"rebasing with cp" the CI of pycv

.github/workflows/dockerWF.yml

@@ -29,3 +29,6 @@ jobs:
     - name: Build and run tests
       run: |
         make -C docker ${{ matrix.variant }}
+    - name: PyCV tests
+      run: |
+        make -C docker ${{ matrix.variant }}-pycv

.github/workflows/linuxWF.yml

@@ -27,6 +27,7 @@ jobs:
 # temporarily commented out
 # see https://github.com/plumed/plumed2/issues/976
         - -intel-
+        - -pycv-mpi-
     steps:
     - uses: actions/checkout@v4
     - uses: actions/cache@v3
@@ -152,7 +153,7 @@ jobs:
         make nmcheck
         ccache -s -M 100M
     - name: Run tests
-      if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) }}
+      if: ${{ ! contains( matrix.variant, '-doc-mpi-' ) && ! contains( matrix.variant, '-pycv-mpi-' ) }}
       run: |
          (while true; do  # see https://github.com/actions/virtual-environments/issues/1860
               df -h
@@ -185,3 +186,12 @@ jobs:
         GIT_TOKEN: ${{ secrets.GIT_TOKEN_PLUMEDBOT }}
       run: |
          .ci/push doc
+    - name: Compile and test pycv
+      if: contains( matrix.variant, '-pycv-' )
+      working-directory: ./plugins/pycv/
+      run: |
+            pip install --user pybind11
+            source ../../sourceme.sh
+            ln -s $(realpath ../../regtest/scripts) ./regtest/scripts
+            ./prepareMakeForDevelop.sh
+            make check

docker/Makefile

@@ -1,14 +1,20 @@
 
-.PHONY: ubuntu plumed2.tgz clean fedora39 rocky8
+.PHONY: ubuntu plumed2.tgz clean fedora39 fedora39-pycv rocky8 rocky8-pycv 
 
 ubuntu: plumed2.tgz
-	docker build -t plumed .
+	docker build -t plumed --progress=plain .
 
 fedora39: plumed2.tgz
-	docker build -t plumed -f fedora39 .
+	docker build -t plumed:fedora39 --progress=plain -f fedora39 .
+fedora39-pycv: plumed2.tgz
+	docker build -t plumed:fedora39-pycv --progress=plain -f fedora39-pycv .
+
 
 rocky8: plumed2.tgz
-	docker build -t plumed -f rocky8 .
+	docker build -t plumed:rocky8 --progress=plain -f rocky8 .
+
+rocky8-pycv: plumed2.tgz
+	docker build -t plumed:rocky8-pycv --progress=plain -f rocky8-pycv .
 
 plumed2.tgz:
 	cd ../ ; git archive HEAD -o "$(CURDIR)"/plumed2.tgz --prefix plumed2/ ; cd -

docker/fedora39-pycv

@@ -0,0 +1,11 @@
+FROM plumed:fedora39
+
+RUN source /etc/bashrc \
+ && module load mpi \
+ && cd plumed2 \
+ && source ./sourceme.sh \
+ && cd plugins/pycv \
+ && pip3 install pybind11 \
+ && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \
+ && ./prepareMakeForDevelop.sh \
+ && make check

docker/rocky8

@@ -7,23 +7,40 @@ RUN yum -y update \
  && dnf config-manager --set-enabled powertools \
  && yum -y group install "Development Tools" \
  && yum -y install environment-modules gawk vim wget \
-                   lapack-devel blas-devel zlib-devel gsl-devel fftw-devel openmpi-devel boost-devel \
-                   python3 python3-devel python3-pip \
- && pip3 install pillow==8.3.2 \
- && pip3 install numpy==1.19 \
- && pip3 install "cython<3" numpy pandas mdtraj \
- && pip3 install MDAnalysis==1.0.0
+ lapack-devel blas-devel zlib-devel gsl-devel fftw-devel openmpi-devel boost-devel \
+ openssl-devel libffi-devel 
 
 RUN useradd -ms /bin/bash plumed
+#These are needed for installing python
+
 USER plumed
 WORKDIR /home/plumed
 
+#Install python with --embedded enabled
+RUN PYVERSION="3.9.16" \
+ && curl -LO https://www.python.org/ftp/python/${PYVERSION}/Python-${PYVERSION}.tgz \
+ && tar xzf Python-${PYVERSION}.tgz \
+ && cd Python-${PYVERSION} \
+ && ./configure --enable-shared --prefix=$HOME/.local \
+ && make -j 4 \
+ && make install \
+ && echo "export LD_LIBRARY_PATH=$HOME/.local/lib/${LD_LIBRARY_PATH:+:}${LD_LIBRARY_PATH}" >> "$HOME/.bashrc"
+
+RUN . ./.bashrc \                
+ && pip3 install --user -U pip \
+ && pip3 install --user pillow==8.3.2 \
+ && pip3 install --user "Cython<3" \
+ && pip3 install --user pandas \
+ && pip3 install --user mdtraj     \
+ && pip3 install --user MDAnalysis==1.0.0
+#  && pip3 install --user numpy==1.19
+
 # import plumed code.
 # assumes a file plumed2.tgz is present in the Dockerfile directory
 COPY plumed2.tgz /home/plumed
 
 # build and test plumed (no install)
-RUN . /etc/bashrc \
+RUN . ./.bashrc \
  && module load mpi \
  && export OMPI_MCA_btl_base_warn_component_unused=0 \
  && export OMPI_MCA_btl_base_verbose=0 \
@@ -42,4 +59,3 @@ RUN . /etc/bashrc \
  && ./configure --enable-modules=all --enable-boost_serialization \
  && make -j 4 \
  && make check
-

docker/rocky8-pycv

@@ -0,0 +1,11 @@
+FROM plumed:rocky8
+
+RUN source ./.bashrc \
+ && module load mpi \
+ && cd plumed2 \
+ && source ./sourceme.sh \
+ && cd plugins/pycv \
+ && pip3 install --user pybind11  \
+ && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \
+ && ./prepareMakeForDevelop.sh \
+ && make check