feat: update pre-commit to align with rest of ek

.pre-commit-config.yaml

@@ -1,40 +1,43 @@
+default_language_version:
+  python: python3
+default_stages:
+- pre-commit
+- pre-push
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v6.0.0
   hooks:
-  - id: trailing-whitespace     # Trailing whitespace checker
-  - id: end-of-file-fixer     # Ensure files end in a newline
-  - id: check-json
-  - id: check-yaml     # Check YAML files for syntax errors only
-    args: [--unsafe, --allow-multiple-documents]
-  - id: check-toml
-          # - id: check-added-large-files
-  - id: debug-statements     # Check for debugger imports and py37+ breakpoint()
+  - id: detect-private-key
+  - id: check-ast
+  - id: end-of-file-fixer
   - id: mixed-line-ending
-  - id: no-commit-to-branch     # Prevent committing to main / master
-  - id: check-merge-conflict     # Check for files that contain merge conflict
-    exclude: /README\.rst$|^docs/.*\.rst$
+    args: [--fix=lf]
+  - id: trailing-whitespace
+  - id: check-case-conflict
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.9
+  rev: v0.15.4
   hooks:
   - id: ruff-check
+    exclude: '(dev/.*|.*_)\.py$'
     args:
+    - --line-length=120
     - --fix
     - --exit-non-zero-on-fix
+    - --preview
   - id: ruff-format
-- repo: https://github.com/executablebooks/mdformat
-  rev: 0.7.14
-  hooks:
-  - id: mdformat
-    exclude: cruft-update-template.md
 - repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
   rev: v2.16.0
   hooks:
   - id: pretty-format-yaml
     args: [--autofix, --preserve-quotes]
   - id: pretty-format-toml
     args: [--autofix]
-- repo: https://github.com/sphinx-contrib/sphinx-lint
-  rev: v1.0.0
+- repo: local
   hooks:
-  - id: sphinx-lint
+  - id: forbid-to-commit
+    name: Don't commit rej files
+    entry: |
+      Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+      Fix the merge conflicts manually and remove the .rej files.
+    language: fail
+    files: '.*\.rej$'

docs/conf.py

@@ -30,9 +30,7 @@
 else:
     source_branch = "main"
 
-src_path = os.path.normpath(
-    os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "src")
-)
+src_path = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "src"))
 sys.path.insert(0, src_path)
 
 # Adds path to the folder _ext, where extensions are stored
@@ -128,19 +126,11 @@
 # clean_autodocs.py feature flags
 # Set to False/None to disable or soften the corresponding processing step.
 autodocs_delete_hidden = True  # delete RST files for private/hidden modules
-autodocs_replace_automodule = (
-    True  # replace automodule directives with autosummary tables
-)
-autodocs_short_display_names = (
-    True  # shorten toctree labels to the last module component
-)
-autodocs_top_level_maxdepth = (
-    1  # :maxdepth: on top-level page (None = keep sphinx-apidoc value)
-)
+autodocs_replace_automodule = True  # replace automodule directives with autosummary tables
+autodocs_short_display_names = True  # shorten toctree labels to the last module component
+autodocs_top_level_maxdepth = 1  # :maxdepth: on top-level page (None = keep sphinx-apidoc value)
 autodocs_rename_titles = False  # strip " package"/" module" from RST page headings
-autodocs_top_level_title = (
-    "API Reference"  # top-level page heading (used when rename_titles=True)
-)
+autodocs_top_level_title = "API Reference"  # top-level page heading (used when rename_titles=True)
 autodocs_titlesonly = False  # inject :titlesonly: into toctree directives
 
