interp traceinv

ameli · Mar 6, 2022 · 1009e0a · 1009e0a
1 parent 50ca6ee
commit 1009e0a
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diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -21,15 +21,14 @@ jobs:
                   ACCESS_TOKEN: ${{ secrets.IMATE_DOCS }}
                   BASE_BRANCH: main
                   BRANCH: gh-pages
-                  FOLDER: docs/_build/html
+                  FOLDER: docs/build/html
                   BUILD_SCRIPT: |
                       apt-get update
                       apt-get install graphviz -y
                       pip install --upgrade pip
                       pip install .[docs]
                       export PATH=$HOME/.local/bin:$PATH
-                      sphinx-apidoc -f -o docs/_modules/ ./imate
-                      python setup.py build_sphinx
+                      make html --directory=docs
                       touch docs/_build/html/.nojekyll
                       echo 'Visit [Documentation](https://ameli.github.io/imate/index.html).' > docs/_build/html/README.md
 
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -16,10 +16,12 @@ recursive-include docs *.py
 recursive-include docs *.rst
 recursive-include docs *.svg
 recursive-include docs Makefile
-recursive-include _modules *.rst
-recursive-exclude docs/images *.pdf
 recursive-include docs *.bib
 recursive-include docs *.in
+recursive-include docs *.txt
+recursive-exclude docs *.html
+recursive-exclude docs *.pdf
+recursive-include docs/source *.html
 
 recursive-include imate *.rst
 recursive-include examples *.py
@@ -28,6 +30,7 @@ recursive-include notebooks *.ipynb
 recursive-include tests *.py
 recursive-include tests *.rst
 recursive-exclude tests *.svg
+recursive-include tests *.txt
 
 include CHANGELOG.rst
 include README.rst
@@ -46,6 +49,7 @@ exclude .travis.yml
 exclude .coverage
 exclude .gitattributes
 
+prune docs/build
 prune .git
 prune tmp
 prune .tox

diff --git a/docs/Makefile b/docs/Makefile
@@ -5,8 +5,8 @@
 # from the environment for the first two.
 SPHINXOPTS    ?=
 SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
+SOURCEDIR     = source
+BUILDDIR      = build
 
 # Put it first so that "make" without argument is like "make help".
 help:

diff --git a/docs/_modules/imate.functions.rst b/docs/_modules/imate.functions.rst
diff --git a/docs/_modules/imate.generate_matrix.rst b/docs/_modules/imate.generate_matrix.rst
diff --git a/docs/_modules/imate.interpolate_traceinv.rst b/docs/_modules/imate.interpolate_traceinv.rst
diff --git a/docs/_modules/imate.linear_operator.rst b/docs/_modules/imate.linear_operator.rst
diff --git a/docs/_modules/imate.logdet.rst b/docs/_modules/imate.logdet.rst
diff --git a/docs/_modules/imate.rst b/docs/_modules/imate.rst
diff --git a/docs/_modules/imate.sample_matrices.rst b/docs/_modules/imate.sample_matrices.rst
diff --git a/docs/_modules/imate.trace.rst b/docs/_modules/imate.trace.rst
diff --git a/docs/_modules/imate.traceinv.rst b/docs/_modules/imate.traceinv.rst
diff --git a/docs/_modules/modules.rst b/docs/_modules/modules.rst
diff --git a/docs/make.bat b/docs/make.bat
@@ -7,8 +7,8 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=sphinx-build
 )
-set SOURCEDIR=.
-set BUILDDIR=_build
+set SOURCEDIR=source
+set BUILDDIR=build
 
