Update dev branch

.gitattributes

@@ -1,6 +1,5 @@
 # Basic .gitattributes for a python repo.
 # Taken from https://github.com/gitattributes/gitattributes/blob/master/Python.gitattributes
-
 # Source files
 # ============
 *.pxd    text diff=python
@@ -10,7 +9,6 @@
 *.pyx    text diff=python
 *.pyz    text diff=python
 *.pyi    text diff=python
-
 # Binary files
 # ============
 *.db     binary
@@ -20,16 +18,14 @@
 *.pyc    binary export-ignore
 *.pyo    binary export-ignore
 *.pyd    binary
-
 # Data files
 # ============
 *.nc
-
 # Jupyter notebook
 *.ipynb  text eol=lf
-
 # Note: .db, .p, and .pkl files are associated
 # with the python modules ``pickle``, ``dbm.*``,
 # ``shelve``, ``marshal``, ``anydbm``, & ``bsddb``
 # (among others).
 tests/_static/test_era5_data.nc filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text

.github/dependabot.yml

@@ -13,4 +13,3 @@ updates:
     directory: "/"
     schedule:
       interval: "weekly"
-

.github/workflows/cd.yml

@@ -5,6 +5,11 @@ on:
     branches: [ "master" ]
   pull_request:
     branches: [ "master" ]
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
   workflow_dispatch:
 
 jobs:
@@ -14,7 +19,9 @@ jobs:
       pages: write # To push to a GitHub Pages site
       id-token: write # To update the deployment status
     uses: ./.github/workflows/sphinx.yml
+    if: ${{ !github.event.pull_request.draft }}
   call-release-workflow:
     permissions:
       id-token: write
-    uses: ./.github/workflows/release.yml
+    uses: ./.github/workflows/release.yml
+    if: ${{ !github.event.pull_request.draft }}

.github/workflows/ci.yml

@@ -11,6 +11,11 @@ on:
       - .github/workflows/release.yml
       - .github/workflows/sphinx.yml
   pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
     branches: [ "master" , "dev" ]
     paths-ignore:
       - .github/workflows/cd.yml
@@ -30,31 +35,38 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [ "3.12", "3.13" ]
+        python-version: [ "3.12", "3.13", "3.14" ]
     environment:
       name: CI
+    if: ${{ !github.event.pull_request.draft }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           lfs: true
       - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
           cache-dependency-glob: "uv.lock"
       - name: Install the project
-        run: uv sync --locked --all-groups --no-group docs
+        run: uv sync --locked --all-groups --no-group docs --all-extras
       - name: Install ruff and lint code
         uses: astral-sh/ruff-action@v3
       - name: Run pyright
-        uses: jakebailey/pyright-action@v2
+        uses: jakebailey/pyright-action@v3
         with:
           python-version: ${{ matrix.python-version }}
       - name: Test with pytest
+        timeout-minutes: 60
         run: |
           uv run pytest --cov=rojak --cov-branch --cov-report=xml -n auto
+        env:
+          # CDSAPI will look for these env vars before loading from ~/.cdsapirc
+          # See https://github.com/ecmwf/cdsapi/blob/72d7cec0b611c2f71c1a69da4668368df5118cdb/cdsapi/api.py#L48
+          CDSAPI_URL: ${{ secrets.CDSAPI_URL }}
+          CDSAPI_KEY: ${{ secrets.CDSAPI_KEY }}
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v5
         with:

