Fix GitHub Actions workflows: install dependencies and pin Python version

[Copilot]

The pyright, pytest, and ruff workflows were failing due to missing dependencies and Python version compatibility issues.

Changes Made

• Added uv installation: Added uv package manager installation step using astral-sh/setup-uv@v5 in all three workflow files
• Installed hatch-pip-compile plugin: Added hatch-pip-compile to the installation command, as required by the dev environment configuration in pyproject.toml
• Used uv for package installation: Changed from python -m pip install to uv pip install --system for better compatibility with the uv-based hatch environment
• Pinned Python version: Set Python version to 3.13 in pyright and ruff workflows to avoid PyO3/libcst compatibility issues with Python 3.14
• Fixed pytest matrix: Corrected pytest workflow to use ${{ matrix.python-version }} instead of '3.x', ensuring tests run on all specified Python versions
• Updated Python version range: Removed Python 3.9 from the test matrix due to dependency constraints (click 8.3.0 requires Python >=3.10). Tests now run on Python 3.10-3.13.

Workflow Files Updated

• .github/workflows/pyright.yaml
• .github/workflows/pytest.yaml
• .github/workflows/ruff.yaml

Technical Details

The dev environment in pyproject.toml uses type = "pip-compile" with installer = "uv" and pip-compile-resolver = "uv". The --system flag tells uv to install packages into the system Python environment managed by GitHub Actions.

Python 3.13 is used as the maximum version due to current PyO3 Rust crate limitations in the libcst dependency, which only supports up to Python 3.13. Python 3.10 is used as the minimum version to satisfy the requirements of current development dependencies (specifically click 8.3.0 via mutmut).

Original prompt

Fix the failing GitHub Actions workflow pyright

Analyze the workflow logs, identify the root cause of the failure, and implement a fix.

Job ID: 59093395823

Job URL: https://github.com/github/annotated-logger/actions/runs/20576121897/job/59093395823

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[sophiagavrila]

@copilot There are still some failing checks within the work flows. Please make appropriate changes to correct this:

https://github.com/github/annotated-logger/actions/runs/20576462843/job/59094644754?pr=99

https://github.com/github/annotated-logger/actions/runs/20576462863/job/59094644845?pr=99

[Copilot]

@copilot There are still some failing checks within the work flows. Please make appropriate changes to correct this:

https://github.com/github/annotated-logger/actions/runs/20576462843/job/59094644...

I've identified the issue. The workflows were failing because the hatch-pip-compile plugin requires the uv package manager to be installed (as specified in pyproject.toml with installer = "uv"), but it wasn't being installed in the GitHub Actions environment.

I've added the uv installation step using astral-sh/setup-uv@v5 to all three workflow files in commit 5713227. This should resolve the failing checks.

[sophiagavrila]

@copilot The following workflows continue to fail. Please investigate and resolve:

https://github.com/github/annotated-logger/actions/runs/20576751601/job/59095516091?pr=99
https://github.com/github/annotated-logger/actions/runs/20576751614/job/59095516226?pr=99
https://github.com/github/annotated-logger/actions/runs/20576751598/job/59095515997?pr=99

[Copilot]

@copilot The following workflows continue to fail. Please investigate and resolve:

https://github.com/github/annotated-logger/actions/runs/20576751601/job/59095516091?pr=99...

I've updated the workflows to use uv pip install instead of python -m pip install for installing hatch and hatch-pip-compile. This should provide better compatibility with the uv package manager that's being used by hatch-pip-compile (commit 67784ea).

[sophiagavrila]

@copilot Several workflows continue to fail. It seems that the environment lacks a proper Python virtual environment before installing dependencies, as informed by this error:

error: No virtual environment found; run `uv venv` to create an environment, or pass `--system` to install into a non-virtual environment

Failing workflows:
https://github.com/github/annotated-logger/actions/runs/20576994013/job/59096244642?pr=99
https://github.com/github/annotated-logger/actions/runs/20576994020/job/59096244639?pr=99
https://github.com/github/annotated-logger/actions/runs/20576994016/job/59096244605?pr=99

[Copilot]

@copilot Several workflows continue to fail. It seems that the environment lacks a proper Python virtual environment before installing dependencies, as informed by this error:

...

I've added the --system flag to the uv pip install command in all three workflow files. This tells uv to install packages into the system Python environment managed by GitHub Actions, rather than requiring a virtual environment (commit 9ea47f9).

