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Numpy docstrings api #253

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merged 81 commits into from Oct 6, 2021
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f51c1f5
coordinate and interpolation utils docstrings update
dccowan Oct 13, 2020
018e44d
More docstrings and examples added
dccowan Oct 14, 2020
8e7042e
Finish mesh utils and fix syntax errors in docstrings
dccowan Oct 14, 2020
10e46ee
Update some syntax. Add example. Change method name to 'closest_point…
dccowan Oct 14, 2020
c384a7a
Update closest points function. Add examples and docstrings for inver…
dccowan Oct 15, 2020
a10b54b
Fix syntax for defining parameters. Added some math to docstrings and…
dccowan Oct 15, 2020
8e57079
Merge branch 'restructure' into numpy_docstrings_api
dccowan Oct 16, 2020
b0d3b13
Merge branch 'restructure' into numpy_docstrings_api
dccowan Nov 4, 2020
6313d6d
Add more docstrings to base mesh and base tensor mesh
dccowan Nov 11, 2020
f05e70c
Add docstrings to tensor mesh
dccowan Nov 15, 2020
b51ed4d
Merge branch 'restructure' into numpy_docstrings_api
dccowan Nov 16, 2020
cee7c74
switch for a pydata sphinx theme, and move around some items.
jcapriot Dec 3, 2020
ffb4f58
updates for formatting
jcapriot Dec 7, 2020
0d667eb
Merge branch 'de-prop' into pydata_retheme
jcapriot Dec 11, 2020
cfd5aa9
Merge branch 'de-prop' into pydata_retheme
jcapriot Dec 11, 2020
e86c02e
apply stash
jcapriot Dec 12, 2020
8cea4ea
updating documentation for base_mesh
jcapriot Dec 12, 2020
ff6e4eb
update documentation of BaseMesh
jcapriot Dec 12, 2020
8b51db9
make deprecate_* functions include a See Also link
jcapriot Dec 12, 2020
7d351d2
put links to examples/tutorials back in for classes.
jcapriot Dec 12, 2020
645d95d
Merge branch 'de-prop' into pydata_retheme
jcapriot Dec 16, 2020
9cb0016
Merge branch 'master' into numpy_docstrings_api
dccowan Apr 1, 2021
8de2448
Merge branch 'de-prop' into numpy_docstrings_api
dccowan Apr 1, 2021
cd71b14
update some docstrings
dccowan Apr 2, 2021
27a2ea0
Merge branch 'de-prop' into pydata_retheme
jcapriot Apr 2, 2021
2961d3e
Merge branch 'pydata_retheme' into numpy_docstrings_api
dccowan Apr 2, 2021
64beea3
some global api organization
dccowan Apr 7, 2021
f2f4a20
Merge branch 'de-prop' into numpy_docstrings_api
dccowan Apr 28, 2021
25030f4
Merge branch 'main' into pydata_retheme
jcapriot Apr 30, 2021
dc7e335
Merge branch 'pydata_retheme' into numpy_docstrings_api
jcapriot Apr 30, 2021
0b3bb97
Merge branch 'main' into pydata_retheme
jcapriot Apr 30, 2021
753c485
remove duplicate function
dccowan May 3, 2021
8d9dae8
docstrings and examples for mesh_utils, matrix_utils and curvilinear_…
dccowan May 11, 2021
3a8e6a2
First draft of API for utilities
dccowan May 12, 2021
1c9d0f7
Docstring progress on mesh classes
dccowan Jun 4, 2021
33bc5e7
Edits to mesh properties and methods
dccowan Jun 8, 2021
43c909c
Add links to other classes and functions in utils
dccowan Jun 9, 2021
ac1c249
Move exampe curvilinear grid to curvilinear utils
dccowan Jun 9, 2021
4bd37bf
Merge branch 'pydata_retheme' into numpy_docstrings_api
dccowan Jun 9, 2021
527baeb
Most base tensor mesh docstrings
dccowan Jun 11, 2021
0dc4141
TreeMesh and TreeCell docstring
dccowan Jun 16, 2021
3cf4027
Docstrings for curvilinear meshes
dccowan Jun 17, 2021
d954f82
Instantiation parameters and examples for mesh types
dccowan Jun 18, 2021
4027ea7
Docstrings for meshIO mixins
dccowan Jun 21, 2021
db4dc1e
Docstrings for VTK Mixins
dccowan Jun 22, 2021
28344eb
Some formatting of docstrings
dccowan Jun 22, 2021
d5c7e1a
More docstring formatting
dccowan Jun 22, 2021
08476f6
Fix syntax for plotting mesh examples
dccowan Jun 22, 2021
460435b
Some docstrings for differential operators (incomplete)
dccowan Jul 5, 2021
e110dcb
Document inner product matrices
dccowan Jul 7, 2021
84cd539
edits to differential operators
dccowan Jul 7, 2021
b2badec
Cell grad boundary conditions edits
dccowan Jul 8, 2021
47cc10e
Differential operators and complete averaging operators documentation
dccowan Jul 10, 2021
ee3f629
doc projection matrices
dccowan Jul 12, 2021
7f2b690
Typos
dccowan Jul 12, 2021
44e2868
Fix grammar and some examples
dccowan Jul 21, 2021
6c16fb4
Update link check to look at platform
dccowan Jul 21, 2021
972d05f
add import platform
dccowan Jul 21, 2021
e46b7e3
formatting updates
jcapriot Jul 28, 2021
e4defc0
More cleanups
jcapriot Jul 30, 2021
c3e1233
no message
jcapriot Aug 4, 2021
cef8554
undo doc test change for linux/mac
jcapriot Aug 5, 2021
e98fb73
intersphinx update
jcapriot Aug 5, 2021
cd3cec1
formatting updates
jcapriot Aug 6, 2021
2000636
update navbar icon colors
jcapriot Aug 6, 2021
dd95fd4
minor mixin edits
jcapriot Aug 6, 2021
3f096b0
master -> main
jcapriot Aug 6, 2021
b1c089f
Add at least a line of text to each of these introducing the section.
jcapriot Aug 6, 2021
f4b9c57
update the installation recommendation for current best practices
jcapriot Aug 6, 2021
c753649
some more formatting updates
jcapriot Aug 7, 2021
d60680e
remove old documentation config options
jcapriot Aug 9, 2021
f500359
add graphviz to the documentation build option (for 3.8)
jcapriot Aug 9, 2021
5d29b35
add 3.9 to windows wheel build
jcapriot Aug 9, 2021
9992897
update some wording on these two landing pages.
jcapriot Aug 9, 2021
f963275
update incorrect references to classes in discretize.base
jcapriot Aug 9, 2021
128c475
add conda-forge badge
jcapriot Aug 9, 2021
66bf256
Merge pull request #258 from jcapriot/numpy_docstrings_api_review
dccowan Aug 16, 2021
b98a184
add pydata theme to dev requirements
dccowan Aug 16, 2021
b217e92
Use toolbox collapse extension for long plotting scripts
dccowan Aug 16, 2021
b3165b3
add sphinx-toolbox to the requirements-dev file
jcapriot Oct 5, 2021
3bdd8a6
updates for deprecations in pyvista
jcapriot Oct 5, 2021
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4 changes: 2 additions & 2 deletions .azure-pipelines/azure-pipelines-linux.yml
Expand Up @@ -26,7 +26,7 @@ jobs:
- script: |
eval "$(conda shell.bash hook)"
conda activate test
conda install --yes --quiet -c conda-forge numpy scipy matplotlib cython vtk properties vectormath pyvista pymatsolver
conda install --yes --quiet -c conda-forge numpy scipy matplotlib cython vtk pyvista pymatsolver graphviz
pip install -r requirements_dev.txt
pip install -e .
displayName: Install requirements and build
Expand All @@ -43,7 +43,7 @@ jobs:
- script: |
eval "$(conda shell.bash hook)"
conda activate test
conda install --yes --quiet -c conda-forge numpy scipy matplotlib cython vtk properties vectormath pyvista pymatsolver
conda install --yes --quiet -c conda-forge numpy scipy matplotlib cython vtk pyvista pymatsolver graphviz
conda install --yes --quiet -c conda-forge pytest pytest-cov
pip install -r requirements_dev.txt
pip install pytest-azurepipelines
Expand Down
2 changes: 1 addition & 1 deletion .azure-pipelines/azure-pipelines-osx.yml
Expand Up @@ -26,7 +26,7 @@ jobs:
- script: |
eval "$(conda shell.bash hook)"
conda activate test
conda install --yes --quiet -c conda-forge numpy scipy matplotlib">=3.0.0" cython vtk properties vectormath pyvista pymatsolver
conda install --yes --quiet -c conda-forge numpy scipy matplotlib">=3.0.0" cython vtk pyvista pymatsolver graphviz
conda install --yes --quiet -c conda-forge pytest
pip install -r requirements_dev.txt
pip install pytest-azurepipelines
Expand Down
2 changes: 1 addition & 1 deletion .azure-pipelines/azure-pipelines-win.yml
Expand Up @@ -17,7 +17,7 @@ jobs:
displayName: Add conda to PATH

