Fix #839, move `setup.py` metadata & config settings into `pyproject.toml`, & remove `requirements.txt` #959

mhucka · 2025-11-18T03:12:01Z

This addresses deprecation warnings originating from the use of outdated setuptools functions, and takes the opportunity to modernize the management of the version number and the dependencies in accordance with current Python practices (PEP 621, 735).

Key changes include:

All declarative package metadata (e.g., name, author, classifiers) has been moved from setup.py to pyproject.toml. What's left in setup.py has been simplified to only contain the logic necessary for building the C++ extensions.
The qsim version number is now stored in only on file, qsimcirq/_version.py, and both pyproject.toml and setup.py read it from there. In the case of setup.py, the use of the deprecated self.distribution.get_version() has been replaced with the use of runpy to read the version number from qsimcirq/_version.py. (The latter change fixes Fix use of deprecated setuptools functions #839.)
Development dependencies are no longer stored as "extras" but rather use the pyproject.toml [dependency-groups] section introduced in 2024 by PEP 735 and recognized by pip version 25.1+. This means both requirements.txt and dev-requirements.txt are gone, and development dependencies are installed using
```
 pip install --group dev
```
pyproject.toml defines the versions of Python for which cibuildwheel builds wheels (in section [tool.cibuildwheel]).

The modern approach is to put more things into `pyproject.toml`. This moves most things out of `setup.py`, with the exception of the native code extensions parts, and the version number. (Still to do: figure out how to move the version number too.)

gemini-code-assist

Code Review

This pull request modernizes the project's packaging by migrating metadata from setup.py to pyproject.toml in line with PEP 621. The changes are well-executed and correctly move dependencies, project information, and other configurations. My main feedback is to eliminate the duplication of the version string, which is currently present in both pyproject.toml and setup.py. By fetching the version from the distribution metadata within setup.py, you can make pyproject.toml the single source of truth for the version, which improves maintainability and prevents potential inconsistencies.

setup.py

pyproject.toml

setup.py

pavoljuhas

LGTM after addressing inline comments.

Have you tested if wheel building - especially with cibuildwheel - works with these changes?

Dockerfile

This makes use of 2 facilities in setuptools and pip. 1. Take advantage of the `--group` feature of pip for the development dependencies. Developers can install them with the command ```shell pip install --group dev ``` This makes files `requirements.txt` and `dev-requirements.txt` no longer necessary, and also puts all the requirements into one file for better clarity and maintenance. 2. Take advantage of the feature of `setuptools` and `setuptools_scm` to get the version number from a file automatically. The setup here makes it read `__version_`` from `qsimcirq/_version.py`.