.github/workflows/release.yml

@@ -32,8 +32,8 @@ jobs:
 #        os: [ubuntu-latest, windows-latest, macos-latest]
 #
 #    steps:
-#      - uses: actions/checkout@v4
-#      - uses: astral-sh/setup-uv@v6
+#      - uses: actions/checkout@v6
+#      - uses: astral-sh/setup-uv@v7
 #      - name: Build wheels
 #        uses: pypa/cibuildwheel@v3.0.1
 #        env:
@@ -43,7 +43,7 @@ jobs:
 #          CIBW_TEST_COMMAND: >
 #            pytest {project}/tests
 #      - name: Upload wheels
-#        uses: actions/upload-artifact@v4
+#        uses: actions/upload-artifact@v6
 #        with:
 #          name: wheels-${{ matrix.os }}
 #          path: ./dist/*.whl
@@ -52,11 +52,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v6
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
       - run: uv build --wheel
       - name: Upload wheel
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: wheel
           path: ./dist/*.whl
@@ -66,14 +66,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
-      - uses: astral-sh/setup-uv@v6
+      - uses: actions/checkout@v6
+      - uses: astral-sh/setup-uv@v7
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"
       - run: uv build --sdist
       - name: Upload sdist
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: sdist
           path: ./dist/*.tar.gz
@@ -91,7 +91,7 @@ jobs:
     if: ${{ github.ref_type == 'tag' }}
 
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v7
         with:
           path: dist
           merge-multiple: true
@@ -114,7 +114,7 @@ jobs:
       id-token: write
 
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v7
         with:
           path: dist
           merge-multiple: true

.github/workflows/sphinx.yml

@@ -8,22 +8,22 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv and set the python version
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           enable-cache: true
           cache-dependency-glob: "uv.lock"
       - name: Install the project
-        run: uv sync --all-groups
+        run: uv sync --all-groups --all-extras
       - name: Build docs using makefile
         run: |
           cd docs
           make html
       - name: Setup Pages
         uses: actions/configure-pages@v5
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v3
+        uses: actions/upload-pages-artifact@v4
         with:
           # Build directory of sphinx
           path: 'docs/_build/html'

.gitignore

@@ -177,4 +177,4 @@ cython_debug/
 
 # output directories that are created by CLI tool if not specified in config
 output/
-plots/
+plots/

.pre-commit-config.yaml

@@ -1,7 +1,17 @@
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks  # Enables fast path
+    rev: v6.0.0  # This is ignored for fast path detection
+    hooks:
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: end-of-file-fixer
+      - id: check-toml
+      - id: check-yaml
+      - id: mixed-line-ending
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.11.8
+    rev: v0.15.0
     hooks:
       # Run the linter.
       - id: ruff
@@ -10,7 +20,7 @@ repos:
       - id: ruff-format
   - repo: https://github.com/astral-sh/uv-pre-commit
     # uv version.
-    rev: 0.7.8
+    rev: 0.10.0
     hooks:
       - id: uv-lock
   - repo: local
@@ -23,6 +33,6 @@ repos:
         types: [ file ]
         files: \.(rst)$
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.403
+    rev: v1.1.408
     hooks:
-      - id: pyright
+      - id: pyright

CITATION.cff

@@ -0,0 +1,40 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Wong
+  given-names: Hui Ling
+  orcid: "https://orcid.org/0009-0006-2314-2660"
+- family-names: Palacios
+  given-names: Rafael
+  orcid: "https://orcid.org/0000-0002-6706-3220"
+- family-names: Gryspeerdt
+  given-names: Edward
+  orcid: "https://orcid.org/0000-0002-3815-4756"
+doi: 10.5281/zenodo.17882683
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Wong
+    given-names: Hui Ling
+    orcid: "https://orcid.org/0009-0006-2314-2660"
+  - family-names: Palacios
+    given-names: Rafael
+    orcid: "https://orcid.org/0000-0002-6706-3220"
+  - family-names: Gryspeerdt
+    given-names: Edward
+    orcid: "https://orcid.org/0000-0002-3815-4756"
+  date-published: 2025-12-13
+  doi: 10.21105/joss.09282
+  issn: 2475-9066
+  issue: 116
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 9282
+  title: "rojak: A Python library and tool for aviation turbulence
+    diagnostics"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.09282"
+  volume: 10
+title: "rojak: A Python library and tool for aviation turbulence
+  diagnostics"