 # List of patterns, relative to source directory, that match files and

docs/tutorials/comparing-models-solutions.ipynb

@@ -49,8 +49,8 @@
    "outputs": [],
    "source": [
     "import earthkit.data as ekd\n",
-    "import earthkit.transforms as ekt\n",
-    "import earthkit.plots as ekp"
+    "import earthkit.plots as ekp\n",
+    "import earthkit.transforms as ekt"
    ]
   },
   {
@@ -1899,9 +1899,7 @@
     "# We can directly access the underlying matplotlib objects to do this\n",
     "x = [-180, -180, 180, 180, -180]\n",
     "y = [-90, 90, 90, -90, -90]\n",
-    "figure[0].ax.fill(\n",
-    "    x, y, transform=ccrs.PlateCarree(), hatch=\"///////\", fill=False, zorder=0\n",
-    ")\n",
+    "figure[0].ax.fill(x, y, transform=ccrs.PlateCarree(), hatch=\"///////\", fill=False, zorder=0)\n",
     "\n",
     "figure.show()"
    ]
@@ -2066,9 +2064,7 @@
     "# We can directly access the underlying matplotlib objects to do this\n",
     "x = [-180, -180, 180, 180, -180]\n",
     "y = [-90, 90, 90, -90, -90]\n",
-    "figure[0].ax.fill(\n",
-    "    x, y, transform=ccrs.PlateCarree(), hatch=\"///////\", fill=False, zorder=0\n",
-    ")\n",
+    "figure[0].ax.fill(x, y, transform=ccrs.PlateCarree(), hatch=\"///////\", fill=False, zorder=0)\n",
     "\n",
     "figure.show()"
    ]
@@ -2138,9 +2134,7 @@
     "# We can directly access the underlying matplotlib objects to do this\n",
     "x = [-180, -180, 180, 180, -180]\n",
     "y = [-90, 90, 90, -90, -90]\n",
-    "figure[0].ax.fill(\n",
-    "    x, y, transform=ccrs.PlateCarree(), hatch=\"///////\", fill=False, zorder=0\n",
-    ")\n",
+    "figure[0].ax.fill(x, y, transform=ccrs.PlateCarree(), hatch=\"///////\", fill=False, zorder=0)\n",
     "\n",
     "figure.show()"
    ]

