Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Redesign #216

Merged
merged 110 commits into from
Jun 15, 2023
Merged
Show file tree
Hide file tree
Changes from 100 commits
Commits
Show all changes
110 commits
Select commit Hold shift + click to select a range
2eaa755
Redesign prototype (#215)
erogluorhan Feb 2, 2023
82c6f03
Redesign (#217)
erogluorhan Feb 2, 2023
828c273
Add UxDataArray and convert xr.DataArrays of UxDataset to this class'…
erogluorhan Feb 17, 2023
f7d7ca1
Add the forgotten dataarray.py
erogluorhan Feb 17, 2023
fc5fa79
Fix test_api.py
erogluorhan Feb 17, 2023
5082ca2
Merge branch 'main' of github.com:UXARRAY/uxarray into prototype_rede…
erogluorhan Feb 17, 2023
f8311d3
o Fix __setitem__ function, it was causing the uxarray dataset object…
rajeeja Mar 4, 2023
9576556
o fix pre-commit
rajeeja Mar 4, 2023
57ffcc9
o Remove TODO comments
rajeeja Mar 4, 2023
a051a70
o reorganize files into folders, fix tests and docs (#224)
rajeeja Mar 7, 2023
3866d8b
refelct restructure in docs test (#227)
anissa111 Mar 7, 2023
8078b0b
Equals and Not Equals Operators
philipc2 Mar 10, 2023
56eccb6
remove leftover code
philipc2 Mar 10, 2023
08f477d
typo fix
philipc2 Mar 10, 2023
8a60d2e
refelct restructure in docs test (#227)
anissa111 Mar 7, 2023
5e9d3b2
Merge branch 'prototype_redesign' into philipc2/grid_eq
philipc2 Mar 10, 2023
b784bf4
Merge pull request #231 from UXARRAY/philipc2/grid_eq
rajeeja Mar 10, 2023
96395d0
o Try to fix the warning message: FutureWarning: xarray subclass UxDa…
rajeeja Mar 10, 2023
45fa6b5
`Info` Method for `ux.Dataset` (#236)
philipc2 Mar 18, 2023
c9f1748
o Fix slot errors
rajeeja Mar 21, 2023
bbe2488
o Add cosmetic fixes
rajeeja Mar 24, 2023
fea09e5
Merge branch 'prototype_redesign' into rajeeja/slots_warning_fix
philipc2 Mar 24, 2023
00e9a9e
Update uxarray/core/dataarray.py
rajeeja Mar 25, 2023
2c8c70c
Update uxarray/core/dataarray.py
rajeeja Mar 25, 2023
c8419f9
Update uxarray/core/dataset.py
rajeeja Mar 25, 2023
f05e33b
Update uxarray/core/dataset.py
rajeeja Mar 25, 2023
f289425
Update uxarray/core/dataset.py
rajeeja Mar 25, 2023
d88165f
o use ugrid_obj instead of ugrid as ugrid is used a string to testing…
rajeeja Mar 25, 2023
e27c7af
Merge branch 'rajeeja/slots_warning_fix' of github.com:UXARRAY/uxarra…
rajeeja Mar 25, 2023
0f01ac1
o accepting changes from comment can be dangerous
rajeeja Mar 25, 2023
918da51
Merge pull request #235 from UXARRAY/rajeeja/slots_warning_fix
rajeeja Mar 26, 2023
17ce01e
Fix conflicts after merging main
erogluorhan Mar 31, 2023
8c6341c
Fix errors after conflict resolutions
erogluorhan Mar 31, 2023
9e7c419
Attempt to fix sphinx-book-theme not importing issue
erogluorhan Mar 31, 2023
f8e7798
Attempt #2 to fix sphinx-book-theme not importing issue
erogluorhan Mar 31, 2023
67fc369
Fixed sphinx_book_theme issue but trying another thing
erogluorhan Mar 31, 2023
318f617
Attempt to fix sphinx_book_theme via actual reason pydata-sphinx-theme
erogluorhan Mar 31, 2023
75a7c71
Turning back to the only working fix
erogluorhan Mar 31, 2023
6152fb3
add (use_dual) to api (#260)
philipc2 Apr 4, 2023
04197d2
Fix conflicts after merging main branch here
erogluorhan Apr 17, 2023
1177703
Reflected the design changes on example notebooks 1 and 2
