Chore/update linting tools

.github/workflows/cd.yml

@@ -3,7 +3,7 @@ name: cd
 on:
   push:
     tags:
-      - '**'
+    - '**'
 
 jobs:
   pypi_binwheels:

.github/workflows/ci.yml

@@ -2,9 +2,9 @@ name: ci
 
 on:
   push:
-    branches: [ "main", "develop" ]
+    branches: ["main", "develop"]
   pull_request:
-    branches: [ "main", "develop" ]
+    branches: ["main", "develop"]
 
 jobs:
   qa-pre-commit:

.github/workflows/downstream-ci.yml

@@ -4,16 +4,16 @@ on:
   # Trigger the workflow on push to master or develop, except tag creation
   push:
     branches:
-      - 'main'
-      - 'develop'
+    - 'main'
+    - 'develop'
     tags-ignore:
-      - '**'
+    - '**'
 
   # Trigger the workflow on pull request
-  pull_request: ~
+  pull_request:
 
   # Trigger the workflow manually
-  workflow_dispatch: ~
+  workflow_dispatch:
 
   # Trigger after public PR approved for CI
   pull_request_target:

.github/workflows/test-pypi.yml

@@ -2,7 +2,7 @@ name: test-cd
 
 on:
   pull_request:
-    branches: [ "main" ]
+    branches: ["main"]
 
 jobs:
   pypi_binwheels:

.pre-commit-config.yaml

@@ -1,45 +1,43 @@
 default_language_version:
-    python: python3
+  python: python3
 default_stages:
-    - pre-commit
-    - pre-push
+- pre-commit
+- pre-push
 repos:
-    - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.5.6
-      hooks:
-          - id: ruff # fix linting violations
-            types_or: [ python, pyi, jupyter ]
-            args: [ --fix ]
-          # - id: ruff-format # fix formatting
-          #   types_or: [ python, pyi, jupyter ]
-    - repo: https://github.com/psf/black
-      rev: 25.1.0
-      hooks:
-        - id: black
-    - repo: https://github.com/pycqa/isort
-      rev: 5.13.2
-      hooks:
-        - id: isort
-    - repo: https://github.com/pycqa/flake8
-      rev: 7.0.0
-      hooks:
-        - id: flake8
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
-      hooks:
-          - id: detect-private-key
-          - id: check-ast
-          - id: end-of-file-fixer
-          - id: mixed-line-ending
-            args: [--fix=lf]
-          - id: trailing-whitespace
-          - id: check-case-conflict
-    - repo: local
-      hooks:
-          - 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$'
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: detect-private-key
+  - id: check-ast
+  - id: end-of-file-fixer
+  - id: mixed-line-ending
+    args: [--fix=lf]
+  - id: trailing-whitespace
+  - id: check-case-conflict
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.15.4
+  hooks:
+  - id: ruff-check
+    exclude: '(dev/.*|.*_)\.py$'
+    args:
+    - --line-length=120
+    - --fix
+    - --exit-non-zero-on-fix
+    - --preview
+  - id: ruff-format
+- repo: https://github.com/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: local
+  hooks:
+  - 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$'

.readthedocs.yml

@@ -6,16 +6,16 @@ build:
     python: "3.11"
   jobs:
     pre_build:
-      - rm -rf _build
-      - rm -rf docs/_build
-      - cd docs && make rst
+    - rm -rf _build
+    - rm -rf docs/_build
+    - cd docs && make rst
 
 python:
   install:
-    - method: pip
-      path: .
-      extra_requirements:
-      - docs
+  - method: pip
+    path: .
+    extra_requirements:
+    - docs
 
 sphinx:
   configuration: docs/source/conf.py

Cargo.toml

@@ -1,18 +1,18 @@
-[package]
-name = "earthkit-hydro"
-version = "0.0.0" # placeholder, will be overwritten
-edition = "2021"
-
 [dependencies]
-pyo3 = { version = "0.26", features = ["extension-module"] }
+fixedbitset = "0.5"
 numpy = "0.26"
+pyo3 = {version = "0.26", features = ["extension-module"]}
 rayon = "1.7"
-fixedbitset = "0.5"
 
 [lib]
+crate-type = ["cdylib"]
 # See https://github.com/PyO3/pyo3 for details
 name = "_rust"  # private module to be nested into Python package
 path = "rust/lib.rs"
-crate-type = ["cdylib"]
+
+[package]
+edition = "2021"
+name = "earthkit-hydro"
+version = "0.0.0"  # placeholder, will be overwritten
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html