docs/tutorials/ensemble.ipynb

@@ -1203,16 +1203,15 @@
     }
    ],
    "source": [
-    "import cartopy.crs as ccrs\n",
     "import datetime\n",
     "\n",
+    "import cartopy.crs as ccrs\n",
+    "\n",
     "# define step\n",
     "step_hours = 78\n",
     "step = datetime.timedelta(hours=step_hours)\n",
     "\n",
-    "figure = ekp.Figure(\n",
-    "    crs=ccrs.PlateCarree(), domain=[-15, 15, 65, 45], size=(7, 6), rows=2, columns=2\n",
-    ")\n",
+    "figure = ekp.Figure(crs=ccrs.PlateCarree(), domain=[-15, 15, 65, 45], size=(7, 6), rows=2, columns=2)\n",
     "\n",
     "gust_style = ekp.styles.Style(\n",
     "    colors=[\"#85AAEE\", \"#208EFC\", \"#6CA632\", \"#FFB000\", \"#FF0000\", \"#7A11B1\"],\n",
@@ -1224,17 +1223,13 @@
     "\n",
     "# the hres forecast, GRIB\n",
     "subplot = figure.add_map(0, 0)\n",
-    "subplot.contourf(\n",
-    "    fl_fc.sel({\"parameter.variable\": \"10fg3\", \"time.step\": step}), style=gust_style\n",
-    ")\n",
+    "subplot.contourf(fl_fc.sel({\"parameter.variable\": \"10fg3\", \"time.step\": step}), style=gust_style)\n",
     "subplot.title(\"HRES {base_time:%Y-%m-%d %H} UTC (+{lead_time}h)\")\n",
     "subplot.legend(label=\"\")\n",
     "\n",
     "# the control forecast, GRIB\n",
     "subplot = figure.add_map(0, 1)\n",
-    "subplot.contourf(\n",
-    "    fl_fg.sel({\"metadata.marsType\": \"cf\", \"time.step\": step}), style=gust_style\n",
-    ")\n",
+    "subplot.contourf(fl_fg.sel({\"metadata.marsType\": \"cf\", \"time.step\": step}), style=gust_style)\n",
     "subplot.title(\"CF {base_time:%Y-%m-%d %H} UTC (+{lead_time}h)\")\n",
     "subplot.legend(label=\"\")\n",
     "\n",
@@ -1301,16 +1296,14 @@
     }
    ],
    "source": [
-    "import matplotlib.pyplot as plt\n",
     "import cartopy.crs as ccrs\n",
+    "import matplotlib.pyplot as plt\n",
     "\n",
     "# define step\n",
     "step_hours = 78\n",
     "step = datetime.timedelta(hours=step_hours)\n",
     "\n",
-    "figure = ekp.Figure(\n",
-    "    crs=ccrs.PlateCarree(), domain=[-15, 15, 65, 45], figsize=(7, 7), rows=8, columns=8\n",
-    ")\n",
+    "figure = ekp.Figure(crs=ccrs.PlateCarree(), domain=[-15, 15, 65, 45], figsize=(7, 7), rows=8, columns=8)\n",
     "\n",
     "gust_style = ekp.styles.Style(\n",
     "    colors=[\"#85AAEE\", \"#208EFC\", \"#6CA632\", \"#FFB000\", \"#FF0000\", \"#7A11B1\"],\n",
@@ -1325,16 +1318,12 @@
     "\n",
     "# HRES forecast, GRIB\n",
     "subplot = figure.add_map(0, 6)\n",
-    "subplot.contourf(\n",
-    "    fl_fc.sel({\"parameter.variable\": \"10fg3\", \"time.step\": step}), style=gust_style\n",
-    ")\n",
+    "subplot.contourf(fl_fc.sel({\"parameter.variable\": \"10fg3\", \"time.step\": step}), style=gust_style)\n",
     "subplot.title(\"HRES\")\n",
     "\n",
     "# control forecast, GRIB\n",
     "subplot = figure.add_map(0, 7)\n",
-    "subplot.contourf(\n",
-    "    fl_fg.sel({\"metadata.marsType\": \"cf\", \"time.step\": step}), style=gust_style\n",
-    ")\n",
+    "subplot.contourf(fl_fg.sel({\"metadata.marsType\": \"cf\", \"time.step\": step}), style=gust_style)\n",
     "subplot.title(\"CF\")\n",
     "\n",
     "# perturbed members, GRIB\n",
@@ -1427,9 +1416,7 @@
     "\n",
     "# perturbed members\n",
     "for f in z_en.sel({\"metadata.marsType\": \"pf\"}):\n",
-    "    chart.contour(\n",
-    "        f, levels=cont_level, linewidths=[0.2, 0.2], colors=\"blue\", labels=False\n",
-    "    )\n",
+    "    chart.contour(f, levels=cont_level, linewidths=[0.2, 0.2], colors=\"blue\", labels=False)\n",
     "\n",
     "# control forecast\n",
     "chart.contour(\n",
@@ -1567,9 +1554,7 @@
    "outputs": [],
    "source": [
     "perc = 0.8  # 80%\n",
-    "perc_xr = fl_fg.to_xarray(ensure_dims=\"forecast_reference_time\").quantile(\n",
-    "    perc, dim=\"member\"\n",
-    ")"
+    "perc_xr = fl_fg.to_xarray(ensure_dims=\"forecast_reference_time\").quantile(perc, dim=\"member\")"
    ]
   },
   {

docs/tutorials/polytope_polygon.ipynb

@@ -582,9 +582,7 @@
     "    \"feature\": {\"type\": \"polygon\", \"shape\": coords},\n",
     "}\n",
     "\n",
-    "ds = ekd.from_source(\n",
-    "    \"polytope\", \"ecmwf-mars\", request, stream=False, address=\"polytope.ecmwf.int\"\n",
-    ").to_xarray()\n",
+    "ds = ekd.from_source(\"polytope\", \"ecmwf-mars\", request, stream=False, address=\"polytope.ecmwf.int\").to_xarray()\n",
     "ds"
    ]
   },

