Merge branch 'master' of

git@git.metabarcoding.org:obitools/obitools3.git

Conflicts:
	doc/source/formats.rst
	src/obicolumn.h

doc/Makefile

@@ -6,6 +6,7 @@ SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = build
+DOXYGENDIR    = doxygen
 
 # User-friendly check for sphinx-build
 ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
@@ -50,8 +51,12 @@ help:
 
 clean:
 	rm -rf $(BUILDDIR)/*
+	rm -rf $(DOXYGENDIR)/*
 
 html:
+	@echo "Generating Doxygen documentation..."
+	doxygen Doxyfile
+	@echo "Doxygen documentation generated. \n"
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
@@ -114,6 +119,9 @@ epub:
 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
 
 latex:
+	@echo "Generating Doxygen documentation..."
+	doxygen Doxyfile
+	@echo "Doxygen documentation generated. \n"
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo
 	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@@ -121,6 +129,9 @@ latex:
 	      "(use \`make latexpdf' here to do that automatically)."
 
 latexpdf:
+	@echo "Generating Doxygen documentation..."
+	doxygen Doxyfile
+	@echo "Doxygen documentation generated. \n"
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo "Running LaTeX files through pdflatex..."
 	$(MAKE) -C $(BUILDDIR)/latex all-pdf

doc/source/DMS.rst

@@ -98,7 +98,7 @@ or more (if there are several versions), and that there is one file per version.
 Versioning
 ----------
 
-The first version of a column file is numbered 1, and each new version increments that
+The first version of a column file is numbered 0, and each new version increments that
 number by 1.
 
 The number of the latest version of an OBIDMS column is stored in an `OBIDMS release file <formats.html#obidms-release-files>`_.
@@ -133,13 +133,17 @@ OBIDMS history file
 An OBIDMS history file consists of an ordered list of views and commands, those commands leading
 from one view to the next one.
 
-This history can be represented in the form of a --- showing all the
+This history can be represented in the form of a ?? showing all the
 operations ever done in the OBIDMS directory and the views in between them :
 
 .. image:: ./images/history.png
     :width: 150 px
     :align: center
 
+OBIType header file
+========================
+
+.. doxygenfile:: obitypes.h
 
 
 OBIIntColumn header file

doc/source/pistes.rst

@@ -9,7 +9,8 @@ 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 d'une colonne en cours d'ecriture (mmap)
+    * Ajouter des valeurs a la fin du fichier d'une colonne en cours d'ecriture (mmap)
+    * 
 
 
 ******
@@ -17,4 +18,4 @@ Divers
 ******
 
 * Si l'ordre d'une colonne est change, elle est reecrite (pas d'index).
-* Truc pour verrouiller l'acces en lecture a un programme a la fois...
+* Utilisation de semaphores pour la lecture