Add Github actions for CI and PyPi release

.github/workflows/ci.yml

@@ -0,0 +1,78 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Run the full pre-commit suite (ruff, pyright, validate-pyproject, uv-lock,
+  # and the local pytest hook) exactly as developers do locally. Uses the
+  # committed uv.lock via --frozen, so any lockfile drift fails loudly.
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 8
+    env:
+      # Uniform cache path across OSes so the actions/cache `path` below
+      # matches what conftest.py writes (it honors this env var via
+      # expanduser). Local dev uses the platform-canonical default instead.
+      JAX_COMPILATION_CACHE_DIR: ~/.cache/jax-compilation-cache
+    steps:
+      - uses: actions/checkout@main
+      - uses: astral-sh/setup-uv@d31148d669074a8d0a63714ba94f3201e7020bc3
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - name: Cache JAX compilations
+        uses: actions/cache@v5
+        with:
+          path: ~/.cache/jax-compilation-cache
+          key: jax-cc-precommit-py3.12-${{ hashFiles('uv.lock') }}
+          restore-keys: |
+            jax-cc-precommit-py3.12-
+      - run: uv run --frozen pre-commit run --all-files --show-diff-on-failure
+
+  # Portability matrix: prove the declared floors and the latest versions both
+  # work across the supported Python versions and operating systems. Each cell
+  # re-resolves dependencies directly from pyproject.toml (--no-project bypasses
+  # uv.lock), so the lowest-direct cell exercises the real lower bounds.
+  test:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 8
+    env:
+      JAX_COMPILATION_CACHE_DIR: ~/.cache/jax-compilation-cache
+      # Self-diagnosing safety net for hangs: dump all thread stacks on
+      # SIGABRT/crash, and log every JAX JIT compilation with its timing so a
+      # stuck job shows exactly which compile/test was in flight.
+      PYTHONFAULTHANDLER: "1"
+      JAX_LOG_COMPILES: "1"
+      # Disable BLAS threads for now because they have shown to cause deadlocks
+      # in our test suite.
+      OMP_NUM_THREADS: "1"
+      OPENBLAS_NUM_THREADS: "1"
+      MKL_NUM_THREADS: "1"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python: ["3.12", "3.13"]
+        resolution: [highest, lowest-direct]
+    steps:
+      - uses: actions/checkout@main
+      - uses: astral-sh/setup-uv@d31148d669074a8d0a63714ba94f3201e7020bc3
+        with:
+          enable-cache: true
+          python-version: ${{ matrix.python }}
+      - name: Cache JAX compilations
+        uses: actions/cache@v5
+        with:
+          path: ~/.cache/jax-compilation-cache
+          key: jax-cc-${{ runner.os }}-py${{ matrix.python }}-${{ matrix.resolution }}-${{ hashFiles('uv.lock') }}
+          restore-keys: |
+            jax-cc-${{ runner.os }}-py${{ matrix.python }}-${{ matrix.resolution }}-
+            jax-cc-${{ runner.os }}-py${{ matrix.python }}-
+      - run: uv run --no-project --with-editable . --with "pytest>=8.0" --with "pytest-timeout>=2.4" --python ${{ matrix.python }} --resolution ${{ matrix.resolution }} pytest --timeout=180 --timeout-method=thread -v --durations=20

