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Moved documentation in share/doc

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This commit is contained in:
Anthony Scemama 2021-04-30 01:26:19 +02:00
parent 79c9651021
commit e2e46d0714
24 changed files with 451 additions and 404 deletions
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12
.github/workflows/gh-pages.yml vendored
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@ -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/

3
.gitmodules vendored
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@ -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

50
Makefile
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@ -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 src/*.c src/*.h src/*.f90 $(distdir)/src/
cp src/Makefile.generated $(distdir)/src/Makefile
cp include/* $(distdir)/include
cp Makefile $(distdir)/
cp docs/*.html $(distdir)/share/doc/qmckl/html/
cp docs/*.css $(distdir)/share/doc/qmckl/html/
cp docs/*.txt $(distdir)/share/doc/qmckl/text/
cp share/qmckl/fortran/* $(distdir)/share/qmckl/fortran
cp $(QMCKL_ROOT)/munit/munit.h munit/munit.c $(distdir)/munit/
cp $(QMCKL_ROOT)/src/*.c src/*.h src/*.f90 $(distdir)/src/
cp $(QMCKL_ROOT)/src/Makefile.generated $(distdir)/src/Makefile
cp $(qmckl_h) $(distdir)/include
cp $(QMCKL_ROOT)/Makefile $(distdir)/
cp $(QMCKL_ROOT)/share/doc/qmckl/html/*.html $(distdir)/share/doc/qmckl/html/
cp $(QMCKL_ROOT)/share/doc/qmckl/html/*.css $(distdir)/share/doc/qmckl/html/
cp $(QMCKL_ROOT)/share/doc/qmckl/text/*.txt $(distdir)/share/doc/qmckl/text/
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
rm $(distdir)/lib/libqmckl.so
rm $(distdir)/include/qmckl.h
rm $(distdir)/share/qmckl/fortran/qmckl_f.f90
rm $(distdir)/share/doc/qmckl/html/*.html
rm $(distdir)/share/doc/qmckl/html/*.css
rm $(distdir)/share/doc/qmckl/text/*.txt
cd $(distdir) && $(MAKE) all
cd $(distdir) && $(MAKE) check
cd $(distdir) && $(MAKE) prefix=$${PWD}/_inst install
cd $(distdir) && $(MAKE) prefix=$${PWD}/_inst uninstall
@remaining="`find $${PWD}/$(distdir)/_inst -type f | wc -l`" ;\
if test "$${remaining}" -ne 0; then \
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

1
docs/.gitignore vendored
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@ -1 +0,0 @@
*.txt

1
docs/org-html-themes

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

16
docs/theme.setup
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@ -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

12
qmckl.pc Normal file
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@ -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

0
share/doc/qmckl/html/.gitignore vendored Normal file
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0
docs/qmckl.css → share/doc/qmckl/html/qmckl.css
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0
share/doc/qmckl/text/.gitignore vendored Normal file
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20
src/Makefile
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@ -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 --addon=cert qmckl_*.c
cppcheck:
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 \
$(QMCKL_ROOT)/docs/*.txt
- $(RM) $(QMCKL_ROOT)/share/doc/qmckl/html/*.html \
$(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

2
src/README.org
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@ -1,6 +1,6 @@
#+TITLE: QMCkl source code documentation
#+PROPERTY: comments org
#+SETUPFILE: ../docs/theme.setup
#+SETUPFILE: ../tools/theme.setup
------------------

2
src/qmckl.org
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@ -1,6 +1,6 @@
#+TITLE: Introduction
#+PROPERTY: comments org
#+SETUPFILE: ../docs/theme.setup
#+SETUPFILE: ../tools/theme.setup
# -*- mode: org -*-
* Using QMCkl

2
src/qmckl_ao.org
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@ -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

2
src/qmckl_context.org
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@ -1,5 +1,5 @@
#+TITLE: Context
#+SETUPFILE: ../docs/theme.setup
#+SETUPFILE: ../tools/theme.setup
#+INCLUDE: ../tools/lib.org
* Headers :noexport:

2
src/qmckl_distance.org
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@ -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.

3
src/qmckl_electron.org
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@ -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) {

2
src/qmckl_error.org
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@ -1,5 +1,5 @@
#+TITLE: Error handling
#+SETUPFILE: ../docs/theme.setup
#+SETUPFILE: ../tools/theme.setup
#+INCLUDE: ../tools/lib.org
* Headers :noexport:

2
src/qmckl_memory.org
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@ -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

2
src/qmckl_numprec.org
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@ -1,5 +1,5 @@
#+TITLE: Numerical precision
#+SETUPFILE: ../docs/theme.setup
#+SETUPFILE: ../tools/theme.setup
#+INCLUDE: ../tools/lib.org
* Headers :noexport:

2
src/test_qmckl.org
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@ -1,5 +1,5 @@
#+TITLE: Testing
#+SETUPFILE: ../docs/theme.setup
#+SETUPFILE: ../tools/theme.setup
* QMCkl test :noexport:

51
tools/Building.org
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@ -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 \
$(QMCKL_ROOT)/docs/*.txt
- $(RM) $(QMCKL_ROOT)/share/doc/qmckl/html/*.html \
$(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

16
tools/build_doc.sh
View File

@ -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

18
tools/create_makefile.sh
View File

@ -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