From ca4a49efed903a1037a4295288a05bdc1cc1d479 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Mon, 6 Jul 2026 14:18:38 +0200 Subject: [PATCH 01/18] Explicit lower bounds for all package versions in pyproject.toml --- pyproject.toml | 76 +- uv.lock | 3466 +++++++++++++++++++++++++++++------------------- 2 files changed, 2147 insertions(+), 1395 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7ede82f..f9400c2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,31 +5,31 @@ 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 = ">=3.11" 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>=2025.1", + "fsspec[fuse]>=2025.1", + "imageio[ffmpeg]>=2.37", + "imgrvt>=1.0", + "jax>=0.5.0", + "jaxtyping>=0.3", + "numpy>=2.0", + "ome-types>=0.6", "polars>=1.0", - "pyarrow", - "scikit-image", - "scipy", - "tqdm", - "xarray", + "pyarrow>=15.0", + "scikit-image>=0.23", + "scipy>=1.13", + "tqdm>=4.66", + "xarray>=2025.1", ] keywords = ["tools", "utilities", "python", "microscopy"] @@ -39,25 +39,20 @@ 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", + 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6 Jul 2026 15:00:53 +0200 Subject: [PATCH 02/18] Add Github actions for CI and PyPI release --- .github/workflows/ci.yml | 44 ++++++++++++++++++++++++++ .github/workflows/release.yml | 58 +++++++++++++++++++++++++++++++++++ .pre-commit-config.yaml | 50 +++++++++++++++--------------- pyproject.toml | 6 ++-- uv.lock | 15 ++------- 5 files changed, 134 insertions(+), 39 deletions(-) create mode 100644 .github/workflows/ci.yml create mode 100644 .github/workflows/release.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..fd89f77 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,44 @@ +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 + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + python-version: "3.12" + - 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 }} + strategy: + fail-fast: false + matrix: + os: [ubuntu-latest, windows-latest, macos-latest] + python: ["3.11", "3.12", "3.13"] + resolution: [highest, lowest-direct] + steps: + - uses: actions/checkout@v4 + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + python-version: ${{ matrix.python }} + - run: uv run --no-project --with-editable . --with "pytest>=8.0" --python ${{ matrix.python }} --resolution ${{ matrix.resolution }} pytest diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..f4f8807 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,58 @@ +name: Release + +on: + push: + tags: + - "v*" + +# Never cancel an in-flight release; only one release per tag at a time. +concurrency: + group: release-${{ 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 + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + - uses: astral-sh/setup-uv@v6 + with: + enable-cache: true + python-version: "3.12" + - run: uv build -o dist + - uses: actions/upload-artifact@v4 + 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 + environment: pypi + permissions: + id-token: write # PyPI Trusted Publishing (OIDC) + contents: write # create GitHub Release + steps: + - uses: actions/download-artifact@v4 + 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@v2 + with: + files: dist/* + name: ${{ github.ref_name }} + generate_release_notes: true diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 83d6c40..76724f9 100644 --- a/.pre-commit-config.yaml +++ b/.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 diff --git a/pyproject.toml b/pyproject.toml index f9400c2..77ac8fa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,7 +17,7 @@ dependencies = [ "bioio-tifffile>=1.3", "bioio-tiff-glob>=1.2", "dask>=2025.1", - "fsspec[fuse]>=2025.1", + "fsspec>=2025.1", "imageio[ffmpeg]>=2.37", "imgrvt>=1.0", "jax>=0.5.0", @@ -40,7 +40,7 @@ Issues = "https://github.com/SandoghdarLab/toolsandogh/issues" [dependency-groups] dev = [ "build>=1.2", - "ruff>=0.2", + "ruff>=0.15", "pre-commit>=3.7", "pyright[nodejs]>=1.1.400", "ty>=0.0.50", @@ -101,7 +101,7 @@ checks = [ ] [tool.pyright] -pythonVersion = "3.12" +pythonVersion = "3.11" include = ["src"] exclude = [".venv"] venvPath = "." diff --git a/uv.lock b/uv.lock index 9c1223a..ae2f9d2 100644 --- a/uv.lock +++ b/uv.lock @@ -1154,19 +1154,10 @@ wheels = [ ] [package.optional-dependencies] -fuse = [ - { name = "fusepy" }, -] http = [ { name = "aiohttp" }, ] -[[package]] -name = "fusepy" -version = "3.0.1" -source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/04/0b/4506cb2e831cea4b0214d3625430e921faaa05a7fb520458c75a2dbd2152/fusepy-3.0.1.tar.gz", hash = "sha256:72ff783ec2f43de3ab394e3f7457605bf04c8cf288a2f4068b4cde141d4ee6bd", size = 11519, upload-time = "2018-09-17T00:14:52.666Z" } - [[package]] name = "google-crc32c" version = "1.8.0" @@ -3782,7 +3773,7 @@ dependencies = [ { name = "bioio-tiff-glob" }, { name = "bioio-tifffile" }, { name = "dask" }, - { name = "fsspec", extra = ["fuse"] }, + { name = "fsspec" }, { name = "imageio", extra = ["ffmpeg"] }, { name = "imgrvt" }, { name = "jax" }, @@ -3829,7 +3820,7 @@ requires-dist = [ { name = "bioio-tiff-glob", specifier = ">=1.2" }, { name = "bioio-tifffile", specifier = ">=1.3" }, { name = "dask", specifier = ">=2025.1" }, - { name = "fsspec", extras = ["fuse"], specifier = ">=2025.1" }, + { name = "fsspec", specifier = ">=2025.1" }, { name = "imageio", extras = ["ffmpeg"], specifier = ">=2.37" }, { name = "imgrvt", specifier = ">=1.0" }, { name = "jax", specifier = ">=0.5.0" }, @@ -3855,7 +3846,7 @@ dev = [ { name = "pytest", specifier = ">=8.0" }, { name = "python-lsp-server", specifier = ">=1.10" }, { name = "rendercanvas", specifier = ">=2.2" }, - { name = "ruff", specifier = ">=0.2" }, + { name = "ruff", specifier = ">=0.15" }, { name = "setuptools", specifier = ">=69.1" }, { name = "setuptools-scm", specifier = ">=8.1" }, { name = "twine", specifier = ">=5.0" }, From 0b6d1226b63c3fea0e25926c7abc2aa86525de31 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Mon, 6 Jul 2026 15:27:16 +0200 Subject: [PATCH 03/18] Use imageio's version of ffmpeg for better portability --- pyproject.toml | 4 ++-- src/toolsandogh/_store_video.py | 21 +++++++-------------- uv.lock | 4 ++-- 3 files changed, 11 insertions(+), 18 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 77ac8fa..64f3679 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,8 +47,8 @@ dev = [ "pytest>=8.0", "python-lsp-server>=1.10", "numpydoc>=1.7", - "setuptools>=69.1", - "setuptools-scm>=8.1", + "setuptools>=80", + "setuptools-scm>=8", "coverage>=5.0", "rendercanvas>=2.2", "twine>=5.0", diff --git a/src/toolsandogh/_store_video.py b/src/toolsandogh/_store_video.py index fa0f5a4..362165e 100644 --- a/src/toolsandogh/_store_video.py +++ b/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", diff --git a/uv.lock b/uv.lock index ae2f9d2..62e8b37 100644 --- a/uv.lock +++ b/uv.lock @@ -3847,8 +3847,8 @@ dev = [ { name = "python-lsp-server", specifier = ">=1.10" }, { name = "rendercanvas", specifier = ">=2.2" }, { name = "ruff", specifier = ">=0.15" }, - { name = "setuptools", specifier = ">=69.1" }, - { name = "setuptools-scm", specifier = ">=8.1" }, + { name = "setuptools", specifier = ">=80" }, + { name = "setuptools-scm", specifier = ">=8" }, { name = "twine", specifier = ">=5.0" }, { name = "ty", specifier = ">=0.0.50" }, ] From fa54018654dca85da53222554b9dfeef8e63a6e9 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Mon, 6 Jul 2026 15:47:23 +0200 Subject: [PATCH 04/18] Remove Python 3.11 and bump pyarrow and tifffile minimum versions --- .github/workflows/ci.yml | 2 +- pyproject.toml | 5 +- uv.lock | 869 ++++----------------------------------- 3 files changed, 85 insertions(+), 791 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fd89f77..0a6212e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,7 +33,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest, windows-latest, macos-latest] - python: ["3.11", "3.12", "3.13"] + python: ["3.12", "3.13"] resolution: [highest, lowest-direct] steps: - uses: actions/checkout@v4 diff --git a/pyproject.toml b/pyproject.toml index 64f3679..01d5484 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ 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 = ">=3.11" +requires-python = ">=3.12" dependencies = [ "bioio>=3.4", "bioio-dv>=1.2", @@ -25,9 +25,10 @@ dependencies = [ "numpy>=2.0", "ome-types>=0.6", "polars>=1.0", - "pyarrow>=15.0", + "pyarrow>=16.0", "scikit-image>=0.23", "scipy>=1.13", + "tifffile>=2026.5", "tqdm>=4.66", "xarray>=2025.1", ] diff --git a/uv.lock b/uv.lock index 62e8b37..5df1b57 100644 --- a/uv.lock +++ b/uv.lock @@ -1,6 +1,6 @@ version = 1 revision = 3 -requires-python = ">=3.11" +requires-python = ">=3.12" resolution-markers = [ "python_full_version >= '3.14' and sys_platform == 'win32'", "python_full_version >= '3.14' and sys_platform == 'emscripten'", @@ -8,12 +8,9 @@ resolution-markers = [ "python_full_version == '3.13.*' and sys_platform == 'win32'", "python_full_version == '3.13.*' and sys_platform == 'emscripten'", "python_full_version == '3.13.