Updated the documentation and restructured a bit because it wasn't

compiling (note: Breathe not working)

doc/Makefile

@@ -57,7 +57,7 @@ html:
 	@echo "Generating Doxygen documentation..."
 	doxygen Doxyfile
 	@echo "Doxygen documentation generated. \n"
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	$(SPHINXBUILD) -b html -c ./ $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

doc/conf.py

@@ -36,7 +36,7 @@ extensions = [
     'sphinx.ext.pngmath',
     'sphinx.ext.ifconfig',
     'sphinx.ext.viewcode',
-    'breathe',
+#    'breathe',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -292,7 +292,7 @@ texinfo_documents = [
 #texinfo_no_detailmenu = False
 
 #Breathe configuration
-sys.path.append( "../breathe/" )
+sys.path.append( "breathe/" )
-breathe_projects = { "OBITools3": "../doxygen/xml/" }
+breathe_projects = { "OBITools3": "doxygen/xml/" }
 breathe_default_project = "OBITools3"
 

doc/source/DMS.rst

@@ -13,7 +13,7 @@ Up to now, each of these categories of data were stored in separate
 files, and nothing made it mandatory to keep them together.
 
 
-The `Data Management System` (DMS) of OBITools3 can be regarded as a basic 
+The `Data Management System` (DMS) of OBITools3 can be viewed like a basic 
 database system.
 
 
@@ -27,9 +27,7 @@ OBIDMS UML
 
 An OBIDMS directory contains :
   * one `OBIDMS history file <#obidms-history-files>`_
-  * Two different kinds of directories :
+  * OBIDMS column directories
-     * OBIDMS column directories
-     * OBIDMS column group directories containing OBIDMS column directories
 
 
 OBIDMS column directories
@@ -39,16 +37,9 @@ OBIDMS column directories contain :
     * all the different versions of one OBIDMS column, under the form of different files (`OBIDMS column files <#obidms-column-files>`_)
     * one `OBIDMS version file <#obidms-version-files>`_
 
-The directory name is the column attribute, or sub-attribute if the column directory is in a column group directory.
+The directory name is the column attribute with the extension ``.obicol``.
 
-
+Example: ``count.obicol``
-OBIDMS column group directories
-===============================
-
-OBIDMS column group directories contain OBIDMS column directories. They are used to store dictionary-like data, where 
-each key corresponds to an OBIDMS column.
-
-The directory name is the dictionary attribute. Each key is considered a sub-attribute and is associated to its column.
 
 
 OBIDMS column files
@@ -57,7 +48,7 @@ OBIDMS column files
 Each OBIDMS column file contains :
 	* a header of a size equal to a multiple of PAGESIZE (PAGESIZE being equal to 4096 bytes
 	  on most systems) containing metadata
-	* one column of data with the same `OBIType <types.html#obitypes>`_
+	* Lines of data with the same `OBIType <types.html#obitypes>`_
 
 
 Header
@@ -79,7 +70,14 @@ The header of an OBIDMS column contains :
 Data
 ----
 
-A column of data with the same `OBIType <types.html#obitypes>`_.
+A line of data corresponds to a vector of elements. Each element is associated with an element name. 
+Elements names are stored in the header. The correspondance between an element and its name is done 
+using their order in the lists of elements and elements names.  This structure allows the storage of 
+dictionary-like data.
+
+Example: In the header, the attribute ``elements_names`` will be associated with the value ``"sample_1;
+sample_2;sample_3"``, and a line of data with the type ``OBInt_t`` will be stored as an ``OBInt_t`` vector 
+of size three e.g. ``5|8|4``.
 
 
 Mandatory columns
@@ -158,3 +156,5 @@ operations ever done in the OBIDMS directory and the views in between them :
 .. image:: ./images/history.png
     :width: 150 px
     :align: center
+
+

doc/source/data.rst

@@ -2,8 +2,8 @@
 Data in OBITools3
 #################
 
-The OBITools3 inaugure a new way to manage DNA metabarcoding data. 
+The OBITools3 introduce a new way to manage DNA metabarcoding data. 
-They rely on a `Data management System` (DMS) that can be considered as
+They rely on a `Data management System` (DMS) that can be viewed like 
 a simplified database system.
 
 

doc/source/guidelines.rst

@@ -70,7 +70,7 @@ Tickets should always be labeled with the branches for which they are relevant.
 Documentation
 *************
 
-C functions are documented in the header files.
+C functions are documented in the header files for public functions, and in the source file for private functions.
 
 
 **************
@@ -92,7 +92,7 @@ C99 :
 	* Object layer
 	* OBITools3 library
 
-`Python 3 <https://www.python.org/>`_ :
+`Python 3.5 <https://www.python.org/>`_ :
 	* Top layer code (scripts)	
 	
 For the documentation, `Sphinx <http://sphinx-doc.org/>`_ should be used for both the original 
@@ -111,6 +111,8 @@ Enum members, macros, constants:                ``ALL_CAPS``
 
 Functions, local variables:                     ``lower_case``
 
+Public functions:                               ``obi_lower_case``
+
 Functions that shouldn't be called directly:    ``_lower_case`` (``_`` prefix)
 
 Global variables:                                ``g_lower_case`` (``g_`` prefix)
@@ -120,9 +122,6 @@ Pointers:                                        ``pointer_ptr`` (``_ptr`` suffi
 .. note::
     Underscores are used to delimit 'words'.
 
-.. todo::
-    ``obi_function`` for public functions names?
-
 
 *****************
 Programming rules

doc/source/index.rst

@@ -11,7 +11,6 @@ OBITools3 documentation
 
    Programming guidelines <guidelines>
    Data structures <data>
-   Pistes de reflexion <pistes>
 
 
 Indices and tables

doc/source/specialvalues.rst

@@ -7,13 +7,16 @@ NA values
 =========
 
 All OBITypes have an associated NA (Not Available) value. 
-NA values are implemented by specifying an explicit NA value for each type, corresponding to the R standards:
+NA values are implemented by specifying an explicit NA value for each type, 
+corresponding to the R standards as much as possible:
 
-* For the types ``OBIInt_t``, ``OBIBool_t``, ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``INT_MIN``.
+* For the type ``OBIInt_t``, the NA value is ``INT_MIN``.
 
-* For the type ``OBIChar_t``: the NA value is ``\0`` (?).
+* For the type ``OBIBool_t``, the NA value is ``2``.
 
-* For the type ``OBIStr_t`` : the NA value is ``\0`` (?).
+* For the type ``OBIIdx_t`` and ``OBITaxid_t``, the NA value is ``SIZE_MAX``.
+
+* For the type ``OBIChar_t``: the NA value is ``\0``.
 
 * For the type ``OBIFloat_t``::
 

doc/sphinx/source/pistes.rst

@@ -1,23 +0,0 @@
-###################
-Pistes de reflexion
-###################
-
-
-******************************
-Ce que l'on veut pouvoir faire
-******************************
-
-    * Gerer les valeurs manquantes
-    * Modifier une colonne en cours d'ecriture (mmap)
-    * Ajouter des valeurs a la fin du fichier d'une colonne en cours d'ecriture (mmap)
-    
-
-******
-Divers
-******
-
-* Si l'ordre d'une colonne est change, elle est reecrite (pas d'index).
-* Utilisation de semaphores pour la lecture
-* Utilisation de tas pour l'indexation des chaines de caracteres. Chaque colonne dont 
-  le type est OBIStr_t est stockee dans 3 fichiers : un fichier contenant les chaines, un 
-  fichier contenant les index, et un fichier contenant le tas.