Merge branch 'main' into rajeeja/yac

Author: rajeeja

.github/upstream-failure-issue-template.md

@@ -0,0 +1,11 @@
+# Upstream testing failure
+
+**Workflow:** {{WORKFLOW}}
+**Run:** [{{RUN_ID}}]({{RUN_URL}})
+**Date:** {{DATE}}
+
+Upstream testing has failed.
+
+Please check the [workflow run]({{RUN_URL}}) for details.
+
+This issue was automatically generated from the CI Upstream workflow.

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
         python-version: [ "3.11", "3.12", "3.13"]
     steps:
       - name: Cancel previous runs
-        uses: styfle/cancel-workflow-action@0.13.0
+        uses: styfle/cancel-workflow-action@0.13.1
         with:
           access_token: ${{ github.token }}
 
@@ -67,6 +67,7 @@ jobs:
           python -m pytest test
 
   link-check:
+      if: github.event_name != 'pull_request'
       runs-on: ubuntu-latest
       defaults:
         run:
@@ -106,12 +107,13 @@ jobs:
             conda list
 
         - name: Make docs with linkcheck
-          uses: nick-fields/retry@ce71cc2ab81d554ebbe88c79ab5975992d79ba08 # v3
+          uses: nick-fields/retry@ad984534de44a9489a53aefd81eb77f87c70dc60 # v4.0.0
           with:
             timeout_minutes: 20
             max_attempts: 3
             command: |
               eval "$(micromamba shell hook --shell bash)"
               micromamba activate uxarray-docs
               cd docs
+              echo 'nb_execution_mode = "off"' >> conf.py
               make linkcheck

.github/workflows/upstream-dev-ci.yml

@@ -12,13 +12,16 @@ jobs:
   upstream-dev:
     name: upstream-dev
     runs-on: ubuntu-latest
+    continue-on-error: true
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.12" ]
+        python-version: [ "3.13" ]
+    outputs:
+      testresults: ${{ steps.tests.outcome }}
 
     steps:
       - name: Checkout
@@ -50,5 +53,66 @@ jobs:
           conda list
 
       - name: Running Tests
+        id: tests
         run: |
           python -m pytest test -v --cov=./uxarray --cov-report=xml
+
+  failure-issue:
+    name: failure-issue
+    needs: [upstream-dev]
+    if: |
+      needs.upstream-dev.testresults != 'success'
+      && github.repository == 'UXARRAY/uxarray'
+      && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: checkout
+        uses: actions/checkout@v6.0.2
+
+      - name: Create or update failure issue
+        shell: bash
+        run: |
+          # Read the template
+          template=$(cat .github/upstream-failure-issue-template.md)
+
+          # Replace placeholders
+          issue_body="${template//\{\{WORKFLOW\}\}/${{ github.workflow }}}"
+          issue_body="${issue_body//\{\{RUN_ID\}\}/${{ github.run_id }}}"
+          issue_body="${issue_body//\{\{RUN_URL\}\}/${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}}"
+          issue_body="${issue_body//\{\{DATE\}\}/$(date -u)}"
+
+          # Check for existing open issue with same title
+          issue_title="🤖 Upstream testing failure"
+          existing_issue=$(gh issue list --state open --label "CI" --search "\"$issue_title\" in:title" --json number --jq '.[0].number // empty')
+
+          if [ -n "$existing_issue" ]; then
+            echo "Found existing open issue #$existing_issue, updating it..."
+            echo "$issue_body" | gh issue edit "$existing_issue" --body-file -
+            echo "Updated existing issue #$existing_issue"
+          else
+            echo "No existing open issue found, creating new one..."
+            echo "$issue_body" | gh issue create \
+              --title "$issue_title" \
+              --body-file - \
+              --label "CI"
+            echo "Created new issue"
+          fi
+        env:
+          GH_TOKEN: ${{ github.token }}
+
+  report-failed:
+    name: report-failed
+    needs: [ upstream-dev, failure-issue ]
+    if: ${{needs.upstream-dev.outputs.testresults != 'success'}}
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: make sure to report a failed workflow
+        shell: bash
+        run: |
+          exit 1;

