Merge branch 'main' into ahijevyc/neighborhood_filter

.github/workflows/pypi.yaml

@@ -50,7 +50,7 @@ jobs:
           python -m twine check dist/*
 
       - name: Publish package to PyPI
-        uses: pypa/[email protected].1
+        uses: pypa/[email protected].2
         with:
           skip-existing: true
           verbose: true

CODE_OF_CONDUCT.md

@@ -0,0 +1,148 @@
+# Code of Conduct
+
+## Our Pledge
+
+We, as members, contributors, creators, stewards, and maintainers, i.e. all the
+participants, of UXarray pledge to make participation in our software, system
+or hardware project and community a safe, healthy, open, productive, welcoming,
+diverse, inclusive, and harassment-free experience for everyone, regardless of
+age, body size, visible or invisible disability, ethnicity, sex characteristics,
+gender identity and expression, level of experience, education, socio-economic
+status, nationality, personal appearance, race, caste, color, religion, or
+sexual identity and orientation, as well as any other characteristic protected
+under applicable US federal or state law.
+
+All participants are required to abide by this Code of Conduct.
+
+## Our Standards
+
+Examples of behaviors that contribute to a positive environment for our community
+include:
+
+- Demonstrating empathy and kindness toward other people
+- Being considerate and respectful of and collaborative with differing opinions,
+  viewpoints, and experiences
+- Acknowledging the contributions of others
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+- Focusing on what is best not just for us as individuals, but for the overall
+  community
+- Respecting the rules and policies of the project and venue
+
+Examples of unacceptable behavior include, but are not limited to:
+
+- Public or private harassment, intimidation, or discrimination in any form
+- Physical, verbal, or written abuse by anyone to anyone, including repeated
+  use of pronouns other than those requested
+- The use of sexualized language or imagery, and sexual attention or advances
+  of any kind
+- Personal attacks directed at other guests, members, participants, etc.
+- Publishing others’ private information, such as a physical or electronic
+  address, without explicit permission
+- Alarming, intimidating, threatening, or hostile comments or conduct
+- Threatening or stalking anyone, including a participant
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies to all community spaces managed by UXarray whether
+they be physical, online or face-to-face, and also applies when an individual is
+officially representing the community in public spaces. This includes but is not
+limited to project code, code repository, associated web pages, documentation,
+mailing lists, project websites and wiki pages, issue tracker, meetings, telecons,
+events, use of official email or social media accounts, and any other forums
+created by the project team which the community uses for communication. In
+addition, violations of this Code of Conduct outside these spaces may affect a
+person's ability to participate within them. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the the `@UXARRAY/uxarray-dev` GitHub handle as the community leaders
+in this group can view and manage the reported content, and hence are responsible
+for enforcement.
+
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant Code of Conduct,
+version 2.1][homepage], [version 2.1][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

README.md

@@ -1,8 +1,5 @@
-<picture>
-  <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/UXARRAY/uxarray/e252a7669acc6a733bca14ac244bbf02e665dbb0/docs/_static/images/logos/uxarray_logo_h_light.svg">
-  <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/UXARRAY/uxarray/e252a7669acc6a733bca14ac244bbf02e665dbb0/docs/_static/images/logos/uxarray_logo_h_dark.svg">
-  <img alt="Shows a black logo in light color mode and a white one in dark color mode." src="https://user-images.githubusercontent.com/25423296/163456779-a8556205-d0a5-45e2-ac17-42d089e3c3f8.png" width="450">
-</picture>
+<img src="https://github.com/UXARRAY/uxarray/raw/main/docs/_static/images/logos/uxarray_logo_h_dark.svg" data-canonical-src="https://github.com/UXARRAY/uxarray/raw/main/docs/_static/images/logos/uxarray_logo_h_dark.svg" width="450"/><br>
+
 
 -----------------
 

benchmarks/asv.conf.json

@@ -94,7 +94,7 @@
         "setuptools_scm": [""],
         "xarray": [""],
         "netcdf4": [""],
-        "pip+git+https://github.com/philipc2/pyfma.git": [""]
+        "pip+pyfma": [""]
     },
 