CODE_OF_CONDUCT.md

@@ -131,4 +131,3 @@ For answers to common questions about this code of conduct, see the FAQ at
 [Mozilla CoC]: https://github.com/mozilla/diversity
 [FAQ]: https://www.contributor-covenant.org/faq
 [translations]: https://www.contributor-covenant.org/translations
-

CONTRIBUTING.md

@@ -16,7 +16,7 @@ Please follow the [Code of Conduct](CODE_OF_CONDUCT.md) in all your interactions
 
 ## Found a bug?
 
-Open an [issue](https://github.com/ImperialCollegeLondon/rojak/issues)! Fill out the issue template accordingly and we'll figure it out from there. 
+Open an [issue](https://github.com/ImperialCollegeLondon/rojak/issues)! Fill out the issue template accordingly and we'll figure it out from there.
 
 ## Need Help with the Library?
 

README.md

@@ -1,17 +1,17 @@
-# rojak : A Library and CLI Tool for Aviation Turbulence Analysis
+# `rojak`: A Library and CLI Tool for Aviation Turbulence Analysis
 
 [![CI](https://github.com/ImperialCollegeLondon/rojak/actions/workflows/ci.yml/badge.svg?branch=master)](https://github.com/ImperialCollegeLondon/rojak/actions/workflows/ci.yml)
 [![CD](https://github.com/ImperialCollegeLondon/rojak/actions/workflows/cd.yml/badge.svg?branch=master)](https://github.com/ImperialCollegeLondon/rojak/actions/workflows/cd.yml)
 [![codecov](https://codecov.io/gh/ImperialCollegeLondon/rojak/graph/badge.svg?token=0COCM07N7R)](https://codecov.io/gh/ImperialCollegeLondon/rojak)
 
+[![status](https://joss.theoj.org/papers/efb0bc9eab2eadeebc1203d15a3203e5/status.svg)](https://joss.theoj.org/papers/efb0bc9eab2eadeebc1203d15a3203e5)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17882683.svg)](https://doi.org/10.5281/zenodo.17882683)
+
+[![python](https://img.shields.io/pypi/pyversions/rojak-cat.svg)](https://github.com/ImperialCollegeLondon/rojak)
 [![Checked with pyright](https://microsoft.github.io/pyright/img/pyright_badge.svg)](https://microsoft.github.io/pyright/)
 [![Formatted with ruff](https://img.shields.io/badge/code%20style-ruff-d7ff64)](https://github.com/astral-sh/ruff)
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
 
-Rojak is salad with Javanese origins. Colloquially (in Singlish), it means a mixture of things.
-This package is for a traditionally unconventional mixture of aviation meteorology (turbulence diagnostics) and (coming
-soon) aeroelasticity.
-
 `rojak` is a distributed python library and command-line tool for using meterological data to forecast CAT and evaluating the effectiveness of CAT diagnostics against turbulence observations.
 Currently, it supports,
 
@@ -22,11 +22,22 @@ Currently, it supports,
 
 >[!NOTE]
 > This repository is under active development. As a result,
+>
 > 1. The API is subject to change and may not be stable
 > 2. The documentation is incomplete and will be updated as development progresses.
 >
 > We appreciate your understanding and encourage you to check back for updates.
 
+Rojak is also a salad with Javanese origins. Colloquially (in Singlish), it means a mixture of things.
+This package is for a traditionally unconventional mixture of aviation meteorology (turbulence diagnostics) and (coming
+soon) aeroelasticity.
+
+## What could I use `rojak` for?
+
+If you're an aviation meteorologist, `rojak` can be used to computing the various turbulence diagnostics and converting it into EDR like [this map from the Aviation Weather Center](https://aviationweather.gov/gfa/#turb).
+
+Or if you're a researcher and you'd like to understand how turbulence is impacted by climate change, `rojak` can be used to compute the probability of encountering turbulence and examining how that has changed over time.
+
 ## Documentation
 
 Learn more about `rojak` at [imperialcollegelondon.github.io/rojak/](https://imperialcollegelondon.github.io/rojak/).