Merge branch 'master' into CROCO_fix_sigma_calculation

Author: erikvansebille

.github/workflows/ci.yml

@@ -24,12 +24,14 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos, ubuntu, windows]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
         include:
           - os: ubuntu
             python-version: "3.10"
           - os: ubuntu
             python-version: "3.11"
+          - os: ubuntu
+            python-version: "3.12"
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -43,10 +45,10 @@ jobs:
           coverage run -m pytest -v -s --html=${{ matrix.os }}_${{ matrix.python-version }}_unit_test_report.html --self-contained-html tests
           coverage xml
       - name: Codecov
-        uses: codecov/codecov-action@v4.6.0
+        uses: codecov/codecov-action@v5.0.7
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-        if: matrix.python-version == '3.12'
+        if: matrix.python-version == '3.13'
         with:
           flags: unit-tests
       - name: Upload test results
@@ -62,7 +64,10 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos, ubuntu, windows]
-        python-version: ["3.12"]
+        python-version: ["3.13"]
+        include:
+          - os: ubuntu
+            python-version: "3.10"
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -72,10 +77,10 @@ jobs:
           environment-file: environment.yml
       - name: Integration test
         run: |
-          coverage run -m pytest -v -s --nbval-lax -k "not documentation" --html="${{ matrix.os }}_integration_test_report.html" --self-contained-html docs/examples
+          coverage run -m pytest -v -s --nbval-lax -k "not documentation" --html="${{ matrix.os }}_${{ matrix.python-version }}_integration_test_report.html" --self-contained-html docs/examples
           coverage xml
       - name: Codecov
-        uses: codecov/codecov-action@v4.6.0
+        uses: codecov/codecov-action@v5.0.7
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
@@ -84,8 +89,8 @@ jobs:
         if: ${{ always() }} # Always run this step, even if tests fail
         uses: actions/upload-artifact@v4
         with:
-          name: Integration test report ${{ matrix.os }}
-          path: ${{ matrix.os }}_integration_test_report.html
+          name: Integration test report ${{ matrix.os }}-${{ matrix.python-version }}
+          path: ${{ matrix.os }}_${{ matrix.python-version }}_integration_test_report.html
   merge-test-artifacts:
     runs-on: ubuntu-latest
     needs:
@@ -112,7 +117,7 @@ jobs:
         run: |
           mypy --install-types --non-interactive parcels --cobertura-xml-report mypy_report
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v4.6.0
+        uses: codecov/codecov-action@v5.0.7
         if: ${{ always() }} # Upload even on error of mypy
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/pypi-release.yml

@@ -72,7 +72,7 @@ jobs:
 
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/gh-action-pypi-publish@v1.11.0
+        uses: pypa/gh-action-pypi-publish@v1.12.2
         with:
           user: __token__
           password: ${{ secrets.PARCELS_PYPI_TEST_TOKEN }}
@@ -89,7 +89,7 @@ jobs:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.11.0
+        uses: pypa/gh-action-pypi-publish@v1.12.2
         with:
           user: __token__
           password: ${{ secrets.PARCELS_PYPI_PROD_TOKEN }}

.pre-commit-config.yaml

@@ -10,18 +10,20 @@ repos:
         types: [text]
         files: \.(json|ipynb)$
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.4
+    rev: v0.8.1
     hooks:
       - id: ruff
+        name: ruff lint (.py)
         args: [--fix, --show-fixes]
+        types_or: [python]
       - id: ruff
-        name: ruff (isort jupyter)
+        name: ruff isort (.ipynb)
         args: [--select, I, --fix]
         types_or: [jupyter]
       - id: ruff-format
         types_or: [python, jupyter]
   - repo: https://github.com/rbubley/mirrors-prettier # Update mirror as official mirror is deprecated
-    rev: v3.3.3
+    rev: v3.4.1
     hooks:
       - id: prettier
 

docs/examples/documentation_indexing.ipynb

@@ -54,9 +54,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import warnings\n",
     "from glob import glob\n",
     "from os import path\n",
-    "import warnings\n",
     "\n",
     "import numpy as np\n",
     "\n",

docs/examples/example_brownian.py

@@ -1,9 +1,10 @@
 from datetime import timedelta
 
 import numpy as np
-import parcels
 import pytest
 
+import parcels
+
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 
 

docs/examples/example_dask_chunk_OCMs.py

@@ -4,8 +4,9 @@
 
 import dask
 import numpy as np
-import parcels
 import pytest
+
+import parcels
 from parcels.tools.statuscodes import DaskChunkingError
 