erogluorhan Apr 20, 2023
2ff4835
Added a failing test for geoflow-small's 'unable to repr' issue
erogluorhan Apr 20, 2023
673f3a0
Update from main and resolve conflicts
erogluorhan Apr 27, 2023
5c2872b
Fix datarray.py uxgrid requirements
erogluorhan May 1, 2023
bc429a5
Fix dataset to get Anissa's notebook to execute
erogluorhan May 2, 2023
e7da6e0
o Add a failing test for copy of dataset object losing uxgrid
rajeeja May 5, 2023
4ee6dd6
Add UxDataset._copy and Grid.copy
erogluorhan May 9, 2023
c30ffca
Merge branch 'main' of github.com:UXARRAY/uxarray into prototype_rede…
erogluorhan May 9, 2023
3ad81ab
Fix dual mesh-related nMaxMesh2_face_nodes issue
erogluorhan May 9, 2023
e93b3e6
o Add support for shallow and deep copy for uxarray object
rajeeja May 15, 2023
a920de6
Merge main into redesign and resolve conflicts
erogluorhan May 15, 2023
c220101
Override _replace for UxDataset and UxDataArray
erogluorhan May 19, 2023
c1dd8d9
Merge branch 'main' into prototype_redesign
erogluorhan May 21, 2023
d6bab59
Merge branch 'main' into prototype_redesign
erogluorhan May 21, 2023
5168867
fix merge conflicts
philipc2 May 24, 2023
a376b76
fix some more merge issues
philipc2 May 24, 2023
d5e8d40
precommit
philipc2 May 24, 2023
3e339be
Merge branch 'main' into prototype_redesign
philipc2 May 24, 2023
7ec6bc9
Fix internal API docs after updates with main
erogluorhan May 24, 2023
9cad7e8
version bump for dev release (#327)
anissa111 May 24, 2023
9af34e5
Resolve issues with to_array() and arithmetic ops in Philip's notebook
erogluorhan May 30, 2023
600edb0
Merge branch 'main' of github.com:UXARRAY/uxarray into prototype_rede…
erogluorhan May 30, 2023
f784a69
Resolve conflicts after udpdating with main
erogluorhan May 30, 2023
34f0d2b
resolve conflicts
philipc2 Jun 5, 2023
cce1c6e
init imports
philipc2 Jun 5, 2023
f16dbf1
update init
philipc2 Jun 5, 2023
d5fd604
Improved Access & Representation of UGRID Topology Variables (#325)
philipc2 Jun 8, 2023
46cd021
Fix Grid vs open_grid usages
erogluorhan Jun 9, 2023
a318fbc
Update Documentation & Clean-Up Code for Redesign (#336)
philipc2 Jun 9, 2023
58fe551
updated PR template
philipc2 Jun 9, 2023
349090e
Address reviews from @philipc2 on return type and @dcherian on __get_…
erogluorhan Jun 9, 2023
80e982f
Update uxarray/core/api.py
erogluorhan Jun 9, 2023
cb25f77
Update uxarray/core/api.py
erogluorhan Jun 9, 2023
852f3ee
Merge branch 'prototype_redesign' of github.com:UXARRAY/uxarray into …
erogluorhan Jun 9, 2023
c58be37
Address reviews from @philipc2 on doc strings
erogluorhan Jun 9, 2023
cc61e41
Update uxarray/core/dataset.py
erogluorhan Jun 9, 2023
adf88c0
Update uxarray/core/dataset.py
erogluorhan Jun 9, 2023
c29b1cd
Update uxarray/core/grid.py
erogluorhan Jun 9, 2023
e6b9c8d
Address more reviews
erogluorhan Jun 9, 2023
c14b262
Merge branch 'prototype_redesign' of github.com:UXARRAY/uxarray into …
erogluorhan Jun 9, 2023
b36122a
Update uxarray/core/grid.py
erogluorhan Jun 9, 2023
8e9d75a
Comment out UxDataset.__setitem__ for now, unpin sphinx-book-theme
erogluorhan Jun 9, 2023
2c245c8
Merge branch 'prototype_redesign' of github.com:UXARRAY/uxarray into …
erogluorhan Jun 9, 2023
e9add52
some small changes to overview
philipc2 Jun 12, 2023
f220030
modified example to better showcase attributes
