Updated to PhyloToAST docs.

Updated conf.py with name change. Modified the names of qiime-tools pipeline to phylotoast pipeline. Updated reST code for main page to display 'PhyloToAST' changes. Updated documentation for biom calc and util scripts. Deleted multiple occurrence of -h option in merge_otu_results reST file.
smdabdoub · Jan 28, 2015 · dafdc72 · dafdc72
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Showing 5 changed files with 24 additions and 27 deletions.
diff --git a/conf.py b/conf.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# QIIME-tools documentation build configuration file, created by
+# PhyloToAST documentation build configuration file, created by
 # sphinx-quickstart on Wed Nov  5 14:24:32 2014.
 #
 # This file is execfile()d with the current directory set to its
@@ -48,17 +48,17 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'QIIME-tools'
-copyright = u'2014, Shareef Dabdoub'
+project = u'PhyloToAST'
+copyright = u'2015, Shareef Dabdoub'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.1'
+version = '1.2'
 # The full version, including alpha/beta/rc tags.
-release = '1.1.3'
+release = '1.2.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -181,7 +181,7 @@
 #html_file_suffix = None
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'QIIME-toolsdoc'
+htmlhelp_basename = 'PhyloToASTdoc'
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -201,7 +201,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'QIIME-tools.tex', u'QIIME-tools Documentation',
+  ('index', 'PhyloToAST.tex', u'PhyloToAST Documentation',
    u'Shareef Dabdoub', 'manual'),
 ]
 
@@ -231,7 +231,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'QIIME-tools', u'QIIME-tools Documentation',
+    ('index', 'PhyloToAST', u'PhyloToAST Documentation',
      [u'Shareef Dabdoub'], 1)
 ]
 
@@ -245,8 +245,8 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'QIIME-tools', u'QIIME-tools Documentation',
-   u'Shareef Dabdoub', 'QIIME-tools', 'One line description of project.',
+  ('index', 'PhyloToAST', u'PhyloToASTs Documentation',
+   u'Shareef Dabdoub', 'PhyloToAST', 'One line description of project.',
    'Miscellaneous'),
 ]
 
@@ -266,13 +266,13 @@
 # -- Options for Epub output ----------------------------------------------
 
 # Bibliographic Dublin Core info.
-epub_title = u'QIIME-tools'
+epub_title = u'PhyloToAST'
 epub_author = u'Shareef Dabdoub'
 epub_publisher = u'Shareef Dabdoub'
-epub_copyright = u'2014, Shareef Dabdoub'
+epub_copyright = u'2015, Shareef Dabdoub'
 
 # The basename for the epub file. It defaults to the project name.
-#epub_basename = u'QIIME-tools'
+#epub_basename = u'PhyloToAST'
 
 # The HTML theme for the epub output. Since the default themes are not optimized
 # for small screen space, using the same theme for HTML and epub output is

diff --git a/figures/qiime-tools-pipeline.png → figures/phylotoast-pipeline.png b/figures/qiime-tools-pipeline.png → figures/phylotoast-pipeline.png
diff --git a/index.txt b/index.txt
@@ -1,15 +1,15 @@
-Welcome to qiime-tools documentation!
+Welcome to PhyloToAST documentation!
 =======================================
 
-The qiime-tools project is a collection of python scripts that modifies the original QIIME [1]_ pipeline:
+The PhyloToAST project is a collection of python scripts that modifies the original QIIME [1]_ pipeline:
 
 .. figure:: figures/qiime-pipeline.png
    :scale: 45 %
    :align: center
 
 by adding or modifying several steps (as seen below) including support for PBS-based cluster-computing, multiple primer support [2]_, enhanced support for species-specific analysis, and additional visualization tools.
 
-.. figure:: figures/qiime-tools-pipeline.png
+.. figure:: figures/phylotoast-pipeline.png
    :scale: 45 %
    :align: center
 
@@ -21,7 +21,7 @@ Contents:
    :maxdepth: 2
 
    scripts/index.txt
-   qiime_tools
+   phylotoast
 
 
 Citations:

diff --git a/qiime_tools.txt → phylotoast.txt b/qiime_tools.txt → phylotoast.txt
@@ -4,7 +4,7 @@ API
 biom_calc module
 ----------------------------
 
-.. automodule:: qiime_tools.biom_calc
+.. automodule:: phylotoast.biom_calc
     :members:
     :undoc-members:
     :show-inheritance:
@@ -14,7 +14,7 @@ biom_calc module
 util module
 -----------------------
 
-.. automodule:: qiime_tools.util
+.. automodule:: phylotoast.util
     :members:
     :undoc-members:
     :show-inheritance:

diff --git a/scripts/merge_otu_results.txt b/scripts/merge_otu_results.txt
@@ -6,12 +6,12 @@ Distributing sequence data across the cluster for OTU picking results in a set
 of result files that need to be merged into a single pick otus result.
 
     .. code-block:: bash
-    
+
         usage: merge_otu_results.py [-h] [-o OUTPUT_FN] [-v] pick_otus_results [pick_otus_results ...]
 
 Required arguments
 ^^^^^^^^^^^^^^^^^^
-    
+
 .. cmdoption:: pick_otus_results
 
     The result files from multiple runs of a pick otus script that need to be merged.
@@ -24,13 +24,10 @@ Optional arguments
     The name of the file the merged results will be written to.
 
 .. cmdoption:: -h, --help
-    
+
     Show the help message and exit.
 
-.. cmdoption:: -h, --help
-
-    Show the help message and exit
-
+
 .. cmdoption::  -v, --verbose
 
-    Print detailed information about script operation.
+    Print detailed information about script operation.