From 05140aaaa6a6eb1879351be4c86bb2d319473879 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Beno=C3=AEt=20J=2E=20T=2E=20GIRARD?= <53222414+BenoitJT-GIRARD@users.noreply.github.com> Date: Thu, 20 Aug 2026 01:49:32 +0200 Subject: [PATCH 1/5] chore: require python 3.11 or newer --- README.md | 4 ++-- pyproject.toml | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index eab4038..8b02c77 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![PyPI](https://img.shields.io/pypi/v/banos)](https://pypi.org/project/banos/) [![PyPI Downloads](https://static.pepy.tech/badge/banos)](https://pepy.tech/project/banos) [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE) -[![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/) +[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/) [![CI](https://github.com/BelloneLab/BANOS/actions/workflows/ci.yml/badge.svg)](https://github.com/BelloneLab/BANOS/actions/workflows/ci.yml) [![MATLAB File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://www.mathworks.com/matlabcentral/fileexchange/157916-banos) @@ -52,7 +52,7 @@ BANOS addresses these questions with four complementary metrics. pip install banos ``` -Requires Python 3.9+. Core dependency: `pandas`. Optional: `scipy` (for +Requires Python 3.11+. Core dependency: `pandas`. Optional: `scipy` (for `matching='optimal'`). ## Quick Start diff --git a/pyproject.toml b/pyproject.toml index baae9ea..a6efefc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,17 +4,17 @@ version = "0.2.3" description = "Behavior ANnOtation Score: ethological metrics for evaluating behavior annotation quality" readme = "README.md" license = { text = "MIT" } -requires-python = ">=3.9" +requires-python = ">=3.11" keywords = ["behavior", "annotation", "ethology", "video", "scoring", "metrics"] classifiers = [ "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.9", - "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", "Topic :: Scientific/Engineering :: Bio-Informatics", ] 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run: uv sync --locked --dev - name: Run ruff check run: uv run ruff check src/ tests/ @@ -36,18 +36,18 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.11", "3.12", "3.13", "3.14"] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 - name: Install uv - uses: astral-sh/setup-uv@v3 + uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1 with: python-version: ${{ matrix.python-version }} - name: Install dependencies - run: uv sync --dev + run: uv sync --locked --dev - name: Run tests run: uv run pytest tests/ --ignore=tests/test_parity.py -v diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index e6c176d..3d9b3f5 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -15,15 +15,15 @@ jobs: contents: read # Required for actions/checkout steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1 - name: Install uv - uses: astral-sh/setup-uv@v3 + uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1 with: python-version: "3.11" - name: Install dependencies - run: uv sync --dev + run: uv sync --locked --dev - name: Run tests before publishing run: uv run pytest tests/ --ignore=tests/test_parity.py --cov=banos --cov-fail-under=80 @@ -32,4 +32,4 @@ jobs: run: uv build - name: Publish to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2 From e903725f1fbaaccd8c7b9f021c71d8bb12849be6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Beno=C3=AEt=20J=2E=20T=2E=20GIRARD?= <53222414+BenoitJT-GIRARD@users.noreply.github.com> Date: Thu, 20 Aug 2026 01:49:32 +0200 Subject: [PATCH 4/5] chore: add dependabot config for github actions --- .github/dependabot.yml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..fcf4ed2 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,21 @@ +# Dependabot is intentionally scoped to GitHub Actions only. +# +# BANOS is a published, maintenance-only scientific package: its numerical +# output must not change. Python dependencies are therefore pinned in +# uv.lock and updated by hand, for security reasons only, and every update +# is validated against the golden regression tests before it is merged. +# Automatic pull requests on that ecosystem would work against this. +# +# GitHub Actions are a different matter. They execute with access to this +# repository and to the OIDC identity used to publish on PyPI, and they +# cannot influence any computed metric, so keeping them current carries no +# scientific risk. Dependabot also keeps the pinned commit SHAs up to date, +# which is what makes SHA pinning maintainable on a dormant project. +version: 2 +updates: + - package-ecosystem: "github-actions" + directory: "/" + schedule: + interval: "monthly" + commit-message: + prefix: "chore" From 45c7a5571f49c657eac10b68fc28f509207bb965 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Beno=C3=AEt=20J=2E=20T=2E=20GIRARD?= <53222414+BenoitJT-GIRARD@users.noreply.github.com> Date: Thu, 20 Aug 2026 01:49:32 +0200 Subject: [PATCH 5/5] docs: document the dependency policy --- SECURITY.md | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/SECURITY.md b/SECURITY.md index 785b6fc..a988ae6 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -37,3 +37,29 @@ BANOS is a pure-Python / MATLAB computation library. It: The attack surface is minimal. Security reports are most relevant to dependency vulnerabilities (e.g., malicious `pandas` or `scipy` releases) or unsafe handling of user-supplied CSV input. + +## Dependency Policy + +BANOS accompanies a peer-reviewed publication and is maintained in security-only mode. +Dependency handling follows two rules. + +**Numerical results must not change.** Runtime dependencies are pinned in `uv.lock`. +Every update is validated by the golden regression tests +(`tests/test_regression.py`, tolerance `1e-10`) across the whole supported Python +matrix before it is merged. An update that moves a metric is rejected — the golden +fixtures are never regenerated to accommodate a dependency bump. + +**Updates are deliberate, never automatic.** Dependabot alerts are enabled for +monitoring, but automatic security updates and version updates are disabled. Each +alert is triaged by hand and remediated with a targeted `uv lock --upgrade-package`, +never a blanket `uv lock --upgrade`. + +Dependabot itself is configured for GitHub Actions only (see +[`.github/dependabot.yml`](.github/dependabot.yml)). Actions are pinned to commit +SHAs: they run with access to this repository and to the OIDC identity used for PyPI +publishing, and unlike Python packages they cannot affect a computed result. + +One caveat when reading alerts: Dependabot reports every entry of `uv.lock` as +`runtime` scope. In practice the BANOS runtime closure is limited to `numpy`, +`pandas`, `scipy`, `matplotlib` and `seaborn`. The `notebook` and `calms21` extras +are optional tutorial environments and are not needed to import or use BANOS.