philipc2 Jun 12, 2023
f236ed4
attributes for cart_x_y_z and updated notebook
philipc2 Jun 12, 2023
34d4f09
allow open_dataset to operate without data file
philipc2 Jun 12, 2023
e7b20f6
Revert "allow open_dataset to operate without data file"
erogluorhan Jun 13, 2023
7077bd6
Comment out integrate from Grid
erogluorhan Jun 13, 2023
ccb368e
Initialize updating uxarray-api.md and creating announcement.rst
erogluorhan Jun 13, 2023
b7ae87d
More uodates on uxarray_api.md
erogluorhan Jun 14, 2023
f5b7e17
Last updates to uxarray_api.md and announcement
erogluorhan Jun 15, 2023
2f62ba9
Address @hongyuchen1030's requests
erogluorhan Jun 15, 2023
49482d6
Apply @ifranda's typo fix
erogluorhan Jun 15, 2023
07f6fdd
fix some typos
philipc2 Jun 15, 2023
aa49c79
Xarray methods and operator showcase in notebook
philipc2 Jun 15, 2023
98dab17
FIx the formatting issues in the announcement
erogluorhan Jun 15, 2023
80eaaae
Merge branch 'prototype_redesign' of github.com:UXARRAY/uxarray into …
erogluorhan Jun 15, 2023
84eb190
section to describe fill value and int dtype
philipc2 Jun 15, 2023
9ae6ac7
Merge branch 'prototype_redesign' of https://github.com/UXARRAY/uxarr…
philipc2 Jun 15, 2023
45a508d
Update docs/getting-started/overview.rst
philipc2 Jun 15, 2023
7c7017c
update notebook
philipc2 Jun 15, 2023
150135f
pre commit
philipc2 Jun 15, 2023
536ba3a
Update uxarray/core/dataset.py
philipc2 Jun 15, 2023
3607202
Update uxarray/core/dataset.py
philipc2 Jun 15, 2023
1cc0ff1
Update uxarray/core/dataarray.py
philipc2 Jun 15, 2023
ffb5475
Update uxarray/core/dataarray.py
philipc2 Jun 15, 2023
857aea1
Update uxarray/core/dataarray.py
philipc2 Jun 15, 2023
209e3d9
pre commit
philipc2 Jun 15, 2023
44f00b3
fix hyperlinks in announcement
philipc2 Jun 15, 2023
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 4 additions & 3 deletions .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -18,13 +18,14 @@ import uxarray as ux
grid_path = "/path/to/grid.nc"
data_path = "/path/to/data.nc"

uxgrid = ux.Grid(grid_path)
uxds = ux.open_dataset(grid_path, data_path)

# this is how you use this function
some_output = uxgrid.some_function()
some_output = uxds.some_function()

# this is another way to use this function
other_output = uxgrid.some_function(some_param = True)
other_output = uxds.some_function(some_param = True)

```

## PR Checklist
Expand Down
10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,9 @@

UXarray aims to address the geoscience community need for tools that enable
standard data analysis techniques to operate directly on unstructured grid
data. UXarray will provide Xarray styled functions to better read in and use
data. UXarray provides Xarray styled functions to better read in and use
unstructured grid datasets that follow standard conventions, including UGRID,
SCRIP, Exodus and shapefile formats. This effort is a result of the
MPAS, SCRIP, and Exodus formats. This effort is a result of the
collaboration between Project Raijin (NCAR and Pennsylvania State University)
and the SEATS Project (Argonne National Laboratory, UC Davis, and Lawrence
Livermore National Laboratory). The UXarray team welcomes other community
Expand All @@ -26,11 +26,11 @@ under the `Issues` tab in the UXarray repository.