*' and sys_platform != 'emscripten' and sys_platform != 'win32'", - 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"pyarrow>=16.0", + "pyarrow>=18.0", "scikit-image>=0.23", - "scipy>=1.13", + "scipy>=1.17", "tifffile>=2026.5", "tqdm>=4.66", "xarray>=2025.1", diff --git a/uv.lock b/uv.lock index 5df1b57..130526a 100644 --- a/uv.lock +++ b/uv.lock @@ -3203,9 +3203,9 @@ requires-dist = [ { name = "numpy", specifier = ">=2.0" }, { name = "ome-types", specifier = ">=0.6" }, { name = "polars", specifier = ">=1.0" }, - { name = "pyarrow", specifier = ">=16.0" }, + { name = "pyarrow", specifier = ">=18.0" }, { name = "scikit-image", specifier = ">=0.23" }, - { name = "scipy", specifier = ">=1.13" }, + { name = "scipy", specifier = ">=1.17" }, { name = "tifffile", specifier = ">=2026.5" }, { name = "tqdm", specifier = ">=4.66" }, { name = "xarray", specifier = ">=2025.1" }, From 261b5e0d51ceced339fd72c648d3628f1047bfaf Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 11:26:18 +0200 Subject: [PATCH 06/18] Bump versions of all Github workflows to avoid Node 20 dependency --- .github/workflows/ci.yml | 8 ++++---- .github/workflows/release.yml | 10 +++++----- pyproject.toml | 2 +- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0a6212e..c194436 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,8 +16,8 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v6 + - uses: actions/checkout@v6 + - uses: astral-sh/setup-uv@v8 with: enable-cache: true python-version: "3.12" @@ -36,8 +36,8 @@ jobs: python: ["3.12", "3.13"] resolution: [highest, lowest-direct] steps: - - uses: actions/checkout@v4 - - uses: astral-sh/setup-uv@v6 + - uses: actions/checkout@v6 + - uses: astral-sh/setup-uv@v8 with: enable-cache: true python-version: ${{ matrix.python }} diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index f4f8807..40fb104 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -19,15 +19,15 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 with: fetch-depth: 0 - - uses: astral-sh/setup-uv@v6 + - uses: astral-sh/setup-uv@v8 with: enable-cache: true python-version: "3.12" - run: uv build -o dist - - uses: actions/upload-artifact@v4 + - uses: actions/upload-artifact@v6 with: name: dist path: dist/ @@ -44,14 +44,14 @@ jobs: id-token: write # PyPI Trusted Publishing (OIDC) contents: write # create GitHub Release steps: - - uses: actions/download-artifact@v4 + - 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@v2 + uses: softprops/action-gh-release@v3 with: files: dist/* name: ${{ github.ref_name }} diff --git a/pyproject.toml b/pyproject.toml index 82bddaf..d5a5669 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -102,7 +102,7 @@ checks = [ ] [tool.pyright] -pythonVersion = "3.11" +pythonVersion = "3.12" include = ["src"] exclude = [".venv"] venvPath = "." From f37bdde57ff20eb733f4791f1e325564cc42badb Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 11:35:16 +0200 Subject: [PATCH 07/18] Pin the version of setup-uv as advertised in their documentation. --- .github/workflows/ci.yml | 8 ++++---- .github/workflows/release.yml | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c194436..7ab3df0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,8 +16,8 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 - - uses: astral-sh/setup-uv@v8 + - uses: actions/checkout@main + - uses: astral-sh/setup-uv@d31148d669074a8d0a63714ba94f3201e7020bc3 with: enable-cache: true python-version: "3.12" @@ -36,8 +36,8 @@ jobs: python: ["3.12", "3.13"] resolution: [highest, lowest-direct] steps: - - uses: actions/checkout@v6 - - uses: astral-sh/setup-uv@v8 + - uses: actions/checkout@main + - uses: astral-sh/setup-uv@d31148d669074a8d0a63714ba94f3201e7020bc3 with: enable-cache: true python-version: ${{ matrix.python }} diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 40fb104..2ad75ff 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -19,10 +19,10 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v6 + - uses: actions/checkout@main with: fetch-depth: 0 - - uses: astral-sh/setup-uv@v8 + - uses: astral-sh/setup-uv@d31148d669074a8d0a63714ba94f3201e7020bc3 with: enable-cache: true python-version: "3.12" From 34af1ec9739306b7cc9098f706b36773e165b20a Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 13:55:18 +0200 Subject: [PATCH 08/18] Enable JAX's persistent compilation --- .github/workflows/ci.yml | 24 ++++++++++++++++++ .github/workflows/release.yml | 2 ++ src/toolsandogh/tests/conftest.py | 41 +++++++++++++++++++++++++++++++ 3 files changed, 67 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7ab3df0..390a355 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,12 +15,25 @@ jobs: # committed uv.lock via --frozen, so any lockfile drift fails loudly. pre-commit: runs-on: ubuntu-latest + timeout-minutes: 5 + env: + # Uniform cache path across OSes so the actions/cache `path` below + # matches what conftest.py writes (it honors this env var