Merge pull request #371 from spacetelescope/release-0.19.0

Release 0.19.0

.pyup.yml

@@ -13,7 +13,7 @@ pin: True
 
 # set the default branch
 # default: empty, the default branch on GitHub
-branch: master
+branch: develop
 
 # update schedule
 # default: empty

CHANGES.rst

@@ -1,3 +1,49 @@
+0.19.0 (2019-04-19)
+===================
+
+New Features
+------------
+
+Project & API Documentation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Added guidelines to the style guide for logging the execution of instrument monitors
+- Added example useage of logging in the ``example.py`` module
+
+Web Application
+~~~~~~~~~~~~~~~
+
+- Modified various web app views to enable faster loading times
+- Modified archive and preview image views to only display data for an authenticated user
+- Added views for MIRI and NIRSpec Data Trending Monitors, which monitors the behavior of select MIRI and NIRSpec Engineering Database mnemonics over time
+
+``jwql`` Repository
+~~~~~~~~~~~~~~~~~~~
+
+- Added Dark Monitor module, which monitors the dark current and hot pixel populations for each JWST instrument
+- Added software for producing MIRI and NIRSpec Data Trending Monitors (described above)
+- Modified ``generate_preview_images`` module to support the creation of preview images for stage 3 data products
+- Refactored ``monitor_filesystem`` to utilize PostgreSQL database tables to store archive filesystem statistics
+- Configured ``codecov`` for the project.  The project homepage can be found at https://codecov.io/gh/spacetelescope/jwql
+- Modified ``logging_functions`` module to enable dev, test, and production logging environments
+- Added convenience decorator to ``logging_functions`` module to time the execution of a function or method
+- Modified ``monitor_cron_jobs`` module to make use of updated ``logging_functions``
+
+Bug Fixes
+---------
+
+Web Application
+~~~~~~~~~~~~~~~
+
+- Fixed API views to only return the basenames of file paths, instead of full directory names
+
+``jwql`` Repository
+~~~~~~~~~~~~~~~~~~~
+
+- Fixed ``logging_functions`` module to properly parse new format of ``INSTALL_REQUIRES`` dependency in ``setup.py`` for logging system dependencies and their versions
+- Fixed ``Jenkinsfile`` to not allow for one failed unit test in Jenkins builds
+
+
 0.18.0 (2019-03-14)
 ===================
 

Jenkinsfile

@@ -1,20 +1,26 @@
 // Obtain files from source control system.
 if (utils.scm_checkout()) return
 
+withCredentials([string(
+    credentialsId: 'jwql-codecov',
+    variable: 'codecov_token')]) {
+
 // Define each build configuration, copying and overriding values as necessary.
 bc0 = new BuildConfig()
 bc0.nodetype = "linux-stable"
 bc0.name = "debug"
-bc0.build_cmds = ["conda env update --file=environment.yml",
-	       	  "with_env -n jwql python setup.py install"]
-bc0.test_cmds = ["with_env -n jwql pytest -s --junitxml=result.xml"]
-bc0.failedUnstableThresh = 1
-bc0.failedFailureThresh = 1
-
+bc0.build_cmds = [
+    "conda env update --file=environment.yml",
+    "pip install codecov pytest-cov",
+    "with_env -n jwql python setup.py install"]
+bc0.test_cmds = [
+    "with_env -n jwql pytest -s --junitxml=results.xml --cov=./jwql/ --cov-report xml",
+    "codecov --token=${codecov_token}"]
 
 // bc1 = utils.copy(bc0)
 // bc1.build_cmds[0] = "conda install -q -y python=3.5"
 
 // Iterate over configurations that define the (distibuted) build matrix.
 // Spawn a host of the given nodetype for each combination and run in parallel.
 utils.run([bc0])
+}

JenkinsfileRT

@@ -0,0 +1,22 @@
+// Obtain files from source control system.
+if (utils.scm_checkout()) return
+
+// Define each build configuration, copying and overriding values as necessary.
+bc0 = new BuildConfig()
+bc0.nodetype = "linux-stable"
+bc0.name = "debug"
+bc0.build_cmds = ["conda env update --file=environment.yml",
+	       	  "with_env -n jwql python setup.py install"]
+bc0.test_cmds = ["cp JWQL_CONFIG jwql/utils/",
+                 "with_env -n jwql pytest -s --junitxml=result.xml"]
+bc0.failedUnstableThresh = 1
+bc0.failedFailureThresh = 1
+
+
+
+// bc1 = utils.copy(bc0)
+// bc1.build_cmds[0] = "conda install -q -y python=3.5"
+
+// Iterate over configurations that define the (distibuted) build matrix.
+// Spawn a host of the given nodetype for each combination and run in parallel.
+utils.run([bc0])