.github/workflows/release.yml

@@ -0,0 +1,60 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+# Never cancel an in-flight release; only one release per tag at a time.
+concurrency:
+  group: release-${{ github.ref }}
+  cancel-in-progress: false
+
+permissions:
+  contents: read
+
+jobs:
+  # Build the sdist and wheel from the tagged commit. setuptools-scm derives
+  # the version from git, so a full history checkout is required.
+  build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@main
+        with:
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@d31148d669074a8d0a63714ba94f3201e7020bc3
+        with:
+          enable-cache: true
+          python-version: "3.12"
+      - run: uv build -o dist
+      - uses: actions/upload-artifact@v6
+        with:
+          name: dist
+          path: dist/
+
+  # Publish to PyPI via Trusted Publishing (OIDC, no stored tokens) and create
+  # a GitHub Release with the built artifacts attached. Requires a one-time
+  # Trusted Publisher registration on pypi.org pointing at this workflow file
+  # (release.yml), the `pypi` environment, and this repository.
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 5
+    environment: pypi
+    permissions:
+      id-token: write   # PyPI Trusted Publishing (OIDC)
+      contents: write   # create GitHub Release
+    steps:
+      - uses: actions/download-artifact@v6
+        with:
+          name: dist
+          path: dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v3
+        with:
+          files: dist/*
+          name: ${{ github.ref_name }}
+          generate_release_notes: true

.pre-commit-config.yaml

@@ -16,35 +16,37 @@ repos:
   hooks:
     - id: uv-lock
 
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.20
-  hooks:
-    - id: ruff-check
-      args: [ --fix ]
-    - id: ruff-format
-
-# - repo: https://github.com/numpy/numpydoc
-#   rev: v1.10.0
-#   hooks:
-#     - id: numpydoc-validation
-
 - repo: https://github.com/abravalheri/validate-pyproject
   rev: v0.25
   hooks:
     - id: validate-pyproject
       additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
-- repo: https://github.com/RobertCraigie/pyright-python
-  rev: v1.1.411
-  hooks:
-    - id: pyright
-
 - repo: local
   hooks:
-  - id: pytest
-    name: pytest
-    entry: uv run ./.venv/bin/pytest
-    language: system
-    types: [python]
-    pass_filenames: false
-    always_run: true
+    - id: ruff-check
+      name: ruff check
+      entry: uv run ruff check --fix --exit-non-zero-on-fix
+      language: system
+      types: [python]
+      require_serial: true
+    - id: ruff-format
+      name: ruff format
+      entry: uv run ruff format
+      language: system
+      types: [python]
+      require_serial: true
+    - id: pyright
+      name: pyright
+      entry: uv run pyright
+      language: system
+      types: [python]
+      pass_filenames: false
+      always_run: true
+    - id: pytest
+      name: pytest
+      entry: uv run pytest
+      language: system
+      types: [python]
+      pass_filenames: false
+      always_run: true

pyproject.toml

@@ -5,31 +5,32 @@ description = "A collection of Python scripts for iSCAT microscopy data analysis
 authors = [{ name = "Marco Heisig", email = "marco.heisig@mpl.mpg.de" }]
 readme = "README.md"
 license = "GPL-3.0-or-later"
-requires-python = ">=3.12,<3.13"
+requires-python = ">=3.12"
 dependencies = [
-    "bioio",
-    "bioio-dv",
-    "bioio-imageio>=1.2",
-    "bioio-lif",
-    "bioio-nd2",
+    "bioio>=3.4",
+    "bioio-dv>=1.2",
+    "bioio-imageio>=1.3",
+    "bioio-lif>=1.3",
+    "bioio-nd2>=2.0",
     "bioio-ome-tiff>=1.4",
-    "bioio-ome-zarr>=2.2",
-    "bioio-tifffile",
-    "bioio-tiff-glob",
-    "dask",
-    "fsspec[fuse]",
-    "imageio[ffmpeg]",
-    "imgrvt",
-    "jax[cpu]",
-    "jaxtyping",
-    "numpy",
-    "ome-types",
+    "bioio-ome-zarr>=3.5",
+    "bioio-tifffile>=1.3",
+    "bioio-tiff-glob>=1.2",
+    "dask>=2026.1",
+    "fsspec>=2025.3",
+    "imageio[ffmpeg]>=2.37",
+    "imgrvt>=1.0",
+    "jax>=0.10.2",
+    "jaxtyping>=0.3",
+    "numpy>=2.3",
+    "ome-types>=0.6",
     "polars>=1.0",
-    "pyarrow",
-    "scikit-image",
-    "scipy",
-    "tqdm",
-    "xarray",
+    "pyarrow>=22.0",
+    "scikit-image>=0.23",
+    "scipy>=1.17",
+    "tifffile>=2026.5",
+    "tqdm>=4.66",
+    "xarray>=2026.1",
 ]
 keywords = ["tools", "utilities", "python", "microscopy"]
 
