Release 0.22.0 [master]

CHANGES.rst

@@ -1,3 +1,32 @@
+0.22.0 (2019-08-26)
+===================
+
+New Features
+------------
+
+Project & API Documentation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Added slides from July 2019 TIPS presentation to ``presentations/`` directory
+
+
+``jwql`` Repository
+~~~~~~~~~~~~~~~~~~~
+
+- Updated dark monitor to support all five JWST instruments, instead of only NIRCam
+- Changed the ``jwql-3.5`` and ``jwql-3.6`` conda environments to be more simple and to work on Linux distributions
+- Added library code for creating instrument monitoring ``bokeh`` plots with new ``bokeh`` templating software
+
+
+Bug Fixes
+---------
+
+Project & API Documentation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Fixed various bugs that were causing the ``sphinx`` API documentation to crash on ReadTheDocs
+
+
 0.21.0 (2019-07-23)
 ===================
 

MANIFEST.in

@@ -7,5 +7,6 @@ include setup.py
 recursive-include notebooks *
 recursive-include style_guide *
 recursive-include typing_demo *
+recursive-include jwql/database/monitor_table_definitions *.txt
 
 exclude *.pyc

codecov.yml

@@ -1,6 +1,6 @@
 codecov:
   notify:
-    require_ci_to_pass: yes
+    require_ci_to_pass: no
 
 coverage:
   precision: 2
@@ -27,6 +27,7 @@ comment:
 
 ignore:
   - "jwql/database/"
+  - "jwql/tests/"
   - "jwql/instrument_monitors/miri_monitors/data_trending/plots/"
   - "jwql/instrument_monitors/nirspec_monitors/data_trending/plots/"
   - "*__init__.py*"

docs/source/tests.rst

@@ -14,14 +14,26 @@ test_calculations.py
     :members:
     :undoc-members:
 
+test_context_processors.py
+--------------------------
+.. automodule:: jwql.tests.test_context_processors
+    :members:
+    :undoc-members:
+
 test_dark_monitor.py
 --------------------
 .. automodule:: jwql.tests.test_dark_monitor
     :members:
     :undoc-members:
 
-test_edb_interface.py
----------------------
+test_data_containers.py
+-----------------------
+.. automodule:: jwql.tests.test_data_containers
+    :members:
+    :undoc-members:
+
+test_edb.py
+-----------
 .. automodule:: jwql.tests.test_edb
     :members:
     :undoc-members:
@@ -33,7 +45,7 @@ test_instrument_properties.py
     :undoc-members:
 
 test_loading_times.py
---------------------
+---------------------
 .. automodule:: jwql.tests.test_loading_times
     :members:
     :undoc-members:

environment_python_3_5.yml

@@ -1,37 +1,37 @@
 channels:
-- http://ssb.stsci.edu/astroconda-dev
 - defaults
+- http://ssb.stsci.edu/astroconda-dev
 dependencies:
-- asdf=2.3.0
-- astropy>=3.1.2
 - astroquery=0.3.9
-- bokeh=0.13.0
-- crds>=7.2.7
-- django=2.1.1
+- bokeh=1.3.2
+- django=2.2.1
+- flake8=3.7.7
 - inflection=0.3.1
-- ipython=6.5.0
+- ipython=7.7.0
 - jinja2=2.10
-- jsonschema>=2.6.0
+- jsonschema=2.6.0
 - jwst=0.13.0
-- matplotlib=3.0.0
-- numpy=1.15.2
-- numpydoc=0.8.0
-- pandas=0.23.4
+- matplotlib=3.1.0
+- numpy=1.16.4
+- numpydoc=0.9.0
+- pandas=0.24.2
+- pip=19.1.1
 - postgresql=9.6.6
 - psycopg2=2.7.5
-- python=3.5.6
-- python-dateutil=2.7.3
-- pytest=3.8.1
-- pytest-cov=2.6.0
-- pytest-html=1.19.0
-- sphinx=2.0.1
-- sphinx_rtd_theme=0.1.9
-- sqlalchemy=1.2.11
+- python=3.6.4
+- pytest=5.0.1
+- pytest-cov=2.7.1
+- scipy=1.3.0
+- setuptools=41.0.1
+- sphinx=2.1.0
+- sqlalchemy=1.3.5
 - stsci_rtd_theme=0.0.2
-- twine=1.11.0
+- twine=1.13.0
 - pip:
-  - authlib==0.10
+  - asdf==2.3.3
+  - astropy==3.2.1
+  - authlib==0.11
   - codecov==2.0.15
   - jwedb>=0.0.3
-  - pysiaf==0.2.5
-  - sphinx-automodapi==0.10
+  - pysiaf==0.3.1
+  - pysqlite3==0.2.2