 if "%1" == "" goto help
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1,8 @@
+sphinx
+sphinx-math-dollar
+sphinx-toggleprompt
+sphinx_rtd_theme
+pydata_sphinx_theme
+graphviz
+sphinx-automodapi
+numpydoc
diff --git a/docs/_static/css/custom-anaconda-doc.css → ...ource/_static/css/custom-anaconda-doc.css b/docs/_static/css/custom-anaconda-doc.css → ...ource/_static/css/custom-anaconda-doc.css
diff --git a/docs/_static/css/custom.css → docs/source/_static/css/custom.css b/docs/_static/css/custom.css → docs/source/_static/css/custom.css
diff --git a/docs/images/CorrelationMatrix.svg → ...urce/_static/images/CorrelationMatrix.svg b/docs/images/CorrelationMatrix.svg → ...urce/_static/images/CorrelationMatrix.svg
diff --git a/docs/images/Example1.pdf → docs/source/_static/images/Example1.pdf b/docs/images/Example1.pdf → docs/source/_static/images/Example1.pdf
diff --git a/docs/images/Example1.svg → docs/source/_static/images/Example1.svg b/docs/images/Example1.svg → docs/source/_static/images/Example1.svg
diff --git a/docs/images/Example2.pdf → docs/source/_static/images/Example2.pdf b/docs/images/Example2.pdf → docs/source/_static/images/Example2.pdf
diff --git a/docs/images/Example2.svg → docs/source/_static/images/Example2.svg b/docs/images/Example2.svg → docs/source/_static/images/Example2.svg
diff --git a/docs/images/GeneralizedCrossValidation.pdf → ...tic/images/GeneralizedCrossValidation.pdf b/docs/images/GeneralizedCrossValidation.pdf → ...tic/images/GeneralizedCrossValidation.pdf
diff --git a/docs/images/GeneralizedCrossValidation.svg → ...tic/images/GeneralizedCrossValidation.svg b/docs/images/GeneralizedCrossValidation.svg → ...tic/images/GeneralizedCrossValidation.svg
diff --git a/docs/images/InterpolationResults.svg → ...e/_static/images/InterpolationResults.svg b/docs/images/InterpolationResults.svg → ...e/_static/images/InterpolationResults.svg
diff --git a/docs/images/generalized_cross_validation.pdf → ...c/images/generalized_cross_validation.pdf b/docs/images/generalized_cross_validation.pdf → ...c/images/generalized_cross_validation.pdf
diff --git a/docs/images/generalized_cross_validation.svg → ...c/images/generalized_cross_validation.svg b/docs/images/generalized_cross_validation.svg → ...c/images/generalized_cross_validation.svg
diff --git a/docs/images/image00.svg → docs/source/_static/images/image00.svg b/docs/images/image00.svg → docs/source/_static/images/image00.svg
diff --git a/docs/images/image01.svg → docs/source/_static/images/image01.svg b/docs/images/image01.svg → docs/source/_static/images/image01.svg
diff --git a/docs/images/image02.svg → docs/source/_static/images/image02.svg b/docs/images/image02.svg → docs/source/_static/images/image02.svg
diff --git a/docs/images/image03.svg → docs/source/_static/images/image03.svg b/docs/images/image03.svg → docs/source/_static/images/image03.svg
diff --git a/docs/images/image04.svg → docs/source/_static/images/image04.svg b/docs/images/image04.svg → docs/source/_static/images/image04.svg
diff --git a/docs/images/image05.svg → docs/source/_static/images/image05.svg b/docs/images/image05.svg → docs/source/_static/images/image05.svg
diff --git a/docs/images/image06.svg → docs/source/_static/images/image06.svg b/docs/images/image06.svg → docs/source/_static/images/image06.svg
diff --git a/docs/images/test_Example1.pdf → docs/source/_static/images/test_Example1.pdf b/docs/images/test_Example1.pdf → docs/source/_static/images/test_Example1.pdf
diff --git a/docs/images/test_Example1.svg → docs/source/_static/images/test_Example1.svg b/docs/images/test_Example1.svg → docs/source/_static/images/test_Example1.svg
diff --git a/docs/images/test_Example2.pdf → docs/source/_static/images/test_Example2.pdf b/docs/images/test_Example2.pdf → docs/source/_static/images/test_Example2.pdf
diff --git a/docs/images/test_Example2.svg → docs/source/_static/images/test_Example2.svg b/docs/images/test_Example2.svg → docs/source/_static/images/test_Example2.svg
diff --git a/...mages/test_GeneralizedCrossValidation.pdf → ...mages/test_GeneralizedCrossValidation.pdf b/...mages/test_GeneralizedCrossValidation.pdf → ...mages/test_GeneralizedCrossValidation.pdf
diff --git a/...mages/test_GeneralizedCrossValidation.svg → ...mages/test_GeneralizedCrossValidation.svg b/...mages/test_GeneralizedCrossValidation.svg → ...mages/test_GeneralizedCrossValidation.svg
diff --git a/docs/source/_templates/autosummary/attribute.rst b/docs/source/_templates/autosummary/attribute.rst
@@ -0,0 +1,8 @@
+:orphan:
+
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoattribute:: {{ objname }}
diff --git a/docs/source/_templates/autosummary/class.rst b/docs/source/_templates/autosummary/class.rst
@@ -0,0 +1,38 @@
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
+
+  {% block methods %}
+   .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages.
+      .. autosummary::
+         :toctree:
+      {% for item in all_methods %}
+         {%- if not item.startswith('_') or item in ['__call__', '__mul__', '__getitem__', '__len__'] %}
+         {{ name }}.{{ item }}
+         {%- endif -%}
+      {%- endfor %}
+      {% for item in inherited_members %}
+         {%- if item in ['__call__', '__mul__', '__getitem__', '__len__'] %}
+         {{ name }}.{{ item }}
+         {%- endif -%}
+      {%- endfor %}
+  {% endblock %}
+
+  {% block attributes %}
+  {% if attributes %}
+   .. HACK -- the point here is that we don't want this to appear in the output, but the autosummary should still generate the pages.
+      .. autosummary::
+         :toctree:
+      {% for item in all_attributes %}
+         {%- if not item.startswith('_') %}
+         {{ name }}.{{ item }}
+         {%- endif -%}
+      {%- endfor %}
+  {% endif %}
+  {% endblock %}
diff --git a/docs/source/_templates/autosummary/method.rst b/docs/source/_templates/autosummary/method.rst
@@ -0,0 +1,8 @@
+:orphan:
+
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. automethod:: {{ objname }}
diff --git a/docs/source/_templates/autosummary/ndarray_subclass.rst b/docs/source/_templates/autosummary/ndarray_subclass.rst
@@ -0,0 +1,10 @@
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. class:: {{ objname }}
+
+This is an ndarray wrapper for a native MATLAB object. This class is not meant
+to be instantiated directly, but can be used for type checking
+:func:`scipy.io.loadmat` outputs.
diff --git a/docs/source/_templates/autosummary/property.rst b/docs/source/_templates/autosummary/property.rst
@@ -0,0 +1,8 @@
+:orphan:
+
+{{ fullname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoproperty:: {{ objname }}