Merge branch 'UXARRAY:main' into main

.github/ISSUE_TEMPLATE/release_request.md

@@ -11,7 +11,6 @@ Date of intended release:
 ## Release progress checklist
 
 - [ ] CI tests are passing
-- [ ] update version number in `meta.yaml`
 - [ ] a new tag and release has been made on GitHub
 - [ ] feedstock PR has been merged
 - [ ] release on pypi action has been triggered and run successfully

.github/workflows/asv-benchmarking.yml

@@ -9,6 +9,9 @@ on:
 jobs:
   benchmark:
     runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
     env:
       CONDA_ENV_FILE: ./ci/asv.yml
       ASV_DIR: ./benchmarks
@@ -18,36 +21,51 @@ jobs:
         uses: actions/checkout@v4
         with:
           repository: UXARRAY/uxarray
+          ref: main
           fetch-depth: 0
+
+      - name: Fetch all tags and branches for uxarray
+        run: |
+          git fetch --all --tags
+
       - name: Checkout uxarray-asv
         uses: actions/checkout@v4
         with:
-          repository: uxarray/uxarray-asv
+          repository: UXARRAY/uxarray-asv
           persist-credentials: false
           fetch-depth: 0
           ref: main
           path: uxarray-asv
-      - name: Set environment variables
-        run: |
-          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
 
-      - name: Set up conda environment
-        id: env-setup
-        continue-on-error: true
-        uses: mamba-org/setup-micromamba@v1
+      - name: Setup Miniforge
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          environment-file: ./ci/asv.yml
-          cache-environment: true
-          cache-environment-key: "benchmark-${{runner.os}}-${{runner.arch}}-${{env.TODAY}}"
+          miniforge-version: "24.1.2-0"
+          activate-environment: asv
+
+      - name: Get date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
 
-      - name: retry environment set up if failed
-        if: steps.env-setup.outcome == 'failure'
-        uses: mamba-org/setup-micromamba@v1
+      - name: Cache environment
+        uses: actions/cache@v4
         with:
-          download-micromamba: false
-          environment-file: ./ci/asv.yml
-          cache-environment: true
-          cache-environment-key: "benchmark-${{runner.os}}-${{runner.arch}}-${{env.TODAY}}"
+          path: ${{ env.CONDA }}/envs
+          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('./ci/asv.yml') }}-${{ env.CACHE_NUMBER }}
+        env:
+          CACHE_NUMBER: 0
+        id: cache
+
+      - name: Update environment
+        run:
+          conda env update -n asv -f ./ci/asv.yml
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Conda list
+        run: |
+          conda info
+          conda list
 
       - name: Copy existing results
         run: |

.github/workflows/ci.yml

@@ -71,7 +71,10 @@ jobs:
           python -m pytest test -v --cov=./uxarray --cov-report=xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/[email protected]
+        if: github.repository == 'UXARRAY/uxarray'
+        uses: codecov/[email protected]
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
           file: ./coverage.xml
           flags: unittests

.github/workflows/pre-commit.yml

@@ -11,5 +11,5 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5.0.0
+      - uses: actions/setup-python@v5.1.0
       - uses: pre-commit/[email protected]

.github/workflows/pypi.yaml

@@ -10,7 +10,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v5.0.0
+        uses: actions/setup-python@v5.1.0
         with:
           python-version: '3.x'
       - name: Install dependencies
@@ -34,7 +34,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v5.0.0
+        uses: actions/setup-python@v5.1.0
         with:
           python-version: '3.x'
       - name: Install dependencies
@@ -50,7 +50,7 @@ jobs:
           python -m twine check dist/*
 
       - name: Publish package to PyPI
-        uses: pypa/[email protected].11
+        uses: pypa/[email protected].14
         with:
           skip-existing: true
           verbose: true

