Clean up packaging, CI and docs: drop Python 3.10, add 3.14, test minimum dependencies

[m-reuter]

Housekeeping for packaging, CI and the docs. No change to the LaPy API.

Packaging

• Remove setup.py. It only called setup(), which pyproject.toml makes unnecessary.
• Build requirements: numpy is no longer listed, since building a pure Python package does not need it. The minimum
  setuptools is now 77, the first version that understands license = 'MIT' and license-files.
• Drop Python 3.10 and add 3.14: requires-python >= 3.11 and classifiers for 3.11 to 3.14. Python 3.10 reaches its end
  of life this month, and current numpy and scipy releases already need 3.11.
• Set real minimum versions for all runtime dependencies: numpy>=1.23.2 and scipy>=1.9.2, the first releases with
  Python 3.11 wheels, plus nibabel>=4.0, plotly>=5.0 and psutil>=5.9. Before, numpy allowed versions that do not
  run on any supported Python, and the other packages had no minimum at all.
• Remove the full extra, which only repeated all.

CI

• pytest runs the oldest and newest Python (3.11 and 3.14) on ubuntu, macOS and Windows, and 3.12 and 3.13 on ubuntu
  only: 8 jobs instead of 12, or 15 with 3.14 added to the old matrix. Coverage is uploaded from ubuntu with 3.14.
• A new job installs the lowest dependency versions that pyproject.toml allows
  (uv pip install --resolution lowest-direct) on Python 3.11 and runs the tests, so the minimums stay true.
• pytest also runs when only pyproject.toml or its own workflow changes, so dependency and CI changes get tested too.
• The build workflow is a single ubuntu job on 3.14 instead of 12 jobs, and now runs twine check --strict on the
  built files. The package is pure Python and builds one py3-none-any wheel for every platform, the release files are
  built on ubuntu by the publish workflow, and the pytest jobs already install the package and run its entry point on
  every OS.
• Docstrings are checked with ruff's pydocstyle rules (numpy convention, same ignores and scope as before) instead of
  pydocstyle, which is no longer maintained. This found 3 extra blank lines after docstrings, which are fixed.

Docs

• Remove the changelog. It still described version 1.0 and was not maintained; GitHub release notes cover the same
  ground. The sphinx-issues extension was only used there and is removed as well.
• Remove sphinx-gallery. Its file pattern matched no example, so it only produced an empty gallery page and empty
  minigallery sections. The notebook tutorials are rendered by nbsphinx and are unchanged. memory-profiler was only
  needed for the gallery and is dropped from the doc extras.
• Remove the empty top-level tutorials/ folder and the gallery header examples/README.rst.

Checks

• ruff check . passes and the 145 tests pass with the current dependencies.
• With the minimum versions on Python 3.11 (numpy 1.23.2, scipy 1.9.2, nibabel 4.0.0, plotly 5.0.0, psutil 5.9.0) the
  145 tests pass as well.
• The docs build with sphinx-build -W --keep-going as in CI. Compared with a build before these changes, only the two
  empty gallery pages are gone.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 61.72%. Comparing base (cbb70b4) to head (a3bd402).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #124      +/-   ##
==========================================
- Coverage   61.84%   61.72%   -0.13%     
==========================================
  Files          16       16              
  Lines        3182     3182              
  Branches      417      417              
==========================================
- Hits         1968     1964       -4     
- Misses       1046     1049       +3     
- Partials      168      169       +1     

Flag	Coverage Δ
unittests	61.72% <ø> (-0.13%)	⬇️

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[Copilot]

🟢 Approval recommended

No unresolved review issues were identified, and the approval assessments are unanimous.

0 open findings

What changed in this PR

Modernizes packaging, CI, and documentation for Python 3.11–3.14, with updated dependency minimums and no API changes.

Changes:

• Updates packaging metadata and dependency requirements.
• Streamlines CI, build validation, and style checks.
• Removes obsolete setup, changelog, gallery, and tutorial placeholders.
• Cleans up affected docstrings and documentation configuration.

File	Summary
tutorials/​README.rst	Removes empty tutorial placeholder.
setup.py	Removes redundant setup shim.
pyproject.toml	Updates packaging, dependencies, and Ruff configuration.
lapy/​utils/​_imports.py	Fixes docstring spacing.
lapy/​utils/​_config.py	Fixes docstring spacing.
examples/​README.rst	Removes empty gallery header.
doc/​index.rst	Removes changelog navigation.
doc/​conf.py	Removes obsolete documentation extensions.
doc/​changes/​latest.rst.template	Removes obsolete changelog template.
doc/​changes/​latest.rst	Removes obsolete changelog content.
doc/​changes/​index.rst	Removes obsolete changelog index.
doc/​changes/​authors.inc	Removes obsolete changelog authors file.
doc/​_templates/​autosummary/​function.rst	Removes gallery sections.
doc/​_templates/​autosummary/​class.rst	Removes gallery sections.
.github/​workflows/​pytest.yml	Updates Python matrices and adds minimum-dependency tests.
.github/​workflows/​code-style.yml	Replaces standalone pydocstyle checks with Ruff.
.github/​workflows/​build.yml	Simplifies builds and adds distribution validation.

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