environment_python_3_6.yml

@@ -1,38 +1,37 @@
 channels:
-- http://ssb.stsci.edu/astroconda-dev
 - defaults
+- http://ssb.stsci.edu/astroconda-dev
 dependencies:
-- asdf=2.3.1
-- astropy>=3.1.2
 - astroquery=0.3.9
-- bokeh=1.2.0
-- crds>=7.2.7
+- bokeh=1.3.4
 - django=2.2.1
+- flake8=3.7.7
 - inflection=0.3.1
-- ipython=7.6.1
+- ipython=7.7.0
 - jinja2=2.10
-- jsonschema>=3.0.1
-- jwst=0.13.1
+- jsonschema=2.6.0
+- jwst=0.13.0
 - matplotlib=3.1.0
 - numpy=1.16.4
 - numpydoc=0.9.0
 - pandas=0.24.2
+- pip=19.1.1
 - postgresql=9.6.6
 - psycopg2=2.7.5
 - python=3.6.4
-- python-dateutil=2.7.5
 - pytest=5.0.1
-- pytest-cov=2.6.1
-- pytest-html=1.19.0
-- sphinx=2.1.0
-- sphinx_rtd_theme=0.1.9
-- sqlalchemy=1.3.5
-- sqlparse=0.3.0
+- pytest-cov=2.7.1
+- scipy=1.3.0
+- setuptools=41.0.1
+- sphinx=2.1.2
+- sqlalchemy=1.3.7
 - stsci_rtd_theme=0.0.2
 - twine=1.13.0
 - pip:
-  - authlib==0.10
+  - asdf==2.3.3
+  - astropy==3.2.1
+  - authlib==0.11
   - codecov==2.0.15
   - jwedb>=0.0.3
-  - pysiaf==0.3.1
-  - sphinx-automodapi==0.10
+  - pysiaf==0.4.0
+  - pysqlite3==0.2.2

