configure fixed in other directory

Makefile.am

@@ -47,27 +47,26 @@ pkgconfig_DATA = pkgconfig/qmckl.pc
 qmckl_h = include/qmckl.h
 include_HEADERS = $(qmckl_h)
 
-qmckl_f       = share/qmckl/fortran/qmckl_f.f90
 test_qmckl_f  = tests/qmckl_f.f90
 test_qmckl_fo = tests/qmckl_f.o
 src_qmckl_f   = src/qmckl_f.f90
 src_qmckl_fo  = src/qmckl_f.o
 header_tests  = tests/chbrclf.h tests/n2.h
 
 fortrandir = $(datadir)/fortran
-fortran_DATA = $(qmckl_f)
+fortran_DATA = $(src_qmckl_f)
 
 
-AM_CPPFLAGS  = -I$(srcdir)/src -I$(srcdir)/include
+AM_CPPFLAGS  = -I$(top_builddir)/src -I$(top_builddir)/include
+AM_CPPFLAGS += -I$(srcdir)/src -I$(srcdir)/include
 AM_CPPFLAGS += -DQMCKL_TEST_DIR="\"$(abs_srcdir)/share/qmckl/test_data/\""
 
 
 lib_LTLIBRARIES = src/libqmckl.la
 src_libqmckl_la_SOURCES = $(qmckl_h) $(src_qmckl_f) $(C_FILES) $(F_FILES) $(H_PRIVATE_FUNC_FILES) $(H_PRIVATE_TYPE_FILES) $(header_tests)
 
-CLEANFILES+=$(test_qmckl_f) $(test_qmckl_fo) $(src_qmckl_f) $(src_qmckl_fo) $(test_qmckl_o) $(src_qmckl_o)
+CLEANFILES+=$(test_qmckl_fo) $(src_qmckl_fo) $(test_qmckl_o) $(src_qmckl_o) $(FH_TYPE_FILES) $(FH_FUNC_FILES)
 
-htmlize_el=share/doc/qmckl/html/htmlize.el
 
 include generated.mk
 
@@ -76,16 +75,17 @@ ln_s_verbose   = $(ln_s_verbose_@AM_V@)
 ln_s_verbose_  = $(ln_s_verbose_@AM_DEFAULT_V@)
 ln_s_verbose_0 = @echo "  LN_S     $<";
 
-htmldir = $(docdir)/html
+htmldir = share/doc/qmckl/html
+textdir = share/doc/qmckl/text
+htmlize_el=$(htmldir)/htmlize.el
 dist_html_DATA = $(HTML_FILES) \
-        share/doc/qmckl/html/index.html \
-        share/doc/qmckl/html/qmckl.css
+        $(htmldir)/index.html \
+        $(htmldir)/qmckl.css
 
-textdir = $(docdir)/text
 dist_text_DATA = $(TEXT_FILES)
 
-share/doc/qmckl/html/index.html: share/doc/qmckl/html/README.html
-	$(ln_s_verbose)cd share/doc/qmckl/html/ && \
+$(htmldir)/index.html: $(htmldir)/README.html
+	$(ln_s_verbose)cd $(htmldir)/ && \
         rm -rf index.html && \
 	$(LN_S) README.html index.html
 
@@ -103,11 +103,11 @@ if VFC_CI
 AM_LDFLAGS=-lvfc_probes -lvfc_probes_f
 endif
 
-dist_src_DATA = $(ORG_FILES) $(TANGLED_FILES) $(EXPORTED_FILES) $(qmckl_f) $(test_qmckl_f)
+dist_src_DATA = $(ORG_FILES) $(TANGLED_FILES) $(EXPORTED_FILES) $(test_qmckl_f)
 
-BUILT_SOURCES = $(C_FILES) $(F_FILES) $(FH_FUNC_FILES) $(FH_TYPE_FILES) $(H_FUNC_FILES) $(H_TYPE_FILES) $(H_PRIVATE_FUNC_FILES) $(H_PRIVATE_TYPE_FILES) $(qmckl_f) $(src_qmckl_f) $(test_qmckl_f) $(qmckl_h) $(header_tests)
+BUILT_SOURCES = $(C_FILES) $(F_FILES) $(FH_FUNC_FILES) $(FH_TYPE_FILES) $(H_FUNC_FILES) $(H_TYPE_FILES) $(H_PRIVATE_FUNC_FILES) $(H_PRIVATE_TYPE_FILES) $(src_qmckl_f) $(test_qmckl_f) $(qmckl_h) $(header_tests)
 
