Adding uv to the Github CI and requirements to `pyproject` by emlynsg · Pull Request #452 · TeamGraphix/graphix

emlynsg · 2026-02-26T17:32:35Z

This PR changes Graphix to use uv instead of pip in the nox routine for CI tests.
To adhere to the requirements of uv, it also includes a uv.lock file locking dependencies for CI reproducibility, and has merged requirements into the pyproject.toml file in line with PEP best practice (https://packaging.python.org/en/latest/specifications/pyproject-toml/). A new Github action has been created to check the uv lockfile matches the pyproject.

The installation process remains the same with this change - either pip install -e . or uv sync (the latter preferred for reproducibility and speed). See changes to the CONTRIBUTING.md and README.md for more details.

This PR also turns off ruff preview mode, to keep linting more stable, alongside changing the dependabot to use uv. Changes to Graphix internal files are due to linting changes introduced by this reversion.

codecov · 2026-02-26T17:36:32Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.98%. Comparing base (aa0d407) to head (4db8fef).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #452   +/-   ##
=======================================
  Coverage   88.98%   88.98%           
=======================================
  Files          44       44           
  Lines        6545     6545           
=======================================
  Hits         5824     5824           
  Misses        721      721

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.github/workflows/typecheck.yml

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README.md

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thierry-martinez

Very nice! Thanks. I have some minor remarks. I also question whether we should version uv.lock, since it appears to be a large generated file likely to cause merge conflicts. I'd prefer to stick with our policy of specifying version constraints in pyproject.toml on a case-by-case basis.

thierry-martinez · 2026-03-10T21:03:23Z

docs/source/conf.py


 project = "graphix"
-copyright = "2022, Team Graphix"
+copyright = "2026, Team Graphix"


We could put a year range: 2022-2026.

thierry-martinez · 2026-03-10T21:10:08Z

docs/source/contributing.rst

+    uv run ruff check --select I --fix .
+    uv run ruff format .


Could we add an equivalent to the code coverage command from before:

uv run pytest --cov=./graphix --cov-report=xml --cov-report=term --doctest-modules

thierry-martinez · 2026-03-11T12:01:47Z

.github/workflows/ruff.yml


      - name: Run Ruff Linter
-        run: ruff check --output-format=github
+        run: uv run --extra dev ruff check --output-format=github


Previously, we installed just ruff (constrained by requirements-dev.txt) instead of all dev dependencies: pip install ruff -c requirements-dev.txt

With uv, the equivalent is:

Suggested change

run: uv run --extra dev ruff check --output-format=github

run: uv run --with ruff ruff check --output-format=github

thierry-martinez · 2026-03-11T12:02:24Z

.github/workflows/ruff.yml


      - name: Run Ruff Formatter Check
-        run: ruff format --check
+        run: uv run --extra dev ruff format --check


Suggested change

run: uv run --extra dev ruff format --check

run: uv run --with ruff ruff format --check

thierry-martinez · 2026-03-11T12:12:01Z

docs/source/contributing.rst

+
+    git clone https://github.com/TeamGraphix/graphix.git
+    cd graphix
+    uv sync --extra dev --extra extra


I would add the step pip install uv, since uv is not part of the standard Python distribution.

thierry-martinez · 2026-03-11T12:13:58Z

CONTRIBUTING.md

+git clone git@github.com:TeamGraphix/graphix.git
 cd graphix
-pip install -e .[dev]
+uv sync --extra dev --extra extra


I would recommend to add pip install uv here as well.

thierry-martinez · 2026-03-11T12:17:03Z

CONTRIBUTING.md

 ```bash
-pip install .[dev]
-pytest --cov=./graphix --cov-report=xml --cov-report=term
+uv run ruff check --select I --fix .


If I understand correctly, the rule I is already selected in pyproject.toml.

Suggested change

uv run ruff check --select I --fix .

uv run ruff check --fix .

I would add a point about test coverage: uv run pytest --cov=./graphix --cov-report=xml --cov-report=term --doctest-modules

thierry-martinez · 2026-03-11T12:23:05Z

CONTRIBUTING.md


 ```bash
-pip install -e . --config-settings editable_mode=strict
+pip install . --config-settings editable_mode=strict


The --config-settings editable_mode=strict flag is only useful with -e (editable installs); it ensures type-checking works correctly with editable packages. I don't know if uv offers an equivalent setting for installing packages as editable while preserving type-checking support.