# Why is the name "UXarray"?

We have created UXarray based on [Xarray](https://docs.xarray.dev/en/stable/)
(via composition of a Xarray dataset object), a Pangeo ecosystem package
(via inheritance of Xarray Dataset and DataArray classes), a Pangeo ecosystem package
commonly-used for structured grids recognition, to support reading and
recognizing unstructured grid model outputs. We picked the name "UXarray"
and preferred to capitalize the first two letters to emphasize it is Xarray
for Unstructured grids.
(pronounced "you-ex-array") and preferred to capitalize the first two letters to
emphasize it builds upon Xarray for Unstructured grids.

# UXarray Functionality

Expand Down
24 changes: 24 additions & 0 deletions docs/announcement.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
.. currentmodule:: uxarray

.. _announcement:

Announcement
============

v2023.6.0 of UXarray includes significant code design & API changes
to address the user needs and requests better. Further information
about the design change can be found in several places such as:

- v2023.6.0 Release notes

- [GitHub Discussion - UXarray Redesign Thoughts and
Options](https://github.com/UXARRAY/uxarray/discussions/185)

- [GitHub Pull Request #216 -
Redesign](https://github.com/UXARRAY/uxarray/pull/216) that implemented
the new design with all the code and documentation changes

- [Usage examples](https://uxarray.readthedocs.io/en/latest/examples.html)
can be utilized to get to know the new design

Feel free to reach out to us with any questions/concerns.
6 changes: 4 additions & 2 deletions docs/api.rst
Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,10 @@
API Reference
=============

Below user API and internal API pages show already-implemented Uxarray functionality.
You can also check the draft `Uxarray API


Below user API and internal API pages show already-implemented UXarray functionality.
You can also check the draft `UXarray API
<https://github.com/UXARRAY/uxarray/blob/main/docs/user_api/uxarray_api.md>`_
documentation to see the tentative whole API and let us know if you have any feedback!

Expand Down
14 changes: 7 additions & 7 deletions docs/citation.rst
Original file line number Diff line number Diff line change
Expand Up @@ -2,17 +2,17 @@

.. _citation:

How to Cite Uxarray
How to Cite UXarray
===================

Cite Uxarray using the following text:
Cite UXarray using the following text:

**UXARRAY Organization. (Year).
Uxarray (version \<version\>) [Software].
**UXarray Organization. (Year).
UXarray (version \<version\>) [Software].
Project Raijin & Project SEATS. doi:10.5281/zenodo.<doi-part-per-version>.**

Update the year, Uxarray version, and DOI part for UXarray version as appropriate. For example:
Update the year, UXarray version, and DOI part for UXarray version as appropriate. For example:

**UXARRAY Organization. (2021).
Uxarray (version 0.0.2) [Software].
**UXarray Organization. (2021).
UXarray (version 0.0.2) [Software].
Project Raijin & Project SEATS. doi:10.5281/zenodo.5658256.**
9 changes: 4 additions & 5 deletions docs/examples.rst
Original file line number Diff line number Diff line change
Expand Up @@ -5,16 +5,15 @@
Usage Examples
==============

Here's some examples of how to use the uxarray. We are always planning to add
more examples! If you are interested in contributing your own examples, please
see the :doc:`contributing`.
Below is a list of usage examples showcasing how to use UXarray. If you are interested in contributing
your own examples or suggesting one for us to create, please see the :doc:`contributing`.

.. include:: notebook-examples.txt

.. toctree::
:maxdepth: 1
:hidden:

examples/001-read-grid-data.ipynb
examples/002-access-grid-info.ipynb
examples/001-working-with-unstructured-grids.ipynb
examples/002-grid-topology.ipynb
examples/003-area-calc.ipynb
240 changes: 0 additions & 240 deletions docs/examples/001-read-grid-data.ipynb

This file was deleted.

Loading