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Unverified Commit 2dc2ca8d authored by Lauren Adoram-Kershner's avatar Lauren Adoram-Kershner Committed by GitHub
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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
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# .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
...@@ -180,3 +180,4 @@ pseudoxml: ...@@ -180,3 +180,4 @@ pseudoxml:
$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
@echo @echo
@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
...@@ -45,6 +45,59 @@ sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES) ...@@ -45,6 +45,59 @@ sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
sys.path.insert(0, os.path.abspath('../')) 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 import autocnet
# -- General configuration --------------------------------------------- # -- General configuration ---------------------------------------------
...@@ -52,6 +105,7 @@ import autocnet ...@@ -52,6 +105,7 @@ import autocnet
# If your documentation needs a minimal Sphinx version, state it here. # If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = '1.3' needs_sphinx = '1.3'
nbsphinx_allow_errors = True nbsphinx_allow_errors = True
nbsphinx_execute = 'never'
# Add any Sphinx extension module names here, as strings. They can be # Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
......
name: autocnet
channels:
- conda-forge
- default
dependencies:
- cmake
- nbsphinx
- networkx
- sphinx
- sqlalchemy
- yaml
:mod:`matcher.ciratefi` --- RST-BC Invariant template match algorithm :mod:`matcher.ciratefi` --- RST-BC Invariant template match algorithm
==================================================================== =====================================================================
The :mod:`matcher.ciratefi` module The :mod:`matcher.ciratefi` module
......
:mod:`matcher.cpu_outlier_detector` --- Finding outliers in both the keypoints and the matches :mod:`matcher.cpu_outlier_detector` --- Finding outliers in both the keypoints and the matches
========================================================================================== ==============================================================================================
The :mod:`matcher.cpu_outlier_detector` module The :mod:`matcher.cpu_outlier_detector` module
......
:mod:`matcher.cuda_outlier_detector` --- Finding outliers in both the keypoints and the matches :mod:`matcher.cuda_outlier_detector` --- Finding outliers in both the keypoints and the matches
========================================================================================== ===============================================================================================
The :mod:`matcher.cpu_outlier_detector` module The :mod:`matcher.cpu_outlier_detector` module
......
...@@ -3,3 +3,4 @@ ...@@ -3,3 +3,4 @@
installation installation
tutorials/index tutorials/index
workshops/index
...@@ -8,7 +8,8 @@ Working With ISIS Control Networks ...@@ -8,7 +8,8 @@ Working With ISIS Control Networks
.. toctree:: .. toctree::
:maxdepth: 1 :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> Using outlier detection to check for bad measures<outlier_detection/outlier_detection.ipynb>
...@@ -31,9 +32,9 @@ Working With Apollo Pan ...@@ -31,9 +32,9 @@ Working With Apollo Pan
Creating a Control Network <apollopan/9. Creating a Control Network.ipynb> Creating a Control Network <apollopan/9. Creating a Control Network.ipynb>
Advanced: Extending the CandidateGraph<apollopan/Advanced 1. Extending the CandidateGraph.ipynb> Advanced: Extending the CandidateGraph<apollopan/Advanced 1. Extending the CandidateGraph.ipynb>
Coupled Decomposition Change Detection
--------------------- ----------------
.. toctree:: .. toctree::
:maxdepth: 1 :maxdepth: 1
Apollo Metric Coupled Decomposition<coupleddecomposition/CoupledDecomposition.ipynb> Change detection examples<change_detection/Change_Detection.ipynb>
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>
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