Merge pull request #314 from zakandrewking/finalize-1.7-docs

updated dev docs and js/py apis

.gitignore

@@ -30,4 +30,6 @@ node_modules/
 
 # docs
 docs/iJO1366.json
-docs/e_coli_core.json
+docs/e_coli_core.json
+docs/iAB_RBC_283.json
+docs/example_map.html

README.md

@@ -89,28 +89,27 @@ pip install escher
 
 ## Jupyter extensions
 
-To install the Jupyter lab extension, simply install Escher with pip then
-install the extension:
-
-```bash
-pip install escher
-jupyter labextension install @jupyter-widgets/jupyterlab-manager
-jupyter labextension install escher
-```
-
-To install the Jupyter notebook extension, run the following:
+When you `pip install escher`, the Jupyter notebook extension should be
+installed automatically. If that doesn't work, try:
 
 ```bash
-pip install escher
-# you'll need version >=5 of the `notebook` package
+# The notebook extenstion should install automatically. You can check by running:
+jupyter nbextension list
+# Make sure you have version >=5 of the `notebook` package
 pip install "notebook>=5"
+# To manually install the extension
 jupyter nbextension install --py escher
 jupyter nbextension enable --py escher
+# depending on you environment, you might need the `--sysprefix` flag with those commands
 ```
 
-Note: depending on you environment, you might want to add the `--sysprefix` flag
-to the nbextension commands. You might also need to use `sudo` to get around
-permissions issues.
+To install the Jupyter lab extension, simply install Escher with `pip install escher` then
+install the extension:
+
+```bash
+jupyter labextension install @jupyter-widgets/jupyterlab-manager
+jupyter labextension install escher
+```
 
 ## Python/Jupyter Development
 
@@ -174,7 +173,7 @@ Build and run the docs::
 
 ```
 cd docs
-make html
+./build_docs
 cd _build/html
 python -m SimpleHTTPServer # python 2
 python -m http.server # python 3

docs/convert_maps.rst

@@ -1,8 +1,5 @@
-Validate and convert maps
--------------------------
-
-Validate an Escher map
-======================
+Validate Escher maps
+--------------------
 
 Escher maps follow a specification using the `JSON Schema`_ format. Therefore,
 any JSON Schema validator can be used to validate an Escher map by comparing it

docs/development.rst

@@ -43,6 +43,9 @@ For an example of the boilerplate code that is required to begin developing with
 Escher, have a look at the `escher-demo repository`_. For projects built with
 npm, use the `escher-test repository`_ as a guide.
 
+You can also follow the :doc:`Developer Tutorial <developer-tutorial>` for an
+example of extending Escher to create custom tooltips.
+
 Import Escher
 =============
 
@@ -110,12 +113,28 @@ COBRA models are also saved as JSON files. This format has not been documented
 with a schema, but you can browse through the `core metabolism model`_ as a
 guide to generating valid COBRA models.
 
+Contributing to the Escher Source Code
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+We welcome open source contributions to the Escher source code. You can find
+installation instructions for developing Escher in the README:
+
+https://github.com/zakandrewking/escher/blob/master/README.md
+
+And instructions (work in progress :):
+
+https://github.com/zakandrewking/escher/blob/master/CONTRIBUTING.md
+
+And our code of conduct:
+
+https://github.com/zakandrewking/escher/blob/master/CODE_OF_CONDUCT.md
+
 I still need help!
 ^^^^^^^^^^^^^^^^^^
 
-If you are interested in developing with Escher and you need more information
-than what is provided in the documentation, please contact Zachary King
-<[email protected]>.
+If you are interested in developing with or contributing to Escher and you need
+more information than what is provided in the documentation, please contact
+Zachary King <[email protected]>.
 
 .. _`Gitter chat room`: https://gitter.im/zakandrewking/escher
 .. _`Development roadmap`: https://github.com/zakandrewking/escher/wiki/Development-Roadmap