Merge pull request #809 from spacetelescope/v1.0.0

Release v1.0.0 [main]

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,22 @@
+---
+name: Bug Report
+about: Create a report to help us improve.
+title: (Concise description of bug)
+labels: bug
+---
+
+**Describe the bug**
+A clear and detailed description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A description of what you expected to happen.
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,18 @@
+---
+name: Feature Request
+about: Suggest an idea for the JWQL project.
+title: Concise description of the feature request
+labels: enhancement
+---
+
+**Is your feature request related to a problem? Please describe.**
+A detailed description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/ci.yml

@@ -21,6 +21,11 @@ jobs:
         with:
           activate-environment: jwql-${{ matrix.python-version }}
 
+      - name: Bandit Check
+        uses: jpetrucciani/bandit-check@1.6.2
+        continue-on-error: true
+        if: runner.os == 'Linux'
+
       - name: Build jwql conda environment and run tests
         shell: bash -l {0}
         run: |

.gitignore

@@ -1,7 +1,7 @@
 *.pyc
 *.fits
 *.ipynb_checkpoints/
-/jwql/utils/config.json
+config.json
 build/
 dist/
 jwql.egg-info/

CHANGES.rst

@@ -1,3 +1,70 @@
+1.0.0 (2021-10-05)
+===================
+
+New Features
+------------
+
+Project & API Documentation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Included documentation describing the algorithms used for instrument monitors
+- Included templates for bug reports and feature requests as well as a link to submit issues on the ``home`` page
+- Included ``Documentation`` option on instrument drop down menu in the navigation bar
+
+
+Web Application
+~~~~~~~~~~~~~~~
+
+- All relevant instruments (NIRCam, NIRISS, NIRSpec) are incorporated into the Bias Monitor
+- The generalized pipeline function from ``pipeline_tools.py`` is used for image calibration
+- For exposures containing multiple integrations, created thumbnail image for only a single ingtegration
+- Implemented tests for all Monitor webpages
+
+
+``jwql`` Repository
+~~~~~~~~~~~~~~~~~~~
+
+- Modified filesystem to reflect MAST-like organizational structure
+- Implemented application security tools into GitHub Actions builds
+- Switched filesystem to use latest DMS build
+- Improved configuration file handling
+
+
+Bug Fixes
+---------
+
+Project & API Documentation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Include API Docs for all modules, classes, and functions in ReadTheDocs
+
+
+Web Application
+~~~~~~~~~~~~~~~
+
+- Included various fixes and improvements suggested during stakeholder demonstrations
+- Fixed ``View Image``, ``View Proposal``, and ``View Header`` buttons
+- Updated dashboard such that ``NULL`` Monitor Status values were fixed
+- Updated options that users can select for general image queries
+- Eliminated pop-up warning when viewing fits file headers in the web app
+- Removed login button on homepage and supporting authentication code and replaced with SSO authentication
+
+
+``jwql`` Repository
+~~~~~~~~~~~~~~~~~~~
+
+- Fixed Dark Monitor failure due to dither point keyword values in data
+- Addressed Dark Monitor failure with data including 64-bit integers
+- Resolved the NIRSpec amp boundary issue
+- Fixed missing reference file error handling with latest DMS build in Readnoise Monitor
+- Ensured Dark, Bias, and Readnoise Monitors complete successfully with latest DMS build
+- Included read persmissions for database tables
+- Performed flake8 sweep of the code repository
+- Updated software to support the latest versions of ``bokeh`` and ``pysiaf``
+- Removed dependencies on the astroconda channel
+
+
+
 0.26.0 (2021-03-30)
 ===================
 

MANIFEST.in

@@ -1,12 +1,17 @@
+include CODE_OF_CONDUCT.md
 include README.md
 include LICENSE
-include environment_python_3_5.yml
-include environment_python_3_6.yml
+include CHANGES.rst
+include environment_python_3_7.yml
+include environment_python_3_8.yml
 include setup.py
+include requirements.txt
+include rtd_requirements.txt
+include jwql/example_config.json
 
 recursive-include notebooks *
 recursive-include style_guide *
 recursive-include typing_demo *
 recursive-include jwql/database/monitor_table_definitions *.txt
 
-exclude *.pyc
+exclude *.pyc

README.md

@@ -104,7 +104,7 @@ The package should now appear if you run `conda list jwql`.
 