docs/source/tutorials/array_backend.ipynb

@@ -7,11 +7,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import earthkit.hydro as ekh\n",
-    "import numpy as np\n",
     "import cupy as cp\n",
+    "import numpy as np\n",
     "import torch\n",
-    "import xarray as xr"
+    "import xarray as xr\n",
+    "\n",
+    "import earthkit.hydro as ekh"
    ]
   },
   {
@@ -208,7 +209,9 @@
     }
    ],
    "source": [
-    "ekh.upstream.array.sum(torch_network, torch.ones(numpy_network.shape, device=torch_network.device), return_type=\"masked\")"
+    "ekh.upstream.array.sum(\n",
+    "    torch_network, torch.ones(numpy_network.shape, device=torch_network.device), return_type=\"masked\"\n",
+    ")"
    ]
   },
   {
@@ -231,24 +234,24 @@
     "example_arr_numpy = np.random.rand(10, *numpy_network.shape)\n",
     "example_arr_cupy = cp.random.rand(10, *numpy_network.shape)\n",
     "\n",
-    "lat = numpy_network.coords['lat']\n",
-    "lon = numpy_network.coords['lon']\n",
+    "lat = numpy_network.coords[\"lat\"]\n",
+    "lon = numpy_network.coords[\"lon\"]\n",
     "step = np.arange(10)\n",
     "\n",
     "example_da_numpy = xr.DataArray(\n",
     "    example_arr_numpy,\n",
-    "    dims = [\"step\", \"lat\", \"lon\"],\n",
-    "    coords = {\"step\": step, \"lat\": lat, \"lon\": lon},\n",
-    "    name = \"precip\",\n",
-    "    attrs={\"units\": \"m\", \"description\": \"Sample precipitation data\"}\n",
+    "    dims=[\"step\", \"lat\", \"lon\"],\n",
+    "    coords={\"step\": step, \"lat\": lat, \"lon\": lon},\n",
+    "    name=\"precip\",\n",
+    "    attrs={\"units\": \"m\", \"description\": \"Sample precipitation data\"},\n",
     ")\n",
     "\n",
     "example_da_cupy = xr.DataArray(\n",
     "    example_arr_cupy,\n",
-    "    dims = [\"step\", \"lat\", \"lon\"],\n",
-    "    coords = {\"step\": step, \"lat\": lat, \"lon\": lon},\n",
-    "    name = \"precip\",\n",
-    "    attrs={\"units\": \"m\", \"description\": \"Sample precipitation data\"}\n",
+    "    dims=[\"step\", \"lat\", \"lon\"],\n",
+    "    coords={\"step\": step, \"lat\": lat, \"lon\": lon},\n",
+    "    name=\"precip\",\n",
+    "    attrs={\"units\": \"m\", \"description\": \"Sample precipitation data\"},\n",
     ")"
    ]
   },

docs/source/tutorials/catchment_statistics.ipynb

@@ -15,9 +15,10 @@
     }
    ],
    "source": [
-    "import earthkit.hydro as ekh\n",
     "import numpy as np\n",
     "\n",
+    "import earthkit.hydro as ekh\n",
+    "\n",
     "network = ekh.river_network.load(\"efas\", \"5\", use_cache=False)"
    ]
   },
@@ -507,12 +508,9 @@
     }
    ],
    "source": [
-    "field = np.ones(network.shape) # or load array/xarray from file\n",
+    "field = np.ones(network.shape)  # or load array/xarray from file\n",
     "\n",
-    "ekh.catchments.sum(network, field, locations = {\n",
-    "    \"gauge_1\": (70.475, 28.32),\n",
-    "    \"gauge_2\": (42.225, 50.24)\n",
-    "})"
+    "ekh.catchments.sum(network, field, locations={\"gauge_1\": (70.475, 28.32), \"gauge_2\": (42.225, 50.24)})"
    ]
   }
  ],

docs/source/tutorials/computing_accumulations.ipynb

@@ -15,9 +15,10 @@
     }
    ],
    "source": [
-    "import earthkit.hydro as ekh\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
+    "import earthkit.hydro as ekh\n",
     "\n",
     "network = ekh.river_network.load(\"efas\", \"5\", use_cache=False)"
    ]
@@ -64,7 +65,7 @@
     }
    ],
    "source": [
-    "field = np.ones(network.shape) # or load array/xarray from file\n",
+    "field = np.ones(network.shape)  # or load array/xarray from file\n",
     "\n",
     "da = ekh.upstream.sum(network, field)\n",
     "\n",

docs/source/tutorials/creating_subnetworks.ipynb

@@ -15,9 +15,10 @@
     }
    ],
    "source": [
-    "import earthkit.hydro as ekh\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
+    "import earthkit.hydro as ekh\n",
     "\n",
     "network = ekh.river_network.load(\"efas\", \"5\", use_cache=False)"
    ]
@@ -64,7 +65,7 @@
     }
    ],
    "source": [
-    "node_mask = ekh.catchments.array.find(network, locations = {\"gauge_1\": (42.225, 50.24)})\n",
+    "node_mask = ekh.catchments.array.find(network, locations={\"gauge_1\": (42.225, 50.24)})\n",
     "# has nans for missing, and 0s for the catchment\n",
     "# => convert to boolean mask\n",
     "node_mask = node_mask == 0\n",