Merge pull request #87 from ocefpaf/docs

Docs

.github/workflows/deploy-docs.yml

@@ -27,7 +27,7 @@ jobs:
     - name: Build environment
       shell: bash -l {0}
       run: |
-        micromamba create --name TEST python=3 --file requirements.txt --file tests/requirements.txt --channel conda-forge
+        micromamba create --name TEST python=3 --file requirements.txt --file docs/requirements.txt --channel conda-forge
         micromamba activate TEST
         python -m pip install -e . --no-deps --force-reinstall
 
@@ -41,7 +41,6 @@ jobs:
         set -e
         micromamba activate TEST
         pushd docs
-        micromamba install --file requirements.txt --channel conda-forge
         make clean html linkcheck
         popd
 

docs/requirements.txt

@@ -1,4 +1,7 @@
+bokeh
 ipykernel
+matplotlib
 nbsphinx
+pynco
 sphinx
 sphinx-autodoc-typehints

docs/source/api/ioos_qc.rst

@@ -40,6 +40,7 @@ ioos\_qc.config module
    :members:
    :undoc-members:
    :show-inheritance:
+   :noindex:
 
 ioos\_qc.gliders module
 -----------------------

docs/source/other.rst

@@ -11,8 +11,7 @@ Here is a collection of other QARTOD implementations or contacts for reference.
 Python
 
 - `Ocean Observatories Initiative (OOI) Quality Control Algorithm <https://github.com/ooici/ion-functions/tree/master/ion_functions/qc>`_
-	- `OOI Quality Control Algorithm Tables <https://github.com/ooi-integration/qc-lookup>`_
-- `QARTOD in Practice <https://drive.google.com/open?id=0BwGScp7mjYjyNGVRUG5ZTTNPdUU>`_
+- `OOI Quality Control Algorithm Tables <https://github.com/ooi-integration/qc-lookup>`_
 
 R
 

docs/source/usage.rst

@@ -5,9 +5,9 @@ At its core, ``ioos_qc`` is a collection of modules and methods to run various q
 
 The following implementations are available in ``ioos_qc``:
 
-* `IOOS QARTOD <https://ioos.noaa.gov/project/qartod/>`_ - `API </api/ioos_qc.html#module-ioos_qc.qartod>`_
-* `ARGO - API </api/ioos_qc.html#module-ioos_qc.argo>`_
-* `AXDS - API </api/ioos_qc.html#module-ioos_qc.axds>`_ - A collection of checks used by `Axiom Data Science <https://axiomdatascience.com>`_
+* `IOOS QARTOD <https://ioos.noaa.gov/project/qartod/>`_ - :mod:`API <ioos_qc.qartod>`
+* :mod:`ARGO - API <ioos_qc.argo>`
+* :mod:`AXDS - API <ioos_qc.axds>` - A collection of checks used by `Axiom Data Science <https://axiomdatascience.com>`_
 
 Basic usage
 -----------
@@ -211,7 +211,7 @@ Usage
 Streams
 -------
 
-Streams represent the data input types for running quality control tests. A user "runs" a stream of data through a collection of quality control tests defined by a Config_. A list of possible Streams can be found in the `Streams API </api/ioos_qc.html#module-ioos_qc.streams>`_.
+Streams represent the data input types for running quality control tests. A user "runs" a stream of data through a collection of quality control tests defined by a Config_. A list of possible Streams can be found in the :mod:`Streams API <ioos_qc.streams>`.
 All streams return a generator of QC results that contain contextual information that can be useful when using the results. You can iterate over the results generator directly or you can collect them into more familiar ``list`` or ``dict`` objects before usage. If you are
 working in a streaming environment you will want to use generator result objects yourself. If you are running one-time or batch process quality checks you likely want to collect the results or use one of the Stores_ provided by ``ioos_qc``.
 
