Moved documentation in share/doc

.github/workflows/gh-pages.yml

@@ -21,29 +21,29 @@ jobs:
         run: sudo apt-get install emacs26
 
       - name: install htmlize
-        run: git clone https://github.com/hniksic/emacs-htmlize && cp emacs-htmlize/htmlize.el docs/
+        run: git clone https://github.com/hniksic/emacs-htmlize && cp emacs-htmlize/htmlize.el share/doc/qmckl/html/
 
       - name: make
-        run: make -C src/ doc && ls -sh ./docs/
+        run: make -C src/ doc && ls -sh ./share/doc/qmckl/html/
 
       - name: pwd
         run: pwd
 
       - name: ls
-        run: ls -sh ./docs
+        run: ls -sh ./share/doc/qmckl/html/
 
 #     - name: Deploy
 #       uses: peaceiris/actions-gh-pages@v3
 #       with:
 #         github_token: ${{ secrets.GITHUB_TOKEN }}
-#         publish_dir: ./docs
+#         publish_dir: ./share/doc/qmckl/html/
 
       - name: Deploy
         uses: JamesIves/github-pages-deploy-action@4.1.0
         with:
            branch: gh-pages
-           folder: ./docs
+           folder: ./share/doc/qmckl/html/
 
 #          github_token: ${{ secrets.GITHUB_TOKEN }}
-#          publish_dir: ./docs
+#          publish_dir: ./share/doc/qmckl/html/
 

.gitmodules

@@ -1,6 +1,3 @@
 [submodule "munit"]
 	path = munit
 	url = https://github.com/nemequ/munit/
-[submodule "docs/org-html-themes"]
-	path = docs/org-html-themes
-	url = https://github.com/fniessen/org-html-themes.git

Makefile

@@ -16,15 +16,19 @@ static_lib=$(QMCKL_ROOT)/lib/libqmckl.a
 qmckl_h=$(QMCKL_ROOT)/include/qmckl.h
 qmckl_f=$(QMCKL_ROOT)/share/qmckl/fortran/qmckl_f.f90
 
+docdir=$(prefix)/share/doc/qmckl
+libdir=$(prefix)/lib
+includedir=$(prefix)/include
+fortrandir=$(prefix)/share/qmckl/fortran
+
 export prefix shared_lib static_lib qmckl_h qmckl_f
 
 
-all clean doc check install uninstall:
+all clean doc install uninstall check:
 	$(MAKE) -C src $@
 
 dist: $(distdir).tar.gz
 
-
 $(distdir).tar.gz: $(distdir)
 	tar chof - $(distdir) | gzip -9 -c > $@
 	rm -rf $(distdir)
@@ -39,15 +43,15 @@ $(distdir): $(qmckl_h) $(qmckl_f) $(static_lib) $(shared_lib) src/Makefile.gener
 	mkdir -p $(distdir)/share/doc/qmckl/html/
 	mkdir -p $(distdir)/share/doc/qmckl/text/
 	mkdir -p $(distdir)/man
-	cp munit/munit.h munit/munit.c $(distdir)/munit/
+	cp $(QMCKL_ROOT)/munit/munit.h munit/munit.c $(distdir)/munit/
-	cp src/*.c src/*.h src/*.f90 $(distdir)/src/
+	cp $(QMCKL_ROOT)/src/*.c src/*.h src/*.f90 $(distdir)/src/
-	cp src/Makefile.generated $(distdir)/src/Makefile
+	cp $(QMCKL_ROOT)/src/Makefile.generated $(distdir)/src/Makefile
-	cp include/* $(distdir)/include
+	cp $(qmckl_h) $(distdir)/include
-	cp Makefile $(distdir)/
+	cp $(QMCKL_ROOT)/Makefile $(distdir)/
-	cp docs/*.html $(distdir)/share/doc/qmckl/html/
+	cp $(QMCKL_ROOT)/share/doc/qmckl/html/*.html $(distdir)/share/doc/qmckl/html/
-	cp docs/*.css  $(distdir)/share/doc/qmckl/html/
+	cp $(QMCKL_ROOT)/share/doc/qmckl/html/*.css  $(distdir)/share/doc/qmckl/html/
-	cp docs/*.txt  $(distdir)/share/doc/qmckl/text/
+	cp $(QMCKL_ROOT)/share/doc/qmckl/text/*.txt  $(distdir)/share/doc/qmckl/text/
-	cp share/qmckl/fortran/*  $(distdir)/share/qmckl/fortran
+	cp $(qmckl_f) $(distdir)/share/qmckl/fortran/
 	mkdir -p $(distdir)/lib
 