README.md

@@ -103,7 +103,7 @@ The following is a bare-bones example of a best work flow for contributing to th
 4. Create a branch on that personal fork.
 5. Make your software changes.
 6. Push that branch to your personal GitHub repository (i.e. `origin`).
-7. On the `spacetelescope` `jwql` repository, create a pull request that merges the branch into `spacetelescope:master`.
+7. On the `spacetelescope` `jwql` repository, create a pull request that merges the branch into `spacetelescope:develop`.
 8. Assign a reviewer from the team for the pull request.
 9. Iterate with the reviewer over any needed changes until the reviewer accepts and merges your branch.
 10. Delete your local copy of your branch.

codecov.yml

@@ -0,0 +1,31 @@
+codecov:
+  notify:
+    require_ci_to_pass: yes
+
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+
+  status:
+    project: yes
+    patch: yes
+    changes: no
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+comment:
+  layout: "header, diff"
+  behavior: default
+  require_changes: no
+
+ignore:
+  - "jwql/website/"
+  - "jwql/database/"
+  - "*__init__.py*"

docs/source/common_monitors.rst

@@ -0,0 +1,9 @@
+***************
+common_monitors
+***************
+
+dark_monitor.py
+---------------
+.. automodule:: jwql.instrument_monitors.common_monitors.dark_monitor
+    :members:
+    :undoc-members:

docs/source/index.rst

@@ -23,9 +23,11 @@ API documentation
    :maxdepth: 1
    :caption: Contents:
 
+   common_monitors.rst
    database.rst
    edb.rst
    jwql_monitors.rst
+   instrument_monitors.rst
    tests.rst
    utils.rst
    website.rst

docs/source/instrument_monitors.rst

@@ -0,0 +1,9 @@
+*******************
+instrument_monitors
+*******************
+
+pipeline_tools.py
+-----------------
+.. automodule:: jwql.instrument_monitors.pipeline_tools
+    :members:
+    :undoc-members:

docs/source/tests.rst

@@ -8,12 +8,36 @@ test_api_views.py
     :members:
     :undoc-members:
 
+test_calculations.py
+--------------------
+.. automodule:: jwql.tests.test_calculations
+    :members:
+    :undoc-members:
+
+test_dark_monitor.py
+--------------------
+.. automodule:: jwql.tests.test_dark_monitor
+    :members:
+    :undoc-members:
+
 test_edb_interface.py
 ---------------------
 .. automodule:: jwql.tests.test_edb_interface
     :members:
     :undoc-members:
 
+test_instrument_properties.py
+-----------------------------
+.. automodule:: jwql.tests.test_instrument_properties
+    :members:
+    :undoc-members:
+
+test_loading_times.py
+--------------------
+.. automodule:: jwql.tests.test_loading_times
+    :members:
+    :undoc-members:
+
 test_monitor_mast.py
 --------------------
 .. automodule:: jwql.tests.test_monitor_mast
@@ -26,6 +50,12 @@ test_permissions.py
     :members:
     :undoc-members:
 
+test_pipeline_tools.py
+----------------------
+.. automodule:: jwql.tests.test_pipeline_tools
+    :members:
+    :undoc-members:
+
 test_plotting.py
 ----------------
 .. automodule:: jwql.tests.test_plotting

docs/source/utils.rst

@@ -2,12 +2,24 @@
 utils
 *****
 
+calculations.py
+---------------
+.. automodule:: jwql.utils.calculations
+    :members:
+    :undoc-members:
+
 constants.py
 ------------
 .. automodule:: jwql.utils.constants
     :members:
     :undoc-members:
 
+instrument_properties.py
+------------------------
+.. automodule:: jwql.utils.instrument_properties
+    :members:
+    :undoc-members:
+
 logging_functions.py
 --------------------
 .. automodule:: jwql.utils.logging_functions

environment.yml

@@ -3,29 +3,32 @@ channels:
 - http://ssb.stsci.edu/astroconda-dev
 - defaults
 dependencies:
-- asdf>=2.3.0
-- astropy
+- asdf=2.3.1
+- astropy>=3.1.2
 - astroquery=0.3.9
-- bokeh=1.0.4
-- django=2.1.5
+- bokeh=1.1.0
+- crds>=7.2.7
+- django=2.1.7
 - ipython=7.3.0
 - jinja2=2.10
-- jwst
+- jwst=0.13.1
 - matplotlib=3.0.2
 - numpy=1.16.2
 - numpydoc=0.8.0
-- pandas=0.24.0
+- pandas=0.24.2
 - postgresql=9.6.6
 - psycopg2=2.7.5
 - python=3.6.4
 - python-dateutil=2.7.5
-- pytest=4.3.0
+- pytest=4.4.0
 - pytest-cov=2.6.1
 - pytest-html=1.19.0
 - sphinx=1.8.5
 - sphinx_rtd_theme=0.1.9
-- sqlalchemy=1.3.1
+- sqlalchemy=1.3.3
 - stsci_rtd_theme=0.0.2
 - pip:
   - authlib==0.10
+  - codecov==2.0.15
+  - pysiaf==0.2.5
   - sphinx-automodapi==0.10