updating sphinx docs to include ipython tutorials

Author: kaeldai

README.md

@@ -7,7 +7,7 @@ We are releasing this code to the public as a tool we expect others to use. Ques
 
 
 ## Quickstart
-bmtk requires Python 2.7 plus [additional python dependicies](https://alleninstitute.github.io/bmtk/index.html#base-installation). To install with
+bmtk requires Python 2.7 or 3.5+, plus [additional python dependicies](https://alleninstitute.github.io/bmtk/index.html#base-installation). To install with
 base requirements from a command-line:
 
 ```bash

docs/autodocs/Makefile

@@ -18,8 +18,11 @@ html:
 	sphinx-apidoc -f -o source/bmtk/ ../../bmtk
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
+tutorials:
+	cp ../tutorial/\d\d_single_cell_clamped.ipynb source
+
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/autodocs/source/conf.py

@@ -18,6 +18,9 @@
 #
 import os
 import sys
+import glob
+import shutil
+
 sys.path.insert(0, os.path.abspath('../../..'))
 
 
@@ -35,7 +38,8 @@
     'sphinx.ext.githubpages',
     'sphinx.ext.viewcode',
     'numpydoc',
-    'sphinx.ext.autosummary'
+    'sphinx.ext.autosummary',
+    'nbsphinx',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -46,7 +50,7 @@
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ['.rst', '.ipynb']
 
 # The master toctree document.
 master_doc = 'index'
@@ -185,4 +189,21 @@
 ]
 
 
+def copy_tutorials():
+    source_dir = os.path.dirname(os.path.abspath(__file__))
+    tutorials_dir = os.path.abspath('../tutorial')
+    tutorials = os.path.join(tutorials_dir, '*.ipynb')
+
+    for ipynb_file in glob.glob(tutorials):
+        tut_fname = os.path.basename(ipynb_file)
+        if ipynb_file.startswith('00'):
+            continue
+        elif tut_fname[:2].isnumeric():
+            tut_fname = tut_fname[3:]
+
+        tut_path = os.path.join(source_dir, 'tutorial_{}'.format(tut_fname))
+        shutil.copy(ipynb_file, tut_path)
+
 
+def setup(app):
+    copy_tutorials()

docs/autodocs/source/index.rst

@@ -16,7 +16,7 @@ Welcome to the Brain Modeling Toolkit
    Building Networks <builder>
    simulators
    analyzer
-   Tutorials <https://github.com/AllenInstitute/bmtk/blob/develop/docs/tutorial/00_introduction.ipynb>
+   tutorials
    Github Profile <https://github.com/AllenInstitute/bmtk.git>
    contributors
    Source Documentation <bmtk/bmtk>