From 0bff7ae259189ca6f2a3726209f079517f10ad3d Mon Sep 17 00:00:00 2001 From: Ramdam17 Date: Sat, 3 Oct 2026 17:27:37 -0400 Subject: [PATCH 1/2] chore(deps): upgrade vulnerable packages and slim the docs requirements Upgrade only the 20 packages of the lock file that carry a known vulnerability (19 reported by Dependabot, plus click, reported by pip-audit only). No numerical dependency changes version: numpy, scipy, mne, numba, pandas, statsmodels and torch are untouched. torch stays at 2.10.0; its two advisories concern torch.jit.script and .pt2 loading, which HyPyP does not use, and its upgrade is scheduled separately. Remove mistune, pillow and urllib3 from the direct dependencies. HyPyP never imported them; they were security pins on indirect dependencies, a role the lock file now plays. Create a `docs` dependency group with the five documentation tools, include it in `dev`, and export docs/requirements.txt from it alone. The export no longer appends `hypyp==`: mkdocstrings reads the source statically, so the site builds without installing the package, and the build no longer depends on the version being on PyPI already. Move Read the Docs from Python 3.10 to 3.12, since the project requires 3.11 or later. Add the changelog entries for #278 and #279, which were merged after 0.6.0 without one. Verified on macOS arm64: 218 passed, 48 skipped, as before the change; `mkdocs build --strict` succeeds in a clean Python 3.12 environment holding only docs/requirements.txt; pip-audit on the full lock reports torch only. Co-Authored-By: Claude Fable 5.1 --- .readthedocs.yaml | 2 +- CHANGELOG.md | 15 + docs/requirements.txt | 564 ++---------------------------------- pyproject.toml | 18 +- update_docs_requirements.sh | 3 +- uv.lock | 400 +++++++++++++------------ 6 files changed, 257 insertions(+), 745 deletions(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 37ff5ab..8513e40 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -3,7 +3,7 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.10" + python: "3.12" mkdocs: configuration: mkdocs.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index b2ce96e..0a271f0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,21 @@ ## [Unreleased] +### Fixed +- Metal backend: a single command queue is now cached per device instead of one being created on every call. Long loops (for example surrogate tests) used to exhaust the device's command queues and crash with `'NoneType' object has no attribute 'commandBuffer'` after about 7,800 calls (#279) + +### Security +- Upgraded the 20 packages of the lock file that had known vulnerabilities: anyio, bleach, click, idna, jupyter-server, jupyterlab, mistune, mkdocs-material, nbconvert, notebook, pillow, pip, pygments, pymdown-extensions, python-multipart, setuptools, soupsieve, starlette, tornado and urllib3. None of the numerical dependencies (numpy, scipy, mne, numba, torch) changes version +- torch stays at 2.10.0 in the lock file for now. Its two open advisories concern `torch.jit.script` (CVE-2025-3000) and the loading of `.pt2` files (CVE-2026-4538), neither of which HyPyP uses + +### Changed +- `mistune`, `pillow` and `urllib3` are no longer direct dependencies. HyPyP never imported them; they were listed only to force minimum versions of indirect dependencies, which the lock file now does. `pillow` and `urllib3` are still installed through `matplotlib` and `requests` +- New `docs` dependency group holding only the documentation tools. `docs/requirements.txt` is now exported from it (36 packages instead of the whole development environment) and no longer installs `hypyp` itself from PyPI, which the documentation build does not need. The `dev` group includes the new group +- Read the Docs now builds with Python 3.12 instead of 3.10, which the project no longer supports + +### Documentation +- Richer docstrings for the nine `hypyp.sync` metrics and for the CUDA