Silence all plugins' messagaes at stdout of C level to be compatibale with NOMAD parsers.

pymolfile/molfile/external/CMakeLists.txt

@@ -14,7 +14,7 @@ message("GIT_EXECUTABLE='${GIT_EXECUTABLE}'")
 ExternalProject_Add(tng
                     PREFIX ${TNG_PREFIX}
                     GIT_REPOSITORY https://github.com/gromacs/tng.git
-		    GIT_TAG v1.7.6
+		    #GIT_TAG v1.7.6
                     INSTALL_DIR ${TNG_INSTALL_DIR}
                     CMAKE_ARGS ${TNG_CMAKE_ARGS} 
 		    CMAKE_COMMAND CFLAGS=-fPIC CXXFLAGS=-fPIC ${CMAKE_COMMAND}

pymolfile/molfile/molfile_plugins/compile/CMakeLists.txt

@@ -172,6 +172,7 @@ if(UNIX)
    message(MAKE_COMMAND= "make dynlibs staticlibs bins \"ARCH = ${TARGET_ARCH}\" \"COPTO = ${TARGET_COPT} \" \"LOPTO = ${TARGET_LOPT} \" \"CC = ${CMAKE_C_COMPILER} \" \"CXX =     ${CMAKE_CXX_COMPILER} \" \"DEF = ${TARGET_DEF}\" \"CCFLAGS = ${TARGET_CFLAGS} \" \"CXXFLAGS = ${TARGET_CXXFLG} \" \"AR = ${TARGET_AR}\" \"NM = ${TARGET_NM}\" \"RANLIB = ${TARGET_RANLIB}\" \"LIBTOOL = ${TARGET_LIBTOOL} \" ${TARGET_MOL_LIBS}")
    add_custom_command( 
       OUTPUT ${LIB_MOLFILE_FILES}
+      COMMAND ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/silence_plugins.sh
       COMMAND make dynlibs staticlibs bins \"ARCH = ${TARGET_ARCH}\" \"COPTO = ${TARGET_COPT} \" \"LOPTO = ${TARGET_LOPT} \" \"CC = ${CMAKE_C_COMPILER} \" \"CXX = ${CMAKE_CXX_COMPILER} \" \"DEF = ${TARGET_DEF}\" \"CCFLAGS = ${TARGET_CFLAGS} \" \"CXXFLAGS = ${TARGET_CXXFLG} \" \"AR = ${TARGET_AR}\" \"NM = ${TARGET_NM}\" \"RANLIB = ${TARGET_RANLIB}\" \"LIBTOOL = ${TARGET_LIBTOOL} \" ${TARGET_MOL_LIBS}
       COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib ${CMAKE_CURRENT_BINARY_DIR}/lib
       COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib 
@@ -201,6 +202,7 @@ if(WINCOMP)
    endif()
    add_custom_command( 
       OUTPUT ${LIB_MOLFILE_FILES}
+      COMMAND ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/silence_plugins.sh
       COMMAND ${MYMAKE} dynlibs win32staticlibs "\" ARCH = ${TARGET_ARCH} \"" "\" COPTO = /Fo \"" "\" LOPTO = /OUT: \"" "\" ${TARGET_MOL_SETTINGS} \"" "\" DEF = ${TARGET_DEF} \"" "\" AR = ${TARGET_AR} \"" "\" NM = ${TARGET_NM} \"" "\" RANLIB = ${TARGET_RANLIB} \"" "\" SHLDFLAGS = ${TARGET_SHLDFLAGS} \"" "\"${TARGET_MOL_LIBS}\""
       COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib ${CMAKE_CURRENT_BINARY_DIR}/molfile_plugins/compile/lib
       COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_SOURCE_DIR}/molfile_plugins/compile/lib 

