Fixed makefile

src/Makefile

@@ -34,9 +34,10 @@ LIBS=-lm
 endif
 
 
-export CC CFLAGS FC FFLAGS LIBS
+QMCKL_ROOT=$(PWD)/..
+
+export CC CFLAGS FC FFLAGS LIBS QMCKL_ROOT
 
-MERGED_ORG=merged_qmckl.org
 ORG_SOURCE_FILES=$(wildcard *.org)
 OBJECT_FILES=$(filter-out $(EXCLUDED_OBJECTS), $(patsubst %.org,%.o,$(ORG_SOURCE_FILES)))
 
@@ -51,12 +52,12 @@ test: Makefile.generated
 
 
 doc: $(ORG_SOURCE_FILES)
-	./create_doc.sh $(MERGED_ORG)
+	$(QMCKL_ROOT)/tools/create_doc.sh 
 
 
 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)
-	./create_makefile.sh $(MERGED_ORG)
+Makefile.generated: Makefile $(QMCKL_ROOT)/tools/create_makefile.sh  $(ORG_SOURCE_FILES)
+	$(QMCKL_ROOT)/tools/create_makefile.sh 
 

src/README.org

@@ -6,7 +6,7 @@
 
 
 * Introduction
- 
+
 
   The ultimate goal of the QMCkl library is to provide a high-performance
   implementation  of  the main  kernels  of  QMC. In  this  particular
@@ -15,9 +15,9 @@
   HPC experts  to use  this repository as  a reference  for re-writing
   optimized libraries.
 
-  
+
 ** Literate programming
-   
+
    In a traditional source code, most of the lines of source files of a program
    are code, scripts, Makefiles, and only a few lines are comments explaining
    parts of the code that are non-trivial to understand. The documentation of
@@ -49,7 +49,7 @@
    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. 
+   interactively, in the same spirit as Jupyter notebooks.
 
 
 ** Source code editing
@@ -59,7 +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. 
+   ``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=.
@@ -137,9 +137,9 @@
     If the  name of the  org-mode file is =xxx.org=, the name  of the
     produced C files should be =xxx.c= and =xxx.h= and the name of the
     produced Fortran file should be =xxx.f90=.
-   
+
     Arrays are in uppercase and scalars are in lowercase.
-    
+
     In the  names of  the variables and  functions, only  the singular
     form is allowed.
 
@@ -224,7 +224,7 @@
     variable.
 
 ** Algorithms
-  
+
    Reducing the scaling of an  algorithm usually implies also reducing
    its arithmetic  complexity (number  of flops per  byte). Therefore,
    for  small  sizes   \(\mathcal{O}(N^3)\)  and  \(\mathcal{O}(N^2)\)
@@ -233,11 +233,14 @@
    implemented adapted to different problem sizes.
 
 ** Rules for the API
-   
+
    - =stdint= should be used for integers (=int32_t=, =int64_t=)
    - integers used for counting should always be =int64_t=
-   - floats should be by default =double=, unless explicitly mentioned 
+   - floats should be by default =double=, unless explicitly mentioned
    - pointers are converted to =int64_t= to increase portability
 
 * Documentation
 
+  # The .org files will be appended here in the order specified in the
+  # table_of_contents file
+

src/create_doc.sh

@@ -1,41 +0,0 @@
-#!/bin/bash 
-
-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
-  rm -rf $TMPDIR
-  exit 0
-else
-  mv index.html ${SRC}/../docs/
-  rm -rf $TMPDIR
-  exit 2
-fi
-
-

src/merge_org.sh

@@ -1,17 +0,0 @@
-#!/bin/bash
-
-OUTPUT=$1
-
-for i in README.org \
-             qmckl.org \
-             qmckl_context.org \
-             qmckl_error.org \
-             qmckl_precision.org \
-             qmckl_memory.org \
-             qmckl_distance.org \
-             qmckl_ao.org \
-             qmckl_footer.org \
-             test_qmckl.org
-do
-    cat $i >> $1
-done

src/table_of_contents

@@ -0,0 +1,9 @@
+qmckl.org 
+qmckl_context.org 
+qmckl_error.org 
+qmckl_precision.org 
+qmckl_memory.org 
+qmckl_distance.org 
+qmckl_ao.org 
+test_qmckl.org
+qmckl_footer.org 

tools/create_doc.sh

@@ -0,0 +1,45 @@
+#!/bin/bash 
+
+INPUT=merged.org
+if [[ -z $QMCKL_ROOT ]]
+then
+  print "QMCKL_ROOT is not defined"
+  exit 1
+fi
+
+
+# Install htmlize if needed
+[[ -f ${QMCKL_ROOT}/docs/htmlize.el ]] || (
+    cd ${QMCKL_ROOT}/docs/
+    git clone https://github.com/hniksic/emacs-htmlize 
+    cp emacs-htmlize/htmlize.el .
+    rm -rf emacs-htmlize
+    cd -
+)
+
+[[ -f ${QMCKL_ROOT}/docs/htmlize.el ]] || exit 1
+
+
+# Switch to TMPDIR for easy cleanup
+TMPDIR=$(mktemp -d)
+${QMCKL_ROOT}/tools/merge_org.sh $TMPDIR/$INPUT
+cd $TMPDIR
+
+
+# Create documentation
+emacs --batch \
+      --load ${QMCKL_ROOT}/docs/htmlize.el \
+      --load ${QMCKL_ROOT}/tools/init.el  \
+      $INPUT -f org-html-export-to-html
+
+if [[ $? -eq 0 ]]
+then
+  rm -rf $TMPDIR
+  exit 0
+else
+  mv index.html ${QMCKL_ROOT}/docs/
+  rm -rf $TMPDIR
+  exit 2
+fi
+
+

tools/create_makefile.sh

@@ -1,17 +1,18 @@
 #!/bin/bash
 
-INPUT=$1
-./merge_org.sh $INPUT
+MERGED=merged.org
+${QMCKL_ROOT}/tools/merge_org.sh $MERGED
 
 OUTPUT=Makefile.generated
 
 # Tangle org files
 emacs \
-     $INPUT \
+     $MERGED \
      --batch \
      -f org-babel-tangle \
      --kill
 
+rm $MERGED
 
 
 # Create the list of *.o files to be created

tools/merge_org.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+OUTPUT=$1
+
+for i in README.org $(cat $QMCKL_ROOT/src/table_of_contents)
+do
+    cat $i >> $1
+done