v0.3.0: Modern stack, RTD docs, and optimized CI/CD

.gitattributes

@@ -1 +0,0 @@
-data/test/*.nc filter=lfs diff=lfs merge=lfs -text export-ignore

.github/dependabot.yml

@@ -0,0 +1,16 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/ci.yml

@@ -0,0 +1,126 @@
+name: CI
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+    branches: [main, dev]
+    types: [opened, synchronize, reopened]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  prepare:
+    runs-on: ubuntu-latest
+    # Skip PR CI if the head branch is 'dev' to avoid double runs (push trigger covers it)
+    if: github.event_name == 'push' || github.event.pull_request.head.ref != 'dev'
+    outputs:
+      python-versions: ${{ steps.versions.outputs.value }}
+    steps:
+      - id: versions
+        run: echo 'value=["3.11", "3.12", "3.13", "3.14"]' >> $GITHUB_OUTPUT
+
+  ruff-lint:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event.pull_request.head.ref != 'dev'
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - name: Install dependencies
+        run: pip install ruff
+      - name: Lint with Ruff
+        run: ruff check .
+
+  ruff-format:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event.pull_request.head.ref != 'dev'
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - name: Install dependencies
+        run: pip install ruff
+      - name: Check formatting with Ruff
+        run: ruff format --check .
+
+  mypy-typecheck:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' || github.event.pull_request.head.ref != 'dev'
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.11"
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name: Type check with Mypy
+        run: mypy src/ tests/
+
+  unit-tests:
+    name: unit-tests (Python ${{ matrix.python-version }})
+    needs: prepare
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ${{ fromJSON(needs.prepare.outputs.python-versions) }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name: Run Unit Tests
+        run: |
+          pytest -vv
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  integration-tests:
+    name: integration-tests (Python ${{ matrix.python-version }})
+    needs: prepare
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ${{ fromJSON(needs.prepare.outputs.python-versions) }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install MPI
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y openmpi-bin libopenmpi-dev
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name: Run Integration Tests
+        run: |
+          pytest -vv tests/test_integration.py --run-all
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/docker-publish.yml

@@ -0,0 +1,70 @@
+name: Docker Publish
+
+on:
+  workflow_run:
+    workflows: ["CI"]
+    types: [completed]
+
+env:
+  DOCKER_HUB_REPO: xddd/pystormtracker
+  GHCR_REPO: ghcr.io/xddd/pystormtracker
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    # Only run if CI was successful AND it was a push event to main or dev
+    # Added head_repository check to prevent checkout of untrusted code in trusted context
+    if: >
+      github.event.workflow_run.conclusion == 'success' &&
+      github.event.workflow_run.head_repository.full_name == github.repository &&
+      (github.event.workflow_run.event == 'push' || github.event.workflow_run.event == 'workflow_dispatch') &&
+      (github.event.workflow_run.head_branch == 'main' || github.event.workflow_run.head_branch == 'dev')
+
+    steps:
+      - name: Checkout repository
+        # Use the commit from the completed workflow run
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.workflow_run.head_sha }}
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v4
+        with:
+          username: ${{ vars.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v4
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GHCR_PAT }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ${{ env.DOCKER_HUB_REPO }}
+            ${{ env.GHCR_REPO }}
+          tags: |
+            type=raw,value=dev,pattern=dev
+            type=raw,value=latest,pattern=main
+            type=semver,pattern={{version}},pattern=main
+            type=semver,pattern={{major}}.{{minor}},pattern=main
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v7
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/python-publish.yml

@@ -17,7 +17,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: "3.x"
 
@@ -27,7 +27,7 @@ jobs:
           python -m build
 
       - name: Upload distributions
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: release-dists
           path: dist/
@@ -54,7 +54,7 @@ jobs:
           echo "version=${VERSION#v}" >> $GITHUB_OUTPUT
 
       - name: Retrieve release distributions
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v8
         with:
           name: release-dists
           path: dist/

.gitignore

@@ -64,7 +64,10 @@ target/
 
 # netCDF files
 *.nc
-!data/test/*.nc
 
-# CSV files
-*.csv
+# TXT track files
+*.txt
+!data/test/tracks/*.txt
+
+# VSCode
+.vscode/

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -9,16 +9,14 @@ repos:
       - id: debug-statements
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.9.9
     hooks:
-      # Run the linter.
       - id: ruff
         args: [ --fix ]
-      # Run the formatter.
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.15.0
     hooks:
       - id: mypy
-        additional_dependencies: [ types-all ]
+        additional_dependencies: [numpy, pooch, scipy, pytest, pandas, xarray, dask, distributed, h5netcdf]

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.14"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev
+
+sphinx:
+  configuration: docs/conf.py

CITATION.cff

@@ -19,8 +19,8 @@ keywords:
   - dask
   - mpi
 license: BSD-3-Clause
-version: 0.2.2
-date-released: '2026-03-04'
+version: 0.3.0
+date-released: '2026-03-08'
 preferred-citation:
   type: article
   authors:

Dockerfile

@@ -0,0 +1,32 @@
+# Use Python 3.14 slim as the base image
+FROM python:3.14-slim
+
+# Install system dependencies for MPI and building packages
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    libopenmpi-dev \
+    openmpi-bin \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set working directory
+WORKDIR /app
+
+# Create data directory for mounting
+RUN mkdir /data && chmod 777 /data
+
+# Copy the project files
+COPY . .
+
+# Install the package and its dependencies
+RUN pip install --no-cache-dir .
+
+# Add a non-root user for security
+RUN useradd -m pst
+USER pst
+
+# Volume for data persistence
+VOLUME /data
+
+# Default command
+ENTRYPOINT ["stormtracker"]
+CMD ["--help"]