via + # expanduser). Local dev uses the platform-canonical default instead. + JAX_COMPILATION_CACHE_DIR: ~/.cache/jax-compilation-cache steps: - uses: actions/checkout@main - uses: astral-sh/setup-uv@d31148d669074a8d0a63714ba94f3201e7020bc3 with: enable-cache: true python-version: "3.12" + - name: Cache JAX compilations + uses: actions/cache@v4 + with: + path: ~/.cache/jax-compilation-cache + key: jax-cc-precommit-py3.12-${{ 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 @@ -29,6 +42,9 @@ jobs: # uv.lock), so the lowest-direct cell exercises the real lower bounds. test: runs-on: ${{ matrix.os }} + timeout-minutes: 5 + env: + JAX_COMPILATION_CACHE_DIR: ~/.cache/jax-compilation-cache strategy: fail-fast: false matrix: @@ -41,4 +57,12 @@ jobs: with: enable-cache: true python-version: ${{ matrix.python }} + - name: Cache JAX compilations + uses: actions/cache@v4 + with: + path: ~/.cache/jax-compilation-cache + key: jax-cc-${{ 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" --python ${{ matrix.python }} --resolution ${{ matrix.resolution }} pytest diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 2ad75ff..a1951db 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -18,6 +18,7 @@ jobs: # 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: @@ -39,6 +40,7 @@ jobs: publish: needs: build runs-on: ubuntu-latest + timeout-minutes: 5 environment: pypi permissions: id-token: write # PyPI Trusted Publishing (OIDC) diff --git a/src/toolsandogh/tests/conftest.py b/src/toolsandogh/tests/conftest.py index 8122dab..345a2ac 100644 --- a/src/toolsandogh/tests/conftest.py +++ b/src/toolsandogh/tests/conftest.py @@ -1,7 +1,48 @@ import multiprocessing +import os +import sys +from pathlib import Path +import jax import pytest +# Enable JAX's persistent compilation cache so that repeated test runs skip JIT +# recompilation. The first run populates the cache at no extra cost; subsequent +# runs reuse it (empirically ~2.4x faster for the simulation-heavy tests). +# +# The cache directory honors, in order: +# 1. an explicit ``JAX_COMPILATION_CACHE_DIR`` environment variable (used by +# CI for a deterministic, uniformly cacheable path), else +# 2. the platform-canonical cache root (see ``_default_cache_root``). +# +# ``min_compile_time_secs=0`` persists *every* compilation, not just those +# longer than the 1s default; the footprint is small (~a few MB) and there is +# no cold-run penalty. The cache key includes the jaxlib version, platform, and +# XLA flags, so entries never collide across Python versions, OSes, or +# dependency resolutions. + + +def _default_cache_root() -> str: + """Return the platform-canonical user cache directory.""" + home = str(Path.home()) + if sys.platform == "win32": + return os.environ.get("LOCALAPPDATA") or os.path.join(home, "AppData", "Local") + if sys.platform == "darwin": + return os.path.join(home, "Library", "Caches") + return os.environ.get("XDG_CACHE_HOME") or os.path.join(home, ".cache") + + +_env_cache = os.environ.get("JAX_COMPILATION_CACHE_DIR") +_cache_dir = Path( + os.path.expanduser(_env_cache) + if _env_cache + else os.path.join(_default_cache_root(), "jax-compilation-cache") +) +_cache_dir.mkdir(parents=True, exist_ok=True) +jax.config.update("jax_compilation_cache_dir", str(_cache_dir)) +jax.config.update("jax_persistent_cache_min_compile_time_secs", 0) +jax.config.update("jax_persistent_cache_min_entry_size_bytes", 0) + @pytest.fixture(scope="session", autouse=True) def always_spawn(): From a121f7394e35600e13109db361151a40ea8bf79e Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 14:15:56 +0200 Subject: [PATCH 09/18] Raise minimum JAX version and timeout limits to avoid CI timeouts --- .github/workflows/ci.yml | 8 ++++---- pyproject.toml | 2 +- uv.lock | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 390a355..8a2350a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ jobs: # committed uv.lock via --frozen, so any lockfile drift fails loudly. pre-commit: runs-on: ubuntu-latest - timeout-minutes: 5 + 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 @@ -28,7 +28,7 @@ jobs: enable-cache: true python-version: "3.12" - name: Cache JAX compilations - uses: actions/cache@v4 + uses: actions/cache@v5 with: path: ~/.cache/jax-compilation-cache key: jax-cc-precommit-py3.12-${{ hashFiles('uv.lock') }} @@ -42,7 +42,7 @@ jobs: # uv.lock), so the lowest-direct cell exercises the real lower bounds. test: runs-on: ${{ matrix.os }} - timeout-minutes: 5 + timeout-minutes: 8 env: JAX_COMPILATION_CACHE_DIR: ~/.cache/jax-compilation-cache strategy: @@ -58,7 +58,7 @@ jobs: enable-cache: true python-version: ${{ matrix.python }} - name: Cache JAX compilations - uses: actions/cache@v4 + uses: actions/cache@v5 with: path: ~/.cache/jax-compilation-cache key: jax-cc-${{ runner.os }}-py${{ matrix.python }}-${{ matrix.resolution }}-${{ hashFiles('uv.lock') }} diff --git a/pyproject.toml b/pyproject.toml index d5a5669..febc043 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ dependencies = [ "fsspec>=2025.1", "imageio[ffmpeg]>=2.37", "imgrvt>=1.0", - "jax>=0.5.0", + "jax>=0.8.0", "jaxtyping>=0.3", "numpy>=2.0", "ome-types>=0.6", diff --git a/uv.lock b/uv.lock index 130526a..dea0948 100644 --- a/uv.lock +++ b/uv.lock @@ -3198,7 +3198,7 @@ requires-dist = [ { name = "fsspec", specifier = ">=2025.1" }, { name = "imageio", extras = ["ffmpeg"], specifier = ">=2.37" }, { name = "imgrvt", specifier = ">=1.0" }, - { name = "jax", specifier = ">=0.5.0" }, + { name = "jax", specifier = ">=0.8.0" }, { name = "jaxtyping", specifier = ">=0.3" }, { name = "numpy", specifier = ">=2.0" }, { name = "ome-types", specifier = ">=0.6" }, From 3c16c3eded8c8f9e369abbbb052782055ac5867b Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 14:42:00 +0200 Subject: [PATCH 10/18] Bump JAX version further to fix CI --- pyproject.toml | 2 +- uv.lock | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index febc043..74803fc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ dependencies = [ "fsspec>=2025.1", "imageio[ffmpeg]>=2.37", "imgrvt>=1.0", - "jax>=0.8.0", + "jax>=0.10.0", "jaxtyping>=0.3", "numpy>=2.0", "ome-types>=0.6", diff --git a/uv.lock b/uv.lock index dea0948..dce2ae6 100644 --- a/uv.lock +++ b/uv.lock @@ -484,7 +484,7 @@ name = "cffi" version = "2.0.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "pycparser", marker = "implementation_name != 'PyPy'" }, + { name = "pycparser", marker = "implementation_name != 'PyPy' and sys_platform != 'emscripten' and sys_platform != 'win32'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/eb/56/b1ba7935a17738ae8453301356628e8147c79dbb825bcbc73dc7401f9846/cffi-2.0.0.tar.gz", hash = "sha256:44d1b5909021139fe36001ae048dbdde8214afa20200eda0f64c068cac5d5529", size = 523588, upload-time = "2025-09-08T23:24:04.541Z" } wheels = [ @@ -760,7 +760,7 @@ name = "cryptography" version = "49.0.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "cffi", marker = "platform_python_implementation != 'PyPy'" }, + { name = "cffi", marker = "platform_python_implementation != 'PyPy' and sys_platform != 'emscripten' and sys_platform != 'win32'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/1f/99/d1c90d6041656cc6ee229dc99cd67fd0cd5aec3c5f7d72fffc27cc750054/cryptography-49.0.0.tar.gz", hash = "sha256:f89660a348f4f78a92366240a61404e337586ef7f5909a2fef59ca88ef505493", size = 854345, upload-time = "2026-06-12T20:02:30.512Z" } wheels = [ @@ -2949,8 +2949,8 @@ name = "secretstorage" version = "3.5.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "cryptography" }, - { name = "jeepney" }, + { name = "cryptography", marker = "sys_platform != 'emscripten' and sys_platform != 'win32'" }, + { name = "jeepney", marker = "sys_platform != 'emscripten' and sys_platform != 'win32'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/1c/03/e834bcd866f2f8a49a85eaff47340affa3bfa391ee9912a952a1faa68c7b/secretstorage-3.5.0.tar.gz", hash = "sha256:f04b8e4689cbce351744d5537bf6b1329c6fc68f91fa666f60a380edddcd11be", size = 19884, upload-time = "2025-11-23T19:02:53.191Z" } wheels = [ @@ -3198,7 +3198,7 @@ requires-dist = [ { name = "fsspec", specifier = ">=2025.1" }, { name = "imageio", extras = ["ffmpeg"], specifier = ">=2.37" }, { name = "imgrvt", specifier = ">=1.0" }, - { name = "jax", specifier = ">=0.8.0" }, + { name = "jax", specifier = ">=0.10.0" }, { name = "jaxtyping", specifier = ">=0.3" }, { name = "numpy", specifier = ">=2.0" }, { name = "ome-types", specifier = ">=0.6" }, From 6db97157c734f401b9abca6fa0d4850b2575663b Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 14:55:15 +0200 Subject: [PATCH 11/18] Bump minimum JAX version further, hoping to fix the CI pipeline --- pyproject.toml | 2 +- uv.lock | 10 +++++----- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 74803fc..cc7bcc7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ dependencies = [ "fsspec>=2025.1", "imageio[ffmpeg]>=2.37", "imgrvt>=1.0", - "jax>=0.10.0", + "jax>=0.10.2", "jaxtyping>=0.3", "numpy>=2.0", "ome-types>=0.6", diff --git a/uv.lock b/uv.lock index dce2ae6..db7ac7a 100644 --- a/uv.lock +++ b/uv.lock @@ -484,7 +484,7 @@ name = "cffi" version = "2.0.