 

benchmarks/face_bounds.py

@@ -28,13 +28,3 @@ def time_face_bounds(self, grid_path):
     def peakmem_face_bounds(self, grid_path):
         """Peak memory usage obtain ``Grid.face_bounds."""
         face_bounds = self.uxgrid.bounds
-
-class Bounds:
-    def setup(self):
-        self.uxgrid = ux.open_grid(r"C:\Users\chmie\PycharmProjects\ncar-uxarray\uxarray-hongyu\benchmarks\oQU480.grid.nc")
-
-    def teardown(self):
-        del self.uxgrid
-
-    def time_bounds(self):
-        self.uxgrid.bounds

benchmarks/mpas_ocean.py

@@ -140,7 +140,20 @@ def time_nearest_neighbor_remapping(self):
     def time_inverse_distance_weighted_remapping(self):
         self.uxds_480["bottomDepth"].remap.inverse_distance_weighted(self.uxds_120.uxgrid)
 
-
 class HoleEdgeIndices(DatasetBenchmark):
     def time_construct_hole_edge_indices(self, resolution):
         ux.grid.geometry._construct_hole_edge_indices(self.uxds.uxgrid.edge_face_connectivity)
+
+class CheckNorm:
+    param_names = ['resolution']
+    params = ['480km', '120km']
+
+    def setup(self, resolution):
+        self.uxgrid = ux.open_grid(file_path_dict[resolution][0])
+
+    def teardown(self, resolution):
+        del self.uxgrid
+
+    def time_check_norm(self, resolution):
+        from uxarray.grid.validation import _check_normalization
+        _check_normalization(self.uxgrid)

ci/asv.yml

@@ -24,6 +24,7 @@ dependencies:
   - scipy
   - shapely
   - spatialpandas
+  - geopandas
   - xarray
   - asv
   - pip:

ci/docs.yml

@@ -33,6 +33,7 @@ dependencies:
     - pandas
     - geocat-datafiles
     - spatialpandas
+    - geopandas
     - pip:
       - antimeridian
       - git+https://github.com/philipc2/pyfma.git # fix until https://github.com/nschloe/pyfma/pull/17 is merged

ci/environment.yml

@@ -28,6 +28,7 @@ dependencies:
   - scipy
   - shapely
   - spatialpandas
+  - geopandas
   - xarray
   - asv
   - pip:

ci/install-upstream.sh

@@ -33,6 +33,7 @@ python -m pip install \
     pandas \
     scikit-learn \
     scipy \
+    geopandas \
     xarray
 
 # install rest from source

docs/internal_api/index.rst

@@ -286,12 +286,17 @@ SCRIP
    io._scrip._encode_scrip
 
 
-Shapefile
+GeoPandas
 ---------
 .. autosummary::
    :toctree: generated/
 
-   io._shapefile._read_shpfile
+   io._geopandas._read_geodataframe
+   io._geopandas._read_geopandas
+   io._geopandas._encode_geopandas
+   io._geopandas._standardize_geopandas
+   io._geopandas._is_geopandas
+   io._geopandas._validate_minimum_geopandas
 
 Vertices
 --------

pyproject.toml

@@ -42,6 +42,7 @@ dependencies = [
   "scipy",
   "shapely",
   "spatialpandas",
+  "geopandas",
   "xarray",
 ]
 # minimal dependencies end

test/meshfiles/geojson/README.md

@@ -0,0 +1,15 @@
+GeoJSON is a format for encoding a variety of geographic data structures, including points, lines, and polygons.
+
+This repository contains "sample_chicago_buildings" GeoJSON file featuring a selection of buildings in Chicago. The file includes:
+
+        Number of polygons: 10
+        Polygon 1: 26 sides
+        Polygon 2: 36 sides
+        Polygon 3: 29 sides
+        Polygon 4: 10 sides
+        Polygon 5: 30 sides
+        Polygon 6: 8 sides
+        Polygon 7: 7 sides
+        Polygon 8: 9 sides
+        Polygon 9: 7 sides
+        Polygon 10: 19 sides