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tonigi wants to merge 56 commits into Iximiel:pycv-package from tonigi:pycv-package

.github/workflows/linuxWF.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -198,8 +198,7 @@ jobs: @@
           if: contains( matrix.variant, '-pycv-' )
           working-directory: ./plugins/pycv/
           run: |
-                pip install --user -r requirements.txt
                 source ../../sourceme.sh
                 ln -s $(realpath ../../regtest/scripts) ./regtest/scripts
-                ./prepareMakeForDevelop.sh
                 make check

VERSION.txt

-Original file line number
+Diff line change
@@ Expand Up / @@ -5,4 +5,4 @@ @@
     # (this is same as gromacs)
     # Notice that "plumed info --version" will return only 2.X
     # and "plumed info --long-version" will return the full string
-.10b
+.11.0-dev

docker/fedora39-pycv

-Original file line number
+Diff line change
@@ Expand Up / @@ -2,10 +2,18 @@ FROM plumed:fedora39 @@
     RUN source /etc/bashrc \
      && module load mpi \
+     && export OMPI_MCA_btl_base_warn_component_unused=0 \
+     && export OMPI_MCA_btl_base_verbose=0 \
+     && export OMPI_MCA_plm=isolated \
+     && export OMPI_MCA_btl_vader_single_copy_mechanism=none \
+     && export OMPI_MCA_rmaps_base_oversubscribe=yes \
+     && export PATH=$HOME/opt/bin:$PATH \
+     && export CPATH=$HOME/opt/include:$CPATH \
+     && export INCLUDE=$HOME/opt/include:$INCLUDE \
+     && export LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH \
+     && export LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH \
      && cd plumed2 \
      && source ./sourceme.sh \
      && cd plugins/pycv \
-     && pip3 install -r requirements.txt \
-     && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \
-     && python_bin=python3 ./prepareMakeForDevelop.sh \
+     && ./configurePyCV.sh \
      && make check

docker/rocky8-pycv

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -1,11 +1,20 @@
  
    FROM plumed:rocky8

    RUN source ./.bashrc \

    RUN . ./.bashrc \

     && module load mpi \

     && export OMPI_MCA_btl_base_warn_component_unused=0 \

     && export OMPI_MCA_btl_base_verbose=0 \

     && export OMPI_MCA_plm=isolated \

     && export OMPI_MCA_btl_vader_single_copy_mechanism=none \

     && export OMPI_MCA_rmaps_base_oversubscribe=yes \

     && export PATH=$HOME/opt/bin:$PATH \

     && export CPATH=$HOME/opt/include:$CPATH \

     && export INCLUDE=$HOME/opt/include:$INCLUDE \

     && export LIBRARY_PATH=$HOME/opt/lib:$LIBRARY_PATH \

     && export LD_LIBRARY_PATH=$HOME/opt/lib:$LD_LIBRARY_PATH \

     && cd plumed2 \

     && source ./sourceme.sh \

     && cd plugins/pycv \

     && pip3 install --user -r requirements.txt  \

     && ./configurePyCV.sh \

     && ln -s $(realpath ../../regtest/scripts) ./regtest/scripts \

     && python_bin=python3 ./prepareMakeForDevelop.sh \

     && make check

plugins/pycv/.gitignore

-Original file line number
+Diff line change
@@ -1,4 +1,7 @@
     /Makefile.conf
     *.o
     *.so
-    env
+    /env*/
+    /build*/
+    /dist*/
+    *.whl

