Support context configurations (spatial/temporal subsets) and climatology-derived-configs.

.gitignore

@@ -17,3 +17,5 @@ docs/build
 tests/data/*.csv
 __pycache__
 .vscode
+build/
+docs/source/_build

.travis.yml

@@ -10,8 +10,6 @@ env:
 jobs:
   fast_finish: true
   include:
-    - python: 3.6
-      env: TEST_TARGET=default
     - python: 3.7
       env: TEST_TARGET=default
     - python: 3.7
@@ -24,7 +22,7 @@ jobs:
       env: TEST_TARGET=coding_standards
     - python: 3.8
       env: TEST_TARGET=docs
-    - python: 3.6
+    - python: 3.8
       env: TEST_TARGET=makerelease
   allow_failures:
     - python: 3.8

MANIFEST.in

@@ -2,4 +2,5 @@ include *.rst
 include *.txt
 include *.ini
 include VERSION
+include setup.cfg
 recursive-include ioos_qc *.py

conda-recipe/meta.yaml

@@ -18,9 +18,11 @@ requirements:
     - python
     - geojson
     - netCDF4
+    - numba
     - numpy >=1.14
     - pygc
     - ruamel.yaml
+    - shapely
     - simplejson
     - xarray
 

docs/source/api/ioos_qc.config_creator.rst

@@ -0,0 +1,43 @@
+ioos\_qc.config\_creator package
+================================
+
+.. automodule:: ioos_qc.config_creator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+ioos\_qc.config\_creator.config\_creator module
+-----------------------------------------------
+
+.. automodule:: ioos_qc.config_creator.config_creator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ioos\_qc.config\_creator.fx\_parser module
+------------------------------------------
+
+.. automodule:: ioos_qc.config_creator.fx_parser
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ioos\_qc.config\_creator.get\_assets module
+-------------------------------------------
+
+.. automodule:: ioos_qc.config_creator.get_assets
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ioos\_qc.config\_creator.make\_config module
+--------------------------------------------
+
+.. automodule:: ioos_qc.config_creator.make_config
+   :members:
+   :undoc-members:
+   :show-inheritance:
+

docs/source/api/ioos_qc.rst

@@ -2,43 +2,90 @@ ioos\_qc package
 ================
 
 .. automodule:: ioos_qc
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   ioos_qc.config_creator
 
 Submodules
 ----------
 
+ioos\_qc.argo module
+--------------------
+
+.. automodule:: ioos_qc.argo
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 ioos\_qc.config module
 ----------------------
 
 .. automodule:: ioos_qc.config
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-ioos\_qc.argo module
+ioos\_qc.gliders module
 -----------------------
 
-.. automodule:: ioos_qc.argo
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. automodule:: ioos_qc.gliders
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ioos\_qc.plotting module
+------------------------
+
+.. automodule:: ioos_qc.plotting
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 ioos\_qc.qartod module
 ----------------------
 
 .. automodule:: ioos_qc.qartod
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ioos\_qc.results module
+-----------------------
+
+.. automodule:: ioos_qc.results
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ioos\_qc.stores module
+----------------------
+
+.. automodule:: ioos_qc.stores
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ioos\_qc.streams module
+-----------------------
+
+.. automodule:: ioos_qc.streams
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 ioos\_qc.utils module
 ---------------------
 
 .. automodule:: ioos_qc.utils
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
+   :members:
+   :undoc-members:
+   :show-inheritance:
 

docs/source/conf.py

@@ -19,6 +19,7 @@
 #
 import os
 import sys
+
 p = os.path.abspath(
     os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
 )
@@ -41,7 +42,7 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.viewcode',
     'sphinx_autodoc_typehints',
-    "nbsphinx",
+    #"nbsphinx",
 ]
 
 napoleon_google_docstring = True

docs/source/examples.rst

@@ -11,3 +11,5 @@ You can download the source for these notebooks `here <https://github.com/ioos/i
 * :doc:`Run QARTOD on a netCDF file, and store the results </examples/Qartod_netCDF_example>`
 
 * :doc:`Run Attenuated Signal test on Salinity data to detect biofouling in an instrument </examples/QartodTestExample_SalinityAttenuation>`
+
+* **TODO: Add links to new notebooks under usage/**