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 6.0.0 to 6.1.0. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/setup-python/releases">actions/setup-python's releases</a>.</em></p> <blockquote> <h2>v6.1.0</h2> <h2>What's Changed</h2> <h3>Enhancements:</h3> <ul> <li>Add support for <code>pip-install</code> input by <a href="https://github.com/gowridurgad"><code>@gowridurgad</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1201">actions/setup-python#1201</a></li> <li>Add graalpy early-access and windows builds by <a href="https://github.com/timfel"><code>@timfel</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/880">actions/setup-python#880</a></li> </ul> <h3>Dependency and Documentation updates:</h3> <ul> <li>Enhanced wording and updated example usage for <code>allow-prereleases</code> by <a href="https://github.com/yarikoptic"><code>@yarikoptic</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/979">actions/setup-python#979</a></li> <li>Upgrade urllib3 from 1.26.19 to 2.5.0 and document breaking changes in v6 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1139">actions/setup-python#1139</a></li> <li>Upgrade typescript from 5.4.2 to 5.9.3 and Documentation update by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1094">actions/setup-python#1094</a></li> <li>Upgrade actions/publish-action from 0.3.0 to 0.4.0 & Documentation update for pip-install input by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1199">actions/setup-python#1199</a></li> <li>Upgrade requests from 2.32.2 to 2.32.4 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1130">actions/setup-python#1130</a></li> <li>Upgrade prettier from 3.5.3 to 3.6.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1234">actions/setup-python#1234</a></li> <li>Upgrade <code>@types/node</code> from 24.1.0 to 24.9.1 and update macos-13 to macos-15-intel by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1235">actions/setup-python#1235</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/yarikoptic"><code>@yarikoptic</code></a> made their first contribution in <a href="https://redirect.github.com/actions/setup-python/pull/979">actions/setup-python#979</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/setup-python/compare/v6...v6.1.0">https://github.com/actions/setup-python/compare/v6...v6.1.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/setup-python/commit/83679a892e2d95755f2dac6acb0bfd1e9ac5d548"><code>83679a8</code></a> Bump <code>@types/node</code> from 24.1.0 to 24.9.1 and update macos-13 to macos-15-intel ...</li> <li><a href="https://github.com/actions/setup-python/commit/bfc4944b43a5d84377eca3cf6ab5b7992ba61923"><code>bfc4944</code></a> Bump prettier from 3.5.3 to 3.6.2 (<a href="https://redirect.github.com/actions/setup-python/issues/1234">#1234</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/97aeb3efb8a852c559869050c7fb175b4efcc8cf"><code>97aeb3e</code></a> Bump requests from 2.32.2 to 2.32.4 in /<strong>tests</strong>/data (<a href="https://redirect.github.com/actions/setup-python/issues/1130">#1130</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/443da59188462e2402e2942686db5aa6723f4bed"><code>443da59</code></a> Bump actions/publish-action from 0.3.0 to 0.4.0 & Documentation update for pi...</li> <li><a href="https://github.com/actions/setup-python/commit/cfd55ca82492758d853442341ad4d8010466803a"><code>cfd55ca</code></a> graalpy: add graalpy early-access and windows builds (<a href="https://redirect.github.com/actions/setup-python/issues/880">#880</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/bba65e51ff35d50c6dbaaacd8a4681db13aa7cb4"><code>bba65e5</code></a> Bump typescript from 5.4.2 to 5.9.3 and update docs/advanced-usage.md (<a href="https://redirect.github.com/actions/setup-python/issues/1094">#1094</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/18566f86b301499665bd3eb1a2247e0849c64fa5"><code>18566f8</code></a> Improve wording and "fix example" (remove 3.13) on testing against pre-releas...</li> <li><a href="https://github.com/actions/setup-python/commit/2e3e4b15a884dc73a63f962bff250a855150a234"><code>2e3e4b1</code></a> Add support for pip-install input (<a href="https://redirect.github.com/actions/setup-python/issues/1201">#1201</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/4267e283df95c05d9f16ece6624106f44613b489"><code>4267e28</code></a> Bump urllib3 from 1.26.19 to 2.5.0 in /<strong>tests</strong>/data and document breaking c...</li> <li>See full diff in <a href="https://github.com/actions/setup-python/compare/e797f83bcb11b83ae66e0230d6156d7c80228e7c...83679a892e2d95755f2dac6acb0bfd1e9ac5d548">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/setup-python&package-manager=github_actions&previous-version=6.0.0&new-version=6.1.0)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

It turns out that Dependabot uses the same database, so there is little point in running the OSV scanner too.

Changes: - Don't tell it to use full sentences in comments, or it goes overboard when critiquing people's PRs. - Add some guidance for shell scripts. - Add some more points to the overall development approach. - Minor verbiage changes here and there.

This adds the names of custom GitHub runners we've defined for Quantumlib.

…lib#975) Windows CI jobs are a bottleneck right now, so I defined larger GitHub-hosted runners. This adds the new names to the actionlint config file so that they are recognized by actionlint.

Update the commands and instructions to use the new approach.

I run cibuildwheel as a way of testing that everything works, and I forsee writing some instructions around that. It may be time to add it to the development dependencies.

Turns out `setup-python` looks for `pyprojec.toml` automatically.

Its contents are in pyproject.toml now.

Take advantage of setuptools_scm's ability to make dependencies be obtained dynamically.

Move cmake, pybind and numpy here. Also constrain more versions, including of some transitive dependencies, because I'm hitting conflicts on Python < 3.11. Some packages like countourpy were updated in recent times and need Numpy 2+, which leads to conflicts.

Add the `-n auto` flag to pytest in the cibuldwheel configuration

Need to set the working directory before trying to install stuff.

The initial plan to use only group dev didn't work out.