@@ -39,25 +40,21 @@ Issues = "https://github.com/SandoghdarLab/toolsandogh/issues"
 
 [dependency-groups]
 dev = [
-    "build",
-    "ipython",
-    "ipywidgets",
-    "ruff",
-    "pre-commit",
-    "pyright[nodejs]",
-    "ty",
-    "pytest",
-    "python-lsp-server",
-    "numpydoc",
-    "setuptools",
-    "setuptools-scm",
-    "coverage",
-    "jupyter",
-    "jupyter_rfb",
+    "build>=1.2",
+    "ruff>=0.15",
+    "pre-commit>=3.7",
+    "pyright[nodejs]>=1.1.400",
+    "ty>=0.0.50",
+    "pytest>=8.0",
+    "pytest-timeout>=2.4",
+    "python-lsp-server>=1.10",
+    "numpydoc>=1.7",
+    "setuptools>=80",
+    "setuptools-scm>=8",
+    "coverage>=5.0",
     "rendercanvas>=2.2",
-    "sidecar",
-    "twine",
-    "bokeh",
+    "twine>=5.0",
+    "bokeh>=3.4",
 ]
 
 [build-system]
@@ -84,6 +81,7 @@ select = [
     "RET", # flake8-return
     "YTT", # Truthiness
     "TRY", # Try block errors
+    "NPY201" # Use Numpy 2.0
 ]
 ignore = [
     "C901",   # Function too complex

src/toolsandogh/_store_video.py

@@ -1,10 +1,10 @@
 import os
 import pathlib
-import shutil
 import subprocess
 import tempfile
 import urllib.parse
 
+import imageio_ffmpeg
 import numpy as np
 import numpy.typing as npt
 import xarray as xr
@@ -14,14 +14,10 @@
 
 from ._canonicalize_video import canonicalize_video
 
-
-def _check_ffmpeg_installed() -> None:
-    """Ensure ffmpeg is installed and accessible."""
-    if shutil.which("ffmpeg") is None:
-        raise RuntimeError(
-            "ffmpeg is not installed or not found in PATH. "
-            "Please install ffmpeg to use video encoding features."
-        )
+# ffmpeg binary shipped by the `imageio-ffmpeg` wheel. Using this (rather than
+# shelling out to a bare `ffmpeg` on PATH) means users get a working ffmpeg on
+# every supported platform without a separate system install.
+_FFMPEG_EXE = imageio_ffmpeg.get_ffmpeg_exe()
 
 
 def store_video(video: npt.ArrayLike, path: str | os.PathLike, **kwargs) -> None:
@@ -117,9 +113,6 @@ def store_video_as_mp4(video: xr.DataArray, path: str | os.PathLike, fps: int =
     fps : int
         The number of frames per second of the resulting mp4 video.
     """
-    # Check for ffmpeg availability
-    _check_ffmpeg_installed()
-
     # Stack T, C, and Z into a single Frame dimension
     data = video.stack(F=("T", "C", "Z")).transpose("F", "Y", "X")
 
@@ -158,7 +151,7 @@ def store_video_as_mp4(video: xr.DataArray, path: str | os.PathLike, fps: int =
 
             # Run ffmpeg to concatenate
             concat_cmd = [
-                "ffmpeg",
+                _FFMPEG_EXE,
                 "-y",
                 "-f",
                 "concat",
@@ -219,7 +212,7 @@ def chunk_to_mp4(chunk: np.ndarray, path: str | os.PathLike, fps: int = 30) -> N
     pix_fmt = "gray8"
 
     ffmpeg_cmd = [
-        "ffmpeg",
+        _FFMPEG_EXE,
         "-y",
         "-f",
         "rawvideo",