Merge branch 'master' into babel

zakandrewking · Nov 23, 2015 · d47937c · d47937c
2 parents bb9ce35 + 123cb04
commit d47937c
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diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,6 @@
 *.pyc
 .#*
 TAGS
-dist/
 Escher.egg-info/
 .ipynb_checkpoints/
 build/

diff --git a/docs/sphinx/Makefile → docs/Makefile b/docs/sphinx/Makefile → docs/Makefile
diff --git a/docs/sphinx/_static/EscherConverterGUI.png → docs/_static/EscherConverterGUI.png b/docs/sphinx/_static/EscherConverterGUI.png → docs/_static/EscherConverterGUI.png
diff --git a/docs/sphinx/_static/Preferences.png → docs/_static/Preferences.png b/docs/sphinx/_static/Preferences.png → docs/_static/Preferences.png
diff --git a/docs/sphinx/_static/bar.png → docs/_static/bar.png b/docs/sphinx/_static/bar.png → docs/_static/bar.png
diff --git a/docs/sphinx/_static/data/tutorial.r → docs/_static/data/tutorial.r b/docs/sphinx/_static/data/tutorial.r → docs/_static/data/tutorial.r
diff --git a/docs/sphinx/_static/data_menu.png → docs/_static/data_menu.png b/docs/sphinx/_static/data_menu.png → docs/_static/data_menu.png
diff --git a/docs/sphinx/_static/edit_menu.png → docs/_static/edit_menu.png b/docs/sphinx/_static/edit_menu.png → docs/_static/edit_menu.png
diff --git a/docs/sphinx/_static/escher-logo_256.png → docs/_static/escher-logo_256.png b/docs/sphinx/_static/escher-logo_256.png → docs/_static/escher-logo_256.png
diff --git a/docs/sphinx/_static/escherconverter_io.png → docs/_static/escherconverter_io.png b/docs/sphinx/_static/escherconverter_io.png → docs/_static/escherconverter_io.png
diff --git a/docs/sphinx/_static/iJO1366.png → docs/_static/iJO1366.png b/docs/sphinx/_static/iJO1366.png → docs/_static/iJO1366.png
diff --git a/docs/sphinx/_static/jar_icon.png → docs/_static/jar_icon.png b/docs/sphinx/_static/jar_icon.png → docs/_static/jar_icon.png
diff --git a/docs/sphinx/_static/launch_page.png → docs/_static/launch_page.png b/docs/sphinx/_static/launch_page.png → docs/_static/launch_page.png
diff --git a/docs/sphinx/_static/lgplv3-147x51.png → docs/_static/lgplv3-147x51.png b/docs/sphinx/_static/lgplv3-147x51.png → docs/_static/lgplv3-147x51.png
diff --git a/docs/sphinx/_static/map_menu.png → docs/_static/map_menu.png b/docs/sphinx/_static/map_menu.png → docs/_static/map_menu.png
diff --git a/docs/sphinx/_static/menu.png → docs/_static/menu.png b/docs/sphinx/_static/menu.png → docs/_static/menu.png
diff --git a/docs/sphinx/_static/model_menu.png → docs/_static/model_menu.png b/docs/sphinx/_static/model_menu.png → docs/_static/model_menu.png
diff --git a/.../sphinx/_static/reaction_data_with_nd.png → docs/_static/reaction_data_with_nd.png b/.../sphinx/_static/reaction_data_with_nd.png → docs/_static/reaction_data_with_nd.png
diff --git a/docs/sphinx/_static/reaction_settings.png → docs/_static/reaction_settings.png b/docs/sphinx/_static/reaction_settings.png → docs/_static/reaction_settings.png
diff --git a/docs/sphinx/_static/screen1.png → docs/_static/screen1.png b/docs/sphinx/_static/screen1.png → docs/_static/screen1.png
diff --git a/docs/sphinx/_static/settings.png → docs/_static/settings.png b/docs/sphinx/_static/settings.png → docs/_static/settings.png
diff --git a/docs/sphinx/_static/view_menu.png → docs/_static/view_menu.png b/docs/sphinx/_static/view_menu.png → docs/_static/view_menu.png
diff --git a/docs/build_docs b/docs/build_docs
@@ -0,0 +1,9 @@
+#! /usr/bin/env python
+
+import platform
+from subprocess import call
+
+if platform.system() == 'Windows':
+    call('make.bat html', shell=True)
+else:
+    call(['make', 'html'])
diff --git a/docs/sphinx/conf.py → docs/conf.py b/docs/sphinx/conf.py → docs/conf.py
@@ -14,6 +14,8 @@
 
