Added some aid-compile option in autoconf

* Trying to setup pycv into config * forgot to commit configure before pushig * redesigning the compilation with the new ac * changed behaviour of not finding cython * now if no python package is found also python_bin is not set * now configure understands if python is embeddable * moved the variables and added some comments for clarity * rerun autoconf * set up a cleaner instalation * forgot to push the compileconfiguration common sourced file * added some aid for maintainers --------- Co-authored-by: Daniele Rapetti <[email protected]>
Iximiel · Dec 19, 2023 · 534003b · 534003b
1 parent 2ac1f50
commit 534003b
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Showing 10 changed files with 250 additions and 79 deletions.
diff --git a/Makefile.conf.in b/Makefile.conf.in
@@ -38,6 +38,11 @@ datadir=@datadir@
 docdir=@docdir@
 htmldir=@htmldir@
 python_bin=@PYTHON_BIN@
+plumed_found_cython=@CYTHON_FOUND@
+canPyCV=@PLUMED_CAN_PYCV@
+pybind11_cflags=@PYBIND11_CFLAGS@
+python_cf_embedded=@PYTHON_CFLAGS@
+python_ld_embedded=@PYTHON_LDFLAGS@
 mpiexec=@MPIEXEC@
 make_static_archive=@make_static_archive@
 use_absolute_soname=@use_absolute_soname@

diff --git a/configure b/configure
@@ -637,6 +637,11 @@ make_doc
 readelf
 LD_MAIN_RUNPATH
 use_debug_glibcxx
+PYTHON_CFLAGS
+PYTHON_LDFLAGS
+PYBIND11_CFLAGS
+PLUMED_CAN_PYCV
+CYTHON_FOUND
 OPENMP_CXXFLAGS
 EGREP
 GREP
@@ -742,6 +747,7 @@ enable_boost_graph
 enable_boost_serialization
 enable_fftw
 enable_python
+enable_pycv
 enable_af_ocl
 enable_af_cuda
 enable_af_cpu
@@ -1443,6 +1449,7 @@ Optional Features:
                           enable search for boost serialization, default: no
   --enable-fftw           enable search for fftw, default: yes
   --enable-python         enable search for python, default: yes
+  --enable-pycv           enable set up the pycv plugin, default: yes
   --enable-af_ocl         enable search for arrayfire_ocl, default: no
   --enable-af_cuda        enable search for arrayfire_cuda, default: no
   --enable-af_cpu         enable search for arrayfire_cpu, default: no
@@ -3143,6 +3150,24 @@ fi
 
 
 
+pycv=
+# Check whether --enable-pycv was given.
+if test "${enable_pycv+set}" = set; then :
+  enableval=$enable_pycv; case "${enableval}" in
+             (yes) pycv=true ;;
+             (no)  pycv=false ;;
+             (*)   as_fn_error $? "wrong argument to --enable-pycv" "$LINENO" 5 ;;
+  esac
+else
+  case "yes" in
+             (yes) pycv=true ;;
+             (no)  pycv=false ;;
+  esac
+
+fi
+
+
+
 af_ocl=
 # Check whether --enable-af_ocl was given.
 if test "${enable_af_ocl+set}" = set; then :
@@ -3222,7 +3247,6 @@ fi
 
 
 
-
 # by default use -O flag
 # we override the autoconf default (-g) because in release build we do not want to
 # include symbol information (obj files are huge)
@@ -8945,11 +8969,21 @@ $as_echo "$as_me: WARNING: cannot enable __PLUMED_HAS_FFTW" >&2;}
 
 fi
 
-if test $python = true  ; then
+# python executable: if any of CYTHON_FOUND or PLUMED_CAN_PYCV is on will store
+# the python executable
+
+# set if PYTHON_BIN has Cython in its environment
+
+# definitions and variables related to pycv and in general embedding python
+
+
+
+
+
 # if PYTHON_BIN is defined, it is expected to be the full path to python
 # Otherwise, search from a list of names:
-  if test -z "$PYTHON_BIN" ; then
-    for ac_prog in python
+if test -z "$PYTHON_BIN" ; then
+    for ac_prog in python python3
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
 set dummy $ac_prog; ac_word=$2
@@ -8991,14 +9025,54 @@ fi
   test -n "$PYTHON_BIN" && break
 done
 