.github/workflows/ci.yaml

.github/workflows/cirq_compatibility.yml

Dockerfile

+RUN python3 -m pip install --no-cache-dir --upgrade pip && \
+    python3 -m pip install --no-cache-dir -r requirements.txt && \
+    python3 -m pip install --no-cache-dir --group dev


mhucka · 2026-01-02T01:59:24Z

Have you tested if wheel building - especially with cibuildwheel - works with these changes?

Yes. However, I made more changes and now the commit history here on this PR is a mess, so I've redone this PR. The new one is #985.

I will close this one now.

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Fix use of deprecated setuptools functions #839

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mhucka changed the title ~~Fix(deps): Modernize packaging to fix setuptools deprecations~~ Move most setup.py configuration and metadata into pyproject.toml Nov 18, 2025

mhucka changed the title ~~Move most setup.py configuration and metadata into pyproject.toml~~ Fix #839 and move most setup.py metadata and config into pyproject.toml Nov 19, 2025

mhucka requested review from pavoljuhas and sboixo November 19, 2025 17:03

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Merge branch 'main' into mh-more-pyproject

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mhucka mentioned this pull request Dec 31, 2025

Investigate the use of uv for dependency management #977

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mhucka requested review from sergeisakov and removed request for sboixo December 31, 2025 22:02

github-actions bot added size: L 250< lines changed <1000 and removed size: M 50< lines changed <250 labels Jan 1, 2026

mhucka changed the title ~~Fix #839 and move most setup.py metadata and config into pyproject.toml~~ Fix #839, move setup.py metadata & config settings into pyproject.toml, & remove requirements.txt Jan 1, 2026

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mhucka marked this pull request as draft January 1, 2026 02:28

mhucka and others added 8 commits January 1, 2026 04:55

Read version number from qsimcirq/_version.py

ec48e0c

Remove OSV scanner workflow (quantumlib#966)

77eee39

It turns out that Dependabot uses the same database, so there is little point in running the OSV scanner too.

Add more runner names to /.github/actionlint.yaml (quantumlib#970)

3a61840

This adds the names of custom GitHub runners we've defined for Quantumlib.

Add new, larger Windows runners to .github/actionlint.yaml (quantum…

6844a8b

…lib#975) Windows CI jobs are a bottleneck right now, so I defined larger GitHub-hosted runners. This adds the new names to the actionlint config file so that they are recognized by actionlint.

Remove requirements files from MANIFEST.in

6fd22b7

mhucka added 11 commits January 1, 2026 04:55

Replace pip install -r requirements with pip install --group dev

942584a

Update the commands and instructions to use the new approach.

Add cibuildwheel to dev requirements

87826c7

I run cibuildwheel as a way of testing that everything works, and I forsee writing some instructions around that. It may be time to add it to the development dependencies.

Remove unnecessary cache-dependency-path setting for setup-python

7b66cf0

Turns out `setup-python` looks for `pyprojec.toml` automatically.

Remove no-longer-needed dev-requirements.txt

6b1791d

Its contents are in pyproject.toml now.

Make dependencies be read from requirements.txt

bc414de

Take advantage of setuptools_scm's ability to make dependencies be obtained dynamically.

Speed up pytest in cibuildwheel by using parallelism

7dadaf6

Add the `-n auto` flag to pytest in the cibuldwheel configuration

Update installation commands in Dockerfile

c1cf90b

Need to set the working directory before trying to install stuff.

Put back requirements.txt into MANIFEST.in

97be565

Put back installation of requirements.txt

8f2792b

The initial plan to use only group dev didn't work out.

Fix typo and an ambiguity

c796145

mhucka force-pushed the mh-more-pyproject branch from 120874d to c796145 Compare January 1, 2026 06:44

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Fix #839, move `setup.py` metadata & config settings into `pyproject.toml`, & remove `requirements.txt` #959

Fix #839, move `setup.py` metadata & config settings into `pyproject.toml`, & remove `requirements.txt` #959

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Fix #839, move setup.py metadata & config settings into pyproject.toml, & remove requirements.txt #959

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Fix #839, move `setup.py` metadata & config settings into `pyproject.toml`, & remove `requirements.txt` #959

Fix #839, move `setup.py` metadata & config settings into `pyproject.toml`, & remove `requirements.txt` #959

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