Fix packaging: declare build-system, fix package discovery (v0.2.23) - #40
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The project had no [build-system] table, so uv treated it as a virtual project and never installed mtphandler — pytest and `uv add --editable` both failed with ModuleNotFoundError. setuptools' flat-layout discovery also errored on the two top-level dirs (mtphandler, specifications). - Add [build-system] (setuptools) so the project installs - Limit package discovery to mtphandler* (excludes specifications/) - Use SPDX string for license (drops setuptools deprecation warning) - Raw-string a regex in multiskan_spectrum_parser (drops SyntaxWarning) - Bump version 0.2.22 -> 0.2.23 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- tests.yml used `pip install poetry; poetry install --with dev`, but the project moved to uv (uv.lock) with PEP 735 [dependency-groups]; poetry has no `dev` group here, so install failed. Now uses astral-sh/setup-uv + `uv sync --group dev` + `uv run pytest`. - Bump actions/setup-python@v4 -> v5 in mkdocs.yml (v4 runs on EOL Node 16). - Add Python 3.14 to the test matrix (continue-on-error): allowed to fail until pyenzyme's transitive dep `fastobo` ships 3.14 wheels. - Widen requires-python to >=3.10,<3.15. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
pyenzyme pins fastobo<0.14, which has no 3.14 wheel, so 3.14 can't install. Revert requires-python to <3.14 and drop 3.14 from the CI matrix until pyenzyme allows fastobo 0.14.x (which does ship cp314 wheels). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- publish_pypi: gate TestPyPI publish to tag pushes and add skip-existing, so branch pushes no longer 400 on re-uploading an existing version. - tests: run `pytest tests/` instead of executing docs notebooks with --nbval; the notebooks call live PubChem and flake on macOS runners. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
test_define_molecule_without_name does a live PubChem lookup; macOS CI runners get rate-limited and the test fails there while ubuntu/windows pass. Skip on PubChem-specific failure so a network flake doesn't red the build, while still asserting whenever PubChem responds. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Replaces the earlier skip-on-failure band-aid. test_define_molecule_without_name is the only test that does a live PubChem lookup. Mark it `network`; CI runs `pytest -m "not network"` because datacenter runner IPs get rate-limited by PubChem. A plain local `pytest` still runs it. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- actions/checkout v4 -> v7 - actions/setup-python v5 -> v7 - actions/upload-artifact v4 -> v7 - actions/download-artifact v4 -> v8 (v4+ share one backend, cross-compatible) - actions/cache v4 -> v6 - astral-sh/setup-uv v6 -> v9 - sigstore/gh-action-sigstore-python v2.1.1 -> v3.4.0 Left on moving/recommended refs: codespell-project/actions-codespell@v2, pypa/gh-action-pypi-publish@release/v1 (upstream's recommended pin). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
pypa/gh-action-pypi-publish (>=1.11.0) already generates PEP 740 attestations by default, so the manual Sigstore signing + release-upload step duplicated provenance PyPI now provides. PyPA removed it from their canonical workflow. The github-release job now just creates the GitHub Release; the sigstore id-token permission and artifact download are no longer needed. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
- publish: add check-version job (release tag must equal pyproject version), gate both publish jobs on it so a mistagged release can't ship. - add .pre-commit-config.yaml with uv-lock hook so uv.lock can't drift from pyproject.toml; add pre-commit to the dev group. - tests: `uv sync --locked` fails CI if the lock is out of sync (belt to the pre-commit hook's suspenders). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Read the installed version via stdlib importlib.metadata instead of hardcoding, so it stays in sync with pyproject.toml. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
uv add --editable,uv sync, anduv run pytestall failed because the project was never actually installed. Root cause:pyproject.tomlhad no[build-system]table, so uv treated it as a virtual project and skipped installingmtphandler— every test collected withModuleNotFoundError: No module named 'mtphandler'. setuptools' flat-layout discovery separately errored on the two top-level dirs (mtphandler,specifications).Changes
[build-system](setuptools ≥61) so the project installs as a package[tool.setuptools.packages.find] include = ["mtphandler*"]— fixes "Multiple top-level packages discovered" by excludingspecifications/license = "MIT"(SPDX string) — drops the setuptools license-table deprecation warningmultiskan_spectrum_parser.py— drops aSyntaxWarning: invalid escape sequence '\d'0.2.22→0.2.23(bugfix)Verification
uv syncnow installsmtphandler==0.2.23editable;uv run pytest→ 25 passed.uv buildproduces a clean wheel + sdist.🤖 Generated with Claude Code