-  fi
-  if test -n "$PYTHON_BIN"
-  then
+fi
+if test -n "$PYTHON_BIN" ; then
     { $as_echo "$as_me:${as_lineno-$LINENO}: Python executable is $PYTHON_BIN" >&5
 $as_echo "$as_me: Python executable is $PYTHON_BIN" >&6;}
-    { $as_echo "$as_me:${as_lineno-$LINENO}: checking support for required python modules (python3, setuptools, cython)" >&5
-$as_echo_n "checking support for required python modules (python3, setuptools, cython)... " >&6; }
-testimport="
+  if test $pycv = true  ; then
+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking pycv: support for required python modules (python3, pybind11, numpy)" >&5
+$as_echo_n "checking pycv: support for required python modules (python3, pybind11, numpy)... " >&6; }
+  testimport="
+import numpy
+import pybind11
+#no need to check for python3, if you have python2, you don't have pybind11 (and vice-versa)
+"
+    if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null;  then
+
+       pyver=$($PYTHON_BIN -c "import sysconfig;print(sysconfig.get_config_var('VERSION'))")
+       python_config=python${pyver}-config
+
+       if ${python_config} --ldflags --embed 1>/dev/null 2>/dev/null ;then
+          { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+          PYBIND11_CFLAGS="$($PYTHON_BIN -m pybind11 --includes) -fvisibility=hidden"
+          PYTHON_CFLAGS=$(${python_config} --cflags --embed)
+          PYTHON_LDFLAGS=$(${python_config} --ldflags --embed)
+          #TODO: conda_fixup
+          PLUMED_CAN_PYCV=yes
+        else
+          { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+          { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable pycv" >&5
+$as_echo "$as_me: WARNING: cannot enable pycv" >&2;}
+          { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \"PyCV needs python to be embeddable, please rebuild python\"" >&5
+$as_echo "$as_me: WARNING: \"PyCV needs python to be embeddable, please rebuild python\"" >&2;}
+       fi
+    else
+       { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+       { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable pycv" >&5
+$as_echo "$as_me: WARNING: cannot enable pycv" >&2;}
+    fi
+  else
+    { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable pycv" >&5
+$as_echo "$as_me: WARNING: cannot enable pycv" >&2;}
+  fi
+
+  if test $python = true  ; then
+    { $as_echo "$as_me:${as_lineno-$LINENO}: checking python wrapper: support for required python modules (python3, setuptools, cython)" >&5
+$as_echo_n "checking python wrapper: support for required python modules (python3, setuptools, cython)... " >&6; }
+    testimport="
 from setuptools import setup
 from setuptools import Extension
 from Cython.Build import cythonize
@@ -9011,19 +9085,24 @@ if sys.version_info < (3,):
 $as_echo "yes" >&6; }
        $as_echo "#define __PLUMED_HAS_PYTHON 1" >>confdefs.h
 
+       CYTHON_FOUND=yes
     else
        { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
 $as_echo "no" >&6; }
        { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable python interface" >&5
 $as_echo "$as_me: WARNING: cannot enable python interface" >&2;}
-       PYTHON_BIN=
     fi
   else
     { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cannot enable python interface" >&5
 $as_echo "$as_me: WARNING: cannot enable python interface" >&2;}
   fi
 fi
 