@@ -225,15 +225,15 @@ working in a streaming environment you will want to use generator result objects
 Results
 ~~~~~~~
 
-Each yielded result will be a `StreamConfigResult </api/ioos_qc.html#ioos_qc.results.StreamConfigResult>`_ or a `ContextResult </api/ioos_qc.html#ioos_qc.results.ContextResult>`_, depending on which type of Config_ object was used. Collected results are only ever of one type, a `CollectedResult </api/ioos_qc.html#ioos_qc.results.CollectedResult>`_, and only one ``CollectedResult`` will be returned after collecting Results. The benefit of using a ``CollectedResult`` is that it will piece back together all of the different ContextConfig_ objects in a Config_ and return you one result per unique ``stream_id`` and module/test combination.
+Each yielded result will be a :mod:`StreamConfigResult <ioos_qc.results.StreamConfigResult>` or a :mod:`ContextResult <ioos_qc.results.ContextResult>`, depending on which type of Config_ object was used. Collected results are only ever of one type, a :mod:`CollectedResult <ioos_qc.results.CollectedResult>`, and only one ``CollectedResult`` will be returned after collecting Results. The benefit of using a ``CollectedResult`` is that it will piece back together all of the different ContextConfig_ objects in a Config_ and return you one result per unique ``stream_id`` and module/test combination.
 
 .. note::
 
     For example: If you had a Config_ object that contained (3) different ContextConfig_ objects (each defining a time window and test inputs) for a single variable/``stream_id``, running that ``Config`` through any ``Stream`` implementation would yield (3) different ``ContextResult`` objects. You could use them yourself to construct whatever results you wanted to manually, or you could collect those results back into a single ``CollectedResult`` object to only have to deal with one result.
 
 .. warning::
 
-    Historically, test results were returned in a ``dict`` structure. While this is still supported it **should be considered deprecated**. The individually yielded result objects or a list of `CollectedResult objects <api/ioos_qc.html#ioos_qc.results.CollectedResult>`_ should be used in any applications, including any implementation of Stores_, going forward.
+    Historically, test results were returned in a ``dict`` structure. While this is still supported it **should be considered deprecated**. The individually yielded result objects or a list of :mod:`CollectedResult objects <ioos_qc.results.CollectedResult>` should be used in any applications, including any implementation of Stores_, going forward.
 
 
 .. code-block:: python
@@ -517,7 +517,7 @@ A subset of the NumpyStream, the NetcdfStream simply extracts numpy arrays from
 Stores
 ------
 
-Stores represent different data formats for storing quality control Results_ from Streams_. The results from any ``Stream`` should be able to be passed into any ``Store`` implementation defined in the `Stores API </api/ioos_qc.html#module-ioos_qc.stores>`_.
+Stores represent different data formats for storing quality control Results_ from Streams_. The results from any ``Stream`` should be able to be passed into any ``Store`` implementation defined in the :mod:`Stores API <ioos_qc.stores>`.
 
 ``ioos_qc`` comes with some built-in Stores_:
 

ioos_qc/qartod.py

@@ -469,12 +469,14 @@ def spike_test(inp: Sequence[N],
         suspect_threshold: The SUSPECT threshold value, in observations units.
         fail_threshold: The SUSPECT threshold value, in observations units.
         method: ['average'(default),'differential'] optional input to assign the method used to detect spikes.
-            "average": Determine if there is a spike at data point n-1 by subtracting
-                the midpoint of n and n-2 and taking the absolute value of this
-                quantity, and checking if it exceeds a low or high threshold.
-            "differential": Determine if there is a spike at data point n by calculating the difference
-                between n and n-1 and n+1 and n variation. To considered, (n - n-1)*(n+1 - n) should
-                be smaller than zero (in opposite direction).
+
+        "average": Determine if there is a spike at data point n-1 by subtracting
+        the midpoint of n and n-2 and taking the absolute value of this
+        quantity, and checking if it exceeds a low or high threshold.
+
+        "differential": Determine if there is a spike at data point n by calculating the difference
+        between n and n-1 and n+1 and n variation. To considered, (n - n-1)*(n+1 - n) should
+        be smaller than zero (in opposite direction).
 
     Returns:
         A masked array of flag values equal in size to that of the input.

tests/requirements.txt

@@ -2,8 +2,5 @@ dask
 erddapy
 flake8
 isort
-#nco
-#pocean-core
-#pynco
 pytest
 pytest-flake8>=1.0.4  # https://github.com/tholo/pytest-flake8/pull/59