jwql/bokeh_templating/__init__.py

@@ -0,0 +1 @@
+from .template import BokehTemplate

jwql/bokeh_templating/bokeh_surface.py

@@ -0,0 +1,172 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon May 21 13:45:34 2018
+
+@author: gkanarek
+"""
+
+from bokeh.core.properties import Instance, String, Any, Dict
+from bokeh.models import ColumnDataSource, LayoutDOM
+
+DEFAULTS = {
+    'width': '600px',
+    'height': '600px',
+    'style': 'surface',
+    'showPerspective': True,
+    'showGrid': True,
+    'keepAspectRatio': True,
+    'verticalRatio': 1.0,
+    'legendLabel': 'stuff',
+    'cameraPosition': {
+        'horizontal': -0.35,
+        'vertical': 0.22,
+        'distance': 1.8,
+    }
+}
+
+JS_CODE = """
+# This file contains the JavaScript (CoffeeScript) implementation
+# for a Bokeh custom extension. The "surface3d.py" contains the
+# python counterpart.
+#
+# This custom model wraps one part of the third-party vis.js library:
+#
+#     http://visjs.org/index.html
+#
+# Making it easy to hook up python data analytics tools (NumPy, SciPy,
+# Pandas, etc.) to web presentations using the Bokeh server.
+
+# These "require" lines are similar to python "import" statements
+import * as p from "core/properties"
+import {LayoutDOM, LayoutDOMView} from "models/layouts/layout_dom"
+
+# This defines some default options for the Graph3d feature of vis.js
+# See: http://visjs.org/graph3d_examples.html for more details.
+OPTIONS =
+  width:  '600px'
+  height: '600px'
+  style: 'surface'
+  showPerspective: true
+  showGrid: true
+  keepAspectRatio: true
+  verticalRatio: 1.0
+  legendLabel: 'stuff'
+  cameraPosition:
+    horizontal: -0.35
+    vertical: 0.22
+    distance: 1.8
+
+# To create custom model extensions that will render on to the HTML canvas
+# or into the DOM, we must create a View subclass for the model. Currently
+# Bokeh models and views are based on BackBone. More information about
+# using Backbone can be found here:
+#
+#     http://backbonejs.org/
+#
+# In this case we will subclass from the existing BokehJS ``LayoutDOMView``,
+# corresponding to our
+export class Surface3dView extends LayoutDOMView
+
+  initialize: (options) ->
+    super(options)
+
+    url = "https://cdnjs.cloudflare.com/ajax/libs/vis/4.16.1/vis.min.js"
+
+    script = document.createElement('script')
+    script.src = url
+    script.async = false
+    script.onreadystatechange = script.onload = () => @_init()
+    document.querySelector("head").appendChild(script)
+
+  _init: () ->
+    # Create a new Graph3s using the vis.js API. This assumes the vis.js has
+    # already been loaded (e.g. in a custom app template). In the future Bokeh
+    # models will be able to specify and load external scripts automatically.
+    #
+    # Backbone Views create <div> elements by default, accessible as @el. Many
+    # Bokeh views ignore this default <div>, and instead do things like draw
+    # to the HTML canvas. In this case though, we use the <div> to attach a
+    # Graph3d to the DOM.
+    @_graph = new vis.Graph3d(@el, @get_data(), @model.options)
+
+    # Set Backbone listener so that when the Bokeh data source has a change
+    # event, we can process the new data
+    @listenTo(@model.data_source, 'change', () =>
+        @_graph.setData(@get_data())
+    )
+
+  # This is the callback executed when the Bokeh data has an change. Its basic
+  # function is to adapt the Bokeh data source to the vis.js DataSet format.
+  get_data: () ->
+    data = new vis.DataSet()
+    source = @model.data_source
+    for i in [0...source.get_length()]
+      data.add({
+        x:     source.get_column(@model.x)[i]
+        y:     source.get_column(@model.y)[i]
+        z:     source.get_column(@model.z)[i]
+      })
+    return data
+
+# We must also create a corresponding JavaScript Backbone model sublcass to
+# correspond to the python Bokeh model subclass. In this case, since we want
+# an element that can position itself in the DOM according to a Bokeh layout,
+# we subclass from ``LayoutDOM``
+export class Surface3d extends LayoutDOM
+
+  # This is usually boilerplate. In some cases there may not be a view.
+  default_view: Surface3dView
+
+  # The ``type`` class attribute should generally match exactly the name
+  # of the corresponding Python class.
+  type: "Surface3d"
+
+  # The @define block adds corresponding "properties" to the JS model. These
+  # should basically line up 1-1 with the Python model class. Most property
+  # types have counterparts, e.g. ``bokeh.core.properties.String`` will be
+  # ``p.String`` in the JS implementatin. Where the JS type system is not yet
+  # as rich, you can use ``p.Any`` as a "wildcard" property type.
+  @define {
+    x:           [ p.String           ]
+    y:           [ p.String           ]
+    z:           [ p.String           ]
+    data_source: [ p.Instance         ]
+    options:     [ p.Any,     OPTIONS ]
+  }
+"""
+
+
+# This custom extension model will have a DOM view that should layout-able in
+# Bokeh layouts, so use ``LayoutDOM`` as the base class. If you wanted to create
+# a custom tool, you could inherit from ``Tool``, or from ``Glyph`` if you
+# wanted to create a custom glyph, etc.
+class Surface3d(LayoutDOM):
+
+    # The special class attribute ``__implementation__`` should contain a string
+    # of JavaScript (or CoffeeScript) code that implements the JavaScript side
+    # of the custom extension model.
+    __implementation__ = JS_CODE
+
+    # Below are all the "properties" for this model. Bokeh properties are
+    # class attributes that define the fields (and their types) that can be
+    # communicated automatically between Python and the browser. Properties
+    # also support type validation. More information about properties in
+    # can be found here:
+    #
+    #    http://bokeh.pydata.org/en/latest/docs/reference/core.html#bokeh-core-properties
+
+    # This is a Bokeh ColumnDataSource that can be updated in the Bokeh
+    # server by Python code
+    data_source = Instance(ColumnDataSource)
+
+    # The vis.js library that we are wrapping expects data for x, y, z, and
+    # color. The data will actually be stored in the ColumnDataSource, but
+    # these properties let us specify the *name* of the column that should
+    # be used for each field.
+    x = String
+    y = String
+    z = String
+    color = String
+
+    options = Dict(String, Any, default=DEFAULTS)