CI: add weekly test against Parcels main

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

@@ -0,0 +1,111 @@
+# Test VirtualShip against the unreleased `main` branch of Parcels, to catch breaking changes.
+# Environment is defined in `ci/upstream/pixi.toml`. On scheduled runs, failures open (or update) a GitHub issue.
+name: CI (for upstream Parcels main)
+
+on:
+  schedule:
+    - cron: "0 0 * * 1" # 00:00 UTC every Monday
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash -el {0}
+
+env:
+  FORCE_COLOR: 3
+
+permissions: {}
+
+jobs:
+  cache-pixi-lock:
+    if: github.repository == 'Parcels-code/virtualship' || github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-slim
+    permissions:
+      contents: read
+    outputs:
+      cache-key: ${{ steps.pixi-lock.outputs.cache-key }}
+      pixi-version: ${{ steps.pixi-lock.outputs.pixi-version }}
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+      - uses: Parcels-code/pixi-lock/create-and-cache@1fab4c17af8243f6ca1321bc941cf2325f46c05d # v0.1.1
+        id: pixi-lock
+        with:
+          manifest-path: ci/upstream/pixi.toml
+          hash-files: |
+            ci/upstream/pixi.toml
+            pyproject.toml
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: pixi-lock-upstream
+          path: ci/upstream/pixi.lock
+
+  upstream-dev:
+    name: "Upstream tests: pixi run --manifest-path ci/upstream/pixi.toml tests-upstream"
+    runs-on: ubuntu-latest
+    needs: cache-pixi-lock
+    permissions:
+      contents: read
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0 # setuptools_scm needs the git history to version the editable install
+          persist-credentials: false
+      - uses: Parcels-code/pixi-lock/restore@1fab4c17af8243f6ca1321bc941cf2325f46c05d # v0.1.1
+        with:
+          cache-key: ${{ needs.cache-pixi-lock.outputs.cache-key }}
+          manifest-path: ci/upstream/pixi.toml
+      - uses: prefix-dev/setup-pixi@d3f436a425481402e6a95a1d1fc10331c708cd9e # v0.10.2
+        with:
+          manifest-path: ci/upstream/pixi.toml
+          cache: false
+          pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
+
+      - name: Version info
+        run: |
+          pixi list --manifest-path ci/upstream/pixi.toml parcels
+          pixi run --manifest-path ci/upstream/pixi.toml python -c 'import parcels; print(f"parcels {parcels.__version__}")'
+
+      - name: Run tests
+        id: status
+        if: ${{ !cancelled() }} # run even if the import check fails, so a report log is produced for the issue
+        run: >-
+          pixi run --manifest-path ci/upstream/pixi.toml tests-upstream
+          --timeout=120
+          --report-log output-upstream-dev-log.jsonl
+
+      - name: Upload test results
+        if: ${{ failure() && steps.status.outcome == 'failure' }}
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: output-upstream-dev-log
+          path: output-upstream-dev-log.jsonl
+          retention-days: 5
+
+  create-issue:
+    name: Create issue on failure
+    needs: upstream-dev
+    if: |
+      always()
+      && needs.upstream-dev.result == 'failure'
+      && github.event_name == 'schedule'
+      && github.repository == 'Parcels-code/virtualship'
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: output-upstream-dev-log
+      - name: Generate and publish the report
+        uses: scientific-python/issue-from-pytest-log-action@35b4e0a9e06f8e7e261778289cf4b968b722662d # v1.6.2
+        with:
+          log-path: output-upstream-dev-log.jsonl
+          issue-title: "⚠️ CI against Parcels main failed ⚠️"
+          issue-label: automated
+          assignees: erikvansebille

.gitignore

@@ -2,6 +2,8 @@
 .pixi/*
 !.pixi/config.toml
 pixi.lock
+ci/upstream/.pixi/
+output-upstream-dev-log.jsonl
 
 
 # Byte-compiled / optimized / DLL files

ci/upstream/pixi.toml

@@ -0,0 +1,64 @@
+# Environment for testing VirtualShip against the unreleased `main` branch of Parcels (weekly)
+
+[workspace]
+name = "VirtualShip upstream"
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-arm64"]
+exclude-newer = "5d" # security pre-caution against compromised packages (does not apply to the git override)
+requires-pixi = ">=0.82.1"
+
+[dependencies]
+python = "3.14.*"
+# VirtualShip run dependencies, pre-installed as conda packages (keep in sync with `pyproject.toml`)
+click = "*"
+pyproj = ">=3,<4"
+sortedcontainers = "==2.4.0"
+opensimplex = "==0.4.5"
+numpy = ">=2.1.0"
+pydantic = ">=2,<3"
+pyyaml = "*"
+copernicusmarine = ">=2.2.2"
+yaspin = "*"
+textual = "*"
+# Parcels run dependencies, pre-installed as conda packages to avoid PyPI source builds
+# If Parcels `main` adds a dependency that isn't listed here, it is installed from PyPI
+cf_xarray = "*"
+cftime = "*"
+dask = "*"
+netcdf4 = "*"
+pandas = "*"
+polars = "*"
+pooch = "*"
+pyarrow = "*"
+tabulate = "*"
+tqdm = "*"
+uxarray = "*"
+xarray = "*"
+zarr = ">=3.0.0"
+# downstream uxarray deps (see root `pixi.toml`)
+numba = ">=0.59.0"
+healpix = "*"
+cartopy = "*"
+shapely = "*"
+geopandas = "*"
+scipy = "*"
+
+[pypi-dependencies]
+virtualship = { path = "../..", editable = true }
+
+[pypi-options.dependency-overrides]
+parcels = { git = "https://github.com/Parcels-code/Parcels", branch = "main" }
+
+[feature.test.dependencies]
+pytest = "*"
+pytest-asyncio = "*"
+pytest-reportlog = "*" # required: issue-from-pytest-log-action consumes the pytest report log
+pytest-timeout = "*"
+seabird = "*"
+openpyxl = "*"
+
+[feature.test.tasks]
+tests-upstream = { cmd = "pytest -m 'not network'", cwd = "../..", description = "Run the test suite (excluding tests that call external services) against Parcels main" }
+
+[environments]
+default = { features = ["test"] }