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
@@ -246,7 +247,7 @@ def test_pop(mode, chunk_mode):
     filenames = str(data_folder / "t.x1_SAMOC_flux.1690*.nc")
     variables = {"U": "UVEL", "V": "VVEL", "W": "WVEL"}
     timestamps = np.expand_dims(
-        np.array([np.datetime64("2000-%.2d-01" % m) for m in range(1, 7)]), axis=1
+        np.array([np.datetime64(f"2000-{m:02d}-01") for m in range(1, 7)]), axis=1
     )
     dimensions = {"lon": "ULON", "lat": "ULAT", "depth": "w_dep"}
     chs = False

docs/examples/example_decaying_moving_eddy.py

@@ -1,9 +1,10 @@
 from datetime import timedelta
 
 import numpy as np
-import parcels
 import pytest
 
+import parcels
+
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 
 # Define some constants.

docs/examples/example_globcurrent.py

@@ -2,10 +2,11 @@
 from glob import glob
 
 import numpy as np
-import parcels
 import pytest
 import xarray as xr
 
+import parcels
+
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 
 

docs/examples/example_mitgcm.py

@@ -1,13 +1,16 @@
 from datetime import timedelta
+from pathlib import Path
+from typing import Literal
 
 import numpy as np
-import parcels
 import xarray as xr
 
+import parcels
+
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 
 
-def run_mitgcm_zonally_reentrant(mode):
+def run_mitgcm_zonally_reentrant(mode: Literal["scipy", "jit"], path: Path):
     """Function that shows how to load MITgcm data in a zonally periodic domain."""
     data_folder = parcels.download_example_dataset("MITgcm_example_data")
     filenames = {
@@ -41,7 +44,7 @@ def periodicBC(particle, fieldset, time):
         size=10,
     )
     pfile = parcels.ParticleFile(
-        "MIT_particles_" + str(mode) + ".zarr",
+        str(path),
         pset,
         outputdt=timedelta(days=1),
         chunks=(len(pset), 1),
@@ -52,12 +55,15 @@ def periodicBC(particle, fieldset, time):
     )
 
 
-def test_mitgcm_output_compare():
-    run_mitgcm_zonally_reentrant("scipy")
-    run_mitgcm_zonally_reentrant("jit")
+def test_mitgcm_output_compare(tmpdir):
+    def get_path(mode: Literal["scipy", "jit"]) -> Path:
+        return tmpdir / f"MIT_particles_{mode}.zarr"
+
+    for mode in ["scipy", "jit"]:
+        run_mitgcm_zonally_reentrant(mode, get_path(mode))
 
-    ds_jit = xr.open_zarr("MIT_particles_jit.zarr")
-    ds_scipy = xr.open_zarr("MIT_particles_scipy.zarr")
+    ds_jit = xr.open_zarr(get_path("jit"))
+    ds_scipy = xr.open_zarr(get_path("scipy"))
 
     np.testing.assert_allclose(ds_jit.lat.data, ds_scipy.lat.data)
     np.testing.assert_allclose(ds_jit.lon.data, ds_scipy.lon.data)

docs/examples/example_moving_eddies.py

@@ -4,9 +4,10 @@
 from datetime import timedelta
 
 import numpy as np
-import parcels
 import pytest
 
+import parcels
+
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 method = {
     "RK4": parcels.AdvectionRK4,
@@ -145,7 +146,7 @@ def moving_eddies_example(
 
     # Execute for 1 week, with 1 hour timesteps and hourly output
     runtime = timedelta(days=7)
-    print("MovingEddies: Advecting %d particles for %s" % (npart, str(runtime)))
+    print(f"MovingEddies: Advecting {npart} particles for {runtime}")
     pset.execute(
         method,
         runtime=runtime,
@@ -176,7 +177,7 @@ def test_moving_eddies_fwdbwd(mode, mesh, tmpdir, npart=2):
     runtime = timedelta(days=1)
     dt = timedelta(minutes=5)
     outputdt = timedelta(hours=1)
-    print("MovingEddies: Advecting %d particles for %s" % (npart, str(runtime)))
+    print(f"MovingEddies: Advecting {npart} particles for {runtime}")
     outfile = tmpdir.join("EddyParticlefwd")
     pset.execute(
         method,