[sophiagavrila]

@copilot Workflow failures continue. They appear to be caused by an incompatibility between the Python version (3.14) being used in the environment and the PyO3 Rust crate, which currently only supports up to Python 3.13.

        error: the configured Python interpreter version (3.14) is newer than
      PyO3's maximum supported version (3.13)
        = help: please check if an updated version of PyO3 is available.
      Current version: 0.23.5
        = help: set PYO3_USE_ABI3_FORWARD_COMPATIBILITY=1 to suppress this
      check and build anyway using the stable ABI
      warning: build failed, waiting for other jobs to finish...
      error: `cargo rustc --lib --message-format=json-render-diagnostics
      --manifest-path native/libcst/Cargo.toml --release -v --features
      pyo3/extension-module --crate-type cdylib --` failed with code 101

      hint: This usually indicates a problem with the package or the build
      environment.

https://github.com/github/annotated-logger/actions/runs/20577153643/job/59097013682?pr=99
https://github.com/github/annotated-logger/actions/runs/20577153650/job/59097013662?pr=99
https://github.com/github/annotated-logger/actions/runs/20577153695/job/59097013694?pr=99

[Copilot]

@copilot Workflow failures continue. They appear to be caused by an incompatibility between the Python version (3.14) being used in the environment and the PyO3 Rust crate, which currently only suppo...

I've pinned the Python version to 3.13 in the pyright and ruff workflows, and fixed the pytest workflow to use the matrix Python version instead of '3.x'. This avoids installing Python 3.14, which is incompatible with the PyO3 Rust crate used by libcst (commit 8a2a9f1).

[sophiagavrila]

@copilot the ruff and Pyright workflows now pass 🎉 , but there are other workflows that continue to fail like

https://github.com/github/annotated-logger/actions/runs/20577388556/job/59097410782?pr=99

with this error that is due to incompatible Python and click package version requirements:

Python>=3.10 and click==8.3.0 depends on Python>=3.10, we can conclude
that click==8.3.0 cannot be used.
And because you require click==8.3.0, we can conclude that your
requirements are unsatisfiable.

[Copilot]

@copilot the ruff and Pyright workflows now pass 🎉 , but there are other workflows that continue to fail like

https://github.com/github/annotated-logger/actions/runs/20577388556/job/59097410782?...

I've removed Python 3.9 from the test matrix. The current dependencies (specifically click 8.3.0 via mutmut) require Python >=3.10, which is incompatible with Python 3.9. The matrix now tests Python 3.10-3.13 (commit 5a07293).

[github-actions]

Coverage report

This PR does not seem to contain any modification to coverable code.

[Copilot]

Pull request overview

This PR fixes failing GitHub Actions workflows by adding proper dependency installation steps and pinning Python versions for compatibility. The changes address missing uv package manager setup and the hatch-pip-compile plugin required by the project's dev environment configuration, and resolves Python version compatibility issues.

Key Changes:

• Added uv installation and switched to uv pip install --system for dependency management across all three workflow files
• Pinned Python to version 3.13 in pyright and ruff workflows to avoid PyO3/libcst compatibility issues
• Fixed pytest workflow to use matrix Python versions (${{ matrix.python-version }}) and removed Python 3.9 from the test matrix due to dependency constraints

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
.github/workflows/pyright.yaml	Added uv setup and pinned Python to 3.13; switched to uv-based dependency installation
.github/workflows/pytest.yaml	Added uv setup, fixed matrix variable usage, and updated Python version range to 3.10-3.13
.github/workflows/ruff.yaml	Added uv setup and pinned Python to 3.13; switched to uv-based dependency installation
requirements/requirements-dev.txt	Removed pytest-memray and its transitive dependencies (memray, jinja2, markupsafe) from compiled requirements

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[Copilot]

The test matrix now only includes Python 3.10-3.13, but pyproject.toml declares requires-python = ">=3.6". This creates an inconsistency where the package claims to support Python 3.6-3.9, but these versions are no longer being tested in CI.

Consider either:

1. Updating requires-python in pyproject.toml to ">=3.10" to match the tested versions, or
2. If Python 3.6-3.9 support is still needed, add a comment explaining why these versions aren't tested (e.g., due to dev dependency constraints like click 8.3.0 requiring Python >=3.10)

Suggested change

	os: [ubuntu-latest, macos-latest, windows-latest]
	os: [ubuntu-latest, macos-latest, windows-latest]
	# Note: pyproject.toml may declare support for Python >=3.6, but CI only runs on 3.10+
	# here due to tooling/dev-dependency constraints. Python 3.6–3.9 are not exercised by
	# this workflow.

[crimsonknave]

I've pulled some of the findings from here into #88 (namely that libcst was the culprit). The uv changes included here are unneeded and uv was never related to the issues in CI.

[sophiagavrila]

Closing this PR to be superseded by #88