 ### Configuration File
 
-Much of the `jwql` software depends on the existence of a `config.json` file within the `utils` directory.  This file contains data that may be unique to users and/or contain sensitive information.  Please see the [Config File wiki page](https://github.com/spacetelescope/jwql/wiki/Config-file) for instructions on how to provide this file.
+Much of the `jwql` software depends on the existence of a `config.json` file within the `jwql` directory.  This file contains data that may be unique to users and/or contain sensitive information.  Please see the [Config File wiki page](https://github.com/spacetelescope/jwql/wiki/Config-file) for instructions on how to provide this file.
 
 
 ## Citation
@@ -186,6 +186,7 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 - James Davies (DMD) [@jdavies-st](https://github.com/jdavies-st)
 - Rosa Diaz (INS) [@rizeladiaz](https://github.com/rizeladiaz)
 - Van Dixon (INS)
+- Larry Doering (ITSD)
 - Tom Donaldson (DMD) [@tomdonaldson](https://github.com/tomdonaldson)
 - Kim DuPrie (DMD)
 - Jonathan Eisenhamer (DMD) [@stscieisenhamer](https://github.com/stscieisenhamer)
@@ -194,6 +195,7 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 - Mike Fox (DSMO) [@mfox22](https://github.com/mfox22)
 - Scott Friedman (INS)
 - Alex Fullerton (INS) [@awfullerton](https://github.com/awfullerton)
+- Macarena Garcia Marin (INS)
 - Lisa Gardner (DMD)
 - Vera Gibbs (ITSD)
 - Catherine Gosmeyer (INS) [@cgosmeyer](https://github.com/cgosmeyer)
@@ -202,9 +204,12 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 - Sherie Holfeltz (INS) [@stholfeltz](https://github.com/stholfeltz)
 - Joe Hunkeler (DMD) [@jhunkeler](https://github.com/jhunkeler)
 - Catherine Kaleida (DMD) [@ckaleida](https://github.com/ckaleida)
+- Deborah Kenny (DMD)
 - Jenn Kotler (DMD) [@jenneh](https://github.com/jenneh)
 - Daniel Kühbacher (Goddard) [@DanielKuebi](https://github.com/DanielKuebi)
 - Mark Kyprianou (DMD) [@mkyp](https://github.com/mkyp)
+- Stephanie La Massa (INS)
+- Matthew Lallo (INS)
 - Karen Levay (DMD)
 - Crystal Mannfolk (SCOPE) [@cmannfolk](https://github.com/cmannfolk)
 - Greg Masci (ITSD)
@@ -221,13 +226,15 @@ Any questions about the `jwql` project or its software can be directed to `jwql@
 - Matt Rendina (DMD) [@rendinam](https://github.com/rendinam)
 - Massimo Robberto (INS) [@mrobberto](https://github.com/mrobberto)
 - Mary Romelfanger (DMD)
+- Elena Sabbi (INS)
 - Bernie Shiao (DMD)
 - Matthew Sienkiewicz (ITSD)
 - Arfon Smith (DSMO) [@arfon](https://github.com/arfon)
 - Linda Smith (INS)
 - Patrick Taylor (ITSD)
 - Dave Unger (ITSD)
 - Jeff Valenti (JWSTMO) [@JeffValenti](https://github.com/JeffValenti)
+- Jeff Wagner (ITSD)
 - Thomas Walker (ITSD)
 - Geoff Wallace (DMD)
 - Lara Wilkinson (OPO)

docs/source/conf.py

@@ -25,6 +25,13 @@
 
 # -- General configuration ------------------------------------------------
 
+# Configure Django for autodoc usage
+import django
+from django.conf import settings
+
+settings.configure(LOGGING_CONFIG=None)
+django.setup()
+
 # If your documentation needs a minimal Sphinx version, state it here.
 #
 # needs_sphinx = '1.0'
@@ -51,7 +58,7 @@
 # The master toctree document.
 master_doc = 'index'
 
-# Numpy doc setting, right now this supresses some warnings, not exactly sure why?
+# Numpy doc setting, currently supresses some warnings, not exactly sure why?
 numpydoc_show_class_members = False
 
 # General information about the project.
@@ -77,8 +84,8 @@
 # Usually you set "language" from the command line for these cases.
 language = None
 
-# This is a fix for warnings because of sphinx-autodoc interaction for classes, however it removes
-# method table from the docs.
+# This is a fix for warnings because of sphinx-autodoc interaction for classes,
+# however it removes method table from the docs.
 numpydoc_show_class_members = False
 
 # List of patterns, relative to source directory, that match files and

docs/source/index.rst

@@ -9,8 +9,7 @@
 Welcome to the ``jwql`` API documentation!
 ==========================================
 
