Documentation in dist

Makefile.am

@@ -87,6 +87,23 @@ tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
 tests_test_f_LDADD   = src/libtrexio.la
 tests_test_f_LDFLAGS = -no-install
 
+HTML_FILES =  docs/trexio.css            \
+              docs/index.html            \
+              docs/Sparse.html           \
+              docs/templator_hdf5.html   \
+              docs/trex.html             \
+              docs/README.html           \
+              docs/templator_front.html  \
+              docs/templator_text.html
+
+htmldir = $(docdir)
+dist_html_DATA = $(HTML_FILES)
+
+docs/index.html: $(SOURCES) src/README.org
+	cd tools && ./build_doc.sh
+
+$(HTML_FILES): docs/index.html
+
 $(test_trexio_f): $(trexio_f)
 	cp $(trexio_f) $(test_trexio_f)
 
@@ -99,6 +116,7 @@ CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h)
 
 BUILT_SOURCES = $(SOURCES) $(trexio_f) $(test_trexio_f)
 
+
 $(SOURCES): $(trexio_f)
 src/trexio.c: $(trexio_h)
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.69])
-AC_INIT([trexio], [0.2.0], [https://github.com/TREX-CoE/trexio/issues])
+AC_INIT([trexio], [0.3.0], [https://github.com/TREX-CoE/trexio/issues])
 AM_INIT_AUTOMAKE([subdir-objects color-tests parallel-tests silent-rules 1.11])
 AM_MAINTAINER_MODE()
 LT_INIT

src/README.org

@@ -4,6 +4,7 @@
 
 ------------------
 
+   - [[./trex.html][Data stored with TREXIO]]
    - [[./templator_front.html][Front end API]]
    - [[./templator_hdf5.html][HDF5 back end]]
    - [[./templator_text.html][TEXT back end]]

tools/build_doc.sh

@@ -99,10 +99,11 @@ function main() {
     # Create documentation
     cd ${SRC} 
 
-    for dir in ${SRC}/templates_*/
+    for dir in ${SRC}/templates_*/ ${TREXIO_ROOT}/
     do
 	dir=${dir%*/}
 	echo ${dir}
+        OLDPWD=$PWD
 	cd ${dir}
     	for i in *.org
     	do
@@ -110,7 +111,7 @@ function main() {
         	echo "=======  ${i} ======="
         	extract_doc ${i} ${dir}
     	done
-	cd ..
+	cd $OLDPWD
     done
 
     echo

trex.org

@@ -221,12 +221,12 @@ arrays are 0-base. Hence, we introduce the ~index~ type which is an
                        "type" : [ "str"  , []                   ]
         ,               "num" : [ "int"  , []                   ]
         ,          "prim_num" : [ "int"  , []                   ]
-        ,     "nucleus_index" : [ "index"  , [ "nucleus.num" ]    ]
+        ,     "nucleus_index" : [ "index", [ "nucleus.num" ]    ]
         , "nucleus_shell_num" : [ "int"  , [ "nucleus.num" ]    ]
         ,     "shell_ang_mom" : [ "int"  , [ "basis.num" ]      ]
         ,    "shell_prim_num" : [ "int"  , [ "basis.num" ]      ]
         ,      "shell_factor" : [ "float", [ "basis.num" ]      ]
-        ,  "shell_prim_index" : [ "index"  , [ "basis.num" ]      ]
+        ,  "shell_prim_index" : [ "index", [ "basis.num" ]      ]
         ,          "exponent" : [ "float", [ "basis.prim_num" ] ]
         ,       "coefficient" : [ "float", [ "basis.prim_num" ] ]
         ,       "prim_factor" : [ "float", [ "basis.prim_num" ] ]
@@ -460,7 +460,7 @@ prim_factor =
 ** One-electron integrals
 
    The operators as the same as those defined in the
-   [[ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
+   [[#ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
    the basis of molecular orbitals.
 
    #+NAME: mo_1e_int
@@ -490,7 +490,7 @@ prim_factor =
 ** Two-electron integrals
 
    The operators as the same as those defined in the
-   [[ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
+   [[#ao_one_e][AO one-electron integrals section]]. Here, the integrals are given in
    the basis of molecular orbitals.
 
    #+NAME: mo_2e_int
@@ -532,7 +532,7 @@ prim_factor =
   #+end_src
   :end:
 
-* Appendix                                                         :noexport:
+* Appendix
 ** Python script from table to json
 
  #+NAME: json