updated dev docs and js/py apis

zakandrewking · Jul 10, 2019 · 528eafd · 528eafd
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diff --git a/README.md b/README.md
@@ -174,7 +174,7 @@ 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

diff --git a/docs/convert_maps.rst b/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

diff --git a/docs/development.rst b/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
-<zaking@ucsd.edu>.
+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 <zaking@ucsd.edu>.
 
 .. _`Gitter chat room`: https://gitter.im/zakandrewking/escher
 .. _`Development roadmap`: https://github.com/zakandrewking/escher/wiki/Development-Roadmap

diff --git a/docs/javascript_api.rst b/docs/javascript_api.rst
@@ -177,11 +177,7 @@ JavaScript API
 
        .. js:attribute:: options.reaction_scale
 
-          Default::
-
-            [ { type: 'min', color: '#c8c8c8', size: 12 },
-              { type: 'median', color: '#9696ff', size: 20 },
-              { type: 'max', color: '#ff0000', size: 25 } ]
+          Default: ``null`` (``options.reaction_scale_preset`` used instead)
 
           An array of objects that define stops on the data scale.
 
@@ -211,6 +207,13 @@ JavaScript API
           ``{ type: 'value', value: 8.5, color: '#333', size: 50 }`` Specifies
           that reactions near 8.5 value have the given color and size.
 
+       .. js:attribute:: options.reaction_scale_preset
+
+          (Default:: ``'GaBuGeRd'``) A preset metabolite scale that will set
+          ``options.reaction_scale`` for you. The available scales are here:
+
+          https://github.com/zakandrewking/escher/blob/master/src/scalePresets.js
+
        .. js:attribute:: options.reaction_no_data_color
 
           (Default: ``'#dcdcdc'``) The color of reactions with no data value.
@@ -254,16 +257,19 @@ JavaScript API
 
        .. js:attribute:: options.metabolite_scale
 
-          Default::
-
-            [ { type: 'min', color: '#fffaf0', size: 20 },
-              { type: 'median', color: '#f1c470', size: 30 },
-              { type: 'max', color: '#800000', size: 40 } ]
+          Default: ``null`` (``options.metabolite_scale_preset`` used instead)
 
           An array of objects that define stops on the data scale. See the
           description of **options.reaction_scale** for an explanation of the
           format.
 
+       .. js:attribute:: options.metabolite_scale_preset
+
+          (Default: ``'WhYlRd'``) A preset metabolite scale that will set
+          ``options.metabolite_scale`` for you. The available scales are here:
+
+          https://github.com/zakandrewking/escher/blob/master/src/scalePresets.js
+
        .. js:attribute:: options.metabolite_no_data_color
 
           (Default: ``'#ffffff'``) The color of metabolites with no data value.
@@ -303,7 +309,7 @@ JavaScript API
           show when hoving over reactions, metabolites, and genes. See
           ``escher.Tooltip.DefaultTooltip`` in the source code for an example of
           a Preact component that defines the default tooltips. And see the
-          :doc:`Tooltip Tutorial <development-tutorial>` for more tips on
+          :doc:`Tooltip Tutorial <developer-tutorial>` for more tips on
           getting started with custom tooltips.
 
           For correct placement of the tooltip, the tooltip component should

diff --git a/py/escher/plots.py b/py/escher/plots.py
@@ -604,12 +604,7 @@ def save_html(self, filepath):
 
             The name of the HTML file.
 
-        TODO apply options from self
-
         """
-
-        #     options = transform(self.options)
-        # get options
         options = {}
         for key in self.traits(option=True):
             val = getattr(self, key)