Consolidate dependencies into pyproject.toml; drop requirements*.txt

[rly]

Motivation

Fixes #2204. Adopts the hdmf dependency-management pattern: all dependency declarations live in pyproject.toml, and the requirements*.txt files are removed.

Changes

• pyproject.toml: added [project.optional-dependencies] (termset, zarr, stream, and an all aggregate) and PEP 735 [dependency-groups] (test, docs).
• Removed requirements.txt, requirements-dev.txt, requirements-opt.txt, requirements-doc.txt, requirements-min.txt. Kept environment-ros3.yml (conda/ROS3 jobs).
• tox.ini: rewritten to install via extras/dependency_groups; a single build env; upgraded/prerelease use pip install -U/-U --pre; minimum envs use uv pip install --resolution lowest-direct (replaces requirements-min.txt).
• CI workflows: install only tox and run tox -e <env>; ros3/coverage/sphinx jobs now install via pip install --group <group> ".[all]". Converted the test matrices from -pinned to -upgraded and to the single build env.
• .readthedocs.yaml: installs --group docs ".[all]".
• Docs: updated install_developers.rst (pip install --group test -e ".[all]"), software_process.rst, make_a_release.rst, and the release PR template; removed the obsolete update_requirements.rst.
• termset extra: capped linkml and linkml-runtime below 1.11. Those versions require click>=8.2, while dandi (a docs/gallery dependency) requires click<8.2. The gallery tox env installs the termset extra and the docs group in separate pip install -U transactions, so an uncapped termset transaction force-upgrades click to a version that breaks dandi, failing the pip check step. The cap keeps click at 8.1.x, which satisfies the whole stack.

Validation

• pyproject.toml parses; optional-dependencies and dependency-groups resolve.
• tox config resolves for all environment types (validated with tox config -e <env> using tox 4.55 + uv in an isolated venv). The minimum envs share hdmf's known tox config introspection quirk but run normally via tox -e.
• All 11 workflow YAML files and .readthedocs.yaml validate.
• The click cap was verified by reproducing the gallery env's two-stage pip install -U sequence (docs group, then termset extra): with both caps in place the stack resolves to click 8.1.8 and pip check passes.

Notes / needs CI

• The full CI run is the real validation for the tox env matrices, the uv --resolution lowest-direct minimum builds, and the pip install --group commands (requires pip ≥ 25.1, present on the runners).
• The test group drops black/isort (ruff supersedes them). Optional-dependency version floors mirror hdmf where applicable.
• The linkml/linkml-runtime <1.11 cap is a workaround for an upstream click constraint disagreement between dandi and linkml. It can be lifted once dandi relaxes its click<8.2 bound or linkml regains click<8.2 compatibility.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.29%. Comparing base (36cc7c3) to head (e460bf8).

Additional details and impacted files

@@           Coverage Diff           @@
##              dev    #2205   +/-   ##
=======================================
  Coverage   95.29%   95.29%           
=======================================
  Files          30       30           
  Lines        3038     3038           
  Branches      450      450           
=======================================
  Hits         2895     2895           
  Misses         87       87           
  Partials       56       56           

Flag	Coverage Δ
integration	73.14% <ø> (ø)
unit	85.97% <ø> (ø)

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[rly]

The latest dandi and linkml-runtime cannot be installed together currently. dandi requires click <8.2.0 and linkml requires click >=8.2.0. There is an open ticket in dandi: dandi/dandi-cli#1631 and I opened a PR to remove the upper bound in dandi/dandi-cli#1883. Until that is resolved, we are limiting to linkml-runtime <1.11.0