The command I've changed it to seems to work. We can also put this in the pyproject.toml to enforce strict editable mode always, but not sure if that's what we want?

thierry-martinez · 2026-03-11T12:24:19Z

pyproject.toml

+    "pytest-mpl",
+    "qiskit>=1.0",
+    "qiskit_qasm3_import",
+    "qiskit-aer; python_version < '3.14'",


This Python version constraint can be removed (see #462).

Suggested change

"qiskit-aer; python_version < '3.14'",

"qiskit-aer",

github-actions · 2026-03-11T16:49:20Z

.github/workflows/ruff.yml


      - name: Run Ruff Linter
-        run: ruff check --output-format=github
+        run: uv run --with ruff ruff check --output-format=github  


[:art: text-formatter] _{reported by reviewdog 🐶}

Suggested change

run: uv run --with ruff ruff check --output-format=github

run: uv run --with ruff ruff check --output-format=github

github-actions · 2026-03-11T16:49:20Z

.github/workflows/ruff.yml


      - name: Run Ruff Formatter Check
-        run: ruff format --check
+        run: uv run --with ruff ruff format --check  


[:art: text-formatter] _{reported by reviewdog 🐶}

Suggested change

run: uv run --with ruff ruff format --check

run: uv run --with ruff ruff format --check

github-actions · 2026-03-11T17:04:29Z

docs/source/contributing.rst


 These settings enable the linter, format the code on save and turn on basic
-static type checking through the Pylance extension.
+static type checking through the Pylance extension.


[:art: text-formatter] _{reported by reviewdog 🐶}

Suggested change

static type checking through the Pylance extension.

static type checking through the Pylance extension.

matulni

Thanks for the PR!
Here are some comments

matulni · 2026-04-03T13:56:49Z

CONTRIBUTING.md


 We recommend to [fork the repository](https://docs.github.com/en/get-started/quickstart/fork-a-repo) before working on new features, whether that being an existing issue or your own idea.
-Once created, you'll need to clone the repository, and you can follow below to set up the environment. You may want to set up virtual environment, such as `conda env` or `pipenv` before setting up the environment.
+Once created, you'll need to clone the repository, and you can follow below to set up the environment. We recommend you use a virtual environment like `uv`, but you may prefer to use `conda env` or `pipenv`.


Suggested change

Once created, you'll need to clone the repository, and you can follow below to set up the environment. We recommend you use a virtual environment like `uv`, but you may prefer to use `conda env` or `pipenv`.

Once created, you'll need to clone the repository, and you can follow below to set up the environment. We recommend you use a project manager like `uv`, but you may prefer to manage your own virtual environment with `conda env` or `pipenv`.

matulni · 2026-04-03T13:59:26Z

CONTRIBUTING.md

-### Local checks
-
-To replicate the CI pipeline locally, install `nox` and run the tests:
+You can also run the full CI suite locally:


Suggested change

You can also run the full CI suite locally:

You can also run the full CI test suite locally:

My understanding is that our nox file doesn't do anything about typecheckers or linters.

