Change theme (#50)

- (Re)-Write some of the "Manual" docs, mostly stub files - Change to RTD theme - Change to sphinx_automod - Combine the three galleries into one - Create stub for external gallery - Re-worked README; added logo and badges; added readme to docs - Added CHANGELOG-file - Moved contributing and developer instructions to docs - Rework a bit the .gitignore
softwareunderground · Apr 21, 2021 · bcbfdeb · bcbfdeb
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diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,17 @@
+# Documentation
+docs/build/
+docs/source/api/
+docs/source/gen_modules/
+docs/source/examples/
+
+# Versioning
 subsurface/_version.py
 
-# Example data files - we need to handle this better
+# Example data files
 *.nc
+*.json
+*.le
+
 
 # vscode
 .vscode/*
@@ -31,17 +41,6 @@ wheels/
 *.egg-info/
 .installed.cfg
 *.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
 
 # Unit test / coverage reports
 htmlcov/
@@ -55,40 +54,12 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
 # Jupyter Notebook
 .ipynb_checkpoints
 
 # pyenv
 .python-version
 
-# celery beat schedule file
-celerybeat-schedule
-
-# SageMath parsed files
-*.sage.py
-
 # Environments
 .env
 .venv
@@ -101,24 +72,3 @@ venv.bak/
 # Spyder project settings
 .spyderproject
 .spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-/tests/data/.~lock.well_based_temperature.csv#
-/docs/build/
-/docs/source/
-!/docs/source/code.rst
-!/docs/source/conf.py
-!/docs/source/index.rst
-!/docs/source/installation.rst
-!/docs/source/_static/
-!/docs/source/_templates/
-/data/
-
-.idea
diff --git a/docs/source/_static/style.css b/docs/source/_static/style.css
@@ -0,0 +1,25 @@
+/* Customized styles */
+
+/* Sidebar header background */
+.wy-side-nav-search, .wy-nav-top {
+  background: #1DB6ED;
+}
+
+/* Sidebar header text */
+.wy-side-nav-search > div.version {
+  color: #ffffff;
+}
+
+/* Navigation headings */
+.wy-menu .caption-text {
+  color: #de4c13;
+  font-weight: bold;
+}
+
+/*
+
+- red of pyramid: #de4c13;
+- yellow of pyramid: #debc13;
+- "SWUNG" blue: #1DB6ED;
+
+*/
diff --git a/docs/source/_templates/base.rst b/docs/source/_templates/base.rst
diff --git a/docs/source/_templates/class.rst b/docs/source/_templates/class.rst
diff --git a/docs/source/_templates/layout.html b/docs/source/_templates/layout.html
@@ -0,0 +1,16 @@
+{% extends "!layout.html" %}
+
+{% block menu %}
+    {{ super() }}
+
+    {% if menu_links %}
+        <p class="caption">
+            <span class="caption-text">{{ menu_links_name }}</span>
+        </p>
+        <ul>
+            {% for text, link in menu_links %}
+                <li class="toctree-l1"><a href="{{ link }}">{{ text }}</a></li>
+            {% endfor %}
+        </ul>
+    {% endif %}
+{% endblock %}
diff --git a/docs/source/_templates/module.rst b/docs/source/_templates/module.rst
diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -0,0 +1 @@
+.. include:: ../../CHANGELOG.rst
diff --git a/docs/source/code-geological-formats.rst b/docs/source/code-geological-formats.rst
@@ -0,0 +1,16 @@
+Geological Formats
+==================
+
+.. automodule:: subsurface.geological_formats
+
+.. automodapi:: subsurface.geological_formats.boreholes
+   :no-inheritance-diagram:
+
+.. automodapi:: subsurface.geological_formats.fault
+   :no-inheritance-diagram:
