Patch Ruff config (isort in notebooks)

.pre-commit-config.yaml

@@ -13,9 +13,11 @@ repos:
     rev: v0.7.4
     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

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}

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

@@ -3,9 +3,10 @@
 from typing import Literal
 
 import numpy as np
-import parcels
 import xarray as xr
 
+import parcels
+
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 
 

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,

docs/examples/example_nemo_curvilinear.py

@@ -5,9 +5,10 @@
 from glob import glob
 
 import numpy as np
-import parcels
 import pytest
 
+import parcels
+
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 advection = {"RK4": parcels.AdvectionRK4, "AA": parcels.AdvectionAnalytical}
 

docs/examples/example_ofam.py

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

docs/examples/example_peninsula.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,

docs/examples/example_radial_rotation.py

@@ -2,9 +2,10 @@
 from datetime import timedelta
 
 import numpy as np
-import parcels
 import pytest
 
+import parcels
+
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 
 

docs/examples/example_stommel.py

@@ -3,9 +3,10 @@
 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,

docs/examples/tutorial_croco_3D.ipynb

@@ -35,11 +35,13 @@
    "outputs": [],
    "source": [
     "import os\n",
-    "import parcels\n",
-    "import numpy as np\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "import xarray as xr\n",
     "\n",
+    "import parcels\n",
+    "\n",
     "example_dataset_folder = parcels.download_example_dataset(\"CROCOidealized_data\")\n",
     "file = os.path.join(example_dataset_folder, \"CROCO_idealized.nc\")"
    ]

docs/examples/tutorial_nemo_3D.ipynb

@@ -54,9 +54,9 @@
     }
    ],
    "source": [
+    "import warnings\n",
     "from datetime import timedelta\n",
     "from glob import glob\n",
-    "import warnings\n",
     "\n",
     "import matplotlib.pyplot as plt\n",
     "import xarray as xr\n",

docs/examples/tutorial_timestamps.ipynb

@@ -14,8 +14,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from glob import glob\n",
     "import warnings\n",
+    "from glob import glob\n",
     "\n",
     "import numpy as np\n",
     "\n",

pyproject.toml

@@ -68,8 +68,6 @@ filterwarnings = [
 line-length = 120
 
 [tool.ruff.lint]
-exclude = ["*.ipynb"]
-
 select = [
     "D",  # pydocstyle
     "E",  # Error
@@ -132,6 +130,9 @@ ignore = [
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
+[tool.ruff.lint.isort]
+known-first-party = ["parcels"]
+
 [tool.mypy]
 files = [
   "parcels/compilation/codegenerator.py",