 
@@ -58,21 +62,27 @@ FORCE:
 
 distcheck: $(distdir).tar.gz
 	gzip -cd $(distdir).tar.gz | tar xvf -
-	cd $(distdir) && $(MAKE) all check
+	cd $(distdir) && $(MAKE) all 
-	rm $(distdir)/lib/libqmckl.so
+	cd $(distdir) && $(MAKE) check
-	rm $(distdir)/include/qmckl.h 
+	cd $(distdir) && $(MAKE) prefix=$${PWD}/_inst install
-	rm $(distdir)/share/qmckl/fortran/qmckl_f.f90
+	cd $(distdir) && $(MAKE) prefix=$${PWD}/_inst uninstall
-	rm $(distdir)/share/doc/qmckl/html/*.html
+	@remaining="`find $${PWD}/$(distdir)/_inst -type f | wc -l`" ;\
-	rm $(distdir)/share/doc/qmckl/html/*.css
+		if test "$${remaining}" -ne 0; then \
-	rm $(distdir)/share/doc/qmckl/text/*.txt
+			echo "*** $${remaining} file(s) remaining in stage directory"; \
+			exit 1; \
+		fi
 	cd $(distdir) && $(MAKE) clean
 	rm -rf $(distdir)
 	@echo "*** Package $(distdir).tar.gz is ready for distribution."
 
 
-$(qmckl_h) $(qmckl_f) $(static_lib) $(shared_lib) src/Makefile.generated:
+$(qmckl_h) $(qmckl_f) $(static_lib) $(shared_lib):
 	$(MAKE) -C src $@ 
 
+src/Makefile.generated: 
+	$(MAKE) -C src Makefile.generated
+
+veryclean: FORCE clean
 
 
-.PHONY: all clean dist doc install uninstall FORCE
+.PHONY: all veryclean clean dist doc install uninstall FORCE

docs/.gitignore

@@ -1 +0,0 @@
-*.txt

docs/org-html-themes

@@ -1 +0,0 @@
-Subproject commit f7224a489462abc2c2174edbf7d4e82c0e276183

docs/theme.setup

@@ -1,16 +0,0 @@
-# -*- mode: org; -*-
-
-#+HTML_LINK_HOME: index.html
-#+OPTIONS: H:4 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t d:(HIDE)
-
-# SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
-
-#+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
-#+AUTHOR:     TREX CoE
-#+LANGUAGE:   en
-
-
-

qmckl.pc

@@ -0,0 +1,12 @@
+prefix=/usr
+exec_prefix=${prefix}
+includedir=${exec_prefix}/include
+libdir=${exec_prefix}/lib
+
+Name: QMCkl
+Description: Quantum Monte Carlo kernel library
+URL: https://github.com/trex-coe/qmckl
+Version: 1.0.0
+Cflags:  -I${includedir}
+Libs: -L${libdir} -lqmckl
+Requires.private: blas

src/Makefile

@@ -92,10 +92,13 @@ endif
 #    The Makefile.generated is the one that will be distributed with the library.
 
 
-.PHONY: clean shared static doc all check install uninstall syntax
+.PHONY: clean shared static doc all check install uninstall
 .SECONDARY: # Needed to keep the produced C and Fortran files
 
-$(shared_lib) $(static_lib) install uninstall: $(qmckl_h) $(qmckl_f) Makefile.generated
+$(shared_lib) $(static_lib): $(qmckl_h) $(qmckl_f) Makefile.generated
+	$(MAKE) -f Makefile.generated $@
+
+install uninstall: Makefile.generated
 	$(MAKE) -f Makefile.generated $@
 
 $(qmckl_f) $(qmckl_h): Makefile.generated
@@ -108,8 +111,11 @@ all: shared static doc check
 check: $(static_lib)
 	$(MAKE) -f Makefile.generated check
 
-syntax:
+cppcheck:
-	cppcheck --addon=cert qmckl_*.c
+	cppcheck \
+	 --addon=cert \
+	--enable=warning,style,performance,portability,information \
+	 qmckl_*.c
 
 doc: $(ORG_SOURCE_FILES)
 	$(QMCKL_ROOT)/tools/build_doc.sh
@@ -122,10 +128,10 @@ clean:
 		Makefile.generated *.html *.txt
 
 veryclean: clean FORCE
-	- $(RM)	$(QMCKL_ROOT)/docs/*.html \
+	- $(RM)	$(QMCKL_ROOT)/share/doc/qmckl/html/*.html \
-		$(QMCKL_ROOT)/docs/*.txt
+		$(QMCKL_ROOT)/share/doc/qmckl/text/*.txt
 
