Changing pycv into a proper python package

plugins/pycv/.gitignore

@@ -1,4 +1,7 @@
 /Makefile.conf
 *.o
 *.so
-env
+/env*/
+/build*/
+/dist*/
+*.whl

plugins/pycv/CMakeLists.txt

@@ -0,0 +1,96 @@
+cmake_minimum_required(VERSION 3.15...3.27)
+project(
+  ${SKBUILD_PROJECT_NAME}
+  VERSION ${SKBUILD_PROJECT_VERSION}
+  LANGUAGES CXX)
+set (CMAKE_CXX_STANDARD 17)
+
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+find_package(pybind11 CONFIG REQUIRED)
+message(STATUS "pybind11 found: ${pybind11_VERSION}")
+
+exec_program(plumed
+ARGS info --include-dir
+OUTPUT_VARIABLE PLUMED_INCLUDE_DIR
+)
+
+exec_program(plumed
+ARGS info --configuration
+OUTPUT_VARIABLE PLUMED_CONFIG
+)
+set(PLUMED_CXX_FLAGS "")
+set(PLUMED_CPP_FLAGS "")
+set(PLUMED_DYNAMIC_LIBS "")
+
+string(REPLACE "\n" ";" ProcessFile_LINES "${PLUMED_CONFIG}")
+foreach(_line ${ProcessFile_LINES})
+    # message(STATUS "Found PLUMED :${_line}")
+  if (${_line} MATCHES "CXXFLAGS=.*")
+    set(PLUMED_CXX_FLAGS ${_line})
+    string(REGEX REPLACE "CXXFLAGS= *" "" PLUMED_CXX_FLAGS ${PLUMED_CXX_FLAGS})
+    string(REPLACE " " ";" PLUMED_CXX_FLAGS ${PLUMED_CXX_FLAGS})
+    # message(STATUS "Found PLUMED CXX_FLAGS: \"${PLUMED_CXX_FLAGS}\"")
+    message(STATUS "Found PLUMED CXX_FLAGS: ")
+    foreach (_flag ${PLUMED_CXX_FLAGS})
+        message(STATUS "   \"${_flag}\"")
+    endforeach()
+  endif()
+  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 "DYNAMIC_LIBS=.*")
+    set(PLUMED_DYNAMIC_LIBS ${_line})
+    string(REGEX REPLACE "DYNAMIC_LIBS= *" "" PLUMED_DYNAMIC_LIBS ${PLUMED_DYNAMIC_LIBS})
+    string(REPLACE " " ";" PLUMED_DYNAMIC_LIBS ${PLUMED_DYNAMIC_LIBS})
+    # message(STATUS "Found PLUMED DYNAMIC_LIBS: \"${PLUMED_DYNAMIC_LIBS}\"")
+    message(STATUS "Found PLUMED DYNAMIC_LIBS:")
+    foreach(_flag ${PLUMED_DYNAMIC_LIBS})
+        message(STATUS "   \"${_flag}\"")
+    endforeach()
+  endif()
+
+endforeach()
+
+message(STATUS "Plumed include dir: ${PLUMED_INCLUDE_DIR}")
+set(CMAke__extra)
+################################################################################
+################################the pycv library################################
+################################################################################
+#TODO: remove the "lib" prefix
+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_CPP_FLAGS})
+get_target_property(COMPILE_DEFINITIONS PythonCVInterface COMPILE_DEFINITIONS)
+message(STATUS "COMPILE_DEFINITIONS ${COMPILE_DEFINITIONS}")
+target_compile_options(PythonCVInterface PUBLIC ${PLUMED_CXX_FLAGS})
+target_link_libraries(PythonCVInterface PRIVATE pybind11::embed)
+target_link_libraries(PythonCVInterface PUBLIC plumedKernel ${PLUMED_DYNAMIC_LIBS})
+target_include_directories(PythonCVInterface PUBLIC src ${PLUMED_INCLUDE_DIR}/plumed)
+#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)
+#python_add_library(plumedCommunications MODULE PlumedPythonEmbeddedModule.cpp WITH_SOABI)
+# target_link_libraries(plumedCommunications PRIVATE pybind11::headers)
+#target_compile_definitions(plumedCommunications PUBLIC ${PLUMED_CPP_FLAGS})
+target_link_libraries(plumedCommunications PUBLIC plumedKernel ${PLUMED_DYNAMIC_LIBS})
+target_link_libraries(plumedCommunications PUBLIC PythonCVInterface)
+target_include_directories(plumedCommunications PUBLIC src ${PLUMED_INCLUDE_DIR}/plumed)
+
+# The install directory is the output (wheel) directory
+install(TARGETS plumedCommunications DESTINATION .)

plugins/pycv/pyproject.toml

@@ -0,0 +1,61 @@
+[build-system]
+requires = ["scikit-build-core>=0.10", "pybind11>=2.10.3,<=2.11.1", "numpy"]
+build-backend = "scikit_build_core.build"
+
+
+[project]
+name = "pycv"
+dependencies = [
+  "numpy",
+  "pybind11>=2.10.3,<=2.11.1"
+]
+version = "0.0.1"
+description="PyCV support module for plumed"
+readme = "README.md"
+authors = [
+  { name = "Toni Giorgino", email = "[email protected]" },
+  { name = "Daniele Rapetti", email = "[email protected]" },
+]
+requires-python = ">=3.9"
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "License :: OSI Approved :: MIT License",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+]
+
+[project.optional-dependencies]
+test = ["pytest", "plumed"]
+
+[project.scripts]
+pycv = "pycv:main"
+
+[tool.scikit-build]
+wheel.expand-macos-universal-tags = true
+minimum-version = "build-system.requires"
+
+
+[tool.pytest.ini_options]
+minversion = "8.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+log_cli_level = "INFO"
+filterwarnings = [
+  "error",
+  "ignore::pytest.PytestCacheWarning",
+]
+testpaths = ["pythontests"]
+
+
+[tool.cibuildwheel]
+build-frontend = "build[uv]"
+test-command = "pytest {project}/pythontests"
+test-extras = ["test"]
+
+[tool.cibuildwheel.pyodide]
+build-frontend = {name = "build", args = ["--exports", "whole_archive"]}
+

plugins/pycv/pythontests/.gitignore

@@ -0,0 +1,4 @@
+bck*
+*.out
+logfile
+*.log

plugins/pycv/pythontests/mypycv.py

@@ -0,0 +1,19 @@
+import plumedCommunications as PLMD
+import numpy
+from sys import stderr as log
+# log = open("pydist.log", "w")
+
+print("Imported my pydist+.", file=log)
+
+
+def plumedInitio(action: PLMD.PythonCVInterface):
+    # return {"Value": {"period": [None,0,0]}}
+    # return {"Value": {"period": None}}
+    return {"Value": {"period": ["0",0.3]}}
+plumedInit={"Value": {"period": None},"NOPBC":False,
+            "ATOMS":"1,2"}
+
+def plumedCalculate(action: PLMD.PythonCVInterface):
+    ret = [action.nat]
+    print ("Hello from plumedCalculate")
+    return ret