.pre-commit-config.yaml

@@ -14,7 +14,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.2
+  rev: v0.15.7
   hooks:
     - id: ruff
       name: lint with ruff

docs/user-guide/grid-formats.rst

@@ -43,8 +43,8 @@ References
 ----------
 * https://ugrid-conventions.github.io/ugrid-conventions/#ugrid-conventions-v10
 * https://github.com/ugrid-conventions/ugrid-conventions
-* https://cfconventions.org/Data/cf-conventions/cf-conventions-1.11/cf-conventions.html#ugrid-conventions
-* https://cfconventions.org/Data/cf-conventions/cf-conventions-1.11/cf-conventions.html#mesh-topology-variables
+* https://cf-convention.github.io/Data/cf-conventions/cf-conventions-1.13/cf-conventions.html#ugrid-conventions
+* https://cf-convention.github.io/Data/cf-conventions/cf-conventions-1.13/cf-conventions.html#mesh-topology-variables
 
 MPAS
 ====

test/grid/grid/test_io.py

@@ -174,3 +174,26 @@ def test_grid_ugrid_exodus_roundtrip(gridpath):
     for filepath in test_files:
         if os.path.exists(filepath):
             os.remove(filepath)
+
+
+def test_exodus_roundtrip_rll1deg_node_lonlat(gridpath, tmp_path):
+    """Check Exodus round-trip coordinate stability for the RLL1deg grid."""
+    grid = ux.open_grid(gridpath("ugrid", "outRLL1deg", "outRLL1deg.ug"))
+
+    exodus_filepath = tmp_path / "outRLL1deg.exo"
+    grid.to_xarray("Exodus").to_netcdf(exodus_filepath)
+
+    reloaded_exodus = ux.open_grid(exodus_filepath)
+
+    np.testing.assert_allclose(
+        grid.node_lon.values,
+        reloaded_exodus.node_lon.values,
+        err_msg="Exodus longitude mismatch for RLL1deg",
+        rtol=ERROR_TOLERANCE,
+    )
+    np.testing.assert_allclose(
+        grid.node_lat.values,
+        reloaded_exodus.node_lat.values,
+        err_msg="Exodus latitude mismatch for RLL1deg",
+        rtol=ERROR_TOLERANCE,
+    )

test/test_plot.py

@@ -4,6 +4,8 @@
 import pytest
 import numpy as np
 
+import matplotlib
+matplotlib.use("Agg")
 import matplotlib.pyplot as plt
 import cartopy.crs as ccrs
 

uxarray/core/dataarray.py

@@ -745,10 +745,19 @@ def zonal_mean(self, lat=(-90, 90, 10), conservative: bool = False, **kwargs):
             dims = list(self.dims)
             dims[face_axis] = "latitudes"
 
+            # Assign coords from `self` to the result except one that corresponds to `dims[face_axis]`
+            new_coords = {
+                k: v
+                for k, v in self.coords.items()
+                if self.dims[face_axis] not in v.dims
+            }
+            # Add latitudes to the resulting coords
+            new_coords["latitudes"] = centers
+
             return xr.DataArray(
                 res,
                 dims=dims,
-                coords={"latitudes": centers},
+                coords=new_coords,
                 name=self.name + "_zonal_mean"
                 if self.name is not None
                 else "zonal_mean",

uxarray/grid/coordinates.py

@@ -68,10 +68,6 @@ def _xyz_to_lonlat_rad_no_norm(
 def _xyz_to_lonlat_rad_scalar(x, y, z, normalize=True):
     if normalize:
         x, y, z = _normalize_xyz_scalar(x, y, z)
-        denom = abs(x * x + y * y + z * z)
-        x /= denom
-        y /= denom
-        z /= denom
 
     lon = np.arctan2(y, x)
     lat = np.asin(z)
@@ -121,10 +117,6 @@ def _xyz_to_lonlat_rad(
 
     if normalize:
         x, y, z = _normalize_xyz(x, y, z)
-        denom = np.abs(x * x + y * y + z * z)
-        x /= denom
-        y /= denom
-        z /= denom
 
     lon = np.arctan2(y, x)
     lat = np.arcsin(z)