pymolfile/molfile/molfile_plugins/compile/silence_plugins.sh

+#!/bin/bash
+
+fpath="../molfile_plugin/src/"
+#ipath="../include/"
+#incfile="silence_plugins.h"
+
+allpattern="printf"
+pattern1=" printf("
+pattern2=" fprintf(stderr"
+pattern3=" fprintf(stdout"
+addstr1=" sprintf(msgstr"
+addstr2=" sprintf(msgerr"
+addstr3=" sprintf(msgout"
+adddef1="#ifndef SILENCEMESSAGES "
+adddef2="char msgstr[512], msgout[512], msgerr[512];"
+adddef3="#endif"
+alsomatch=");"
+ignore1="/*"
+ignore2="//"
+exclude="("
+
+files=`find -E ${fpath}* -regex '.*\.(c|h|cxx|hxx|C|H)' -type f -exec grep -l -e "$allpattern" {} \; | grep -v "periodic_table"`
+
+echo "Changing lines with $pattern1 $pattern2 and $pattern3 in following files:"
+#echo "Copying $incfile to $ipath"
+#cp $incfile $ipath
+fcount=1
+
+for file in $files
+do
+	if [ -f $file.bak ]; then
+	    cp $file.bak $file
+	fi
+	echo "Processing file $file ..."
+	#incline=` cat $file | grep -n -e "#" | head -n 1 | awk -F":" '{print $1}'`
+	#sed -i.bak $incline'a\'$'\n''#include "silence_plugins.h"'$'\n' $file
+	#sed -i.bak $incline'a\'$'\n''#endif'$'\n' $file
+	#firstline=`cat $file | head -n 1`
+	#sed -i.bak '1a\'$'\n'${firstline}$'\n' $file
+	sed -i.bak '1i\'$'\n''#endif'$'\n' $file
+	sed -i.bak '1i\'$'\n''char msgstr'${fcount}'[512], msgout'${fcount}'[512], msgerr'${fcount}'[512];'$'\n' $file
+	sed -i.bak '1i\'$'\n''#define SILENCE_'${fcount}'_PLUGIN 1'$'\n' $file 
+	sed -i.bak '1i\'$'\n''#ifndef SILENCE_'${fcount}'_PLUGIN'$'\n' $file 
+	#sed -i.bak $incline'a\'$'\n''#define SILENCE_PLUGINS_'${fcount}' 1'$'\n' $file 
+	#sed -i.bak $incline'a\'$'\n''#ifndef SILENCE_PLUGINS_'${fcount}''$'\n' $file 
+	singlelines1=`cat $file | grep -n -e "$pattern1" | grep -v "^--" | awk -F":" '{print $1}'`
+	singlelines2=`cat $file | grep -n -e "$pattern2" | grep -v "^--" | awk -F":" '{print $1}'`
+	singlelines3=`cat $file | grep -n -e "$pattern3" | grep -v "^--" | awk -F":" '{print $1}'`
+	for line in $singlelines1
+	do
+		sed -i "" $line's|'"$pattern1"'|'"${addstr1}${fcount},"'|' $file
+	done
+	for line in $singlelines2
+	do
+		sed -i "" $line's|'"$pattern2"'|'"${addstr2}${fcount}"'|' $file
+	done
+	for line in $singlelines3
+	do
+		sed -i "" $line's|'"$pattern3"'|'"${addstr3}${fcount}"'|' $file
+	done
+	#if [ -f $file.bak2 ]; then
+	#    rm $file.bak2
+        #fi
+	let fcount="$fcount + 1"
+done
+

setup.py

@@ -90,6 +90,14 @@ class BuildExtWithoutPlatformSuffix(build_ext):
         filename = super().get_ext_filename(ext_name)
         return get_ext_filename_without_platform_suffix(filename)
 
+def check_tcl_version():
+    output = subprocess.check_output("echo \"puts \$tcl_version;exit 0\" | tclsh", shell=True)
+    try:
+        val = float(output)
+    except (TypeError,ValueError):
+        val = None
+    return val
+
 VERSION = "0.0.1"
 CLASSIFIERS = [
     "Development Status :: 1 - Alpha",
@@ -110,7 +118,6 @@ CLASSIFIERS = [
     "Operating System :: Microsoft :: Windows",
 ]
 
-
 # from MDAnalysis setup.py (http://www.mdanalysis.org/)
 class NumpyExtension(Extension, object):
     """Derived class to cleanly handle setup-time (numpy) dependencies.
@@ -169,22 +176,33 @@ def get_numpy_include():
     return numpy_include
 
 # from SimpleTraj setup.py (https://github.com/arose/simpletraj)
-
 if __name__ == '__main__':
 
+    tcl_version = None
+    tcl_version = check_tcl_version()
+    if tcl_version is None:
+        library_defs=['netcdf', 'expat']
+    else:
+        library_defs=['netcdf', 'expat', 'tcl']
+
+#    if sys.version_info < (3, 0):
+#        swig_opt_defs=['-Wall', '-c++']
+#    else:
+#        swig_opt_defs=['-py3', '-Wall', '-c++']
+    swig_opt_defs=['-py3', '-Wall', '-c++']
+
     libpymolfile_module = Extension(
             'pymolfile/molfile/_libpymolfile', 
             sources=[
                 'pymolfile/molfile/libpymolfile.i' , 
                 'pymolfile/molfile/pymolfile.cxx',
                 ],
-            swig_opts=['-py3', '-Wall', '-c++'],
+            swig_opts=swig_opt_defs,
             library_dirs=[
                 'build/external/tng/lib',
                 'build/molfile_plugins/compile/lib/'
                 ],
-            #libraries=['netcdf','expat','tcl'],
-            libraries=['netcdf','expat'],
+            libraries=library_defs,
             include_dirs = [
                 get_numpy_include(),
                 'pymolfile/molfile',
@@ -210,7 +228,7 @@ if __name__ == '__main__':
         version = VERSION,
         classifiers = CLASSIFIERS,
         license = "UIUC",
-        url = "https://gitlab.mpcdf.mpg.de/berko/pymolfile",
+        url = "https://gitlab.mpcdf.mpg.de/nomad-lab/pymolfile",
         zip_safe = False,
         packages = find_packages(),
         libraries = [('molfile_plugin', { 'sources' : ['build/molfile_plugins/compile/lib/libmolfile_plugin.a']})],
@@ -228,3 +246,5 @@ if __name__ == '__main__':
         install_requires = [ "numpy" ],
         extras_require = {}
     )
+ 
+