[pre-commit.ci] pre-commit autoupdate

.binder/environment.yml

@@ -3,4 +3,5 @@ channels:
   - conda-forge
 dependencies:
   - parcels
+  - pooch
   - trajan

.gitattributes

@@ -1 +1,3 @@
 .git_archival.txt  export-subst
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true

.github/ci/min-core-deps.yml

@@ -6,18 +6,14 @@ dependencies:
   # MINIMUM VERSIONS POLICY: keep track of minimum versions
   # for core packages. Dev and conda release builds should use this as reference.
   # Run ci/min_deps_check.py to verify that this file respects the policy.
-  - python=3.10
+  - python=3.11
   - cftime=1.6
-  - cgen=2020.1
   - dask=2022.8
   - matplotlib-base=3.5
   # netcdf follows a 1.major.minor[.patch] convention
   # (see https://github.com/Unidata/netcdf4-python/issues/1090)
   - netcdf4=1.6
   - numpy=1.23
-  - platformdirs=2.5
-  - psutil=5.9
-  - pymbolic=2022.1
   - pytest=7.1
   - scipy=1.9
   - tqdm=4.64

.github/ci/min_deps_check.py

@@ -60,8 +60,8 @@ def parse_requirements(fname) -> Iterator[tuple[str, int, int, int | None]]:
 
         try:
             version_tup = tuple(int(x) for x in version.split("."))
-        except ValueError:
-            raise ValueError("non-numerical version: " + row)
+        except ValueError as e:
+            raise ValueError("non-numerical version: " + row) from e
 
         if len(version_tup) == 2:
             yield (pkg, *version_tup, None)  # type: ignore[misc]
@@ -193,7 +193,7 @@ def main() -> None:
         print("\nErrors:")
         print("-------")
         for i, e in enumerate(errors):
-            print(f"{i+1}. {e}")
+            print(f"{i + 1}. {e}")
         sys.exit(1)
 
 

.github/ci/recipe.yaml

@@ -0,0 +1,69 @@
+# Recipe for https://github.com/prefix-dev/rattler-build used for nightly releases of Parcels
+# during version 4 alpha development
+#
+# Adapted from the conda forge recipe
+context:
+  name: parcels
+  version: 4.0.0alpha0 # The last number here needs to be bumped for each new alpha release
+
+package:
+  name: ${{ name|lower }}
+  version: ${{ version }}
+
+source:
+  path: ../..
+
+build:
+  number: 0
+  noarch: python
+  script:
+    - python -m pip install . -vv --no-deps --no-build-isolation
+
+requirements:
+  host:
+    - python 3.11.*
+    - pip
+    - setuptools
+    - setuptools_scm
+    - setuptools_scm_git_archive
+    - wheel
+  run:
+    - python >=3.11
+    - cftime
+    - dask
+    - matplotlib-base >=2.0.2
+    - netcdf4 >=1.1.9
+    - numpy >=1.11
+    - platformdirs
+    - pytest
+    - scipy >=0.16.0
+    - trajan
+    - tqdm
+    - xarray >=0.10.8
+    - zarr >=2.11.0,!=2.18.0,<3
+    - uxarray>=2025.3.0
+    - pyogrio # needed for geopandas (uxarray -> geoviews -> geopandas -> pyogrio, but for some reason conda doesn't pick it up automatically)
+    - pooch
+
+tests:
+  - python:
+      imports:
+        - parcels
+
+about:
+  homepage: https://github.com/OceanParcels/parcels
+  license: MIT
+  license_file: LICENSE.md
+  summary: Probably A Really Computationally Efficient Lagrangian Simulator
+  description: |
+    Parcels (Probably A Really Computationally Efficient Lagrangian Simulator)
+    is a set of Python classes and methods to create customisable particle
+    tracking simulations using output from Ocean Circulation models.
+    Parcels can be used to track passive and active particulates such as
+    water, nutrients, plankton, plastic and fish.
+  documentation: https://oceanparcels.org/
+  repository: https://github.com/OceanParcels/parcels
+
+extra:
+  recipe-maintainers:
+    - VeckoTheGecko

.github/workflows/additional.yml

@@ -29,16 +29,14 @@ jobs:
           python .github/ci/min_deps_check.py .github/ci/min-core-deps.yml
 
   linkcheck:
-    name: Sphinx linkcheck
+    name: pixi run docs-linkcheck
     runs-on: "ubuntu-latest"
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
       - uses: actions/checkout@v4
-      - name: Setup parcels
-        uses: ./.github/actions/install-parcels
-        with:
-          environment-file: environment.yml
-      - run: sphinx-build -b linkcheck docs/ _build/linkcheck
+      - uses: actions/checkout@v4
+      - uses: prefix-dev/[email protected]
+      - run: pixi run docs-linkcheck

.github/workflows/cache-pixi-lock.yml

@@ -0,0 +1,49 @@
+name: Generate and cache Pixi lockfile
+
+on:
+  workflow_call:
+    outputs:
+      cache-id:
+        description: "The lock file contents"
+        value: ${{ jobs.cache-pixi-lock.outputs.cache-id }}
+
+jobs:
+  cache-pixi-lock:
+    name: Generate output
+    runs-on: ubuntu-latest
+    outputs:
+      cache-id: ${{ steps.restore.outputs.cache-primary-key }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          fetch-depth: 0
+          sparse-checkout: pixi.toml
+      - name: Get current date
+        id: date
+        run: echo "date=$(date +'%Y-%m-%d')" >> "$GITHUB_OUTPUT"
+      - uses: actions/cache/restore@v4
+        id: restore
+        with:
+          path: |
+            pixi.lock
+          key: ${{ steps.date.outputs.date }}_${{hashFiles('pixi.toml')}}
+      - uses: prefix-dev/[email protected]
+        if: ${{ !steps.restore.outputs.cache-hit }}
+        with:
+          pixi-version: v0.49.0
+          run-install: false
+      - name: Run pixi lock
+        if: ${{ !steps.restore.outputs.cache-hit }}
+        run: pixi lock
+      - uses: actions/cache/save@v4
+        if: ${{ !steps.restore.outputs.cache-hit }}
+        id: cache
+        with:
+          path: |
+            pixi.lock
+          key: ${{ steps.restore.outputs.cache-primary-key }}
+      - name: Upload pixi.lock
+        uses: actions/upload-artifact@v4
+        with:
+          name: pixi-lock
+          path: pixi.lock