-Makefile.generated: Makefile $(QMCKL_ROOT)/tools/create_makefile.sh  $(ORG_SOURCE_FILES)
+Makefile.generated: Makefile $(QMCKL_ROOT)/tools/create_makefile.sh  $(ORG_SOURCE_FILES) ../tools/Building.org
 	$(QMCKL_ROOT)/tools/create_makefile.sh
 
 

src/README.org

@@ -1,6 +1,6 @@
 #+TITLE: QMCkl source code documentation
 #+PROPERTY: comments org
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 
 ------------------
 

src/qmckl.org

@@ -1,6 +1,6 @@
 #+TITLE: Introduction
 #+PROPERTY: comments org
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 # -*- mode: org -*-
 
 * Using QMCkl

src/qmckl_ao.org

@@ -1,5 +1,5 @@
 #+TITLE: Atomic Orbitals
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 #+INCLUDE: ../tools/lib.org
 
 The atomic basis set is defined as a list of shells. Each shell $s$ is

src/qmckl_context.org

@@ -1,5 +1,5 @@
 #+TITLE: Context
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 #+INCLUDE: ../tools/lib.org
 
 * Headers                                                          :noexport:

src/qmckl_distance.org

@@ -1,5 +1,5 @@
 #+TITLE: Inter-particle distances
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 #+INCLUDE: ../tools/lib.org
 
 Functions for the computation of distances between particles.

src/qmckl_electron.org

@@ -1,5 +1,5 @@
 #+TITLE: Electrons
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 #+INCLUDE: ../tools/lib.org
 
 In conventional QMC simulations, up-spin and down-spin electrons are
@@ -466,7 +466,6 @@ qmckl_exit_code qmckl_provide_ee_distance(qmckl_context context)
  /* Compute if necessary */
   if (ctx->electron.coord_new_date > ctx->electron.ee_distance_date) {
 
-    fprintf(stderr, "%10ld: provide ee_distance", ctx->date);
  /* Allocate array */
     if (ctx->electron.ee_distance == NULL) {
 

src/qmckl_error.org

@@ -1,5 +1,5 @@
 #+TITLE: Error handling
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 #+INCLUDE: ../tools/lib.org
 
 * Headers                                                         :noexport:

src/qmckl_memory.org

@@ -1,5 +1,5 @@
 #+TITLE: Memory management
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 #+INCLUDE: ../tools/lib.org
 
 We override the allocation functions to enable the possibility of

src/qmckl_numprec.org

@@ -1,5 +1,5 @@
 #+TITLE: Numerical precision
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 #+INCLUDE: ../tools/lib.org
 
 * Headers                                                          :noexport:

src/test_qmckl.org

@@ -1,5 +1,5 @@
 #+TITLE: Testing
-#+SETUPFILE: ../docs/theme.setup
+#+SETUPFILE: ../tools/theme.setup
 
 * QMCkl test                                                       :noexport:
 

tools/Building.org

@@ -167,7 +167,10 @@ endif
 .PHONY: clean shared static doc all check install uninstall
 .SECONDARY: # Needed to keep the produced C and Fortran files
 
-$(shared_lib) $(static_lib) install uninstall: $(qmckl_h) $(qmckl_f) Makefile.generated
+$(shared_lib) $(static_lib): $(qmckl_h) $(qmckl_f) Makefile.generated
+	$(MAKE) -f Makefile.generated $@
+
+install uninstall: Makefile.generated
 	$(MAKE) -f Makefile.generated $@
 
 $(qmckl_f) $(qmckl_h): Makefile.generated
@@ -180,6 +183,12 @@ all: shared static doc check
 check: $(static_lib)
 	$(MAKE) -f Makefile.generated check
 
+cppcheck:
+	cppcheck \
+	  --addon=cert \
+	  --enable=warning,style,performance,portability,information \
+	  qmckl_*.c
+
 doc: $(ORG_SOURCE_FILES)
 	$(QMCKL_ROOT)/tools/build_doc.sh
 
@@ -191,10 +200,10 @@ clean:
 		Makefile.generated *.html *.txt
 
 veryclean: clean FORCE
-	- $(RM)	$(QMCKL_ROOT)/docs/*.html \
+	- $(RM)	$(QMCKL_ROOT)/share/doc/qmckl/html/*.html \
-		$(QMCKL_ROOT)/docs/*.txt
+		$(QMCKL_ROOT)/share/doc/qmckl/text/*.txt
 