docs/tutorials/polytope_timeseries.ipynb

@@ -721,9 +721,7 @@
     "    },\n",
     "}\n",
     "\n",
-    "ds = ekd.from_source(\n",
-    "    \"polytope\", \"ecmwf-mars\", request, stream=False, address=\"polytope.ecmwf.int\"\n",
-    ").to_xarray()\n",
+    "ds = ekd.from_source(\"polytope\", \"ecmwf-mars\", request, stream=False, address=\"polytope.ecmwf.int\").to_xarray()\n",
     "ds"
    ]
   },
@@ -753,8 +751,8 @@
     }
    ],
    "source": [
-    "import earthkit.transforms as ekt\n",
     "import earthkit.plots as ekp\n",
+    "import earthkit.transforms as ekt\n",
     "\n",
     "mean_ds = ekt.ensemble.mean(ds)\n",
     "\n",
@@ -795,9 +793,7 @@
     "TIME_FREQUENCY = \"6h\"\n",
     "QUANTILES = [0, 0.1, 0.25, 0.5, 0.75, 0.9, 1]\n",
     "\n",
-    "ekp.timeseries.multiboxplot(ds, resample=TIME_FREQUENCY, quantiles=QUANTILES).line(\n",
-    "    ds.mean(dim=\"number\")\n",
-    ")"
+    "ekp.timeseries.multiboxplot(ds, resample=TIME_FREQUENCY, quantiles=QUANTILES).line(ds.mean(dim=\"number\"))"
    ]
   }
  ],

docs/tutorials/polytope_vertical_profile.ipynb

@@ -613,9 +613,7 @@
     "    },\n",
     "}\n",
     "\n",
-    "ds = ekd.from_source(\n",
-    "    \"polytope\", \"ecmwf-mars\", request, stream=False, address=\"polytope.ecmwf.int\"\n",
-    ").to_xarray()\n",
+    "ds = ekd.from_source(\"polytope\", \"ecmwf-mars\", request, stream=False, address=\"polytope.ecmwf.int\").to_xarray()\n",
     "ds"
    ]
   }

docs/tutorials/time-series-solutions.ipynb

@@ -828,9 +828,7 @@
     "\n",
     "chart.line(data, units=\"celsius\", color=\"red\")\n",
     "\n",
-    "chart.title(\n",
-    "    \"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\"\n",
-    ")\n",
+    "chart.title(\"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\")\n",
     "\n",
     "chart.ylabel()\n",
     "\n",
@@ -880,9 +878,7 @@
     "chart.line(data, units=\"celsius\", label=\"hourly\")\n",
     "chart.line(daily_min, units=\"celsius\", label=\"{name}\")\n",
     "\n",
-    "chart.title(\n",
-    "    \"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\"\n",
-    ")\n",
+    "chart.title(\"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\")\n",
     "\n",
     "chart.ylabel()\n",
     "\n",
@@ -968,9 +964,7 @@
     "chart.line(data, units=\"celsius\", label=\"hourly\")\n",
     "chart.line(daily_min, units=\"celsius\", label=\"{name}\")\n",
     "\n",
-    "chart.title(\n",
-    "    \"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\"\n",
-    ")\n",
+    "chart.title(\"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\")\n",
     "\n",
     "chart.ylabel()\n",
     "\n",
@@ -1019,9 +1013,7 @@
     "chart.line(daily_mean, units=\"celsius\", label=\"{name}\")\n",
     "chart.line(daily_min, units=\"celsius\", label=\"{name}\")\n",
     "\n",
-    "chart.title(\n",
-    "    \"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\"\n",
-    ")\n",
+    "chart.title(\"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\")\n",
     "\n",
     "chart.ylabel()\n",
     "\n",
@@ -1087,9 +1079,7 @@
     "import numpy as np\n",
     "\n",
     "daily_precip = ekt.temporal.daily_mean(ds)\n",
-    "daily_precip = daily_precip.assign_coords(\n",
-    "    valid_time=daily_precip.valid_time + np.timedelta64(12, \"h\")\n",
-    ")"
+    "daily_precip = daily_precip.assign_coords(valid_time=daily_precip.valid_time + np.timedelta64(12, \"h\"))"
    ]
   },
   {
@@ -1114,9 +1104,7 @@
     "\n",
     "chart.bar(daily_precip, units=\"mm\")\n",
     "\n",
-    "chart.title(\n",
-    "    \"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\"\n",
-    ")\n",
+    "chart.title(\"ERA5 hourly {variable_name} at {latitude:%Lt} {longitude:%Ln} ({location:%c}, {location:%C})\")\n",
     "\n",
     "chart.ylabel()\n",
     "\n",