-CLEANFILES += $(BUILT_SOURCES) $(C_TEST_FILES) $(F_TEST_FILES) $(TANGLED_FILES) $(C_TEST_FILES) $(F_TEST_FILES) $(qmckl_f) $(src_qmckl_f) $(test_qmckl_f) $(qmckl_h) $(HTML_FILES) $(TEXT_FILES) share/doc/qmckl/html/index.html $(EXPORTED_FILES) $(header_tests)
+CLEANFILES += $(BUILT_SOURCES) $(C_TEST_FILES) $(F_TEST_FILES) $(TANGLED_FILES) $(C_TEST_FILES) $(F_TEST_FILES) $(src_qmckl_f) $(test_qmckl_f) $(qmckl_h) $(HTML_FILES) $(TEXT_FILES) $(htmldir)/index.html $(EXPORTED_FILES) $(header_tests) 
 
 EXTRA_DIST +=                 \
     tools/build_doc.sh        \
@@ -147,25 +147,22 @@ SUFFIXES = .f90 .h .org .c _f.f90 _func.h _type.h _private_func.h _private_type.
 $(test_qmckl_f): $(src_qmckl_f)
 	cp $(src_qmckl_f) $(test_qmckl_f)
 
-$(qmckl_f): $(src_qmckl_f)
-	cp $(src_qmckl_f) $(qmckl_f) 
-
 $(qmckl_h): $(H_FUNC_FILES) $(H_TYPE_FILES)
-	$(cat_h_verbose)top_builddir=$(top_builddir) srcdir=$(srcdir) qmckl_h=$(qmckl_h) $(srcdir)/tools/build_qmckl_h.sh
+	$(cat_h_verbose)top_builddir=$(abs_top_builddir) srcdir=$(abs_srcdir) qmckl_h=$(qmckl_h) $(srcdir)/tools/build_qmckl_h.sh
 
 $(src_qmckl_f): $(FH_FUNC_FILES) $(FH_TYPE_FILES)
-	$(cat_h_verbose)top_builddir=$(top_builddir) srcdir=$(srcdir) src_qmckl_f=$(src_qmckl_f) $(srcdir)/tools/build_qmckl_f.sh
+	echo $(FH_TYPE_FILES) $(FH_FUNC_FILES)
+	$(cat_h_verbose)top_builddir=$(abs_top_builddir) srcdir=$(abs_srcdir) src_qmckl_f=$(src_qmckl_f) $(srcdir)/tools/build_qmckl_f.sh
 
 $(htmlize_el):
-	$(srcdir)/tools/install_htmlize.sh $(htmlize_el)
+	$(MKDIR_P) $(htmldir)
+	$(MKDIR_P) $(textdir)
+	abs_srcdir=$(abs_srcdir) $(srcdir)/tools/install_htmlize.sh $(htmlize_el)
 
 tests/chbrclf.h: $(qmckl_h)
 
 tests/n2.h: $(qmckl_h)
 
-generated.mk: $(ORG_FILES)
-	top_builddir=$(top_builddir) srcdir=$(srcdir) qmckl_h=$(qmckl_h) src_qmckl_f=$(src_qmckl_f) $(PYTHON) $(srcdir)/tools/build_makefile.py
-
 cppcheck: cppcheck.out
 
 cppcheck.out: $(qmckl_h)
@@ -175,7 +172,7 @@ cppcheck.out: $(qmckl_h)
 	  --suppress="unusedFunction" \
 	  --suppress="missingIncludeSystem" \
           --language=c --std=c99 -rp --platform=unix64  \
-          -I../include *.c *.h 2>../$@
+          -I$(srcdir)/include -I$(top_builddir)/include *.c *.h 2>../$@
 