-Makefile.generated: Makefile $(QMCKL_ROOT)/tools/create_makefile.sh  $(ORG_SOURCE_FILES)
+Makefile.generated: Makefile $(QMCKL_ROOT)/tools/create_makefile.sh  $(ORG_SOURCE_FILES) ../tools/Building.org
 	$(QMCKL_ROOT)/tools/create_makefile.sh
 
 
@@ -361,15 +370,29 @@ check: test_qmckl test_qmckl_shared
 clean:
 	\$(RM) -- *.o *.mod \$(shared_lib) \$(static_lib) test_qmckl
 
+
+
+
 install:
 	install -d \$(prefix)/lib
 	install -d \$(prefix)/include
 	install -d \$(prefix)/share/qmckl/fortran
-	install -d \$(prefix)/man
+	install -d \$(prefix)/share/doc/qmckl/html/
+	install -d \$(prefix)/share/doc/qmckl/text/
 	install    \$(shared_lib) \$(prefix)/lib
 	install    \$(static_lib) \$(prefix)/lib
 	install    \$(qmckl_h) \$(prefix)/include
 	install    \$(qmckl_f) \$(prefix)/share/qmckl/fortran
+	install    \$(QMCKL_ROOT)/share/doc/qmckl/html/*.html \$(prefix)/share/doc/qmckl/html/
+	install    \$(QMCKL_ROOT)/share/doc/qmckl/html/*.css  \$(prefix)/share/doc/qmckl/html/
+	install    \$(QMCKL_ROOT)/share/doc/qmckl/text/*.txt  \$(prefix)/share/doc/qmckl/text/
+
+uninstall:
+	rm \$(prefix)/lib/libqmckl.so
+	rm \$(prefix)/lib/libqmckl.a
+	rm \$(prefix)/include/qmckl.h
+	rm -rf \$(prefix)/share/qmckl/
+	rm -rf \$(prefix)/share/doc/qmckl/
 
 .SUFFIXES: .c .f90 .o
 
@@ -379,7 +402,7 @@ install:
 .f90.o: qmckl_f.o
 	\$(FC) \$(FFLAGS) -c \$*.f90 -o \$*.o
 
-.PHONY: check clean all
+.PHONY: check cppcheck clean all
 EOF
 
   #+end_src
@@ -495,9 +518,9 @@ EOF
   First define readonly global variables.
 
   #+begin_src bash :noweb yes
-readonly DOCS=${QMCKL_ROOT}/docs/
+readonly DOCS=${QMCKL_ROOT}/share/doc/qmckl/
 readonly SRC=${QMCKL_ROOT}/src/
-readonly HTMLIZE=${DOCS}/htmlize.el
+readonly HTMLIZE=${DOCS}/html/htmlize.el
 readonly CONFIG_DOC=${QMCKL_ROOT}/tools/config_doc.el
 readonly CONFIG_TANGLE=${QMCKL_ROOT}/tools/config_tangle.el
   #+end_src
@@ -513,7 +536,7 @@ function check_preconditions()
         exit 1
     fi
 
-    for dir in ${DOCS} ${SRC}
+    for dir in ${DOCS}/html ${DOCS}/text ${SRC}
     do
         if [[ ! -d ${dir} ]]
         then
@@ -543,7 +566,7 @@ function install_htmlize()
     local repo="emacs-htmlize"
 
     [[ -f ${HTMLIZE} ]] || (
-        cd ${DOCS}
+        cd ${DOCS}/html
         git clone ${url} \
             && cp ${repo}/htmlize.el ${HTMLIZE} \
             && rm -rf ${repo}
@@ -564,7 +587,8 @@ function extract_doc()
     local org=$1
     local local_html=${SRC}/${org%.org}.html
     local local_text=${SRC}/${org%.org}.txt
-    local html=${DOCS}/${org%.org}.html
+    local html=${DOCS}/html/${org%.org}.html
+    local text=${DOCS}/text/${org%.org}.txt
 
     if [[ -f ${html} && ${org} -ot ${html} ]]
     then
@@ -577,7 +601,8 @@ function extract_doc()
           --load ${CONFIG_TANGLE}    \
           -f org-html-export-to-html \
           -f org-ascii-export-to-ascii
-    mv ${local_html} ${local_text} ${DOCS}
+    mv ${local_html} ${DOCS}/html
+    mv ${local_text} ${DOCS}/text
 
 }
   #+end_src
@@ -605,7 +630,7 @@ function main() {
 
     if [[ $? -eq 0 ]]
     then
-        cd ${DOCS}
+        cd ${DOCS}/html
         rm -f index.html
         ln README.html index.html
         exit 0

tools/build_doc.sh

@@ -7,9 +7,9 @@
 #   First define readonly global variables.
 
