readding a donfiguration file

docker/fedora39-pycv

@@ -15,5 +15,6 @@ RUN source /etc/bashrc \
  && cd plumed2 \
  && source ./sourceme.sh \
  && cd plugins/pycv \
+ && ./configurePyCV.sh \
  && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \
  && make check

docker/rocky8-pycv

@@ -15,5 +15,6 @@ RUN . ./.bashrc \
  && cd plumed2 \
  && source ./sourceme.sh \
  && cd plugins/pycv \
+ && ./configurePyCV.sh \
  && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \
  && make check

plugins/pycv/Makefile

@@ -1,24 +1,28 @@
+
+PYTHON=python
+#optional, just in case you want to override python with ./configurePyCV.sh
+-include Makefile.conf
 #this makefiles assume that pip and pytest are installed
 .PHONY: clean check check_standalone check_python all
 
 all: pycv_here
 
 pycv_here: src/*.cpp src/*.h src/pycv/*.py
 	@echo installing pycv
-	pip3 install .
-	touch $@
+	$(PYTHON) -m pip install .
+	@touch $@
 
 clean:
-	pip3 uninstall pycv
-	rm -fv pycv_here
+	@$(PYTHON) -m  pip uninstall pycv -y
+	@rm -fv pycv_here
 
 check_standalone: pycv_here
 	$(MAKE) -C regtest testclean
 	$(MAKE) -C regtest checkfail
 
 #just in case  pytest is still not installed we install it before the tests
 check_python: pycv_here
-	pip3 install pytest
-	pytest -v
+	@$(PYTHON) -m pip install pytest
+	@$(PYTHON) -m pytest -v
 
 check: check_standalone check_python

plugins/pycv/configurePyCV.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+#formatted with shfmtv3.36.0 (https://github.com/mvdan/sh/releases)
+
+#A simple script to configure PyCV if python does not work
+PYTHON=""
+if which plumed >/dev/null; then
+    echo "plumed found"
+    PYTHON=$(plumed --no-mpi info --configuration | grep 'python_bin=')
+    PYTHON=${PYTHON#python_bin=}
+fi
+
+if [ -z "$PYTHON" ]; then
+    echo "python not found using plumed"
+    echo "serching for  available python with plumed module installed"
+
+    for python_bin in python python3 python3.12 python3.11 python3.10 python3.9 python3.8 python3.7; do
+        if $python_bin -c "import plumed" 2>/dev/null; then
+            if [ $python_bin != python ]; then
+                PYTHON=$python_bin
+            fi
+            return 1
+        fi
+    done
+
+fi
+
+if [ -z "$PYTHON" ]; then
+    echo "python not found"
+    exit 1
+fi
+
+cat <<EOF >Makefile.conf
+PYTHON=$(which "$PYTHON")
+EOF