Clean configure

.gitignore

@@ -1,17 +1,10 @@
+*.la
+*.lo
 .deps/
-compile
+.dirstamp
-depcomp
+.libs
-generated.mk
-stamp-h1
-libtool
-ltmain.sh
-missing
-m4/libtool.m4
-m4/ltoptions.m4
-m4/ltsugar.m4
-m4/ltversion.m4
-m4/lt~obsolete.m4
 Makefile
+Makefile.in
 aclocal.m4
 autom4te.cache/
 config.guess
@@ -19,13 +12,20 @@ config.log
 config.status
 config.sub
 configure
-install-sh
+generated.mk
-qmckl.pc
+m4/libtool.m4
-Makefile.in
+m4/ltoptions.m4
-test-driver
+m4/ltsugar.m4
-.libs
+m4/ltversion.m4
-.dirstamp
+m4/lt~obsolete.m4
-*.la
-*.lo
 qmckl-*.tar.gz
 qmckl.mod
+qmckl.pc
+stamp-h1
+tools/compile
+tools/depcomp
+tools/install-sh
+tools/libtool
+tools/ltmain.sh
+tools/missing
+tools/test-driver

Makefile.am

@@ -159,7 +159,7 @@ tests/chbrclf.h: $(qmckl_h)
 	
 
 generated.mk: $(ORG_FILES)
-	python $(srcdir)/tools/build_makefile.py
+	$(PYTHON) $(srcdir)/tools/build_makefile.py
 
 cppcheck: cppcheck.out
 	

configure.ac

@@ -38,13 +38,13 @@ AC_PREREQ([2.69])
 AC_INIT([qmckl],[0.1.1],
         [https://github.com/TREX-CoE/qmckl/issues], [],
         [https://trex-coe.github.io/qmckl/index.html])
+AC_CONFIG_AUX_DIR(tools)
 AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
 AM_MAINTAINER_MODE()
 LT_INIT
 AC_CONFIG_SRCDIR([Makefile.in])
 AC_CONFIG_HEADERS([include/config.h])
 AC_CONFIG_MACRO_DIR([m4])
-#AM_MAINTAINER_MODE
 
 VERSION_MAJOR=`echo ${PACKAGE_VERSION} | cut -d. -f1`
 VERSION_MINOR=`echo ${PACKAGE_VERSION} | cut -d. -f2`
@@ -64,6 +64,9 @@ AC_LANG(C)
 
 # Checks for programs.
 AC_PROG_CC
+# Make sure the c compiler supports C99
+m4_version_prereq([2.70],[], [AC_PROG_CC_C99])
+AS_IF([test "$ac_cv_prog_cc_c99" = "no"], [AC_MSG_ERROR([The compiler does not support C99])])
 AC_PROG_CC_C_O
 AC_PROG_FC
 AC_PROG_FC_C_O
@@ -72,13 +75,10 @@ AC_FC_FREEFORM
 AC_PROG_LIBTOOL
 AC_PROG_INSTALL
 AC_PROG_LN_S
-AC_PROG_CC_C99
 PKG_PROG_PKG_CONFIG([])
 PKG_LIBS=""
 PKG_CFLAGS=""
 
-AC_SUBST([HAS_CPPCHECK])
-
 # Checks for libraries.
 
 AC_FC_LIBRARY_LDFLAGS
@@ -178,15 +178,8 @@ if test "x${QMCKL_DEVEL}" != "x"; then
 
   QMCKL_DEVEL=" -- Developer mode"
   AC_PROG_AWK
-  AC_CHECK_PROGS([PYTHON],[python python3 python2],[no])
+  AM_PATH_PYTHON
-  if test x${PYTHON} == xno ; then
+  ${PYTHON} ${srcdir}/tools/build_makefile.py
-    AC_MSG_ERROR([
-    --------------------------------------------
-    Error: Python is required to build makefiles
-    --------------------------------------------
-    ])
-  fi
-  python ${srcdir}/tools/build_makefile.py
 
   AC_CHECK_PROGS([EMACS],[emacs26 emacs],[no])
   if test x${EMACS} == xno ; then
@@ -211,6 +204,8 @@ LIBS="${LAPACK_LIBS} ${BLAS_LIBS} ${LIBS}"
 PKG_LIBS="${PKG_LIBS} ${LIBS}"
 AC_SUBST([PKG_LIBS])
 AC_SUBST([PKG_CFLAGS])
+AC_SUBST([HAS_CPPCHECK])
+
 
