Merge pull request #647 from bourque/v0.24.0

v0.24.0 Release [master]

CHANGES.rst

@@ -1,3 +1,55 @@
+0.24.0 (2020-10-20)
+===================
+
+New Features
+------------
+
+Project & API Documentation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Added API documentation for Bias, Bad Pixel, and Readnoise Monitors
+
+Web Application
+~~~~~~~~~~~~~~~
+
+- Added webpage that describes how to use the JWQL web app API
+- Added webpage that enables a user to query the ``jwqldb`` database contents
+- Enabled more search options and aesthetic improvements for anomaly query webpage
+
+``jwql`` Repository
+~~~~~~~~~~~~~~~~~~~
+
+- Added support for Python versions 3.7 and 3.8
+- Added unit tests for Readnoise Monitor
+- Added unit tests for Bias Monitor
+- Added unit tests for Bad Pixel Monitor
+- Added unit tests for ``bokeh`` templating library
+- Added webpage for displaying Readnoise Monitor results with ``bokeh`` plots
+- Added webpage for displaying Bad Pixel Monitor results with ``bokeh`` plots
+
+
+Bug Fixes
+---------
+
+Project & API Documentation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Updated broken links to JWST instrument JDox pages
+
+Web Application
+~~~~~~~~~~~~~~~
+
+- Fixed various issues that was cuasing authentication through ``auth.mast`` to fail
+
+``jwql`` Repository
+~~~~~~~~~~~~~~~~~~~
+
+- Fixed bug that was causing Dark Monitor to crash on recently added apertures from ``pysiaf``
+- Fixed several bugs in ``bokeh`` templating library
+- Fixed bug that was causing unit tests for ``permissions.py`` to fail
+- Fixed bug that was causing ``most_recent_search`` function in Dark Monitor to fail
+
+
 0.23.0 (2020-07-01)
 ===================
 

Jenkinsfile

@@ -27,7 +27,7 @@ if (utils.scm_checkout()) return
 
 // Establish OS and Python version variables for the matrix
 matrix_os = ["linux-stable"] // (Note that Jenkins can only be run with Linux, not MacOSX/Windows)
-matrix_python = ["3.6"]
+matrix_python = ["3.6", "3.7", "3.8"]
 
 // Set up the matrix of builds
 matrix = []

README.md

@@ -21,7 +21,7 @@ The JWST Quicklook Application (`JWQL`) is a database-driven web application and
 
 Official API documentation can be found on [ReadTheDocs](https://jwql.readthedocs.io)
 
-The `jwql` application is currently under heavy development.  The `1.0` release is expected in 2019.  Currently, a development version of the web application can be found at [https://dljwql.stsci.edu](https://dljwql.stsci.edu).
+The `jwql` application is currently under heavy development.  The `1.0` release is expected in 2021.  Currently, a development version of the web application can be found at [https://dljwql.stsci.edu](https://dljwql.stsci.edu).
 
 ## Installation for Users
 
@@ -177,7 +177,8 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 - Van Dixon (INS)
 - Tom Donaldson (DMD) [@tomdonaldson](https://github.com/tomdonaldson)
 - Kim DuPrie (DMD)
-- Jonathan Eisenhamer (DMD) [@stscieisenhamer](https://githublcom/stscieisenhamer)
+- Jonathan Eisenhamer (DMD) [@stscieisenhamer](https://github.com/stscieisenhamer)
+- Ben Falk (DMD) [@falkben](https://github.com/falkben)
 - Ann Feild (OPO)
 - Mike Fox (DSMO) [@mfox22](https://github.com/mfox22)
 - Scott Friedman (INS)

docs/source/common_monitors.rst

@@ -2,8 +2,26 @@
 common_monitors
 ***************
 
+bad_pixel_monitor.py
+--------------------
+.. automodule:: jwql.instrument_monitors.common_monitors.bad_pixel_monitor
+    :members:
+    :undoc-members:
+
+bias_monitor.py
+---------------
+.. automodule:: jwql.instrument_monitors.common_monitors.bias_monitor
+    :members:
+    :undoc-members:
+
 dark_monitor.py
 ---------------
 .. automodule:: jwql.instrument_monitors.common_monitors.dark_monitor
+    :members:
+    :undoc-members:
+
+readnoise_monitor.py
+--------------------
+.. automodule:: jwql.instrument_monitors.common_monitors.readnoise_monitor
     :members:
     :undoc-members:

docs/source/tests.rst

@@ -8,6 +8,19 @@ test_api_views.py
     :members:
     :undoc-members:
 