+
+.. automodapi:: subsurface.geological_formats.segy_reader
+   :no-inheritance-diagram:
+
+.. automodapi:: subsurface.geological_formats.seismic
+   :no-inheritance-diagram:
diff --git a/docs/source/code-interfaces.rst b/docs/source/code-interfaces.rst
@@ -0,0 +1,4 @@
+Interfaces
+==========
+
+.. automodule:: subsurface.interfaces
diff --git a/docs/source/code-reader.rst b/docs/source/code-reader.rst
@@ -0,0 +1,70 @@
+Reader
+======
+
+.. automodule:: subsurface.reader
+
+.. automodapi:: subsurface.reader.readers_data
+   :no-inheritance-diagram:reader
+
+.. automodapi:: subsurface.reader.read_netcdf
+   :no-inheritance-diagram:reader
+
+
+.. automodule:: subsurface.reader.faults
+
+.. automodapi:: subsurface.reader.faults.faults
+   :no-inheritance-diagram:reader
+
+
+.. automodule:: subsurface.reader.geo_object
+
+
+.. automodule:: subsurface.reader.mesh
+
+.. automodapi:: subsurface.reader.mesh.surface_reader
+   :no-inheritance-diagram:reader
+
+.. automodapi:: subsurface.reader.mesh.surfaces_api
+   :no-inheritance-diagram:reader
+
+
+.. automodule:: subsurface.reader.petrel
+
+
+.. automodule:: subsurface.reader.profiles
+
+.. automodapi:: subsurface.reader.profiles.profiles_core
+   :no-inheritance-diagram:reader
+
+
+.. automodule:: subsurface.reader.topography
+
+.. automodapi:: subsurface.reader.topography.topo_core
+   :no-inheritance-diagram:reader
+
+
+.. automodule:: subsurface.reader.volume
+
+.. automodapi:: subsurface.reader.volume.read_volume
+   :no-inheritance-diagram:reader
+
+.. automodapi:: subsurface.reader.volume.volume_utils
+   :no-inheritance-diagram:reader
+
+
+.. automodule:: subsurface.reader.wells
+
+.. automodapi:: subsurface.reader.wells.pandas_to_welly
+   :no-inheritance-diagram:reader
+
+.. automodapi:: subsurface.reader.wells.well_files_reader
+   :no-inheritance-diagram:reader
+
+.. automodapi:: subsurface.reader.wells.wells_api
+   :no-inheritance-diagram:reader
+
+.. automodapi:: subsurface.reader.wells.wells_utils
+   :no-inheritance-diagram:reader
+
+.. automodapi:: subsurface.reader.wells.welly_reader
+   :no-inheritance-diagram:reader
diff --git a/docs/source/code-structs.rst b/docs/source/code-structs.rst
@@ -0,0 +1,25 @@
+Structures
+==========
+
+.. automodule:: subsurface.structs
+
+.. automodapi:: subsurface.structs.errors
+   :no-inheritance-diagram:
+
+.. automodapi:: subsurface.structs.structured_elements
+   :no-inheritance-diagram:
+
+.. automodapi:: subsurface.structs.unstructured_elements
+   :no-inheritance-diagram:
+
+
+.. automodule:: subsurface.structs.base_structures
+
+.. automodapi:: subsurface.structs.base_structures.common_data_utils
+   :no-inheritance-diagram:
+
+.. automodapi:: subsurface.structs.base_structures.structured_data
+   :no-inheritance-diagram:
+
+.. automodapi:: subsurface.structs.base_structures.unstructured_data
+   :no-inheritance-diagram:
diff --git a/docs/source/code-utils.rst b/docs/source/code-utils.rst
@@ -0,0 +1,7 @@
+Utilities
+=========
+
+.. automodule:: subsurface.utils
+
+.. automodapi:: subsurface.utils.utils_core
+   :no-inheritance-diagram:
diff --git a/docs/source/code-viz.rst b/docs/source/code-viz.rst
@@ -0,0 +1,7 @@
+Visualization
+=============
+
+.. automodule:: subsurface.visualization
+
+.. automodapi:: subsurface.visualization.to_pyvista
+   :no-inheritance-diagram: