WIP: New 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.rst

@@ -2,9 +2,9 @@ ioos\_qc package
 ================
 
 .. automodule:: ioos_qc
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 Submodules
 ----------
@@ -13,9 +13,9 @@ ioos\_qc.config module
 ----------------------
 
 .. automodule:: ioos_qc.config
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 ioos\_qc.argo module
 -----------------------
@@ -29,16 +29,31 @@ ioos\_qc.qartod module
 ----------------------
 
 .. automodule:: ioos_qc.qartod
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :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/**

docs/source/examples/usage/Config.ipynb

@@ -0,0 +1,114 @@
+{
+ "metadata": {
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.2-final"
+  },
+  "orig_nbformat": 2,
+  "kernelspec": {
+   "name": "python_defaultSpec_1597865297299",
+   "display_name": "Python 3.8.2 64-bit ('ioosqc38': conda)"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2,
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Install QC library\n",
+    "#!pip uninstall -y ioos_qc\n",
+    "#!pip install git+git://github.com/ioos/ioos_qc.git\n",
+    "\n",
+    "# # Alternative installation (install specific branch):\n",
+    "# !pip uninstall -y ioos_qc\n",
+    "# !pip install git+git://github.com/ioos/ioos_qc.git@BRANCHNAME\n",
+    "\n",
+    "# Alternative installation (run with local updates):\n",
+    "#!pip uninstall -y ioos_qc\n",
+    "import sys\n",
+    "from pathlib import Path\n",
+    "basedir = Path().absolute()\n",
+    "libdir = basedir.parent.parent.parent.parent\n",
+    "sys.path.append(str(libdir))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Load a Config object from a YAML string"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stderr",
+     "text": "Ignoring region because it could not be parsed, is it valid GeoJSON?\nIgnoring region because it could not be parsed, is it valid GeoJSON?\n"
+    },
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "OrderedDict([('contexts',\n              [{'region': None,\n                'window': {'starting': datetime.datetime(2020, 1, 1, 0, 0),\n                 'ending': datetime.datetime(2020, 4, 1, 0, 0)},\n                'streams': {'variable1': {'qartod': {'location_test': {'bbox': [-80,\n                     40,\n                     -70,\n                     60]}}},\n                 'variable2': {'qartod': {'gross_range_test': {'suspect_span': [1,\n                     11],\n                    'fail_span': [0, 12]}}}}},\n               {'region': None,\n                'window': {'starting': datetime.datetime(2020, 1, 1, 0, 0),\n                 'ending': datetime.datetime(2020, 4, 1, 0, 0)},\n                'streams': {'variable1': {'qartod': {'location_test': {'bbox': [-80,\n                     40,\n                     -70,\n                     60]}}},\n                 'variable2': {'qartod': {'gross_range_test': {'suspect_span': [1,\n                     11],\n                    'fail_span': [0, 12]}}}}}])])"
+     },
+     "metadata": {},
+     "execution_count": 3
+    }
+   ],
+   "source": [
+    "from ioos_qc.config import Config\n",
+    "\n",
+    "config = \"\"\"\n",
+    "    contexts:\n",
+    "        -   region: null\n",
+    "            window:\n",
+    "                starting: 2020-01-01T00:00:00Z\n",
+    "                ending: 2020-04-01T00:00:00Z\n",
+    "            streams:\n",
+    "                variable1:\n",
+    "                    qartod:\n",
+    "                        location_test:\n",
+    "                            bbox: [-80, 40, -70, 60]\n",
+    "                variable2:\n",
+    "                    qartod:\n",
+    "                        gross_range_test:\n",
+    "                            suspect_span: [1, 11]\n",
+    "                            fail_span: [0, 12]\n",
+    "        -   region: null\n",
+    "            window:\n",
+    "                starting: 2020-01-01T00:00:00Z\n",
+    "                ending: 2020-04-01T00:00:00Z\n",
+    "            streams:\n",
+    "                variable1:\n",
+    "                    qartod:\n",
+    "                        location_test:\n",
+    "                            bbox: [-80, 40, -70, 60]\n",
+    "                variable2:\n",
+    "                    qartod:\n",
+    "                        gross_range_test:\n",
+    "                            suspect_span: [1, 11]\n",
+    "                            fail_span: [0, 12]\n",
+    "\"\"\"\n",
+    "c = Config(config)\n",
+    "c.config"
+   ]
+  }
+ ]
+}

docs/source/examples/usage/ContextConfig.ipynb

@@ -0,0 +1,100 @@
+{
+ "metadata": {
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.2-final"
+  },
+  "orig_nbformat": 2,
+  "kernelspec": {
+   "name": "python_defaultSpec_1597865124286",
+   "display_name": "Python 3.8.2 64-bit ('ioosqc38': conda)"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2,
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Install QC library\n",
+    "#!pip uninstall -y ioos_qc\n",
+    "#!pip install git+git://github.com/ioos/ioos_qc.git\n",
+    "\n",
+    "# # Alternative installation (install specific branch):\n",
+    "# !pip uninstall -y ioos_qc\n",
+    "# !pip install git+git://github.com/ioos/ioos_qc.git@BRANCHNAME\n",
+    "\n",
+    "# Alternative installation (run with local updates):\n",
+    "#!pip uninstall -y ioos_qc\n",
+    "import sys\n",
+    "from pathlib import Path\n",
+    "basedir = Path().absolute()\n",
+    "libdir = basedir.parent.parent.parent.parent\n",
+    "sys.path.append(str(libdir))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Load a ContextConfig object from a YAML string"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stderr",
+     "text": "Ignoring region because it could not be parsed, is it valid GeoJSON?\n"
+    },
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": "OrderedDict([('region', None),\n             ('window',\n              {'starting': datetime.datetime(2020, 1, 1, 0, 0),\n               'ending': datetime.datetime(2020, 4, 1, 0, 0)}),\n             ('streams',\n              {'variable1': {'qartod': {'location_test': {'bbox': [-80,\n                   40,\n                   -70,\n                   60]}}},\n               'variable2': {'qartod': {'aggregate': None,\n                 'gross_range_test': {'suspect_span': [1, 11],\n                  'fail_span': [0, 12]}}}})])"
+     },
+     "metadata": {},
+     "execution_count": 6
+    }
+   ],
+   "source": [
+    "from ioos_qc.config import ContextConfig\n",
+    "\n",
+    "config = \"\"\"\n",
+    "    region: null\n",
+    "    window:\n",
+    "        starting: 2020-01-01T00:00:00Z\n",
+    "        ending: 2020-04-01T00:00:00Z\n",
+    "    streams:\n",
+    "        variable1:\n",
+    "            qartod:\n",
+    "                location_test:\n",
+    "                    bbox: [-80, 40, -70, 60]\n",
+    "        variable2:\n",
+    "            qartod:\n",
+    "                aggregate:\n",
+    "                gross_range_test:\n",
+    "                    suspect_span: [1, 11]\n",
+    "                    fail_span: [0, 12]\n",
+    "\"\"\"\n",
+    "c = ContextConfig(config)\n",
+    "c.config"
+   ]
+  }
+ ]
+}