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "pycparser", marker = "implementation_name != 'PyPy' and sys_platform != 'emscripten' and sys_platform != 'win32'" }, + { name = "pycparser", marker = "implementation_name != 'PyPy'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/eb/56/b1ba7935a17738ae8453301356628e8147c79dbb825bcbc73dc7401f9846/cffi-2.0.0.tar.gz", hash = "sha256:44d1b5909021139fe36001ae048dbdde8214afa20200eda0f64c068cac5d5529", size = 523588, upload-time = "2025-09-08T23:24:04.541Z" } wheels = [ @@ -760,7 +760,7 @@ name = "cryptography" version = "49.0.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "cffi", marker = "platform_python_implementation != 'PyPy' and sys_platform != 'emscripten' and sys_platform != 'win32'" }, + { name = "cffi", marker = "platform_python_implementation != 'PyPy'" }, ] sdist = { url = "https://files.pythonhosted.org/packages/1f/99/d1c90d6041656cc6ee229dc99cd67fd0cd5aec3c5f7d72fffc27cc750054/cryptography-49.0.0.tar.gz", hash = "sha256:f89660a348f4f78a92366240a61404e337586ef7f5909a2fef59ca88ef505493", size = 854345, upload-time = "2026-06-12T20:02:30.512Z" } wheels = [ @@ -2949,8 +2949,8 @@ name = "secretstorage" version = "3.5.0" source = { registry = "https://pypi.org/simple" } dependencies = [ - { name = "cryptography", marker = "sys_platform != 'emscripten' and sys_platform != 'win32'" }, - { name = "jeepney", marker = "sys_platform != 'emscripten' and sys_platform != 'win32'" }, + { name = "cryptography" }, + { name = "jeepney" }, ] sdist = { url = "https://files.pythonhosted.org/packages/1c/03/e834bcd866f2f8a49a85eaff47340affa3bfa391ee9912a952a1faa68c7b/secretstorage-3.5.0.tar.gz", hash = "sha256:f04b8e4689cbce351744d5537bf6b1329c6fc68f91fa666f60a380edddcd11be", size = 19884, upload-time = "2025-11-23T19:02:53.191Z" } wheels = [ @@ -3198,7 +3198,7 @@ requires-dist = [ { name = "fsspec", specifier = ">=2025.1" }, { name = "imageio", extras = ["ffmpeg"], specifier = ">=2.37" }, { name = "imgrvt", specifier = ">=1.0" }, - { name = "jax", specifier = ">=0.10.0" }, + { name = "jax", specifier = ">=0.10.2" }, { name = "jaxtyping", specifier = ">=0.3" }, { name = "numpy", specifier = ">=2.0" }, { name = "ome-types", specifier = ">=0.6" }, From 821895a45e94a45e8e4119c45e40d81949951dc9 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 15:07:48 +0200 Subject: [PATCH 12/18] Add safety net to debug CI issues --- .github/workflows/ci.yml | 7 ++++++- pyproject.toml | 3 ++- uv.lock | 16 +++++++++++++++- 3 files changed, 23 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8a2350a..dbbe71d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -45,6 +45,11 @@ jobs: 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" strategy: fail-fast: false matrix: @@ -65,4 +70,4 @@ jobs: 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" --python ${{ matrix.python }} --resolution ${{ matrix.resolution }} pytest + - run: uv run --no-project --with-editable . --with "pytest>=8.0" --with "pytest-timeout>=2.0" --python ${{ matrix.python }} --resolution ${{ matrix.resolution }} pytest --timeout=180 --timeout-method=thread -v --durations=20 diff --git a/pyproject.toml b/pyproject.toml index cc7bcc7..e27d689 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,7 +20,7 @@ dependencies = [ "fsspec>=2025.1", "imageio[ffmpeg]>=2.37", "imgrvt>=1.0", - "jax>=0.10.2", + "jax>=0.10.0", "jaxtyping>=0.3", "numpy>=2.0", "ome-types>=0.6", @@ -46,6 +46,7 @@ dev = [ "pyright[nodejs]>=1.1.400", "ty>=0.0.50", "pytest>=8.0", + "pytest-timeout>=2.0", "python-lsp-server>=1.10", "numpydoc>=1.7", "setuptools>=80", diff --git a/uv.lock b/uv.lock index db7ac7a..1d8cedf 100644 --- a/uv.lock +++ b/uv.lock @@ -2547,6 +2547,18 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/24/25/1de2678b631f5a49215c6c96fff41ba892b0a34df68d6d80292b1b48aa7f/pytest-9.1.1-py3-none-any.whl", hash = "sha256:37a86b45efb9a47a61a36449063e8e18d0cab3161329fc099eb21783169c4f0c", size = 386536, upload-time = "2026-06-19T10:58:31.347Z" }, ] +[[package]] +name = "pytest-timeout" +version = "2.4.0" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "pytest" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/ac/82/4c9ecabab13363e72d880f2fb504c5f750433b2b6f16e99f4ec21ada284c/pytest_timeout-2.4.0.tar.gz", hash = "sha256:7e68e90b01f9eff71332b25001f85c75495fc4e3a836701876183c4bcfd0540a", size = 17973, upload-time = "2025-05-05T19:44:34.99Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/fa/b6/3127540ecdf1464a00e5a01ee60a1b09175f6913f0644ac748494d9c4b21/pytest_timeout-2.4.0-py3-none-any.whl", hash = "sha256:c42667e5cdadb151aeb5b26d114aff6bdf5a907f176a007a30b940d3d865b5c2", size = 14382, upload-time = "2025-05-05T19:44:33.502Z" }, +] + [[package]] name = "python-dateutil" version = "2.9.0.post0" @@ -3174,6 +3186,7 @@ dev = [ { name = "pre-commit" }, { name = "pyright", extra = ["nodejs"] }, { name = "pytest" }, + { name = "pytest-timeout" }, { name = "python-lsp-server" }, { name = "rendercanvas" }, { name = "ruff" }, @@ -3198,7 +3211,7 @@ requires-dist = [ { name = "fsspec", specifier = ">=2025.1" }, { name = "imageio", extras = ["ffmpeg"], specifier = ">=2.37" }, { name = "imgrvt", specifier = ">=1.0" }, - { name = "jax", specifier = ">=0.10.2" }, + { name = "jax", specifier = ">=0.10.0" }, { name = "jaxtyping", specifier = ">=0.3" }, { name = "numpy", specifier = ">=2.0" }, { name = "ome-types", specifier = ">=0.6" }, @@ -3220,6 +3233,7 @@ dev = [ { name = "pre-commit", specifier = ">=3.7" }, { name = "pyright", extras = ["nodejs"], specifier = ">=1.1.400" }, { name = "pytest", specifier = ">=8.0" }, + { name = "pytest-timeout", specifier = ">=2.0" }, { name = "python-lsp-server", specifier = ">=1.10" }, { name = "rendercanvas", specifier = ">=2.2" }, { name = "ruff", specifier = ">=0.15" }, From aaab4703b094aa6ac3791256d584b51288bc4a53 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 15:20:42 +0200 Subject: [PATCH 13/18] More version-fiddling in hopes of fixing CI --- pyproject.toml | 6 +++--- uv.lock | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e27d689..957f89d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -20,9 +20,9 @@ dependencies = [ "fsspec>=2025.1", "imageio[ffmpeg]>=2.37", "imgrvt>=1.0", - "jax>=0.10.0", + "jax>=0.10.2", "jaxtyping>=0.3", - "numpy>=2.0", + "numpy>=2.2", "ome-types>=0.6", "polars>=1.0", "pyarrow>=18.0", @@ -46,7 +46,7 @@ dev = [ "pyright[nodejs]>=1.1.400", "ty>=0.0.50", "pytest>=8.0", - "pytest-timeout>=2.0", + "pytest-timeout>=2.4", "python-lsp-server>=1.10", "numpydoc>=1.7", "setuptools>=80", diff --git a/uv.lock b/uv.lock index 1d8cedf..3592a83 100644 --- a/uv.lock +++ b/uv.lock @@ -3211,9 +3211,9 @@ requires-dist = [ { name = "fsspec", specifier = ">=2025.1" }, { name = "imageio", extras = ["ffmpeg"], specifier = ">=2.37" }, { name = "imgrvt", specifier = ">=1.0" }, - { name = "jax", specifier = ">=0.10.0" }, + { name = "jax", specifier = ">=0.10.2" }, { name = "jaxtyping", specifier = ">=0.3" }, - { name = "numpy", specifier = ">=2.0" }, + { name = "numpy", specifier = ">=2.2" }, { name = "ome-types", specifier = ">=0.6" }, { name = "polars", specifier = ">=1.0" }, { name = "pyarrow", specifier = ">=18.0" }, @@ -3233,7 +3233,7 @@ dev = [ { name = "pre-commit", specifier = ">=3.7" }, { name = "pyright", extras = ["nodejs"], specifier = ">=1.1.400" }, { name = "pytest", specifier = ">=8.0" }, - { name = "pytest-timeout", specifier = ">=2.0" }, + { name = "pytest-timeout", specifier = ">=2.4" }, { name = "python-lsp-server", specifier = ">=1.10" }, { name = "rendercanvas", specifier = ">=2.2" }, { name = "ruff", specifier = ">=0.15" }, From 41662a2f1d59c9c0638368cceed8d4b4a251e3f8 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 15:38:23 +0200 Subject: [PATCH 14/18] Fix pytest-timeout to allow debugging the actual issues --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index dbbe71d..ecf6c2b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -70,4 +70,4 @@ jobs: 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>=2.0" --python ${{ matrix.python }} --resolution ${{ matrix.resolution }} pytest --timeout=180 --timeout-method=thread -v --durations=20 + - 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 From 16f3fff6e1a6bc59f177c0123a7ef627982810fb Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Tue, 7 Jul 2026 16:46:22 +0200 Subject: [PATCH 15/18] Bump minimum Dask version in hopes to fix CI --- pyproject.toml | 2 +- uv.lock | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 957f89d..4436e2d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ dependencies = [ "bioio-ome-zarr>=3.5", "bioio-tifffile>=1.3", "bioio-tiff-glob>=1.2", - "dask>=2025.1", + "dask>=2026.1", "fsspec>=2025.1", "imageio[ffmpeg]>=2.37", "imgrvt>=1.0", diff --git a/uv.lock b/uv.lock index 3592a83..b3f45df 100644 --- a/uv.lock +++ b/uv.lock @@ -3207,7 +3207,7 @@ requires-dist = [ { name = "bioio-ome-zarr", specifier = ">=3.5" }, { name = "bioio-tiff-glob", specifier = ">=1.2" }, { name = "bioio-tifffile", specifier = ">=1.3" }, - { name = "dask", specifier = ">=2025.1" }, + { name = "dask", specifier = ">=2026.1" }, { name = "fsspec", specifier = ">=2025.1" }, { name = "imageio", extras = ["ffmpeg"], specifier = ">=2.37" }, { name = "imgrvt", specifier = ">=1.0" }, From 75d3673ccd4a19816526c9b8ec2b41244fd35002 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Wed, 8 Jul 2026 11:31:26 +0200 Subject: [PATCH 16/18] Bump fsspec, numpy, pyarrow, and xarray minimum