Small changes in documentation structure

karel-brinda · Jul 9, 2015 · 521b581 · 521b581
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diff --git a/docs/conf.py b/docs/conf.py
@@ -56,9 +56,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.1.0'
+version = '0.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.1.0'
+release = '0.2.0b0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/getting_started.rst b/docs/getting_started.rst
@@ -18,6 +18,7 @@ Technically, the entire RNFtools package is based on `SnakeMake`_, a `Make`_-lik
 	* All required software and data files are installed **fully automatically** (using the `SMBL`_ library).
 	* Created pipelines are fully reproducible and they can be distributed as **single SnakeMake files**.
 
+There exists also a console variant of RNFtools with a basic functionality (see :ref:`command_line`).
 
 How to start with RNFtools
 --------------------------

diff --git a/docs/index.rst b/docs/index.rst
@@ -39,9 +39,6 @@ Table of contents
 :ref:`reference`
 	Automatically generated documentation for RNFtools.
 
-:ref:`command_line`
-	Command-line tool for RNFtools.
-
 :ref:`other_information`
  	FAQs and other information about RNFtools and read simulators in general.
 
@@ -54,5 +51,4 @@ Table of contents
 	getting_started
 	tutorial
 	reference
-	command_line
 	other_information
diff --git a/docs/command_line.rst → docs/reference/04_command_line.rst b/docs/command_line.rst → docs/reference/04_command_line.rst
@@ -3,7 +3,7 @@
 Command-line tool
 =================
 
-Even though SnakeMake-based approach is the prefered way how to use RNFtools, we provide also a command-line tool
+Even though SnakeMake-based approach is the prefered way to use RNFtools, we provide also a command-line tool
 ``rnftools`` with most of functionality. Here you can find help messages for its subcommands.
 
 .. contents::

diff --git a/docs/command_line/art2rnf.txt → docs/reference/command_line/art2rnf.txt b/docs/command_line/art2rnf.txt → docs/reference/command_line/art2rnf.txt
diff --git a/docs/command_line/check.txt → docs/reference/command_line/check.txt b/docs/command_line/check.txt → docs/reference/command_line/check.txt
diff --git a/docs/command_line/curesim2rnf.txt → docs/reference/command_line/curesim2rnf.txt b/docs/command_line/curesim2rnf.txt → docs/reference/command_line/curesim2rnf.txt
diff --git a/docs/command_line/dwgsim2rnf.txt → docs/reference/command_line/dwgsim2rnf.txt b/docs/command_line/dwgsim2rnf.txt → docs/reference/command_line/dwgsim2rnf.txt
diff --git a/docs/command_line/es2et.txt → docs/reference/command_line/es2et.txt b/docs/command_line/es2et.txt → docs/reference/command_line/es2et.txt
diff --git a/docs/command_line/et2roc.txt → docs/reference/command_line/et2roc.txt b/docs/command_line/et2roc.txt → docs/reference/command_line/et2roc.txt
diff --git a/docs/command_line/main.txt → docs/reference/command_line/main.txt b/docs/command_line/main.txt → docs/reference/command_line/main.txt
diff --git a/docs/command_line/mason2rnf.txt → docs/reference/command_line/mason2rnf.txt b/docs/command_line/mason2rnf.txt → docs/reference/command_line/mason2rnf.txt
diff --git a/docs/command_line/merge.txt → docs/reference/command_line/merge.txt b/docs/command_line/merge.txt → docs/reference/command_line/merge.txt
diff --git a/docs/command_line/publication.txt → docs/reference/command_line/publication.txt b/docs/command_line/publication.txt → docs/reference/command_line/publication.txt
diff --git a/docs/command_line/sam2es.txt → docs/reference/command_line/sam2es.txt b/docs/command_line/sam2es.txt → docs/reference/command_line/sam2es.txt
diff --git a/docs/command_line/sam2rnf.txt → docs/reference/command_line/sam2rnf.txt b/docs/command_line/sam2rnf.txt → docs/reference/command_line/sam2rnf.txt
diff --git a/docs/command_line/sam2roc.txt → docs/reference/command_line/sam2roc.txt b/docs/command_line/sam2roc.txt → docs/reference/command_line/sam2roc.txt
diff --git a/docs/command_line/save_help.sh → docs/reference/command_line/save_help.sh b/docs/command_line/save_help.sh → docs/reference/command_line/save_help.sh
diff --git a/docs/command_line/wgsim2rnf.txt → docs/reference/command_line/wgsim2rnf.txt b/docs/command_line/wgsim2rnf.txt → docs/reference/command_line/wgsim2rnf.txt
diff --git a/docs/tutorial/05_extending_rnf.rst b/docs/tutorial/05_extending_rnf.rst
@@ -12,16 +12,16 @@ A new simulator
 To add support for another read simulator, you have to make the following four changes in source codes of RNFtools and SMBL. 
 
 
-A. Plugin for installation in SMBL
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Step 1: SMBL plugin for installation of your simulator
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 First you should write a plugin for SMBL (https://github.com/karel-brinda/smbl) for automatic installation
 of the simulator (plugins are located in this directory: https://github.com/karel-brinda/smbl/blob/master/smbl/prog/plugins/). You should get inspired from existing plugins such as https://github.com/karel-brinda/smbl/blob/master/smbl/prog/plugins/wgsim.py.
 When the plugin is written, it should be added to https://github.com/karel-brinda/smbl/blob/master/smbl/prog/plugins/__init__.py.
 
 
-B. Wrapper of the simulator in RNFtools
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Step 2: Wrapper of the simulator in RNFtools
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 All wrappers of read simulators are located in this directory: https://github.com/karel-brinda/rnftools/blob/master/rnftools/mishmash/. To create a
 new wrapper, copy some existing one and modify the code inside.
@@ -39,14 +39,14 @@ When all these functions are created/adjusted, the class should be imported in `
 At this point, it should be tested if the simulator works well in 
 
 
-C. Support in the ``rnftools`` program
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Step 3: Support in the ``rnftools`` program
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 The last step is pluging your converting static function into ``rnftools`` console program, which is contained in this file: https://github.com/karel-brinda/rnftools/blob/master/rnftools/scripts.py. You will  have to add a new subcommand (which will call the static function) and create a parser for it. Again, follow existing code.
 
 
-D. Tests
-~~~~~~~~
+Step 4: Tests
+~~~~~~~~~~~~~
 
 Add corresponding tests (see the test directory).