-The JWST Quicklook Application (``JWQL``) is a database-driven web application and automation framework for JWST instrument monitoring and performance trending.  This site serves as the official API documentation for
-the project.  The ``JWQL`` website can currently be found at `https://dljwql.stsci.edu <http://dljwql.stsci.edu>`_.  The ``JWQL`` source code, installation instructions, and instructions for issue reporting and feature requests can be found in the `jwql GitHub repository <https://github.com/spacetelescope/jwql>`_.
+The JWST Quicklook Application (``JWQL``) is a web application and automation framework for analyzing and monitoring the JWST instruments and their data.  This site serves as the official API documentation for the project.  The ``JWQL`` source code, installation instructions, and instructions for issue reporting and feature requests can be found in the `jwql GitHub repository <https://github.com/spacetelescope/jwql>`_.
 
 .. toctree::
    :maxdepth: 1

docs/source/tests.rst

@@ -14,22 +14,21 @@ test_bad_pixel_monitor.py
     :members:
     :undoc-members:
 
-
 test_bias_monitor.py
 --------------------
 .. automodule:: jwql.tests.test_bias_monitor
     :members:
     :undoc-members:
 
-test_calculations.py
---------------------
-.. automodule:: jwql.tests.test_calculations
+test_bokeh_templating
+---------------------
+.. automodule:: jwql.tests.test_bokeh_templating
     :members:
     :undoc-members:
 
-test_context_processors.py
---------------------------
-.. automodule:: jwql.tests.test_context_processors
+test_calculations.py
+--------------------
+.. automodule:: jwql.tests.test_calculations
     :members:
     :undoc-members:
 
@@ -45,6 +44,12 @@ test_data_containers.py
     :members:
     :undoc-members:
 
+test_database_interface.py
+--------------------------
+.. automodule:: jwql.tests.test_database_interface
+    :members:
+    :undoc-members:
+
 test_edb.py
 -----------
 .. automodule:: jwql.tests.test_edb
@@ -99,6 +104,12 @@ test_preview_image.py
     :members:
     :undoc-members:
 
+test_readnoise_monitor.py
+-------------------------
+.. automodule:: jwql.tests.test_readnoise_monitor
+    :members:
+    :undoc-members:
+
 test_setup.py
 -------------
 .. automodule:: jwql.tests.test_setup

docs/source/utils.rst

@@ -2,6 +2,12 @@
 utils
 *****
 
+anomaly_query_config.py
+-----------------------
+.. automodule:: jwql.utils.anomaly_query_config
+    :members:
+    :undoc-members:
+
 calculations.py
 ---------------
 .. automodule:: jwql.utils.calculations
@@ -14,6 +20,18 @@ constants.py
     :members:
     :undoc-members:
 
+crds_tools.py
+-------------
+.. automodule:: jwql.utils.crds_tools
+    :members:
+    :undoc-members:
+
+credentials.py
+--------------
+.. automodule:: jwql.utils.credentials
+    :members:
+    :undoc-members:
+
 instrument_properties.py
 ------------------------
 .. automodule:: jwql.utils.instrument_properties
@@ -26,12 +44,30 @@ logging_functions.py
     :members:
     :undoc-members:
 
+mast_utils.py
+-------------
+.. automodule:: jwql.utils.mast_utils
+    :members:
+    :undoc-members:
+
 monitor_template.py
 -------------------
 .. automodule:: jwql.utils.monitor_template
     :members:
     :undoc-members:
 
+monitor_utils.py
+----------------
+.. automodule:: jwql.utils.monitor_utils
+    :members:
+    :undoc-members:
+
+organize_filesystem.py
+----------------------
+.. automodule:: jwql.utils.organize_filesystem
+    :members:
+    :undoc-members:
+
 permissions.py
 --------------
 .. automodule:: jwql.utils.permissions

docs/source/website.rst

@@ -38,6 +38,12 @@ manage.py
     :members:
     :undoc-members:
 
+monitor_views.py
+----------------
+.. automodule:: jwql.website.apps.jwql.monitor_views
+    :members:
+    :undoc-members:
+
 oauth.py
 --------
 .. automodule:: jwql.website.apps.jwql.oauth
@@ -50,6 +56,12 @@ settings.py
     :members:
     :undoc-members:
 
+urls.py
+-------
+.. automodule:: jwql.website.apps.jwql.urls
+    :members:
+    :undoc-members:
+
 views.py
 --------
 .. automodule:: jwql.website.apps.jwql.views