Update Docker and venv to python3.9 (gwastro#4115)

* Update Docker files

* Also update venv

* Also thie file

* Probably don't want python38-devel for python39

.github/workflows/build_venv.yml

@@ -12,7 +12,7 @@ jobs:
         name: "Set up Python"
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
       -
         env:
           OSG_ACCESS: "${{secrets.OSG_ACCESS}}"

.github/workflows/docker-build.yml

@@ -12,7 +12,7 @@ jobs:
         name: "Set up Python"
         uses: actions/setup-python@v1
         with:
-          python-version: 3.8
+          python-version: 3.9
       -
         name: "Preparing a host container"
         run: "docker build -t pycbc-docker-tmp ."

Dockerfile

@@ -10,7 +10,7 @@ ADD docker/etc/cvmfs/config-osg.opensciencegrid.org.conf /etc/cvmfs/config-osg.o
 RUN dnf -y install https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest.noarch.rpm && dnf -y install cvmfs cvmfs-config-default && dnf clean all && dnf makecache && \
     dnf -y groupinstall "Development Tools" \
                         "Scientific Support" && \
-    rpm -e --nodeps git perl-Git && dnf -y install @python38 rsync zlib-devel libpng-devel libjpeg-devel sqlite-devel openssl-devel fftw-libs-single fftw-devel fftw fftw-libs-long fftw-libs fftw-libs-double gsl gsl-devel hdf5 hdf5-devel python38-devel swig which osg-ca-certs && python3.8 -m pip install --upgrade pip setuptools wheel cython && python3.8 -m pip install mkl ipython jupyter jupyterhub jupyterlab lalsuite && \
+    rpm -e --nodeps git perl-Git && dnf -y install @python39 rsync zlib-devel libpng-devel libjpeg-devel sqlite-devel openssl-devel fftw-libs-single fftw-devel fftw fftw-libs-long fftw-libs fftw-libs-double gsl gsl-devel hdf5 hdf5-devel python39-devel swig which osg-ca-certs && python3.9 -m pip install --upgrade pip setuptools wheel cython && python3.9 -m pip install mkl ipython jupyter jupyterhub jupyterlab lalsuite && \
     dnf -y install https://repo.opensciencegrid.org/osg/3.5/el8/testing/x86_64/osg-wn-client-3.5-5.osg35.el8.noarch.rpm && dnf clean all
 
 # set up environment
@@ -21,15 +21,15 @@ RUN cd / && \
 # Install MPI software needed for pycbc_inference
 # at the end.
 RUN dnf -y install libibverbs libibverbs-devel libibmad libibmad-devel libibumad libibumad-devel librdmacm librdmacm-devel libmlx5 libmlx4 openmpi openmpi-devel && \
-    python3.8 -m pip install schwimmbad && \
-    MPICC=/lib64/openmpi/bin/mpicc CFLAGS='-I /usr/include/openmpi-x86_64/ -L /usr/lib64/openmpi/lib/ -lmpi' python3.8 -m pip install --no-cache-dir mpi4py
+    python3.9 -m pip install schwimmbad && \
+    MPICC=/lib64/openmpi/bin/mpicc CFLAGS='-I /usr/include/openmpi-x86_64/ -L /usr/lib64/openmpi/lib/ -lmpi' python3.9 -m pip install --no-cache-dir mpi4py
 RUN echo "/usr/lib64/openmpi/lib/" > /etc/ld.so.conf.d/openmpi.conf
 
 # Now update all of our library installations
 RUN rm -f /etc/ld.so.cache && /sbin/ldconfig
 
 # Make python be what we want
-RUN alternatives --set python /usr/bin/python3.8
+RUN alternatives --set python /usr/bin/python3.9
 
 # Explicitly set the path so that it is not inherited from build the environment
 ENV PATH "/usr/local/bin:/usr/bin:/bin:/lib64/openmpi/bin/bin"

docker/etc/docker-install.sh

@@ -1,9 +1,11 @@
 #!/bin/bash -v
 set -e
 cd /scratch
-python3.8 -m pip install --upgrade 'pip<22.0'
-python3.8 -m pip install -r requirements.txt
-python3.8 -m pip install .
+python3.9 -m pip install --upgrade 'pip<22.0'
+python3.9 -m pip install -r requirements.txt
+python3.9 -m pip install -r requirements-igwn.txt
+python3.9 -m pip install -r companion.txt
+python3.9 -m pip install .
 cd /
 mkdir -p /opt/pycbc/src
 cp -a /scratch /opt/pycbc/src/pycbc

tools/docker_build_dist.sh

@@ -37,7 +37,7 @@ fi
 if [ "x${PYCBC_CONTAINER}" == "xpycbc_rhel_virtualenv" ]; then
 
   ENV_OS="x86_64_rhel_8"
-  yum -y install python38 python38-devel
+  yum -y install python39 python39-devel
   yum -y groupinstall "Development Tools"
   yum -y install which rsync
   yum clean all
@@ -51,7 +51,7 @@ if [ "x${PYCBC_CONTAINER}" == "xpycbc_rhel_virtualenv" ]; then
   mkdir -p ${CVMFS_PATH}
 
   VENV_PATH=${CVMFS_PATH}/pycbc-${SOURCE_TAG}
-  virtualenv -p python3.8 ${VENV_PATH}
+  virtualenv -p python3.9 ${VENV_PATH}
   echo 'export PYTHONUSERBASE=${VIRTUAL_ENV}/.local' >> ${VENV_PATH}/bin/activate
   echo "export XDG_CACHE_HOME=\${HOME}/cvmfs-pycbc-${SOURCE_TAG}/.cache" >> ${VENV_PATH}/bin/activate
   source ${VENV_PATH}/bin/activate