.pre-commit-config.yaml

@@ -10,18 +10,19 @@ repos:
     hooks:
     - id: check-yaml               # Checks the syntax of .yaml files.
       args: [--allow-multiple-documents]
-      exclude: 'meta.yaml'    # Exclude this because it gives an error for '%' in Line 1 and couldn't fix yet
     - id: end-of-file-fixer        # Makes sure files end with a newline.
     - id: trailing-whitespace      # Checks for any tabs or spaces after the last non-whitespace character on the line.
     - id: check-docstring-first    # Checks that code comes after the docstrings.
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.1.5
+  rev: v0.4.1
   hooks:
     # Run the linter.
     - id: ruff
       args: [ --fix ]
+      types_or: [ python, pyi, jupyter ]
 
     # Run the formatter.
     - id: ruff-format
+      types_or: [ python, pyi, jupyter ]

MANIFEST.in

@@ -0,0 +1,18 @@
+include LICENSE
+include README.md
+
+recursive-include uxarray *.py
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+exclude .gitignore
+exclude .pre-commit-config.yaml
+exclude .readthedocs.yml
+
+include *.md
+include *.toml
+include *.txt
+prune test*
+prune ci*
+prune .github*
+prune docs*
+prune benchmarks*

benchmarks/asv.conf.json

@@ -60,6 +60,8 @@
     // defaults to 10 min
     "install_timeout": 600,
 
+    "benchmark_timeout": 360,
+
     // the base URL to show a commit for the project.
     "show_commit_url": "https://github.com/UXARRAY/uxarray/commit/",
 

benchmarks/face_bounds.py

@@ -0,0 +1,32 @@
+import os
+from pathlib import Path
+
+import uxarray as ux
+
+current_path = Path(os.path.dirname(os.path.realpath(__file__))).parents[0]
+
+grid_quad_hex = current_path / "test" / "meshfiles" / "ugrid" / "quad-hexagon" / "grid.nc"
+grid_geoflow = current_path / "test" / "meshfiles" / "ugrid" / "geoflow-small" / "grid.nc"
+grid_scrip = current_path / "test" / "meshfiles" / "scrip" / "outCSne8" / "outCSne8.nc"
+grid_mpas= current_path / "test" / "meshfiles" / "mpas" / "QU" / "oQU480.231010.nc"
+
+
+
+class FaceBounds:
+
+    params = [grid_quad_hex, grid_geoflow, grid_scrip, grid_mpas]
+
+
+    def setup(self, grid_path):
+        self.uxgrid = ux.open_grid(grid_path)
+
+    def teardown(self, n):
+        del self.uxgrid
+
+    def time_face_bounds(self, grid_path):
+        """Time to obtain ``Grid.face_bounds``"""
+        self.uxgrid.bounds
+
+    def peakmem_face_bounds(self, grid_path):
+        """Peak memory usage obtain ``Grid.face_bounds."""
+        face_bounds = self.uxgrid.bounds