 AC_CONFIG_FILES([Makefile
                  pkgconfig/qmckl.pc

org/.gitignore

@@ -1,2 +1,3 @@
+ltximg/
 *.tangled
 *.exported

org/qmckl_ao.org

@@ -94,6 +94,7 @@ int main() {
    | ~shell_factor~     | ~[shell_num]~ | Normalization factor for each shell                                  |
    | ~exponent~         | ~[prim_num]~  | Array of exponents                                                   |
    | ~coefficient~      | ~[prim_num]~  | Array of coefficients                                                |
+   | ~prim_factor~      | ~[prim_num]~  | Normalization factors of the primtives                               |
 
    For H_2 with the following basis set,
 
@@ -1661,7 +1662,6 @@ end function test_qmckl_ao_gaussian_vgl
    #+end_src
 
 ** TODO Slater basis functions
-
 ** TODO Radial functions on a grid
 * Combining radial and polynomial parts
 * End of files                                                     :noexport:

pkgconfig/qmckl.pc.in

@@ -7,7 +7,7 @@ Name: @PACKAGE_NAME@
 Description: Quantum Monte Carlo kernel library
 URL: https://github.com/trex-coe/qmckl
 Version: @PACKAGE_VERSION@
-Cflags:  -I${includedir} @PKG_CFLAGS@
+Cflags:  -I${includedir}
-Libs: -L${libdir} -lqmckl @PKG_LIBS@
+Libs: -L${libdir} -lqmckl
-Requires: @PKG_BLAS@
+Libs.private: @PKG_LIBS@
 

tools/build_doc.sh

@@ -19,7 +19,7 @@ function extract_doc()
   html=${DOCS}/html/$(basename ${org%.org}.html)
   text=${DOCS}/text/$(basename ${org%.org}.txt)
 
-  ./missing emacs --batch  \
+  ./tools/missing emacs --batch  \
         --load ${HTMLIZE}          \
         --load ${CONFIG_DOC}       \
         ${org}                     \
@@ -34,8 +34,9 @@ function extract_doc()
 for i in $@
 do
     exported=${i%.org}.exported
+    exported=$(dirname $exported)/.$(basename $exported)
     NOW=$(date +"%m%d%H%M.%S")
-    extract_doc ${i} &> $exported
+    extract_doc ${i} > $exported
 
     # Make log file older than the exported files
     touch -t ${NOW} $exported

tools/build_makefile.py

@@ -33,8 +33,8 @@ def main():
 
     for org in glob("org/*.org"):
         i         =  org.split('/')[-1].rsplit(".",1)[0]
-        tangled   =  "org/"+i+".tangled"
+        tangled   =  "org/."+i+".tangled"
-        exported  =  "org/"+i+".exported"
+        exported  =  "org/."+i+".exported"
         c_test_x  =  "tests/test_"+i
         c_test_o  =  "tests/test_"+i+".$(OBJEXT)"
         f_test_o  =  "tests/test_"+i+"_f.$(OBJEXT)"

tools/tangle.sh

@@ -24,7 +24,7 @@ function tangle()
     elif [[ ${org_file} -ot ${f_file} ]] ; then
         return
     fi
-    ./missing \
+    ./tools/missing \
         emacs --batch ${org_file} \
          --load=${PWD}/tools/config_tangle.el \
         -f org-babel-tangle
@@ -33,8 +33,9 @@ function tangle()
 for i in $@
 do
     tangled=${i%.org}.tangled
+    tangled=$(dirname $tangled)/.$(basename $tangled)
     NOW=$(date +"%m%d%H%M.%S")
-    tangle ${i} &> $tangled
+    tangle ${i} > $tangled
 
     # Make log file older than the tangled files
     touch -t ${NOW} $tangled

tools/theme.setup

@@ -6,7 +6,7 @@
 #+INFOJS_OPT: toc:t mouse:underline path:org-info.js
 #+HTML_HEAD: <link rel="stylesheet" title="Standard" href="qmckl.css" type="text/css" />
 
-#+STARTUP:    align fold nodlcheck hidestars oddeven lognotestate
+#+STARTUP:    align fold nodlcheck hidestars oddeven lognotestate latexpreview
 #+AUTHOR:     TREX CoE
 #+LANGUAGE:   en