+if test "${PLUMED_CAN_PYCV}" != yes &&  test "${CYTHON_FOUND}" != yes; then
+  #this deactivate python bin if no package was found
+  PYTHON_BIN=
+fi
+
 if test "$af_ocl" = true ; then
 
     found=ko
@@ -10062,8 +10141,6 @@ $as_echo "#define _REENTRANT 1" >>confdefs.h
 
 # these are libraries that should be linked also to MD engines
 
-# python executable
-
 
 
 

diff --git a/configure.ac b/configure.ac
@@ -319,6 +319,7 @@ PLUMED_CONFIG_ENABLE([boost_graph],[search for boost graph],[no])
 PLUMED_CONFIG_ENABLE([boost_serialization],[search for boost serialization],[no])
 PLUMED_CONFIG_ENABLE([fftw],[search for fftw],[yes])
 PLUMED_CONFIG_ENABLE([python],[search for python],[yes])
+PLUMED_CONFIG_ENABLE([pycv],[set up the pycv plugin],[yes])
 PLUMED_CONFIG_ENABLE([af_ocl],[search for arrayfire_ocl],[no])
 PLUMED_CONFIG_ENABLE([af_cuda],[search for arrayfire_cuda],[no])
 PLUMED_CONFIG_ENABLE([af_cpu],[search for arrayfire_cpu],[no])
@@ -331,7 +332,6 @@ AC_ARG_VAR(PYTHON_BIN,[python executable (e.g. python2.7 or /opt/local/bin/pytho
 AC_ARG_VAR(BASH_COMPLETION_DIR,[path where bash completion will be installed - default: search with pkg-config])
 AC_ARG_VAR(MPIEXEC,[command to run mpi programs in tests - default not specified, which means use PLUMED_MPIRUN env var at runtime for backward compatibility])
 
-
 # by default use -O flag
 # we override the autoconf default (-g) because in release build we do not want to
 # include symbol information (obj files are huge)
@@ -838,17 +838,59 @@ if test $fftw = true ; then
   PLUMED_CHECK_PACKAGE([fftw3.h],[fftw_execute],[__PLUMED_HAS_FFTW],[fftw3])
 fi
 
-if test $python = true  ; then
+# python executable: if any of CYTHON_FOUND or PLUMED_CAN_PYCV is on will store
+# the python executable
+AC_SUBST(PYTHON_BIN)
+# set if PYTHON_BIN has Cython in its environment
+AC_SUBST(CYTHON_FOUND)
+# definitions and variables related to pycv and in general embedding python
+AC_SUBST(PLUMED_CAN_PYCV)
+AC_SUBST(PYBIND11_CFLAGS)
+AC_SUBST(PYTHON_LDFLAGS)
+AC_SUBST(PYTHON_CFLAGS)
+
 # if PYTHON_BIN is defined, it is expected to be the full path to python
-# Otherwise, search from a list of names:
-  if test -z "$PYTHON_BIN" ; then
-    AC_CHECK_PROGS([PYTHON_BIN],[python])
-  fi
-  if test -n "$PYTHON_BIN"
-  then
+# Otherwise, search from a list of names:  
+if test -z "$PYTHON_BIN" ; then
+    AC_CHECK_PROGS([PYTHON_BIN],[python python3])
+fi
+if test -n "$PYTHON_BIN" ; then
     AC_MSG_NOTICE([Python executable is $PYTHON_BIN])
-    AC_MSG_CHECKING([support for required python modules (python3, setuptools, cython)])
-testimport="
+  if test $pycv = true  ; then
+    AC_MSG_CHECKING([pycv: support for required python modules (python3, pybind11, numpy)])
+  testimport="
+import numpy
+import pybind11
+#no need to check for python3, if you have python2, you don't have pybind11 (and vice-versa)
+"
+    if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null;  then
+
+       pyver=$($PYTHON_BIN -c "import sysconfig;print(sysconfig.get_config_var('VERSION'))")
+       python_config=python${pyver}-config
+
+       if ${python_config} --ldflags --embed 1>/dev/null 2>/dev/null ;then
+          AC_MSG_RESULT([yes])
+          PYBIND11_CFLAGS="$($PYTHON_BIN -m pybind11 --includes) -fvisibility=hidden"
+          PYTHON_CFLAGS=$(${python_config} --cflags --embed)
+          PYTHON_LDFLAGS=$(${python_config} --ldflags --embed)
+          #TODO: conda_fixup
+          PLUMED_CAN_PYCV=yes
+        else
+          AC_MSG_RESULT([no])
+          AC_MSG_WARN([cannot enable pycv])
+          AC_MSG_WARN(["PyCV needs python to be embeddable, please rebuild python"])
+       fi
+    else
+       AC_MSG_RESULT([no])
+       AC_MSG_WARN([cannot enable pycv])
+    fi
+  else
+    AC_MSG_WARN([cannot enable pycv])
+  fi
+
+  if test $python = true  ; then
+    AC_MSG_CHECKING([python wrapper: support for required python modules (python3, setuptools, cython)])
+    testimport="
 from setuptools import setup
 from setuptools import Extension
 from Cython.Build import cythonize
@@ -859,16 +901,21 @@ if sys.version_info < (3,):
     if echo "$testimport" | "$PYTHON_BIN" 1>/dev/null 2>/dev/null;  then
        AC_MSG_RESULT([yes])
        AC_DEFINE([__PLUMED_HAS_PYTHON])
+       CYTHON_FOUND=yes
     else
        AC_MSG_RESULT([no])
        AC_MSG_WARN([cannot enable python interface])
-       PYTHON_BIN=
     fi
   else
     AC_MSG_WARN([cannot enable python interface])
   fi
 fi
 