and Metal kernels, with intent and literature references (#278) + ## [0.6.0] - 2026-04-21 ### Added diff --git a/docs/requirements.txt b/docs/requirements.txt index f9bf003..278dac8 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,220 +1,32 @@ # This file was autogenerated by uv via the following command: -# uv export --no-hashes --group dev --output-file docs/requirements.txt --e . -anyio==4.12.1 - # via - # httpx - # jupyter-server -appnope==0.1.4 ; sys_platform == 'darwin' - # via ipykernel -argon2-cffi==25.1.0 - # via jupyter-server -argon2-cffi-bindings==25.1.0 - # via argon2-cffi -arrow==1.4.0 - # via isoduration -astroid==4.0.4 - # via pylint -asttokens==3.0.1 - # via stack-data -async-lru==2.3.0 - # via jupyterlab -attrs==26.1.0 - # via - # jsonschema - # referencing -autoreject==0.4.3 - # via hypyp +# uv export --no-hashes --only-group docs --output-file docs/requirements.txt babel==2.18.0 - # via - # jupyterlab-server - # mkdocs-material + # via mkdocs-material backrefs==6.2 # via mkdocs-material -beautifulsoup4==4.14.3 - # via nbconvert -black==26.3.1 -bleach==6.3.0 - # via nbconvert bracex==2.6 # via wcmatch certifi==2026.2.25 - # via - # httpcore - # httpx - # hypyp - # netcdf4 - # requests -cffi==2.0.0 - # via - # argon2-cffi-bindings - # pyzmq -cftime==1.6.5 - # via netcdf4 + # via requests charset-normalizer==3.4.6 # via requests -click==8.3.1 - # via - # black - # mkdocs +click==8.5.0 + # via mkdocs colorama==0.4.6 # via - # click - # ipython # mkdocs # mkdocs-material - # pylint - # pytest - # pytest-watch - # snirf - # tqdm -comm==0.2.3 - # via - # ipykernel - # ipywidgets -contourpy==1.3.3 - # via matplotlib -cycler==0.12.1 - # via matplotlib -debugpy==1.8.20 - # via ipykernel -decorator==5.2.1 - # via - # ipython - # mne -defusedxml==0.7.1 - # via nbconvert -dill==0.4.1 - # via pylint -docopt==0.6.2 - # via pytest-watch -executing==2.2.1 - # via stack-data -fastjsonschema==2.21.2 - # via nbformat -fonttools==4.62.1 - # via matplotlib -fqdn==1.5.1 - # via jsonschema ghp-import==2.1.0 # via mkdocs griffelib==2.0.0 # via mkdocstrings-python -h11==0.16.0 - # via httpcore -h5io==0.2.5 - # via mne -h5py==3.16.0 - # via - # h5io - # pymatreader - # snirf -httpcore==1.0.9 - # via httpx -httpx==0.28.1 - # via jupyterlab -idna==3.11 - # via - # anyio - # httpx - # jsonschema - # requests -imageio==2.37.3 - # via scikit-image -importlib-resources==6.5.2 - # via hypyp -iniconfig==2.3.0 - # via pytest -ipykernel==7.2.0 - # via jupyterlab -ipython==9.10.0 ; python_full_version < '3.12' - # via - # ipykernel - # ipywidgets -ipython==9.11.0 ; python_full_version >= '3.12' - # via - # ipykernel - # ipywidgets -ipython-pygments-lexers==1.1.1 - # via ipython -ipywidgets==8.1.8 -isoduration==20.11.0 - # via jsonschema -isort==8.0.1 - # via pylint -jedi==0.19.2 - # via ipython +idna==3.20 + # via requests jinja2==3.1.6 # via - # jupyter-server - # jupyterlab - # jupyterlab-server # mkdocs # mkdocs-material # mkdocstrings - # mne - # nbconvert -joblib==1.5.3 - # via - # autoreject - # scikit-learn -json5==0.13.0 - # via jupyterlab-server -jsonpointer==3.1.0 - # via jsonschema -jsonschema==4.26.0 - # via - # jupyter-events - # jupyterlab-server - # nbformat -jsonschema-specifications==2025.9.1 - # via jsonschema -jupyter-client==8.8.0 - # via - # ipykernel - # jupyter-server - # nbclient -jupyter-core==5.9.1 - # via - # ipykernel - # jupyter-client - # jupyter-server - # jupyterlab - # nbclient - # nbconvert - # nbformat -jupyter-events==0.12.0 - # via jupyter-server -jupyter-lsp==2.3.0 - # via jupyterlab -jupyter-server==2.17.0 - # via - # jupyter-lsp - # jupyterlab - # jupyterlab-server - # notebook - # notebook-shim -jupyter-server-terminals==0.5.4 - # via jupyter-server -jupyterlab==4.5.6 - # via notebook -jupyterlab-pygments==0.3.0 - # via nbconvert -jupyterlab-server==2.28.0 - # via - # jupyterlab - # notebook -jupyterlab-widgets==3.0.16 - # via ipywidgets -kiwisolver==1.5.0 - # via matplotlib -lark==1.3.1 - # via rfc3987-syntax -lazy-loader==0.5 - # via - # mne - # scikit-image -livereload==2.7.1 markdown==3.10.2 # via # mkdocs @@ -222,39 +34,16 @@ markdown==3.10.2 # mkdocs-material # mkdocstrings # pymdown-extensions -markdown-it-py==4.0.0 - # via rich markupsafe==3.0.3 # via # jinja2 # mkdocs # mkdocs-autorefs # mkdocstrings - # nbconvert -matplotlib==3.10.8 - # via - # autoreject - # hypyp - # mne - # seaborn -matplotlib-inline==0.2.1 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via pylint -mdurl==0.1.2 - # via markdown-it-py mergedeep==1.3.4 # via # mkdocs # mkdocs-get-deps -meshio==5.3.5 - # via hypyp -mistune==3.2.0 - # via - # hypyp - # nbconvert mkdocs==1.6.1 # via # mkdocs-autorefs @@ -265,357 +54,46 @@ mkdocs-autorefs==1.4.4 # via # mkdocstrings # mkdocstrings-python - # mkdocstrings-python-legacy mkdocs-get-deps==0.2.2 # via mkdocs mkdocs-include-markdown-plugin==7.2.1 -mkdocs-material==9.7.6 +mkdocs-material==9.7.7 mkdocs-material-extensions==1.3.1 # via mkdocs-material mkdocstrings==1.0.3 - # via - # mkdocstrings-python - # mkdocstrings-python-legacy + # via mkdocstrings-python mkdocstrings-python==2.0.3 -mkdocstrings-python-legacy==0.2.7 -mne==1.11.0 - # via - # autoreject - # hypyp - # mne-connectivity -mne-connectivity==0.7.0 - # via hypyp -mypy-extensions==1.1.0 - # via black -nbclient==0.10.4 - # via nbconvert -nbconvert==7.17.0 - # via jupyter-server -nbformat==5.10.4 - # via - # jupyter-server - # nbclient - # nbconvert -nest-asyncio==1.6.0 - # via ipykernel -netcdf4==1.7.4 - # via mne-connectivity -networkx==3.6.1 - # via scikit-image -notebook==7.5.5 -notebook-shim==0.2.4 - # via - # jupyterlab - # notebook -numpy==2.4.3 - # via - # autoreject - # cftime - # contourpy - # h5io - # h5py - # hypyp - # imageio - # matplotlib - # meshio - # mne - # mne-connectivity - # netcdf4 - # pandas - # patsy - # pymatreader - # pywavelets - # pyxdf - # scikit-image - # scikit-learn - # scipy - # seaborn - # snirf - # statsmodels - # tifffile - # xarray -overrides==7.7.0 ; python_full_version < '3.12' - # via jupyter-server packaging==26.0 - # via - # black - # ipykernel - # jupyter-events - # jupyter-server - # jupyterlab - # jupyterlab-server - # lazy-loader - # matplotlib - # mkdocs - # mne - # nbconvert - # pooch - # pytest - # scikit-image - # statsmodels - # xarray + # via mkdocs paginate==0.5.7 # via mkdocs-material -pandas==3.0.1 - # via - # hypyp - # mne-connectivity - # seaborn - # statsmodels - # xarray -pandocfilters==1.5.1 - # via nbconvert -parso==0.8.6 - # via jedi pathspec==1.0.4 - # via - # black - # mkdocs -patsy==1.0.2 - # via statsmodels -pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' - # via ipython -pillow==12.2.0 - # via - # hypyp - # imageio - # matplotlib - # scikit-image -pip==26.0.1 - # via snirf + # via mkdocs platformdirs==4.9.4 - # via - # black - # jupyter-core - # mkdocs-get-deps - # pooch - # pylint -pluggy==1.6.0 - # via pytest -pooch==1.9.0 - # via - # hypyp - # mne -prometheus-client==0.24.1 - # via jupyter-server -prompt-toolkit==3.0.52 - # via ipython -psutil==7.2.2 - # via ipykernel -ptyprocess==0.7.0 ; os_name != 'nt' or (sys_platform != 'emscripten' and sys_platform != 'win32') - # via - # pexpect - # terminado -pure-eval==0.2.3 - # via stack-data -pyarrow==23.0.1 - # via hypyp -pycparser==3.0 ; implementation_name != 'PyPy' - # via cffi -pygments==2.19.2 - # via - # ipython - # ipython-pygments-lexers - # mkdocs-material - # nbconvert - # pytest - # rich -pylint==4.0.5 -pymatreader==1.2.2 - # via mne -pymdown-extensions==10.21 + # via mkdocs-get-deps +pygments==2.21.0 + # via mkdocs-material +pymdown-extensions==12.1 # via # mkdocs-material # mkdocstrings -pyparsing==3.3.2 - # via matplotlib -pyqt6==6.10.2 -pyqt6-qt6==6.10.2 - # via pyqt6 -pyqt6-sip==13.11.1 - # via pyqt6 -pytest==9.0.3 - # via - # pytest-mock - # pytest-watch -pytest-mock==3.15.1 -pytest-watch==4.2.0 python-dateutil==2.9.0.post0 - # via - # arrow - # ghp-import - # jupyter-client - # matplotlib - # pandas -python-json-logger==4.0.0 - # via jupyter-events -pytkdocs==0.16.5 - # via mkdocstrings-python-legacy -pytokens==0.4.1 - # via black -pywavelets==1.9.0 - # via hypyp -pywinpty==3.0.3 ; os_name == 'nt' - # via - # jupyter-server - # jupyter-server-terminals - # terminado -pyxdf==1.17.3 - # via hypyp + # via ghp-import pyyaml==6.0.3 # via - # jupyter-events # mkdocs # mkdocs-get-deps # pymdown-extensions # pyyaml-env-tag pyyaml-env-tag==1.1 # via mkdocs -pyzmq==27.1.0 - # via - # ipykernel - # jupyter-client - # jupyter-server -referencing==0.37.0 - # via - # jsonschema - # jsonschema-specifications - # jupyter-events requests==2.33.0 - # via - # hypyp - # jupyterlab-server - # mkdocs-material - # pooch -rfc3339-validator==0.1.4 - # via - # jsonschema - # jupyter-events -rfc3986-validator==0.1.1 - # via - # jsonschema - # jupyter-events -rfc3987-syntax==1.1.0 - # via jsonschema -rich==14.3.3 - # via meshio -rpds-py==0.30.0 - # via - # jsonschema - # referencing -scikit-image==0.26.0 - # via hypyp -scikit-learn==1.8.0 - # via autoreject -scipy==1.17.1 - # via - # autoreject - # hypyp - # mne - # mne-connectivity - # pymatreader - # scikit-image - # scikit-learn - # statsmodels -seaborn==0.13.2 - # via hypyp -send2trash==2.1.0 - # via jupyter-server -setuptools==82.0.1 - # via - # jupyterlab - # snirf + # via mkdocs-material six==1.17.0 - # via - # python-dateutil - # rfc3339-validator -snirf==0.8.0 - # via hypyp -soupsieve==2.8.3 - # via beautifulsoup4 -stack-data==0.6.3 - # via ipython -statsmodels==0.14.6 - # via hypyp -tabulate==0.10.0 -termcolor==3.3.0 - # via snirf -terminado==0.18.1 - # via - # jupyter-server - # jupyter-server-terminals 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-webcolors==25.10.0 - # via jsonschema -webencodings==0.5.1 - # via - # bleach - # tinycss2 -websocket-client==1.9.0 - # via jupyter-server -widgetsnbextension==4.0.15 - # via ipywidgets -xarray==2026.2.0 - # via mne-connectivity -xmltodict==1.0.4 - # via pymatreader -hypyp==0.6.0 diff --git a/pyproject.toml b/pyproject.toml index 5f7853f..5acc460 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,12 +17,10 @@ dependencies = [ "importlib-resources>=6.0.0", "matplotlib>=3.7.2", "meshio>=5.3.4", - "mistune>=2.0.4", "mne>=1.3", "mne-connectivity>=0.7.0", "numpy>=2.2.3", "pandas>=2.0.3", - "pillow>=11.3.0", "pooch>=1.8", "pyarrow>=20.0.0", "pywavelets>=1.8.0", @@ -34,7 +32,6 @@ dependencies = [ "snirf>=0.8.0", "statsmodels>=0.14.4", "tqdm>=4.46.0", - "urllib3>=2.5.0", ] [project.optional-dependencies] @@ -51,16 +48,12 @@ Documentation = "https://hypyp.readthedocs.io" [dependency-groups] dev = [ + {include-group = "docs"}, "black>=25.1.0", "ipykernel>=6.19.4", "ipywidgets>=7.5.1", "jupyterlab>=4.3.5", "livereload>=2.6.3", - "mkdocs>=1.3.0", - "mkdocs-include-markdown-plugin>=7.1.5", - "mkdocs-material>=8.2.15", - "mkdocstrings>=0.20.0", - "mkdocstrings-python>=1.1.0", "mkdocstrings-python-legacy>=0.2.3", "notebook>=7.4.3", "pylint>=2.4.4", @@ -71,6 +64,15 @@ dev = [ "tabulate>=0.9.0", "widgetsnbextension>=3.5.1", ] +# Only what the documentation site needs; exported to docs/requirements.txt +# for Read the Docs by update_docs_requirements.sh. +docs = [ + "mkdocs>=1.3.0", + "mkdocs-include-markdown-plugin>=7.1.5", + "mkdocs-material>=8.2.15", + "mkdocstrings>=0.20.0", + "mkdocstrings-python>=1.1.0", +] benchmark = [ "doit>=0.36.0", ] diff --git a/update_docs_requirements.sh b/update_docs_requirements.sh index f2a0b66..2273627 100755 --- a/update_docs_requirements.sh +++ b/update_docs_requirements.sh @@ -1,5 +1,4 @@ REQUIREMENTS_PATH=docs/requirements.txt echo "Exporting docs requirements..." -uv export --no-hashes --group dev --output-file $REQUIREMENTS_PATH 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