI_MCA_btl_base_verbose=0" >> $GITHUB_ENV
echo "OMPI_MCA_plm=isolated" >> $GITHUB_ENV
echo "OMPI_MCA_btl_vader_single_copy_mechanism=none" >> $GITHUB_ENV
echo "OMPI_MCA_rmaps_base_oversubscribe=yes" >> $GITHUB_ENV
- name: Install python packages
run: |
python -m pip install --upgrade pip
pip install --user Cython
pip install --user numpy
pip install --user pytest
pip install --user pybind11
pip install --user six ;
pip install --user pandas ;
pip install --user mdtraj ;
pip install --user MDAnalysis ;
python -c "import MDAnalysis" ;
python -c "import mdtraj" ;
pip install --user mpi4py
python -c "import mpi4py"
- name: compile and test pycv
working-directory: ./plugins/pycv/
run: |
./prepareMakeForDevelop.sh
make check

8 changes: 8 additions & 0 deletions python/requirements.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
#requirements for the tests in the CI
Cython
numpy
pytest
six
pandas
mdtraj
MDAnalysis