+if test "${PLUMED_CAN_PYCV}" != yes &&  test "${CYTHON_FOUND}" != yes; then
+  #this deactivate python bin if no package was found
+  PYTHON_BIN=
+fi
+
 if test "$af_ocl" = true ; then
   PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afopencl])
   PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE_OCL],[afopencl])
@@ -944,8 +991,6 @@ AC_SUBST(LDSHARED)
 AC_SUBST(LD_MAIN_RUNPATH)
 # these are libraries that should be linked also to MD engines
 AC_SUBST(STATIC_LIBS)
-# python executable
-AC_SUBST(PYTHON_BIN)
 
 AC_SUBST(MPIEXEC)
 

diff --git a/plugins/pycv/.gitignore b/plugins/pycv/.gitignore
@@ -1,4 +1,4 @@
-Make.inc
+/Makefile.conf
 *.o
 *.so
 env
diff --git a/plugins/pycv/Makefile b/plugins/pycv/Makefile
@@ -1,12 +1,19 @@
-include Make.inc
+# 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
 
 ifeq ($(SOEXT),dylib)
@@ -18,6 +25,7 @@ endif
 all: PythonCVInterface.$(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)
@@ -35,7 +43,7 @@ include $(wildcard $(DEPFILES))
 #TODO: seems that $PLUMED_KERNEL is not needed, check
 PythonCVInterface.$(SOEXT): $(OBJS)
 	@echo Linking $@
-	$(LDSHARED) $(SONAME_OPTION),"$(notdir $@)" $(DYNAMIC_LIBS) $(PLUMED_KERNEL) $(ADDCLDFLAGS)  $^ -o $@ 
+	$(LDSHARED) $(SONAME_OPTION),"$(notdir $@)" $(DYNAMIC_LIBS) $(PLUMED_KERNEL) $(ADDCLDFLAGS) $^ -o $@ 
 
 clean:
 	rm -f $(OBJS) PythonCVInterface.$(SOEXT)

diff --git a/plugins/pycv/astyle.sh b/plugins/pycv/astyle.sh
@@ -1,20 +1,23 @@
 #! /usr/bin/env bash
 
+#formatted with shfmt  https://github.com/mvdan/sh/releases
+#checked with shellcheck
+
 for file in *.c *.cpp *.h *.inc.in; do
 
   test -f "$file" || continue
 
   echo -n "astyle $file"
 
-  ../../astyle/astyle --options=../../.astyle.options <$file >$file.tmp && {
-    if cmp -s $file $file.tmp; then
+  ../../astyle/astyle --options=../../.astyle.options <"$file" >"${file}.tmp" && {
+    if cmp -s "$file" "${file}.tmp"; then
       echo
     else
-      cp $file.tmp $file
+      cp "${file}.tmp" "$file"
       echo " +++ PATCHED"
     fi
   }
 
-  rm $file.tmp
+  rm "${file}.tmp"
 
 done