matulni · 2026-04-03T14:00:46Z

CONTRIBUTING.md

-ruff format .
+uv run ruff check .
+uv run ruff format --check .
+uv run mypy


Suggested change

uv run mypy

uv run mypy

uv run pyright

matulni · 2026-04-03T14:03:35Z

CONTRIBUTING.md

+Once created, you'll need to clone the repository, and you can follow below to set up the environment. We recommend you use a virtual environment like `uv`, but you may prefer to use `conda env` or `pipenv`.

 ```bash
-git clone git@github.com:<username>/graphix.git


I think this was consistent with the recommendation of forking the repo above.

matulni · 2026-04-03T14:15:01Z

pyproject.toml

+dependencies = [
+    "matplotlib",
+    "networkx",
+    "numpy>=2",
+    "opt_einsum",
+    "quimb",
+    "scipy",
+    "sympy",
+    "typing_extensions",
+]


Should we take the opportunity of this PR to pin all dependencies ?
I believe that this will yield safer and more stable code, not sure if dependabot takes care of updating them...

Suggested change

dependencies = [

"matplotlib",

"networkx",

"numpy>=2",

"opt_einsum",

"quimb",

"scipy",

"sympy",

"typing_extensions",

]

dependencies = [

"matplotlib==3.10.8",

"networkx==3.6.1",

"numpy==2.4.4",

"quimb==1.13.0",

"scipy==1.17.1",

"sympy==1.14.0",

"typing_extensions==4.15.0",

]

Also, I believe that opt_einsum is not used in the codebase (tests pass without), but could someone else double check please?

matulni · 2026-04-03T14:35:29Z

.github/workflows/ci.yml

+          enable-cache: true
+          cache-dependency-glob: "pyproject.toml"


It's suggested to pin the uv version as well

Suggested change

enable-cache: true

cache-dependency-glob: "pyproject.toml"

version: "0.11.3" # Install a specific version of uv.

enable-cache: true

cache-dependency-glob: "pyproject.toml"

matulni · 2026-04-03T14:39:58Z

.github/workflows/ci.yml

+      - name: "Set up Python ${{ matrix.python }}"
+        run: uv python install ${{ matrix.python }}


Is there a difference between this and setting

with: python-version: ${{ matrix.python }}

in the previous action as shown in the docs ?

matulni · 2026-04-03T14:49:29Z

noxfile.py

 if TYPE_CHECKING:
    from collections.abc import Callable

+nox.options.default_venv_backend = "uv"


Let's keep the default as a fallback

Suggested change

nox.options.default_venv_backend = "uv"

nox.options.default_venv_backend = "uv|virtualenv"

matulni · 2026-04-03T14:56:24Z

.github/workflows/ci.yml

-
-      - run: nox --python ${{ matrix.python }}
+      - name: Run nox
+        run: uvx nox -db uv --python ${{ matrix.python }}


Two questions:

If I understood correctly this comment, it seems that nox installs the appropriate Python version. Does this mean that we can skip the uv python install ... above ?

Is there a reason why we are doing uvx nox instead of uv run nox ?

matulni · 2026-04-03T14:57:45Z

.github/workflows/cov.yml

+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
        with:
+          enable-cache: true


See comments in ci.yml about versions

uv CI and tidy reqs

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Emlyn Graham added 3 commits February 26, 2026 18:52

fixing

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fixing typechecking

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Emlyn Graham and others added 8 commits February 26, 2026 19:41

removing references to requirements files

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emlynsg linked an issue Feb 27, 2026 that may be closed by this pull request

Replace nox with uv in CI #443

Open

matulni reviewed Mar 10, 2026

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Emlyn Graham added 3 commits March 10, 2026 14:44

extra docs and turned off ruff preview

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update ruff

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merging changes to master

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emlynsg marked this pull request as ready for review March 10, 2026 13:48

emlynsg and others added 3 commits March 10, 2026 14:51

Update CONTRIBUTING.md

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fixing linting and adding lockfile check Github action

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emlynsg requested review from matulni and thierry-martinez March 10, 2026 14:56

emlynsg added 2 commits March 11, 2026 09:29

Merge branch 'master' into uv-nox

460bf5a

Merge branch 'master' into uv-nox

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fixing nox ReverseDeps tests

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Thierry comments

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Emlyn Graham added 3 commits March 12, 2026 09:59

fixing nox

473a94a

fixing nox

533a571

removed lockfile check Github Action

4db8fef

matulni reviewed Apr 3, 2026

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	run: uv run --extra dev ruff check --output-format=github
	run: uv run --with ruff ruff check --output-format=github

	run: uv run --extra dev ruff format --check
	run: uv run --with ruff ruff format --check

	uv run ruff check --select I --fix .
	uv run ruff check --fix .

	static type checking through the Pylance extension.
	static type checking through the Pylance extension.

	Once created, you'll need to clone the repository, and you can follow below to set up the environment. We recommend you use a virtual environment like `uv`, but you may prefer to use `conda env` or `pipenv`.
	Once created, you'll need to clone the repository, and you can follow below to set up the environment. We recommend you use a project manager like `uv`, but you may prefer to manage your own virtual environment with `conda env` or `pipenv`.

	You can also run the full CI suite locally:
	You can also run the full CI test suite locally:

		- name: "Set up Python ${{ matrix.python }}"
		run: uv python install ${{ matrix.python }}

	nox.options.default_venv_backend = "uv"
	nox.options.default_venv_backend = "uv\|virtualenv"

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emlynsg commented Feb 26, 2026 •

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