 import sys
 import os
+from os.path import join, dirname, abspath
+import json
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -50,10 +52,13 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
+with open(join(dirname(__file__), '..', 'package.json'), 'r') as f:
+    package = json.load(f)
+
 # The short X.Y version.
-version = '1.3.0'
+version = package['version']
 # The full version, including alpha/beta/rc tags.
-release = '1.3.0'
+release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -101,7 +106,7 @@
 
 # Only import and set the theme if we're building docs locally. Otherwise,
 # readthedocs.org uses their theme by default, so no need to specify it.
-if not on_rtd: 
+if not on_rtd:
     import sphinx_rtd_theme
     html_theme = 'sphinx_rtd_theme'
     html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

diff --git a/docs/sphinx/contribute_maps.rst → docs/contribute_maps.rst b/docs/sphinx/contribute_maps.rst → docs/contribute_maps.rst
diff --git a/docs/sphinx/convert_maps.rst → docs/convert_maps.rst b/docs/sphinx/convert_maps.rst → docs/convert_maps.rst
diff --git a/docs/sphinx/development.rst → docs/development.rst b/docs/sphinx/development.rst → docs/development.rst
diff --git a/docs/sphinx/escher_and_cobrapy.rst → docs/escher_and_cobrapy.rst b/docs/sphinx/escher_and_cobrapy.rst → docs/escher_and_cobrapy.rst
diff --git a/docs/sphinx/escherconverter.rst → docs/escherconverter.rst b/docs/sphinx/escherconverter.rst → docs/escherconverter.rst
diff --git a/docs/sphinx/getting_started.rst → docs/getting_started.rst b/docs/sphinx/getting_started.rst → docs/getting_started.rst
@@ -173,7 +173,9 @@ The structure of a CSV file
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 CSV files should have 1 header row, 1 ID column, and either 1 or 2 columns for
-data values. Here is an example with a single data value columns::
+data values. The ID column can contain BiGG IDs or descriptive names for the
+reactions, metabolites, or genes in the dataset. Here is an example with a
+single data value columns::
 
     ID,time 0sec
     glc__D_c,5.4
@@ -187,7 +189,7 @@ ID        time 0sec
 glc__D_c  5.4
 g6p_c     2.3
 ========= =========
-   
+
 If two datasets are provided, then the Escher map will display the difference
 between the datasets. In the Settings menu, the **Comparison** setting allows
 you to choose between comparison functions (Fold Change, Log2(Fold Change), and
@@ -199,7 +201,20 @@ ID        time 0sec time 5s
 glc__D_c  5.4       10.2
 g6p_c     2.3        8.1
 ========= ========= =========
-
+
+..
+   For gene data, an example file could contain the BiGG IDs (generally the locus
+   IDs) or the descriptive names (generally gene names). So, for the RECON1 human
+   model, the following gene data files would be equivalent:
+
+       ID,reads
+       glc__D_c,1220
+       g6p__D_c,35
+
+       descriptive name,reads
+       glc__D_c,1220
+       g6p__D_c,35
+
 Data can also be loaded from a JSON file. This Python code snippet provides an
 example of generating the proper format for single reaction data values and for
 reaction data comparisons::

diff --git a/docs/sphinx/index.rst → docs/index.rst b/docs/sphinx/index.rst → docs/index.rst
diff --git a/docs/sphinx/ipython_notebook.rst → docs/ipython_notebook.rst b/docs/sphinx/ipython_notebook.rst → docs/ipython_notebook.rst