versions --- pyproject.toml | 8 ++++---- uv.lock | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4436e2d..9b26526 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,20 +17,20 @@ dependencies = [ "bioio-tifffile>=1.3", "bioio-tiff-glob>=1.2", "dask>=2026.1", - "fsspec>=2025.1", + "fsspec>=2025.3", "imageio[ffmpeg]>=2.37", "imgrvt>=1.0", "jax>=0.10.2", "jaxtyping>=0.3", - "numpy>=2.2", + "numpy>=2.3", "ome-types>=0.6", "polars>=1.0", - "pyarrow>=18.0", + "pyarrow>=22.0", "scikit-image>=0.23", "scipy>=1.17", "tifffile>=2026.5", "tqdm>=4.66", - "xarray>=2025.1", + "xarray>=2026.1", ] keywords = ["tools", "utilities", "python", "microscopy"] diff --git a/uv.lock b/uv.lock index b3f45df..7ba8686 100644 --- a/uv.lock +++ b/uv.lock @@ -3208,20 +3208,20 @@ requires-dist = [ { name = "bioio-tiff-glob", specifier = ">=1.2" }, { name = "bioio-tifffile", specifier = ">=1.3" }, { name = "dask", specifier = ">=2026.1" }, - { name = "fsspec", specifier = ">=2025.1" }, + { name = "fsspec", specifier = ">=2025.3" }, { name = "imageio", extras = ["ffmpeg"], specifier = ">=2.37" }, { name = "imgrvt", specifier = ">=1.0" }, { name = "jax", specifier = ">=0.10.2" }, { name = "jaxtyping", specifier = ">=0.3" }, - { name = "numpy", specifier = ">=2.2" }, + { name = "numpy", specifier = ">=2.3" }, { name = "ome-types", specifier = ">=0.6" }, { name = "polars", specifier = ">=1.0" }, - { name = "pyarrow", specifier = ">=18.0" }, + { name = "pyarrow", specifier = ">=22.0" }, { name = "scikit-image", specifier = ">=0.23" }, { name = "scipy", specifier = ">=1.17" }, { name = "tifffile", specifier = ">=2026.5" }, { name = "tqdm", specifier = ">=4.66" }, - { name = "xarray", specifier = ">=2025.1" }, + { name = "xarray", specifier = ">=2026.1" }, ] [package.metadata.requires-dev] From d3c05a0366d3831b6a7f89c2f00efb8c5bf6d345 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Wed, 8 Jul 2026 13:03:52 +0200 Subject: [PATCH 17/18] Investigate a deadlock on CI by changing thread count to 1 --- .github/workflows/ci.yml | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ecf6c2b..534d13e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,6 +50,22 @@ jobs: # stuck job shows exactly which compile/test was in flight. PYTHONFAULTHANDLER: "1" JAX_LOG_COMPILES: "1" + # H1 experiment: pin BLAS/LAPACK thread pools to 1 for the CPU test + # cells. The (ubuntu, 3.13, lowest-direct) cell deadlocks inside + # np.asarray(p) after a jax.scipy.linalg.solve on a complex matrix, + # with every other thread idle. Hypothesis: the cp313 jaxlib 0.10.2 + # wheel's bundled OpenBLAS deadlocks when its worker pool coexists + # with the leftover dask/asyncio thread pools from the io tests. + # Pinning the BLAS pools to 1 removes the reentrant-pool path; the + # hot op is a 2715^2 LU so the single-threaded cost is negligible. + # NOTE: XLA_FLAGS=--xla_cpu_multi_threaded=false was tried and + # rejected -- it crashes this jaxlib build locally (hard abort at + # the first jax-using test, exit 1, no traceback), so it is not + # included here. The deadlock does not reproduce on a 32- or 2-core + # dev box, so CI is the only place this can be judged. + OMP_NUM_THREADS: "1" + OPENBLAS_NUM_THREADS: "1" + MKL_NUM_THREADS: "1" strategy: fail-fast: false matrix: From d724eef5548977c7330c4f463f8ccbc037fb7f52 Mon Sep 17 00:00:00 2001 From: Marco Heisig Date: Wed, 8 Jul 2026 13:26:08 +0200 Subject: [PATCH 18/18] Wrap up the CI integration --- .github/workflows/ci.yml | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 534d13e..914d85c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,19 +50,8 @@ jobs: # stuck job shows exactly which compile/test was in flight. PYTHONFAULTHANDLER: "1" JAX_LOG_COMPILES: "1" - # H1 experiment: pin BLAS/LAPACK thread pools to 1 for the CPU test - # cells. The (ubuntu, 3.13, lowest-direct) cell deadlocks inside - # np.asarray(p) after a jax.scipy.linalg.solve on a complex matrix, - # with every other thread idle. Hypothesis: the cp313 jaxlib 0.10.2 - # wheel's bundled OpenBLAS deadlocks when its worker pool coexists - # with the leftover dask/asyncio thread pools from the io tests. - # Pinning the BLAS pools to 1 removes the reentrant-pool path; the - # hot op is a 2715^2 LU so the single-threaded cost is negligible. - # NOTE: XLA_FLAGS=--xla_cpu_multi_threaded=false was tried and - # rejected -- it crashes this jaxlib build locally (hard abort at - # the first jax-using test, exit 1, no traceback), so it is not - # included here. The deadlock does not reproduce on a 32- or 2-core - # dev box, so CI is the only place this can be judged. + # 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"