+test_bad_pixel_monitor.py
+-------------------------
+.. automodule:: jwql.tests.test_bad_pixel_monitor
+    :members:
+    :undoc-members:
+
+
+test_bias_monitor.py
+--------------------
+.. automodule:: jwql.tests.test_bias_monitor
+    :members:
+    :undoc-members:
+
 test_calculations.py
 --------------------
 .. automodule:: jwql.tests.test_calculations

environment_python_3_6.yml

@@ -2,19 +2,21 @@ channels:
 - defaults
 - http://ssb.stsci.edu/astroconda
 dependencies:
-- astroquery=0.3.10
+- astroquery=0.4
+- authlib=0.15.1
 - bokeh>=1.0,<1.4
 - django=2.2.5
+- drizzle=1.13
 - flake8=3.7.9
 - inflection=0.3.1
 - ipython=7.13.0
 - jinja2=2.10.3
 - jsonschema=3.2.0
 - matplotlib=3.1.0
 - nodejs=10.13.0
-- numpy=1.16.4
+- numpy=1.19.1
 - numpydoc=0.9.2
-- pandas=1.0.3
+- pandas=1.1.1
 - pip=19.1.1
 - postgresql=9.6.6
 - psycopg2=2.7.5
@@ -28,13 +30,13 @@ dependencies:
 - sqlalchemy=1.3.17
 - twine=2.0.0
 - pip:
-  - asdf==2.6.0
+  - asdf==2.7.1
   - astropy==4.0.1
-  - authlib==0.14.3
-  - codecov==2.1.3
-  - crds==7.5.0.0
+  - codecov==2.1.9
+  - crds==10.0.0
+  - cryptography==3.1.1
   - jwedb>=0.0.3
+  - jwst==0.17.1
   - pysqlite3==0.2.2
   - stsci_rtd_theme==0.0.2
-  - git+https://github.com/spacetelescope/[email protected]
-  - git+https://github.com/spacetelescope/jwst_reffiles
+  - git+https://github.com/spacetelescope/jwst_reffiles#egg=jwst_reffiles

environment_python_3_7.yml

@@ -0,0 +1,41 @@
+channels:
+- defaults
+- http://ssb.stsci.edu/astroconda
+dependencies:
+- astroquery=0.4
+- authlib=0.15.1
+- bokeh>=1.0,<1.4
+- django=3.0.3
+- flake8=3.8.3
+- inflection=0.3.1
+- ipython=7.16.1
+- jinja2=2.11.2
+- jsonschema=3.2.0
+- matplotlib=3.2.2
+- nodejs=10.13.0
+- numpy=1.18.5
+- numpydoc=1.1.0
+- pandas=1.1.1
+- pip=20.1.1
+- postgresql=12.2
+- psycopg2=2.8.5
+- pysiaf=0.9.0
+- python=3.7.7
+- pytest=5.4.3
+- pytest-cov=2.10.0
+- scipy=1.5.0
+- setuptools=49.2.0
+- sphinx=3.1.2
+- sqlalchemy=1.3.18
+- twine=2.0.0
+- pip:
+  - asdf==2.7.1
+  - astropy==4.0.1.post1
+  - codecov==2.1.9
+  - crds==10.0.0
+  - cryptography==3.1.1
+  - jwedb==0.0.6
+  - jwst==0.17.1
+  - pysqlite3==0.4.3
+  - stsci_rtd_theme==0.0.2
+  - git+https://github.com/spacetelescope/jwst_reffiles

environment_python_3_8.yml

@@ -0,0 +1,41 @@
+channels:
+- defaults
+- http://ssb.stsci.edu/astroconda
+dependencies:
+- authlib=0.15.1
+- django=3.0.3
+- flake8=3.8.3
+- inflection=0.3.1
+- ipython=7.16.1
+- jinja2=2.11.2
+- jsonschema=3.2.0
+- matplotlib=3.2.2
+- nodejs=10.13.0
+- numpy=1.18.5
+- numpydoc=1.1.0
+- pandas=1.1.1
+- pip=20.2.2
+- postgresql=12.2
+- psycopg2=2.8.5
+- python=3.8.5
+- pytest=6.0.1
+- pytest-cov=2.10.1
+- scipy=1.5.0
+- setuptools=49.6.0
+- sphinx=3.2.1
+- twine=2.0.0
+- pip:
+  - asdf==2.7.1
+  - astropy==4.0.1.post1
+  - astroquery==0.4.1
+  - bokeh>=1.0,<1.4
+  - codecov==2.1.9
+  - crds==10.0.0
+  - cryptography==3.1.1
+  - jwedb==0.0.6
+  - jwst==0.17.1
+  - pysiaf==0.9.0
+  - pysqlite3==0.4.3
+  - sqlalchemy==1.3.19
+  - stsci_rtd_theme==0.0.2
+  - git+https://github.com/spacetelescope/jwst_reffiles