 .PHONY: cppcheck
 

autogen.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
 
-python ./tools/build_makefile.py
+export srcdir="."
+${PYTHON} ${srcdir}/tools/build_makefile.py
 autoreconf -i -Wall --no-recursive

configure.ac

@@ -41,7 +41,7 @@ AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
 
 # Activate developer mode when the source is the git repository.
 # Otherwise, it is the source distribution and the developer mode should not be activated.
-AS_IF([test -d .git],
+AS_IF([test -d ${srcdir}/.git],
         [enable_maintainer_mode="yes"],
         [enable_maintainer_mode="no"]
 )
@@ -208,7 +208,6 @@ if test "x${QMCKL_DEVEL}" != "x"; then
 
   AC_PROG_AWK
   AM_PATH_PYTHON
-  ${PYTHON} ${srcdir}/tools/build_makefile.py
 
   AC_CHECK_PROGS([EMACS],[emacs26 emacs],[no])
   if test x${EMACS} == xno ; then

org/qmckl_tests.org

@@ -39,7 +39,7 @@ Br        -1.218470   -0.187436   -0.028227
 
  Nuclear coordinates are stored in atomic units in transposed format.
 
-#+begin_src c :tangle ../tests/chbrclf.h
+#+begin_src c :tangle (concat tests "chbrclf.h")
 #define chbrclf_nucl_num ((int64_t) 5)
 
 double chbrclf_charge[chbrclf_nucl_num] = { 6., 1., 9., 17., 35. };
@@ -523,7 +523,7 @@ F   1
 
     #+END_example
 
-#+begin_src c :tangle ../tests/chbrclf.h
+#+begin_src c :tangle (concat tests "chbrclf.h")
 #define chbrclf_shell_num 72
 #define chbrclf_prim_num 297
 #define chbrclf_ao_num 263
@@ -968,7 +968,7 @@ double chbrclf_basis_prim_factor[chbrclf_prim_num] =
 
 ** Molecular orbitals
 
-#+begin_src c :tangle ../tests/chbrclf.h
+#+begin_src c :tangle (concat tests "chbrclf.h")
 #define chbrclf_mo_num ((int64_t) 224)
 double chbrclf_mo_coef[chbrclf_mo_num*chbrclf_ao_num] =
 {
@@ -59891,7 +59891,7 @@ double chbrclf_mo_coef[chbrclf_mo_num*chbrclf_ao_num] =
 
    Electron coordinates are stored in atomic units in normal format.
 
-#+begin_src c :tangle ../tests/chbrclf.h
+#+begin_src c :tangle (concat tests "chbrclf.h")
 #define chbrclf_elec_up_num  ((int64_t) 34)
 #define chbrclf_elec_dn_num  ((int64_t) 34)
 #define chbrclf_elec_num  ((int64_t) 68)
@@ -60064,7 +60064,7 @@ N2
 
  Nuclear coordinates are stored in atomic units in transposed format.
 
-#+begin_src c :tangle ../tests/n2.h
+#+begin_src c :tangle (concat tests "n2.h")
 #define n2_nucl_num ((int64_t) 2)
 
 double n2_charge[n2_nucl_num] = { 5., 5.};
@@ -60080,7 +60080,7 @@ double n2_nucl_coord[3][n2_nucl_num] =
 
    Electron coordinates are stored in atomic units in normal format.
 
-#+begin_src c :tangle ../tests/n2.h
+#+begin_src c :tangle (concat tests "n2.h")
 #define n2_elec_up_num  ((int64_t) 5)
 #define n2_elec_dn_num  ((int64_t) 5)
 #define n2_elec_num     ((int64_t) 10)
@@ -60105,7 +60105,7 @@ double n2_elec_coord[n2_walk_num][n2_elec_num][3] = { {
   This test is mainly for the Jastrow factor and was supplied by
   Ramon Panades Baruetta.
 
-#+begin_src c :tangle ../tests/n2.h
+#+begin_src c :tangle (concat tests "n2.h")
 /* Jastrow related */
 
 #define n2_type_nucl_num    ((int64_t) 1)

tools/build_doc.sh

@@ -32,7 +32,7 @@ function extract_doc()
         --load="${HTMLIZE}"           \
         --load="${CONFIG_DOC}"        \
         ${org}                           \
-        --load="../${CONFIG_TANGLE}"     \
+        --load="${CONFIG_TANGLE}"     \
         -f org-html-export-to-html       \
         -f org-ascii-export-to-ascii 
 
@@ -47,7 +47,7 @@ function extract_doc()
 for i in $@
 do
     exported=${i%.org}.exported
-    exported=$(dirname $exported)/.$(basename $exported)
+    exported=${top_builddir}/src/$(basename $exported)
     NOW=$(date +"%m%d%H%M.%S")
     extract_doc ${i} &> $exported 
     rc=$?

tools/build_makefile.py

@@ -4,8 +4,16 @@
 
 from __future__ import print_function
 from glob import glob
+import os
 
 def main():
+    wd = os.getcwd()
+    try:
+        srcdir = os.environ["srcdir"]
+        os.chdir(srcdir)
+    except KeyError:
+        pass
+
     C_FILES               =  []
     C_O_FILES             =  []
     F_FILES               =  []
@@ -33,8 +41,8 @@ def main():
 
     for org in glob("org/*.org"):
         i         =  org.split('/')[-1].rsplit(".",1)[0]
-        tangled   =  "org/."+i+".tangled"
-        exported  =  "org/."+i+".exported"
+        tangled   =  "src/"+i+".tangled"
+        exported  =  "src/"+i+".exported"
         c_test_x  =  "tests/test_"+i
         c_test_o  =  "tests/test_"+i+".$(OBJEXT)"
         f_test_o  =  "tests/test_"+i+"_f.$(OBJEXT)"
@@ -181,7 +189,7 @@ def main():
     output = ["",
               "## Source files",
               "",
-              "ORG_FILES="+" ".join(ORG_FILES),
+              "ORG_FILES="+" ".join([ "$(srcdir)/"+ x for x in ORG_FILES]),
               "TANGLED_FILES="+" ".join(TANGLED_FILES),
               "EXPORTED_FILES="+" ".join(EXPORTED_FILES),
               "C_FILES="+" ".join(C_FILES),
@@ -195,7 +203,7 @@ def main():
               "H_PRIVATE_TYPE_FILES="+" ".join(H_PRIVATE_TYPE_FILES),
               "C_TEST_FILES="+" ".join(C_TEST_FILES),
               "F_TEST_FILES="+" ".join(F_TEST_FILES),
-              "TESTS="+" ".join(TESTS.keys()).replace("$(srcdir)/",""),
+              "TESTS="+" ".join(TESTS.keys()),
               "HTML_FILES="+" ".join(HTML.values()),
               "TEXT_FILES="+" ".join(TEXT.values()),
               "" ]
@@ -205,8 +213,8 @@ def main():
               "",
               "if QMCKL_DEVEL" ]
     for f in DEPS_ORG.keys():
-        output += [ DEPS_ORG[f] + ": "+f,
-                    "\t$(tangle_verbose)top_builddir=$(top_builddir) srcdir=$(srcdir) $(srcdir)/tools/missing bash $(srcdir)/tools/tangle.sh "+f,
+        output += [ DEPS_ORG[f] + ": $(srcdir)/"+f,
+                    "\t$(tangle_verbose)top_builddir=$(abs_top_builddir) srcdir=$(abs_srcdir) $(srcdir)/tools/missing bash $(srcdir)/tools/tangle.sh $(srcdir)/"+f,
                     "" ]
     output += [ "endif",
                 "" ]
@@ -233,7 +241,7 @@ def main():
     for f in sorted(TESTS.keys()):
         prefix = "tests_" + f.rsplit("/",1)[-1]
         output += [ prefix + "_SOURCES = " + \
-                    " ".join(TESTS[f]).replace("$(srcdir)",""),
+                    " ".join(TESTS[f]),
                     prefix + "_LDADD   = src/libqmckl.la",
                     prefix + "_LDFLAGS = -no-install",
                     "" ]
@@ -252,16 +260,16 @@ def main():
 
     for f in sorted(ORG_FILES):
         output += [ HTML[f] + ": " + DEPS_DOC[f],
-                    TEXT[f] + ":  " + DEPS_DOC[f],
+                    TEXT[f] + ": " + DEPS_DOC[f],
                     "" ]
 
     for f in sorted(DEPS_DOC.keys()):
-        output += [ DEPS_DOC[f] + ": " + f + " $(htmlize_el)",
-                    "\t$(export_verbose)top_builddir=$(top_builddir) srcdir=$(srcdir) $(srcdir)/tools/missing bash $(srcdir)/tools/build_doc.sh "+f,
+        output += [ DEPS_DOC[f] + ": $(srcdir)/" + f + " $(htmlize_el)",
+                    "\t$(export_verbose)top_builddir=$(abs_top_builddir) srcdir=$(abs_srcdir) $(srcdir)/tools/missing bash $(srcdir)/tools/build_doc.sh $(srcdir)/"+f,
                     "" ]
     output += ["endif"]
 
-    f = open("generated.mk","w")
+    f = open(srcdir+"/generated.mk","w")
     f.write("\n".join(output))
 
 

tools/build_qmckl_h.sh

@@ -99,7 +99,7 @@ EOF
 
 for i in ${HEADERS}
 do
-    header=${srcdir}/src/$i
+    header=${top_builddir}/src/$i
     if [ -f $header ] ; then
         echo "/* $header */" >> ${qmckl_h}
         cat $header >> ${qmckl_h}

tools/config_tangle.el

@@ -33,19 +33,21 @@
 
 
 ; The following is required to compute the file names
-(setq pwd (file-name-directory buffer-file-name))
-(setq wd (concat pwd "/../src/"))
-(setq td (concat pwd "/../tests/"))
+(setq top_builddir (or (getenv "top_builddir") "."))
+(setq srcdir (or (getenv "srcdir") "."))
+
+(setq src (concat top_builddir "/src/"))
+(setq tests (concat top_builddir "/tests/"))
 (setq name (file-name-nondirectory (substring buffer-file-name 0 -4)))
-(setq f  (concat wd name "_f.f90"))
-(setq fh_func (concat wd name "_fh_func.f90"))
-(setq fh_type (concat wd name "_fh_type.f90"))
-(setq c  (concat wd name ".c"))
-(setq h_func  (concat wd name "_func.h"))
-(setq h_type  (concat wd name "_type.h"))
-(setq h_private_type  (concat wd name "_private_type.h"))
-(setq h_private_func  (concat wd name "_private_func.h"))
-(setq c_test  (concat td "test_" name ".c"))
-(setq f_test  (concat td "test_" name "_f.f90"))
-(org-babel-lob-ingest "../tools/lib.org")
+(setq f  (concat src name "_f.f90"))
+(setq fh_func (concat src name "_fh_func.f90"))
+(setq fh_type (concat src name "_fh_type.f90"))
+(setq c  (concat src name ".c"))
+(setq h_func  (concat src name "_func.h"))
+(setq h_type  (concat src name "_type.h"))
+(setq h_private_type  (concat src name "_private_type.h"))
+(setq h_private_func  (concat src name "_private_func.h"))
+(setq c_test  (concat tests "test_" name ".c"))
+(setq f_test  (concat tests "test_" name "_f.f90"))
+(org-babel-lob-ingest (concat srcdir "/tools/lib.org"))
 

tools/install_htmlize.sh

@@ -2,7 +2,7 @@
 #
 # Installs the htmlize Emacs plugin
 
-./tools/missing git clone "https://github.com/hniksic/emacs-htmlize"
+${abs_srcdir}/tools/missing git clone "https://github.com/TREX-CoE/emacs-htmlize"
 mv emacs-htmlize/htmlize.el $1
 rm -rf emacs-htmlize
 

tools/tangle.sh

@@ -14,7 +14,7 @@ if [[ -z ${srcdir} ]] ; then
 fi
 
 if [[ -z ${top_builddir} ]] ; then
-   echo "Error: srcdir environment variable is not defined"
+   echo "Error: top_builddir environment variable is not defined"
    exit 1
 fi
 
@@ -31,14 +31,14 @@ function tangle()
     fi
     ${srcdir}/tools/missing \
         emacs --batch ${org_file} \
-         --load=${PWD}/tools/config_tangle.el \
+         --load=${srcdir}/tools/config_tangle.el \
         -f org-babel-tangle
 }
 
 for i in $@
 do
     tangled=${i%.org}.tangled
-    tangled=$(dirname $tangled)/.$(basename $tangled)
+    tangled=${top_builddir}/src/$(basename $tangled)
     NOW=$(date +"%m%d%H%M.%S")
     tangle ${i} &> $tangled 
     rc=$?
@@ -47,6 +47,6 @@ do
     # Fail if tangling failed
     if [[ $rc -ne 0 ]] ; then
        cat $tangled
-       exit rc
+       exit $rc
     fi
 done