Updated doc generation

src/Makefile

@@ -51,16 +51,12 @@ test: Makefile.generated
 
 
 doc: $(ORG_SOURCE_FILES)
-	./merge_org.sh
 	./create_doc.sh $(MERGED_ORG)
-	rm $(MERGED_ORG)
 
 
 clean:
 	rm -f qmckl.h test_qmckl_* test_qmckl.c test_qmckl qmckl_*.f90 qmckl_*.c qmckl_*.o qmckl_*.h Makefile.generated libqmckl.so *.html *.fh *.mod
 
 Makefile.generated: Makefile create_makefile.sh  $(ORG_SOURCE_FILES)
-	./merge_org.sh 
 	./create_makefile.sh $(MERGED_ORG)
-	rm $(MERGED_ORG)
 

src/README.org

@@ -4,9 +4,9 @@
 
 #+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
 
- bibliography:../docs/references.bib
 
 * Introduction
+ 
 
   The ultimate goal of the QMCkl library is to provide a high-performance
   implementation  of  the main  kernels  of  QMC. In  this  particular
@@ -24,7 +24,7 @@
    the prorgam is usually written in a separate directory, and is often outdated
    compared to the code.
 
-   Literate programming cite:knuth_1992 is a different approach to programming,
+   Literate programming is a different approach to programming,
    where the program is considered as a publishable-quality document. Most of
    the lines of the source files are text, mathematical formulas, tables,
    figures, /etc/, and the lines of code are just the translation in a computer
@@ -43,13 +43,13 @@
    be tested.
 
    We have chosen to write the source files in [[https://karl-voit.at/2017/09/23/orgmode-as-markup-only/][org-mode]] format,
-   cite:schulte_2012 as any text editor can be used to edit org-mode files. To
+   as any text editor can be used to edit org-mode files. To
    produce the documentation, there exists multiple possibilities to convert
    org-mode files into different formats such as HTML or PDF. The source code is
    easily extracted from the org-mode files invoking the Emacs text editor from
    the command-line in the =Makefile=, and then the produced files are compiled.
    Moreover, within the Emacs text editor the source code blocks can be executed
-   interactively, in the same spirit as Jupyter notebooks. cite:Kluyver_2016
+   interactively, in the same spirit as Jupyter notebooks. 
 
 
 ** Source code editing
@@ -59,8 +59,7 @@
    Any text  editor can be used  to edit org-mode files.  For a better
    user experience Emacs  is recommended.  For users  hating Emacs, it
    is good to  know that Emacs can behave like  Vim when switched into
-   ``Evil''  mode.  There  also   exists  [[https://www.spacemacs.org][Spacemacs]]  which  helps  the
-   transition for Vim users.
+   ``Evil''  mode. 
 
    In the =tools/init.el= file, we provide a minimal Emacs configuration
    file for vim users. This file should be copied into =.emacs.d/init.el=.
@@ -78,10 +77,10 @@
    Most of the codes of the TREX CoE are written in Fortran with some scripts in
    Bash and Python. Outside of the CoE, Fortran is also important (Casino, Amolqc),
    and other important languages used by the community are C and C++ (QMCPack,
-   QWalk), and Julia is gaining in popularity. cite:poole_2020 The library we
-   design should be compatible with all of these languages.  The QMCkl API has to
-   be compatible with the C language since libraries with a C-compatible API can be
-   used in every other language.
+   QWalk), and Julia is gaining in popularity. The library we design should be
+   compatible with all of these languages.  The QMCkl API has to be compatible
+   with the C language since libraries with a C-compatible API can be used in
+   every other language.
 
    High-performance versions of the QMCkl, with the same API, will be rewritten by
    the experts in HPC. These optimized libraries will be tuned for specific
@@ -100,7 +99,7 @@
    internal functions related to system programming, the C language is more natural
    than Fortran.
 
-   The <<<Fortran>>> source files should provide a C interface using the
+   The Fortran source files should provide a C interface using the
  ~iso_c_binding~ module. The name of the Fortran source files should end with
  =_f.f90= to be properly handled by the =Makefile=.  The names of the functions
    defined in Fortran should be the same as those exposed in the API suffixed by

src/create_doc.sh

@@ -1,13 +1,41 @@
-#!/bin/bash
-INPUT=$1
+#!/bin/bash 
 
-if [[ -f ../docs/htmlize.el ]]
+INPUT=$1
+SRC=$PWD
+
+
+# Install htmlize if needed
+[[ -f ../docs/htmlize.el ]] || (
+    cd ../docs/
+    git clone https://github.com/hniksic/emacs-htmlize 
+    cp emacs-htmlize/htmlize.el .
+    rm -rf  emacs-htmlize
+    cd -
+)
+
+[[ -f ../docs/htmlize.el ]] || exit 1
+
+
+# Switch to TMPDIR for easy cleanup
+TMPDIR=$(mktemp -d)
+./merge_org.sh $TMPDIR/$INPUT
+cd $TMPDIR
+
+
+# Create documentation
+emacs --batch \
+      --load ${SRC}/../docs/htmlize.el \
+      --load ${SRC}/../toold/init.el  \
+      $INPUT -f org-html-export-to-html
+
+if [[ $? -eq 0 ]]
 then
-    emacs --batch --load ../docs/htmlize.el --load ../docs/config.el $INPUT -f org-html-export-to-html
+  rm -rf $TMPDIR
+  exit 0
 else
-    emacs --batch --load ../docs/config.el $INPUT -f org-html-export-to-html
+  mv index.html ${SRC}/../docs/
+  rm -rf $TMPDIR
+  exit 2
 fi
 
-mv index.html ../docs
-
 

src/create_makefile.sh

@@ -1,6 +1,8 @@
 #!/bin/bash
 
 INPUT=$1
+./merge_org.sh $INPUT
+
 OUTPUT=Makefile.generated
 
 # Tangle org files

src/merge_org.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
+OUTPUT=$1
+
 for i in README.org \
              qmckl.org \
              qmckl_context.org \
@@ -11,5 +13,5 @@ for i in README.org \
              qmckl_footer.org \
              test_qmckl.org
 do
-    cat $i >> merged_qmckl.org
+    cat $i >> $1
 done