- script: |
conda create --yes --quiet -c conda-forge --name test python=$(python.version) numpy scipy matplotlib cython vtk properties vectormath pyvista pymatsolver pip
conda create --yes --quiet -c conda-forge --name test python=$(python.version) numpy scipy matplotlib cython vtk pyvista pymatsolver pip
displayName: Create Anaconda environment

- script: |
Expand Down
12 changes: 8 additions & 4 deletions README.rst
Expand Up @@ -5,15 +5,19 @@ discretize
:target: https://pypi.python.org/pypi/discretize
:alt: Latest PyPI version

.. image:: https://anaconda.org/conda-forge/discretize/badges/version.svg
:target: https://anaconda.org/conda-forge/discretize
:alt: Latest conda-forge version

.. image:: https://img.shields.io/github/license/simpeg/simpeg.svg
:target: https://github.com/simpeg/discretize/blob/master/LICENSE
:target: https://github.com/simpeg/discretize/blob/main/LICENSE
:alt: MIT license

.. image:: https://dev.azure.com/simpeg/discretize/_apis/build/status/simpeg.discretize?branchName=master
:target: https://dev.azure.com/simpeg/discretize/_build/latest?definitionId=1&branchName=master
.. image:: https://dev.azure.com/simpeg/discretize/_apis/build/status/simpeg.discretize?branchName=main
:target: https://dev.azure.com/simpeg/discretize/_build/latest?definitionId=1&branchName=main
:alt: Azure pipelines build status

.. image:: https://codecov.io/gh/simpeg/discretize/branch/master/graph/badge.svg
.. image:: https://codecov.io/gh/simpeg/discretize/branch/main/graph/badge.svg
:target: https://codecov.io/gh/simpeg/discretize
:alt: Coverage status

Expand Down
4 changes: 3 additions & 1 deletion azure-pipelines.yml
Expand Up @@ -48,7 +48,7 @@ stages:
eval "$(conda shell.bash hook)"
conda activate test
conda env list
conda install --yes --quiet -c conda-forge numpy scipy matplotlib cython vtk properties vectormath pyvista
conda install --yes --quiet -c conda-forge numpy scipy matplotlib cython vtk properties vectormath pyvista graphviz
pip install -r requirements_dev.txt
pip install .
displayName: building and installing deps
Expand Down Expand Up @@ -95,6 +95,8 @@ stages:
python.version: '3.7'
win-Python38:
python.version: '3.8'
win-Python39:
python.version: '3.9'
pool:
vmImage: vs2017-win2016
steps:
Expand Down
31 changes: 31 additions & 0 deletions discretize/__init__.py
@@ -1,3 +1,34 @@
"""
=====================================
Discretize Meshes (:mod:`discretize`)
=====================================
.. currentmodule:: discretize

The ``discretize`` package contains four types of meshes for soliving partial differential
equations using the finite volume method.

Mesh Classes
============
.. autosummary::
:toctree: generated/

TensorMesh
CylindricalMesh
CurvilinearMesh
TreeMesh

Tree Mesh Cells
===============
The :class:`~discretize.tree_mesh.TreeCell` class was designed specificialy to define the cells within tree meshes.
Instances of :class:`~discretize.tree_mesh.TreeCell` are not meant to be created on there own.
However, they can be returned directly by indexing a particular cell within a tree mesh.

.. autosummary::
:toctree: generated/

tree_mesh.TreeCell
"""

from discretize.tensor_mesh import TensorMesh
from discretize.cylindrical_mesh import CylMesh, CylindricalMesh
from discretize.curvilinear_mesh import CurvilinearMesh
Expand Down