 
-readonly DOCS=${QMCKL_ROOT}/docs/
+readonly DOCS=${QMCKL_ROOT}/share/doc/qmckl/
 readonly SRC=${QMCKL_ROOT}/src/
-readonly HTMLIZE=${DOCS}/htmlize.el
+readonly HTMLIZE=${DOCS}/html/htmlize.el
 readonly CONFIG_DOC=${QMCKL_ROOT}/tools/config_doc.el
 readonly CONFIG_TANGLE=${QMCKL_ROOT}/tools/config_tangle.el
 
@@ -26,7 +26,7 @@ function check_preconditions()
         exit 1
     fi
 
-    for dir in ${DOCS} ${SRC}
+    for dir in ${DOCS}/html ${DOCS}/text ${SRC}
     do
         if [[ ! -d ${dir} ]]
         then
@@ -57,7 +57,7 @@ function install_htmlize()
     local repo="emacs-htmlize"
 
     [[ -f ${HTMLIZE} ]] || (
-        cd ${DOCS}
+        cd ${DOCS}/html
         git clone ${url} \
             && cp ${repo}/htmlize.el ${HTMLIZE} \
             && rm -rf ${repo}
@@ -79,7 +79,8 @@ function extract_doc()
     local org=$1
     local local_html=${SRC}/${org%.org}.html
     local local_text=${SRC}/${org%.org}.txt
-    local html=${DOCS}/${org%.org}.html
+    local html=${DOCS}/html/${org%.org}.html
+    local text=${DOCS}/text/${org%.org}.txt
 
     if [[ -f ${html} && ${org} -ot ${html} ]]
     then
@@ -92,7 +93,8 @@ function extract_doc()
           --load ${CONFIG_TANGLE}    \
           -f org-html-export-to-html \
           -f org-ascii-export-to-ascii
-    mv ${local_html} ${local_text} ${DOCS}
+    mv ${local_html} ${DOCS}/html
+    mv ${local_text} ${DOCS}/text
 
 }
 
@@ -121,7 +123,7 @@ function main() {
 
     if [[ $? -eq 0 ]]
     then
-        cd ${DOCS}
+        cd ${DOCS}/html
         rm -f index.html
         ln README.html index.html
         exit 0

tools/create_makefile.sh

@@ -117,15 +117,29 @@ check: test_qmckl test_qmckl_shared
 clean:
 	\$(RM) -- *.o *.mod \$(shared_lib) \$(static_lib) test_qmckl
 
+
+
+
 install:
 	install -d \$(prefix)/lib
 	install -d \$(prefix)/include
 	install -d \$(prefix)/share/qmckl/fortran
-	install -d \$(prefix)/man
+	install -d \$(prefix)/share/doc/qmckl/html/
+	install -d \$(prefix)/share/doc/qmckl/text/
 	install    \$(shared_lib) \$(prefix)/lib
 	install    \$(static_lib) \$(prefix)/lib
 	install    \$(qmckl_h) \$(prefix)/include
 	install    \$(qmckl_f) \$(prefix)/share/qmckl/fortran
+	install    \$(QMCKL_ROOT)/share/doc/qmckl/html/*.html \$(prefix)/share/doc/qmckl/html/
+	install    \$(QMCKL_ROOT)/share/doc/qmckl/html/*.css  \$(prefix)/share/doc/qmckl/html/
+	install    \$(QMCKL_ROOT)/share/doc/qmckl/text/*.txt  \$(prefix)/share/doc/qmckl/text/
+
+uninstall:
+	rm \$(prefix)/lib/libqmckl.so
+	rm \$(prefix)/lib/libqmckl.a
+	rm \$(prefix)/include/qmckl.h
+	rm -rf \$(prefix)/share/qmckl/
+	rm -rf \$(prefix)/share/doc/qmckl/
 
 .SUFFIXES: .c .f90 .o
 
@@ -135,5 +149,5 @@ install:
 .f90.o: qmckl_f.o
 	\$(FC) \$(FFLAGS) -c \$*.f90 -o \$*.o
 
-.PHONY: check clean all
+.PHONY: check cppcheck clean all
 EOF