plugins/pycv/CMakeLists.txt

-Original file line number
+Diff line change
@@ -0,0 +1,75 @@
+    cmake_minimum_required(VERSION 3.15...3.27)
+    project(
+      ${SKBUILD_PROJECT_NAME}
+      VERSION ${SKBUILD_PROJECT_VERSION}
+      LANGUAGES CXX)
+    set(CMAKE_CXX_STANDARD 17)
+    message(
+      STATUS
+        "Everithing should work fine if you are in the same environment in which you have compiled plumed"
+    )
+    # FinPlumed is here:
+    list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}")
+    # Finding necessary packages
+    find_package(Python REQUIRED COMPONENTS Interpreter Development)
+    find_package(pybind11 CONFIG REQUIRED)
+    find_package(Plumed REQUIRED)
+    # Finding optionals things
+    if(Plumed_HAS_MPI)
+      find_package(MPI REQUIRED)
+    endif()
+    if(MPI_CXX_FOUND)
+      list(APPEND extraLibs MPI::MPI_CXX)
+    endif()
+    if(Plumed_HAS_OPENMP)
+      find_package(OpenMP REQUIRED)
+    endif()
+    if(OpenMP_CXX_FOUND)
+      list(APPEND extraLibs OpenMP::OpenMP_CXX)
+    endif()
+    include(CheckCXXCompilerFlag)
+    check_cxx_compiler_flag(-fno-gnu-unique USE_NO_GNU_UNIQUE)
+    if(USE_NO_GNU_UNIQUE)
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-gnu-unique")
+    endif()
+    # plumed_STATIC_LDFLAGS_OTHER:INTERNAL=-rdynamic;-Wl,-Bsymbolic;-fopenmp
+    # -rdynamic is automatically set by cmake, and also -fPIC
+    ################################################################################
+    ################################the pycv library################################
+    ################################################################################
+    add_library(
+      PythonCVInterface SHARED src/ActionWithPython.cpp src/PythonCVInterface.cpp
+                               src/PythonFunction.cpp)
+    # public, so they trickle down to the python module
+    target_compile_definitions(PythonCVInterface PUBLIC ${Plumed_CFLAGS})
+    target_include_directories(PythonCVInterface PUBLIC src ${Plumed_INCLUDEDIR})
+    # ####################################################################
+    # uncommenting this brings problems since some symbols here are needed
+    # by the python module even if it should be the correct setting...
+    # https://gcc.gnu.org/wiki/Visibility could be a starting point
+    #######################################################################
+    # target_compile_options(PythonCVInterface PRIVATE -fvisibility=hidden)
+    target_link_libraries(PythonCVInterface PRIVATE pybind11::embed)
+    target_link_libraries(PythonCVInterface PUBLIC plumedKernel ${extraLibs})
+    # this removes the "lib" prefix
+    set_target_properties(PythonCVInterface PROPERTIES PREFIX "")
+    install(TARGETS PythonCVInterface DESTINATION pycv)
+    ################################################################################
+    ###########################The pvCV companion module############################
+    ################################################################################
+    pybind11_add_module(plumedCommunications src/PlumedPythonEmbeddedModule.cpp)
+    target_link_libraries(plumedCommunications PRIVATE pybind11::headers)
+    target_link_libraries(plumedCommunications PUBLIC PythonCVInterface)
+    # The install directory is the output (wheel) directory
+    install(TARGETS plumedCommunications DESTINATION .)

plugins/pycv/FindPlumed.cmake

-Original file line number
+Diff line change
@@ -0,0 +1,87 @@
+    if(NOT Plumed_FOUND)
+      find_package(PkgConfig)
+      if(Plumed_FIND_QUIETLY)
+        function(message)
+          # THIS completely shuts down messages
+        endfunction()
+        pkg_check_modules(PLUMED QUIET plumedInternals)
+      else()
+        pkg_check_modules(PLUMED plumedInternals)
+      endif()
+      if(Plumed_FOUND)
+        if("-D__PLUMED_HAS_MPI=1" IN_LIST Plumed_CFLAGS)
+          set(Plumed_HAS_MPI
+              CACHE INTERNAL "plumed has MPI")
+        endif()
+        if("-fopenmp" IN_LIST Plumed_STATIC_LDFLAGS_OTHER)
+          set(Plumed_HAS_OPENMP
+              CACHE INTERNAL "plumed has OpenMP")
+        endif()
+      else()
+        message(STATUS "plumed not found via pkgconfig, trying executable")
+        execute_process(
+          COMMAND plumed --no-mpi info --include-dir
+          RESULT_VARIABLE PLUMED_EXECUTABLE
+          OUTPUT_QUIET ERROR_QUIET)
+        if(PLUMED_EXECUTABLE EQUAL 0)
+          set(Plumed_FOUND
+              CACHE INTERNAL "plumed found")
+          message(STATUS "Configuring plumed from executable")
+          execute_process(
+            COMMAND plumed --no-mpi info --include-dir
+            OUTPUT_VARIABLE Plumed_INCLUDEDIR
+            OUTPUT_STRIP_TRAILING_WHITESPACE)
+          set(Plumed_INCLUDEDIR
+              ${Plumed_INCLUDEDIR}
+              CACHE INTERNAL "plumed include dir")
+          execute_process(
+            COMMAND plumed --no-mpi info --configuration
+            OUTPUT_VARIABLE Plumed_CONFIG
+            OUTPUT_STRIP_TRAILING_WHITESPACE)
+          set(Plumed_CPP_FLAGS "")
+          string(REPLACE "\n" ";" ProcessFile_LINES "${Plumed_CONFIG}")
+          foreach(_line ${ProcessFile_LINES})
+            if(${_line} MATCHES "CPPFLAGS=.*")
+              set(Plumed_CPP_FLAGS ${_line})
+              string(REGEX REPLACE "CPPFLAGS= *" "" Plumed_CPP_FLAGS
+                                   ${Plumed_CPP_FLAGS})
+              string(REPLACE "\\" "" Plumed_CPP_FLAGS ${Plumed_CPP_FLAGS})
+              string(REPLACE "-D" ";" Plumed_CPP_FLAGS ${Plumed_CPP_FLAGS})
+              # message(STATUS "Found PLUMED CPP_FLAGS: \"${Plumed_CPP_FLAGS}\"")
+              # message(STATUS "Found PLUMED CPP_FLAGS:") foreach(_flag
+              # ${Plumed_CPP_FLAGS}) message(STATUS "   \"${_flag}\"") endforeach()
+            endif()
+            if(${_line} MATCHES ".*-fopenmp.*")
+              set(Plumed_HAS_MPI
+                  CACHE INTERNAL "plumed has MPI")
+            endif()
+          endforeach()
+          set(Plumed_CFLAGS
+              ${Plumed_CPP_FLAGS}
+              CACHE INTERNAL "plumed Definitions flags")
+          execute_process(COMMAND plumed --no-mpi config -q has mpi
+                          RESULT_VARIABLE Plumed_WITH_MPI)
+          if(Plumed_WITH_MPI EQUAL 0)
+            set(Plumed_HAS_MPI
+                CACHE INTERNAL "plumed has MPI")
+          endif()
+        else()
+          if(Plumed_FIND_REQUIRED)
+            message(FATAL_ERROR "plumed not found")
+          endif()
+        endif()
+      endif()
+    endif()

plugins/pycv/Makefile

-Original file line number
+Diff line change
@@ -1,53 +1,28 @@
-    # include the machine dependent configuration
-    ifneq ($(MAKECMDGOALS),clean)
-      -include ../../Makefile.conf
-    	ifndef canPyCV
-      	include ./Makefile.conf
-    	endif
-    endif
-    .PHONY: clean check all
-    #Dependency tracking based on https://make.mad-scientist.net/papers/advanced-auto-dependency-generation/#tldr
-    #this assumes gcc
-    DEPDIR := .deps
-    DEPFLAGS = -MT $@ -MMD -MP -MF $(DEPDIR)/$*.d
-    PYBIND11FLAG =
-    ADDCPPFLAGS:=$(python_cf_embedded) $(pybind11_cflags) $(ADDCPPFLAGS)
-    ADDCLDFLAGS:=$(ADDCLDFLAGS) $(python_ld_embedded)
-    OBJS = ActionWithPython.o PythonCVInterface.o PythonFunction.o PlumedPythonEmbeddedModule.o
+    PYTHON=python
+    #optional, just in case you want to override python with ./configurePyCV.sh
+    -include Makefile.conf
+    #this makefiles assume that pip and pytest are installed
+    .PHONY: clean check check_standalone check_python all
-    ifeq ($(SOEXT),dylib)
-      SONAME_OPTION:=-Wl,-install_name
-    else
-      SONAME_OPTION:=-Wl,-soname
-    endif
+    all: pycv_here
-    all: PythonCVInterface.$(SOEXT)
-    #-fvisibility=hidden is needed for pybind11 (to not conflict with different pybind11 versions)
-    #I think I enforced this nearly everywhere I set up a flag for the compiler
-    ActionWithPython.o PythonCVInterface.o PythonFunction.o PlumedPythonEmbeddedModule.o: PYBIND11FLAG= -fvisibility=hidden
-    %.o: %.cpp $(DEPDIR)/%.d | $(DEPDIR)
-    	@echo Compiling object $@
-    	@$(CXX) -c $(DEPFLAGS) $(CPPFLAGS) $(PYBIND11FLAG) $(ADDCPPFLAGS) $(CXXFLAGS) $< -o $@
-    $(DEPDIR): ; @mkdir -p $@
-    DEPFILES := $(OBJS:%.o=$(DEPDIR)/%.d)
-    $(DEPFILES):
-    include $(wildcard $(DEPFILES))
-    #-Wl,--no-as-needed forces the python library to be linked, without this in a WSL does not work
-    #TODO: seems that $PLUMED_KERNEL is not needed, check
-    PythonCVInterface.$(SOEXT): $(OBJS)
-    	@echo Linking $@
-    	$(LDSHARED) $(SONAME_OPTION),"$(notdir $@)" $(DYNAMIC_LIBS) $(PLUMED_KERNEL) $(ADDCLDFLAGS) $^ -o $@
+    pycv_here: src/*.cpp src/*.h src/pycv/*.py
+    	@echo installing pycv
+    	$(PYTHON) -m pip install .
+    	@touch $@
     clean:
-    	rm -f $(OBJS) PythonCVInterface.$(SOEXT)
+    	@$(PYTHON) -m  pip uninstall pycv -y
+    	@rm -fv pycv_here
-    check: all
+    check_standalone: pycv_here
     	$(MAKE) -C regtest testclean
     	$(MAKE) -C regtest checkfail
+    #just in case  pytest is still not installed we install it before the tests
+    check_python: pycv_here
+    	@$(PYTHON) -m pip install pytest
+    	@$(PYTHON) -m pytest -v
+    check: check_standalone check_python

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