Chore/update linting tools

.github/ci-hpc-config.yml

@@ -1,25 +1,25 @@
 build:
   modules:
-    - ninja
+  - ninja
   dependencies:
-    - ecmwf/ecbuild@develop
-    - MathisRosenhauer/libaec@refs/tags/v1.1.3
-    - ecmwf/eccodes@develop
-    - ecmwf/eckit@develop
-    - ecmwf/odc@develop
-    - ecmwf/metkit@develop
-    - ecmwf/fdb@develop
+  - ecmwf/ecbuild@develop
+  - MathisRosenhauer/libaec@refs/tags/v1.1.3
+  - ecmwf/eccodes@develop
+  - ecmwf/eckit@develop
+  - ecmwf/odc@develop
+  - ecmwf/metkit@develop
+  - ecmwf/fdb@develop
   python_dependencies:
-    - ecmwf/eccodes-python@develop
-    - ecmwf/cfgrib@master
-    - ecmwf/pdbufr@master
-    - ecmwf/pyodc@develop
-    - ecmwf/pyfdb@develop
-    - ecmwf/earthkit-utils@develop
+  - ecmwf/eccodes-python@develop
+  - ecmwf/cfgrib@master
+  - ecmwf/pdbufr@master
+  - ecmwf/pyodc@develop
+  - ecmwf/pyfdb@develop
+  - ecmwf/earthkit-utils@develop
   env:
-    - ECCODES_SAMPLES_PATH=$ECCODES_DIR/share/eccodes/samples
-    - ECCODES_DEFINITION_PATH=$ECCODES_DIR/share/eccodes/definitions
-    - GITHUB_WORKFLOW=anything
+  - ECCODES_SAMPLES_PATH=$ECCODES_DIR/share/eccodes/samples
+  - ECCODES_DEFINITION_PATH=$ECCODES_DIR/share/eccodes/definitions
+  - GITHUB_WORKFLOW=anything
   parallel: 64
   requirements: tests/downstream-ci-requirements.txt
   pytest_cmd: |

.github/ci-hpc-gpu-config.yml

@@ -1,24 +1,24 @@
 build:
   modules:
-    - ninja
+  - ninja
   dependencies:
-    - ecmwf/ecbuild@develop
-    - MathisRosenhauer/libaec@refs/tags/v1.1.3
-    - ecmwf/eccodes@develop
-    - ecmwf/eckit@develop
-    - ecmwf/odc@develop
-    - ecmwf/metkit@develop
-    - ecmwf/fdb@develop
+  - ecmwf/ecbuild@develop
+  - MathisRosenhauer/libaec@refs/tags/v1.1.3
+  - ecmwf/eccodes@develop
+  - ecmwf/eckit@develop
+  - ecmwf/odc@develop
+  - ecmwf/metkit@develop
+  - ecmwf/fdb@develop
   python_dependencies:
-    - ecmwf/eccodes-python@develop
-    - ecmwf/cfgrib@master
-    - ecmwf/pdbufr@master
-    - ecmwf/pyodc@develop
-    - ecmwf/pyfdb@develop
-    - ecmwf/earthkit-utils@develop
+  - ecmwf/eccodes-python@develop
+  - ecmwf/cfgrib@master
+  - ecmwf/pdbufr@master
+  - ecmwf/pyodc@develop
+  - ecmwf/pyfdb@develop
+  - ecmwf/earthkit-utils@develop
   env:
-    - ECCODES_SAMPLES_PATH=$ECCODES_DIR/share/eccodes/samples
-    - ECCODES_DEFINITION_PATH=$ECCODES_DIR/share/eccodes/definitions
+  - ECCODES_SAMPLES_PATH=$ECCODES_DIR/share/eccodes/samples
+  - ECCODES_DEFINITION_PATH=$ECCODES_DIR/share/eccodes/definitions
   parallel: 64
   queue: ng
   gpus: 1

.github/workflows/cd-pypi.yml

@@ -2,7 +2,7 @@ name: cd
 on:
   push:
     tags:
-      - '**'
+    - '**'
 jobs:
   deploy:
     uses: ecmwf/reusable-workflows/.github/workflows/cd-pypi.yml@v2

.github/workflows/ci.yml

@@ -3,26 +3,26 @@ on:
   # Trigger the workflow on push to master or develop, except tag creation
   push:
     branches:
-      - "main"
-      - "develop"
+    - "main"
+    - "develop"
     tags-ignore:
-      - "**"
+    - "**"
     paths-ignore:
-      - "docs/**"
-      - "README.md"
+    - "docs/**"
+    - "README.md"
   # Trigger the workflow on pull request
   pull_request:
     paths-ignore:
-      - "docs/**"
-      - "README.md"
+    - "docs/**"
+    - "README.md"
   # Trigger the workflow manually
   workflow_dispatch:
   # Trigger after public PR approved for CI
   pull_request_target:
     types: [labeled]
     paths-ignore:
-      - "docs/**"
-      - "README.md"
+    - "docs/**"
+    - "README.md"
 jobs:
   # Run CI including downstream packages on self-hosted runners
   downstream-ci:

.github/workflows/nightly-hpc-gpu.yml

@@ -3,16 +3,16 @@ on:
   workflow_dispatch:
   # Run at 04:00 UTC every day (on default branch)
   schedule:
-    - cron: "0 04 * * *"
+  - cron: "0 04 * * *"
 jobs:
   test-hpc-gpu:
     runs-on: [self-hosted, linux, hpc]
     steps:
-      - uses: ecmwf/reusable-workflows/ci-hpc@v2
-        with:
-          github_user: ${{ secrets.BUILD_PACKAGE_HPC_GITHUB_USER }}
-          github_token: ${{ secrets.GH_REPO_READ_TOKEN }}
-          troika_user: ${{ secrets.HPC_CI_TESTING_SSH_USER }}
-          repository: ecmwf/earthkit-data@${{ github.event.pull_request.head.sha || github.sha }}
-          build_config: .github/ci-hpc-gpu-config.yml
-          python_version: "3.10"
+    - uses: ecmwf/reusable-workflows/ci-hpc@v2
+      with:
+        github_user: ${{ secrets.BUILD_PACKAGE_HPC_GITHUB_USER }}
+        github_token: ${{ secrets.GH_REPO_READ_TOKEN }}
+        troika_user: ${{ secrets.HPC_CI_TESTING_SSH_USER }}
+        repository: ecmwf/earthkit-data@${{ github.event.pull_request.head.sha || github.sha }}
+        build_config: .github/ci-hpc-gpu-config.yml
+        python_version: "3.10"

.github/workflows/notify-new-issue.yml

@@ -2,12 +2,12 @@ name: Notify new issue
 on:
   issues:
     types:
-      - "opened"
+    - "opened"
 jobs:
   notify:
     runs-on: ubuntu-latest
     steps:
-      - name: Notify new issue
-        uses: ecmwf/notify-teams-issue@v1
-        with:
-          incoming_webhook: ${{ secrets.MS_TEAMS_INCOMING_WEBHOOK }}
+    - name: Notify new issue
+      uses: ecmwf/notify-teams-issue@v1
+      with:
+        incoming_webhook: ${{ secrets.MS_TEAMS_INCOMING_WEBHOOK }}

.github/workflows/notify-new-pr.yml

@@ -2,12 +2,12 @@ name: Notify new PR
 on:
   pull_request_target:
     types:
-      - "opened"
+    - "opened"
 jobs:
   notify:
     runs-on: ubuntu-latest
     steps:
-      - name: Notify new PR
-        uses: ecmwf/notify-teams-pr@v1
-        with:
-          incoming_webhook: ${{ secrets.MS_TEAMS_INCOMING_WEBHOOK }}
+    - name: Notify new PR
+      uses: ecmwf/notify-teams-pr@v1
+      with:
+        incoming_webhook: ${{ secrets.MS_TEAMS_INCOMING_WEBHOOK }}

.pre-commit-config.yaml

@@ -1,54 +1,41 @@
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
-    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: 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$|^docs/.*\.rst$
-  - repo: https://github.com/psf/black
-    rev: 24.8.0
-    hooks:
-      - id: black
-        args: [--line-length=120]
-  - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.8
-    hooks:
-      - id: blackdoc
-        additional_dependencies: [black==23.3.0]
-        exclude: xr_engine_profile_rst\.py
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
-    hooks:
-      - id: ruff
-        exclude: '(docs/conf|dev/.*|.*_)\.py$|docs/experimental/.*\.ipynb$|polytope_feature\.ipynb$'
-        args:
-          - --line-length=120
-          - --fix
-          - --exit-non-zero-on-fix
-          - --preview
-  - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.14
-    hooks:
-      - id: mdformat
-        exclude: cruft-update-template.md
-  - repo: https://github.com/google/yamlfmt
-    rev: v0.13.0
-    hooks:
-      - id: yamlfmt
-  - repo: https://github.com/sphinx-contrib/sphinx-lint
-    rev: v1.0.0
-    hooks:
-      - id: sphinx-lint
-  - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.5.0"
-    hooks:
-      - id: pyproject-fmt
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace     # Trailing whitespace checker
+  - id: end-of-file-fixer     # Ensure files end in a newline
+  - id: check-json
+  - id: check-yaml     # Check YAML files for syntax errors only
+    args: [--unsafe, --allow-multiple-documents]
+  - id: check-toml
+          # - id: check-added-large-files
+  - id: debug-statements     # Check for debugger imports and py37+ breakpoint()
+  - id: mixed-line-ending
+  - id: no-commit-to-branch     # Prevent committing to main / master
+  - id: check-merge-conflict     # Check for files that contain merge conflict
+    exclude: /README\.rst$|^docs/.*\.rst$
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.15.4
+  hooks:
+  - id: ruff-check
+    exclude: '(dev/.*|.*_)\.py$'
+    args:
+    - --fix
+    - --exit-non-zero-on-fix
+  - 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
+  hooks:
+  - id: sphinx-lint

.readthedocs.yml

@@ -6,8 +6,8 @@ build:
     python: "3.10"
 python:
   install:
-    - requirements: docs/requirements.txt
-    - method: pip
-      path: .
+  - requirements: docs/requirements.txt
+  - method: pip
+    path: .
 sphinx:
   configuration: docs/conf.py

docs/examples/bufr_synop.ipynb

@@ -488,8 +488,7 @@
     }
    ],
    "source": [
-    "df = ds.to_pandas(columns=[\"latitude\", \"longitude\", \n",
-    "                           \"heightOfStation\", \"airTemperatureAt2M\"])\n",
+    "df = ds.to_pandas(columns=[\"latitude\", \"longitude\", \"heightOfStation\", \"airTemperatureAt2M\"])\n",
     "df"
    ]
   },
@@ -576,9 +575,10 @@
     }
    ],
    "source": [
-    "df = ds.to_pandas(columns=[\"latitude\", \"longitude\", \n",
-    "                           \"heightOfStation\", \"airTemperatureAt2M\", \"WMO_station_id\"],\n",
-    "                 filters={\"WMO_station_id\": [30846, 89514]})\n",
+    "df = ds.to_pandas(\n",
+    "    columns=[\"latitude\", \"longitude\", \"heightOfStation\", \"airTemperatureAt2M\", \"WMO_station_id\"],\n",
+    "    filters={\"WMO_station_id\": [30846, 89514]},\n",
+    ")\n",
     "df"
    ]
   },
@@ -662,9 +662,10 @@
     }
    ],
    "source": [
-    "df = ds.to_pandas(columns=[\"latitude\", \"longitude\", \n",
-    "                           \"heightOfStation\", \"airTemperatureAt2M\"],\n",
-    "                 filters={\"airTemperatureAt2M\": slice(None, 290)})\n",
+    "df = ds.to_pandas(\n",
+    "    columns=[\"latitude\", \"longitude\", \"heightOfStation\", \"airTemperatureAt2M\"],\n",
+    "    filters={\"airTemperatureAt2M\": slice(None, 290)},\n",
+    ")\n",
     "df"
    ]
   },
@@ -756,9 +757,10 @@
     }
    ],
    "source": [
-    "df = ds.to_pandas(columns=[\"latitude\", \"longitude\", \n",
-    "                           \"heightOfStation\", \"airTemperatureAt2M\"],\n",
-    "                 filters={\"airTemperatureAt2M\": slice(290, 300)})\n",
+    "df = ds.to_pandas(\n",
+    "    columns=[\"latitude\", \"longitude\", \"heightOfStation\", \"airTemperatureAt2M\"],\n",
+    "    filters={\"airTemperatureAt2M\": slice(290, 300)},\n",
+    ")\n",
     "df"
    ]
   },
@@ -842,9 +844,10 @@
     }
    ],
    "source": [
-    "df = ds.to_pandas(columns=[\"latitude\", \"longitude\", \n",
-    "                           \"heightOfStation\", \"airTemperatureAt2M\"],\n",
-    "                 filters={\"airTemperatureAt2M\": slice(300, None)})\n",
+    "df = ds.to_pandas(\n",
+    "    columns=[\"latitude\", \"longitude\", \"heightOfStation\", \"airTemperatureAt2M\"],\n",
+    "    filters={\"airTemperatureAt2M\": slice(300, None)},\n",
+    ")\n",
     "df"
    ]
   },

docs/examples/bufr_temp.ipynb

@@ -1159,8 +1159,9 @@
     }
    ],
    "source": [
-    "df = ds.to_pandas(columns=(\"WMO_station_id\", \"data_datetime\", \"pressure\", \"airTemperature\"),\n",
-    "    filters={\"WMO_station_id\": 1415})\n",
+    "df = ds.to_pandas(\n",
+    "    columns=(\"WMO_station_id\", \"data_datetime\", \"pressure\", \"airTemperature\"), filters={\"WMO_station_id\": 1415}\n",
+    ")\n",
     "df"
    ]
   },