Setting up AutoCNet to interact with RTDs (#583)

* adding RTD files

* dont build NBs and export ISISROOT to environment

* adding dummy ISISDATA env variable for kalasiris

* adding nbsphinx to environment and incorperating very bad work around to kalasiris import requirements

* addressing warnings

* adding workshops index.rst

* simplifying docs environment requirements and mocking models, reverting junky kalasiris workaround

.readthedocs.yaml

+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+conda:
+  environment: docs/environment.yml

docs/Makefile

@@ -180,3 +180,4 @@ pseudoxml:
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+

docs/conf.py

@@ -45,6 +45,59 @@ sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 
 sys.path.insert(0, os.path.abspath('../'))
 
+for mod_name in (
+	"csmapi",
+	"cv2",
+	"dill",
+	"geoalchemy2",
+	"geoalchemy2.shape",
+	"geopandas",
+	"kalasiris",
+	"knoten",
+	"knoten.csm",
+	"matplotlib",
+	"matplotlib.pyplot",
+	"numpy",
+	"ogr",
+	"osgeo",
+	"pandas",
+	"pandas.core",
+	"pandas.core.indexing",
+	"PIL",
+	"plio",
+	"plio.io",
+	"plio.io.io_gdal",
+	"plio.io.io_controlnetwork",
+	"plio.io.isis_serial_number",
+	"plio.utils",
+	"plurmy",
+	"psycopg2",
+	"psycopg2.extensions",
+	"pvl",
+	"pyproj",
+	"redis",
+	"scipy",
+	"scipy.spatial",
+	"scipy.spatial.distance",
+	"scipy.special",
+	"scipy.stats",
+	"scipy.ndimage",
+	"scipy.ndimage.interpolation",
+	"shapely",
+	"shapely.affinity",
+	"shapely.geometry",
+	"shapely.ops",
+	"shapely.wkt",
+	"shapely.wkb",
+	"skimage",
+	"skimage.transform",
+	"sklearn",
+	"sklearn.cluster",
+	"sklearn.neighbors",
+	"sqlalchemy_utils",
+	"yaml"
+):
+	sys.modules[mod_name]= MagicMock()
 import autocnet
 
 # -- General configuration ---------------------------------------------
@@ -52,6 +105,7 @@ import autocnet
 # If your documentation needs a minimal Sphinx version, state it here.
 needs_sphinx = '1.3'
 nbsphinx_allow_errors = True
+nbsphinx_execute = 'never'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.

docs/environment.yml

+name: autocnet
+channels:
+  - conda-forge
+  - default
+
+dependencies:
+  - cmake
+  - nbsphinx
+  - networkx
+  - sphinx
+  - sqlalchemy
+  - yaml

docs/library/matcher/ciratefi.rst

 :mod:`matcher.ciratefi` --- RST-BC Invariant template match algorithm
-====================================================================
+=====================================================================
 
 The :mod:`matcher.ciratefi` module
 

docs/library/matcher/cpu_outlier_detector.rst

 :mod:`matcher.cpu_outlier_detector` --- Finding outliers in both the keypoints and the matches
-==========================================================================================
+==============================================================================================
 
 The :mod:`matcher.cpu_outlier_detector` module
 

docs/library/matcher/cuda_outlier_detector.rst

 :mod:`matcher.cuda_outlier_detector` --- Finding outliers in both the keypoints and the matches
-==========================================================================================
+===============================================================================================
 
 The :mod:`matcher.cpu_outlier_detector` module
 

docs/users/index.rst

@@ -3,3 +3,4 @@
 
    installation
    tutorials/index
+   workshops/index

docs/users/tutorials/index.rst

@@ -8,7 +8,8 @@ Working With ISIS Control Networks
 .. toctree::
    :maxdepth: 1
 
-    Ingesting from ISIS control network<isis_ingest/from_cnet.ipynb>
+    Ingesting from ISIS control network<isis_ingestion/from_cnet.ipynb>
+    Check for empty overlaps and overlap connectivity<isis_ingestion/overlap_check.ipynb>
     Using outlier detection to check for bad measures<outlier_detection/outlier_detection.ipynb>
 
 
@@ -31,9 +32,9 @@ Working With Apollo Pan
     Creating a Control Network <apollopan/9. Creating a Control Network.ipynb>
     Advanced: Extending the CandidateGraph<apollopan/Advanced 1. Extending the CandidateGraph.ipynb>
 
-Coupled Decomposition
----------------------
+Change Detection
+----------------
 .. toctree::
    :maxdepth: 1
 
-   Apollo Metric Coupled Decomposition<coupleddecomposition/CoupledDecomposition.ipynb>
+   Change detection examples<change_detection/Change_Detection.ipynb>

docs/users/workshops/index.rst

+Astrogeology Science Center Workshop
+------------------------------------
+
+.. toctree::
+   :maxdepth: 1
+
+   Jupyter notebook and jupyter kernel basics<FY21_workshop/0_jupyter_basics.ipynb>
+   Introduction to python packages<FY21_workshop/1_python_software_tutorial.ipynb>
+   Using PLIO to analyze control networks<FY21_workshop/2_plio_analysis.ipynb>
+   Homography and Fundamental matrix outlier detection in AutoCNet<FY21_workshop/3_outlier_detection.ipynb>
+   Generating a Control Network with AutoCNet<FY21_workshop/4_network_generation.ipynb>