benchmarks/mpas_ocean.py

@@ -0,0 +1,99 @@
+import os
+import urllib.request
+from pathlib import Path
+
+import uxarray as ux
+
+current_path = Path(os.path.dirname(os.path.realpath(__file__)))
+
+data_var = 'bottomDepth'
+
+grid_filename_480 = "oQU480.grid.nc"
+data_filename_480 = "oQU480.data.nc"
+
+grid_filename_120 = "oQU120.grid.nc"
+data_filename_120 = "oQU120.data.nc"
+
+filenames = [grid_filename_480, data_filename_480, grid_filename_120, data_filename_120]
+
+for filename in filenames:
+    if not os.path.isfile(current_path / filename):
+        # downloads the files from Cookbook repo, if they haven't been downloaded locally yet
+        url = f"https://github.com/ProjectPythia/unstructured-grid-viz-cookbook/raw/main/meshfiles/{filename}"
+        _, headers = urllib.request.urlretrieve(url, filename=current_path / filename)
+
+
+file_path_dict = {"480km": [current_path / grid_filename_480, current_path / data_filename_480],
+                  "120km": [current_path / grid_filename_120, current_path / data_filename_120]}
+
+
+class Gradient:
+
+    param_names = ['resolution']
+    params = ['480km', '120km']
+
+
+    def setup(self, resolution):
+        self.uxds = ux.open_dataset(file_path_dict[resolution][0], file_path_dict[resolution][1])
+
+    def teardown(self, resolution):
+        del self.uxds
+
+    def time_gradient(self, resolution):
+        self.uxds[data_var].gradient()
+
+    def peakmem_gradient(self, resolution):
+        grad = self.uxds[data_var].gradient()
+
+class Integrate:
+
+    param_names = ['resolution']
+    params = ['480km', '120km']
+
+
+    def setup(self, resolution):
+        self.uxds = ux.open_dataset(file_path_dict[resolution][0], file_path_dict[resolution][1])
+
+    def teardown(self, resolution):
+        del self.uxds
+
+    def time_integrate(self, resolution):
+        self.uxds[data_var].integrate()
+
+    def peakmem_integrate(self, resolution):
+        integral = self.uxds[data_var].integrate()
+
+class GeoDataFrame:
+
+    param_names = ['resolution', 'exclude_antimeridian']
+    params = [['480km', '120km'],
+              [True, False]]
+
+
+    def setup(self, resolution, exclude_antimeridian):
+        self.uxds = ux.open_dataset(file_path_dict[resolution][0], file_path_dict[resolution][1])
+
+    def teardown(self, resolution, exclude_antimeridian):
+        del self.uxds
+
+    def time_to_geodataframe(self, resolution, exclude_antimeridian):
+        self.uxds[data_var].to_geodataframe(exclude_antimeridian=exclude_antimeridian)
+
+    def peakmem_to_geodataframe(self, resolution, exclude_antimeridian):
+        gdf = self.uxds[data_var].to_geodataframe(exclude_antimeridian=exclude_antimeridian)
+
+
+class ConnectivityConstruction:
+
+    param_names = ['resolution']
+    params = ['480km', '120km']
+
+
+    def setup(self, resolution):
+        self.uxds = ux.open_dataset(file_path_dict[resolution][0], file_path_dict[resolution][1])
+
+    def teardown(self, resolution):
+        del self.uxds
+
+    def time_n_nodes_per_face(self, resolution):
+        self.uxds.uxgrid.n_nodes_per_face

ci/asv.yml

@@ -9,13 +9,14 @@ dependencies:
   - gmpy2
   - holoviews
   - matplotlib-base
+  - matplotlib-inline
   - netcdf4
   - numba
   - numpy
   - pandas<2.1.0
   - pathlib
   - pre_commit
-  - pyarrow<13.0.0   # pin due to CI faliures on macOS & ubuntu
+  - pyarrow
   - pytest
   - pytest-cov
   - requests
@@ -27,5 +28,5 @@ dependencies:
   - pip:
     - antimeridian
     - pyfma
-    - asv
+    - asv<0.6.2
     - -e ../

ci/docs.yml

@@ -6,7 +6,7 @@ dependencies:
     - dask
     - netcdf4
     - numba
-    - numpy<=1.24
+    - numpy
     - pathlib
     - pre_commit
     - pytest
@@ -24,6 +24,7 @@ dependencies:
     - sphinx-design
     - nbsphinx
     - matplotlib-base
+    - matplotlib-inline
     - shapely
     - hvplot
     - holoviews

ci/environment.yml

@@ -8,13 +8,14 @@ dependencies:
   - gmpy2
   - holoviews
   - matplotlib-base
+  - matplotlib-inline
   - netcdf4
   - numba
   - numpy
   - pandas<2.1.0
   - pathlib
   - pre_commit
-  - pyarrow<13.0.0   # pin due to CI faliures on macOS & ubuntu
+  - pyarrow
   - pytest
   - pytest-cov
   - requests

docs/api.rst

@@ -14,8 +14,7 @@ high-level understanding of UXarray's future function development milestones and
 Please let us know if you have any feedback!
 
 .. toctree::
-   :maxdepth: 2
-   :hidden:
+   :maxdepth: 1
 
    user_api/index.rst
    internal_api/index.rst