[chaoming0625]

Summary

Prepares the braintools 0.4.0 release, which ships all of the roadmap work merged since 0.3.0 (#129–#133): braintools.analysis, braintools.spike, braintools.fit, quad trajectories, scalable conn networks, readout learning, neuroscience data formats, full type checking and doctested examples.

Changes

• braintools/_version.py: 0.3.0 → 0.4.0.
• changelog.md: the five unreleased phase sections (0.4–0.8) are merged into one 0.4.0 release note, with highlights, upgrade notes, Added / Changed / Deprecated / Removed / Fixed, and packaging.
• Docstrings and docs no longer cite unpublished versions: versionchanged:: 0.7.0 → 0.4.0, and comparisons such as "differs from 0.6" → "0.3".
• Python: requires-python >=3.12, with classifiers for 3.12–3.15. 3.11 is dropped from the CI matrix, and CONTRIBUTING.md is updated to match.
• scripts/run_doctests.py forces the Agg matplotlib backend, matching conftest.py.

Local verification

• pytest, one process per subpackage: all passed (≈6.3k tests, 0 failures).
• mypy: no issues in 148 source files.
• sphinx-build -W --keep-going: succeeded.
• Doctests: all modules pass except braintools.file, which needs pynwb, neo and quantities; those weren't installed locally and are covered by the doctest workflow here.
• python -m build and twine check: passed. The wheel metadata reports Version: 0.4.0 and Requires-Python: >=3.12.

Summary by Sourcery

Prepare braintools 0.4.0 as the consolidated release of the roadmap features and updated Python support.

Enhancements:

• Consolidate the roadmap work into the braintools 0.4.0 release, including analysis, spike, fitting, trajectory integration, scalable connectivity, learning, and neuroscience data tooling.
• Update release documentation, migration guidance, API references, and examples to reflect the unified 0.4.0 release.
• Require Python 3.12 or newer and align contributor guidance and CI support with the new minimum version.

Build:

• Update package metadata and version information for the 0.4.0 release.

CI:

• Align CI with supported Python versions and make doctest execution use a non-interactive matplotlib backend.

Documentation:

• Consolidate unreleased roadmap notes into the 0.4.0 changelog and update version references throughout documentation.

Tests:

• Finalize the release with the project’s tested, type-checked, documented, and build-validated state.

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[sourcery-ai]

Reviewer's Guide

This release-preparation PR publishes braintools 0.4.0 by updating version and release documentation to consolidate all roadmap work since 0.3.0, documenting the resulting API and behavior changes, raising support to Python 3.12+, and aligning CI and doctest execution with the release configuration.

Flow diagram for braintools 0.4.0 compatibility changes

flowchart TD
    Python312[Python 3.12 or newer] --> CI[CI matrix 3.12 to 3.14]
    CI --> Package[Package metadata requires Python 3.12+]
    Package --> Version[braintools version 0.4.0]
    Version --> Release[Published release]
    Python311[Python 3.11] --> Dropped[Support dropped]

Loading

File-Level Changes

Change	Details	Files
Promote the package and consolidate roadmap work into the 0.4.0 release.	Set the runtime version to 0.4.0. Merged the unreleased 0.4–0.8 notes into a single release note covering features, migrations, fixes, deprecations, and packaging. Updated documentation and doctest references from unpublished roadmap versions to 0.4.0 or the prior 0.3 release.	braintools/_version.py changelog.md braintools/_deprecation.py braintools/analysis/spike/_firings.py braintools/conn/_biological.py braintools/conn/_compartment.py braintools/conn/_kernel.py braintools/conn/_random.py braintools/conn/_spatial.py braintools/conn/_topological.py braintools/conn/_topological_test.py docs/analysis/08_analysis_toolbox.ipynb docs/conn/06_networks_and_scale.ipynb docs/migration.md
Raise the supported Python baseline and align packaging and CI with the 0.4.0 support policy.	Changed package metadata and contributor guidance to require Python 3.12+. Removed Python 3.11 from CI and added the Python 3.15 package classifier.	pyproject.toml .github/workflows/CI.yml CONTRIBUTING.md
Make doctest execution use the same headless plotting configuration as the test suite.	Set MPLBACKEND to Agg before importing matplotlib or running module doctests.	scripts/run_doctests.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

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