jwql/bokeh_templating/example/example_interface.yaml

@@ -1,24 +1,15 @@
-- !ColumnDataSource: &dummy # This is a dummy ColumnDataSource used to trigger the controller method whenever a slider is changed.
-    data:
-        value: []
-    on_change: ['data', !self.controller ]
-- !CustomJS: &callback # This callback changes the value of the dummy ColumnDataSource data to trigger the controller method.
-    ref: "callback"
-    args:
-        source: *dummy
-    code: "\n    source.data = { value: [cb_obj.value] }\n"
 - !Slider: &a_slider # a slider for the a value
     ref: "a_slider"
     title: "A"
     value: 4
     range: !!python/tuple [1, 20, 0.1]
-    callback: *callback
+    on_change: ['value', !self.controller ]
 - !Slider: &b_slider # a slider for the b value
     ref: "b_slider"
     title: "B"
     value: 2
     range: !!python/tuple [1, 20, 0.1]
-    callback: *callback
+    on_change: ['value', !self.controller ]
 - !ColumnDataSource: &figure_source # the ColumnDataSource for the figure
     ref: "figure_source"
     data:

jwql/bokeh_templating/example/main.py

@@ -24,6 +24,8 @@
 
 class TestBokehApp(BokehTemplate):
     """This is a minimal ``BokehTemplate`` app."""
+
+    _embed = True
 
     def pre_init(self):
         """Before creating the Bokeh interface (by parsing the interface

jwql/bokeh_templating/factory.py

@@ -66,7 +66,7 @@ def mapping_factory(tool, element_type):
     for an example of how this function is used.
     """
 
-    def mapping_constructor(loader, node): #docstring added below
+    def mapping_constructor(loader, node):  # docstring added below
         fmt = tool.formats.get(element_type, {})
         value = loader.construct_mapping(node, deep=True)
         ref = value.pop("ref", "")
@@ -216,9 +216,10 @@ def figure_constructor(tool, loader, node):
                 figure.js_on_event(*event)
 
     for element in elements:
-        key = element.pop('kind')
+        key = element.pop('kind', 'diamond')
         shape = {'line': ('Line', figure.line),
                  'circle': ('Circle', figure.circle),
+                 'step': ('Step', figure.step),
                  'diamond': ('Diamond', figure.diamond),
                  'triangle': ('Triangle', figure.triangle),
                  'square': ('Square', figure.square),

jwql/bokeh_templating/keyword_map.py

@@ -1,4 +1,5 @@
-"""A script to scrape the Bokeh package and collate dictionaries of
+"""
+A script to scrape the Bokeh package and collate dictionaries of
 classes and functions.
 
 The ``_parse_module`` function iterates over a module, and uses the
@@ -34,19 +35,21 @@
 from bokeh import layouts, models, palettes, plotting, transform
 from inspect import getmembers, isclass, isfunction
 
-from .surface3d import Surface3d
-
 bokeh_sequences = {}
-bokeh_mappings = {"Surface3d": Surface3d}  # Note that abstract base classes *are* included
+bokeh_mappings = {}  # Note that abstract base classes *are* included
 
 
 def _parse_module(module):
-    """Sort the members of a module into dictionaries of functions
-    (sequences) and classes (mappings)."""
-
-    test = lambda nm, mem: (not nm.startswith("_")) and (module.__name__ in mem.__module__)
-    seqs = {nm: mem for nm, mem in getmembers(module, isfunction) if test(nm, mem)}
-    maps = {nm: mem for nm, mem in getmembers(module, isclass) if test(nm, mem)}
+    """
+    Sort the members of a module into dictionaries of functions (sequences)
+    and classes (mappings).
+    """
+
+    def accessible_member(name, member):
+        return (not name.startswith("_")) and (module.__name__ in member.__module__)
+
+    seqs = {nm: mem for nm, mem in getmembers(module, isfunction) if accessible_member(nm, mem)}
+    maps = {nm: mem for nm, mem in getmembers(module, isclass) if accessible_member(nm, mem)}
 
     # these need to be mappings
     if 'gridplot' in seqs: