Merge branch 'v4-dev' into renaming_pyfunc_to_kernels

Author: erikvansebille

.github/ci/recipe.yaml

@@ -4,7 +4,7 @@
 # Adapted from the conda forge recipe
 context:
   name: parcels
-  version: 4.0.0alpha2 # The last number here needs to be bumped for each new alpha release
+  version: ${{ env.get('PARCELS_ALPHA_VERSION') }}
 
 package:
   name: ${{ name|lower }}

.github/workflows/additional.yml

@@ -30,3 +30,38 @@ jobs:
       - uses: actions/checkout@v5
       - uses: prefix-dev/setup-pixi@v0.9.0
       - run: pixi run docs-linkcheck
+
+  create-issue-on-failure:
+    name: Create issue on failure
+    runs-on: ubuntu-latest
+    needs: [min-version-policy, linkcheck]
+    if: |
+      always() &&
+      (needs.min-version-policy.result == 'failure' || needs.linkcheck.result == 'failure') &&
+      github.event_name == 'schedule'
+    permissions:
+      issues: write
+    steps:
+      - name: Create issue
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const workflowUrl = `${context.serverUrl}/${context.repo.owner}/${context.repo.repo}/actions/runs/${context.runId}`;
+            const title = `CI Additional workflow failed - ${new Date().toISOString().split('T')[0]}`;
+            const body = `The [CI Additional workflow](${workflowUrl}) failed on its scheduled run.
+
+            **Workflow Run:** ${context.runId}
+            **Trigger:** ${context.eventName}
+            **Branch:** ${context.ref}
+
+            Please investigate the failure and fix the issues.
+
+            _This issue was automatically created by the workflow._`;
+
+            await github.rest.issues.create({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              title: title,
+              body: body,
+              labels: ['bug', 'automated']
+            });

.github/workflows/ci.yml

@@ -3,10 +3,9 @@ on:
   push:
     branches:
       - "main"
+      - "v4-dev"
       - "test-me/*"
   pull_request:
-  schedule:
-    - cron: "0 7 * * 1" # Run every Monday at 7:00 UTC
 
 concurrency:
   group: branch-${{ github.head_ref }}
@@ -16,9 +15,6 @@ defaults:
   run:
     shell: bash -el {0}
 
-env:
-  PIXI_VERSION: "v0.63.0"
-
 jobs:
   should-run-ci:
     name: should run ci
@@ -41,17 +37,15 @@ jobs:
           exit 1
 
   cache-pixi-lock:
-    runs-on: ubuntu-slim
+    runs-on: ubuntu-latest
     needs: [should-run-ci]
     outputs:
       cache-key: ${{ steps.pixi-lock.outputs.cache-key }}
       pixi-version: ${{ steps.pixi-lock.outputs.pixi-version }}
     steps:
       - uses: actions/checkout@v4
-      - uses: Parcels-code/pixi-lock/create-and-cache@2b823a4a804631370fbde7e6088ee5db71a26c60 # TODO: Update to action in prefix-dev once available
+      - uses: Parcels-code/pixi-lock/create-and-cache@2b823a4a804631370fbde7e6088ee5db71a26c60
         id: pixi-lock
-        with:
-          pixi-version: ${{env.PIXI_VERSION}}
       - uses: actions/upload-artifact@v6
         with:
           name: pixi-lock
@@ -200,3 +194,36 @@ jobs:
         with:
           name: Mypy report
           path: mypy-report
+  build-and-upload-nightly-parcels: # for alpha testing
+    needs: [cache-pixi-lock]
+    permissions:
+      contents: read
+      id-token: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+      - name: Restore cached pixi lockfile
+        uses: Parcels-code/pixi-lock/restore@2b823a4a804631370fbde7e6088ee5db71a26c60 # TODO: Update to action in prefix-dev once available
+        with:
+          cache-key: ${{ needs.cache-pixi-lock.outputs.cache-key }}
+      - uses: prefix-dev/setup-pixi@v0.9.0
+        with:
+          pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
+          cache: true
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'v4-dev' }} # TODO: Update v4-dev to main when v4 is released
+      - run: pixi run get-parcels-alpha-version >> $GITHUB_ENV
+      - run: echo "PARCELS_ALPHA_VERSION is $PARCELS_ALPHA_VERSION"
+      - name: Build conda package
+        uses: prefix-dev/rattler-build-action@v0.2.34
+        with:
+          recipe-path: .github/ci/recipe.yaml
+      - if: github.ref == 'refs/heads/v4-dev'
+        run: |
+          for pkg in $(find output -type f \( -name "*.conda" -o -name "*.tar.bz2" \) ); do
+            echo "Uploading ${pkg}"
+            rattler-build upload prefix -c parcels "${pkg}"
+          done
+        env:
+          PREFIX_API_KEY: ${{ secrets.PREFIX_API_KEY }}

.github/workflows/nightly.yml

@@ -18,7 +18,6 @@ The pages below provide further background on the development of Parcels v4. You
 
 ```{toctree}
 installation
-api
 nojit
 TODO
 Parcels v4 Project Board <https://github.com/orgs/Parcels-code/projects/5>

docs/v4/api.md

@@ -3,11 +3,11 @@ name = "Parcels"
 preview = ["pixi-build"]
 channels = ["conda-forge"]
 platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
+requires-pixi = ">=0.63.0"
 
 [package]
 name = "parcels"
 version = "dynamic" # dynamic versioning needs better support in pixi https://github.com/prefix-dev/pixi/issues/2923#issuecomment-2598460666 . Putting `version = "dynamic"` here for now until pixi recommends something else.
-license = "MIT" # can remove this once https://github.com/prefix-dev/pixi-build-backends/issues/397 is resolved
 
 [package.build]
 backend = { name = "pixi-build-python", version = "0.4.*" }
@@ -35,6 +35,12 @@ py-triangle = ">=20250106,<20250107"
 [dependencies]
 parcels = { path = "." }
 
+[feature.alpha-parcels.dependencies]
+git = "*"
+
+[feature.alpha-parcels.tasks]
+get-parcels-alpha-version = { cmd = "python tools/get-parcels-alpha-version.py" }
+
 [feature.minimum.dependencies]
 python = "3.11.*"
 netcdf4 = "1.6.*"
@@ -63,8 +69,8 @@ pytest-html = "*"
 pytest-cov = "*"
 
 [feature.test.tasks]
-tests = "pytest"
-tests-notebooks = "pytest --nbval-lax docs/user_guide/examples"
+tests = { cmd = "pytest", description = "Run the test suite." }
+tests-notebooks = { cmd = "pytest --nbval-lax docs/user_guide/examples", description = "Run the user guide example notebooks as tests." }
 
 
 [feature.notebooks.dependencies]
@@ -87,29 +93,29 @@ sphinx-design = "*"
 sphinx-autoapi = "*"
 
 [feature.docs.tasks]
-docs = "sphinx-build docs docs/_build"
-docs-watch = 'sphinx-autobuild docs docs/_build'
-docs-linkcheck = "sphinx-build -b linkcheck docs/ docs/_build/linkcheck"
+docs = { cmd = "sphinx-build docs docs/_build", description = "Build the documentation." }
+docs-watch = { cmd = "sphinx-autobuild docs docs/_build", description = "Build and auto-rebuild the documentation on changes." }
+docs-linkcheck = { cmd = "sphinx-build -b linkcheck docs/ docs/_build/linkcheck", description = "Verify all links in documentation don't 404." }
 
 [feature.pre-commit.dependencies]
 pre_commit = "*"
 
 [feature.pre-commit.tasks]
-lint = "pre-commit run --all-files"
+lint = { cmd = "pre-commit run --all-files", description = "Run all pre-commit linting hooks." }
 
 [feature.numpydoc.dependencies]
 numpydoc = "*"
 
 [feature.numpydoc.tasks]
-numpydoc-lint = "python tools/numpydoc-public-api.py"
+numpydoc-lint = { cmd = "python tools/numpydoc-public-api.py", description = "Lint public API docstrings with numpydoc." }
 
 [feature.typing.dependencies]
 mypy = "*"
 lxml = "*" # in CI
 types-tqdm = "*"
 
 [feature.typing.tasks]
-typing = "mypy src/parcels --install-types"
+typing = { cmd = "mypy src/parcels --install-types", description = "Run static type checking with mypy." }
 
 
 [environments]
@@ -127,3 +133,4 @@ test-py313 = { features = ["test", "py313"] }
 test-notebooks = { features = ["test", "notebooks"], solve-group = "main" }
 docs = { features = ["docs", "notebooks"], solve-group = "docs" }
 typing = { features = ["typing"], solve-group = "main" }
+alpha-parcels = { features = ["alpha-parcels"] }

docs/v4/index.md

@@ -26,7 +26,6 @@ dependencies = [
   "netCDF4 >=1.7.2",
   "zarr >=2.15.0,!=2.18.0,<3",
   "tqdm >=4.50.0",
-  "pytest",
   "xarray >=2024.5.0",
   "uxarray >=2025.3.0",
   "pooch >=1.8.0",

pixi.toml

@@ -0,0 +1,30 @@
+"""Get a Parcels v4 alpha version string based on commits since the last tag.
+
+Sets the PARCELS_ALPHA_VERSION environment variable (via GITHUB_ENV in CI,
+or prints the version to stdout for local use).
+"""
+
+import subprocess
+
+
+def get_alpha_version():
+    result = subprocess.run(
+        ["git", "describe", "--tags", "--long"],
+        capture_output=True,
+        text=True,
+        check=True,
+    )
+    # Format: <tag>-<n>-g<hash>
+    # e.g. v3.1.2-1967-g1857d5219
+    parts = result.stdout.strip().rsplit("-", 2)
+    n_commits = parts[1]
+    return f"4.0.0alpha{n_commits}"
+
+
+def main():
+    version = get_alpha_version()
+    print(f"PARCELS_ALPHA_VERSION={version}")
+
+
+if __name__ == "__main__":
+    main()