Enable pure pip/uv installations

[niksirbi]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?

Since tables>=3.10, PyTables has published wheels for Apple Silicon (arm64) Macs — see release notes. Previously, the lack of these wheels required us to install pytables from conda-forge, see #125.

Now that the necessary wheels are available directly on PyPI, we can simplify installation and CI:

• 1-line installation with pip or uv
• no necessary dependency on conda-specific tooling

What does this PR do?

• Adds a dependency on tables>=3.10.1 to pyproject.toml
• Removes tox-conda from the tox config in pyproject.toml
• Updates docs/requirements.txt (no separate tables requirement needed now that it’s a runtime dependency)
• Overhauls the installation guide and adds uv as an option (alongside conda and pip)
• Updates developer environment instructions to mention uv as an alternative to the existing workflow (see Note below)
• Removes references to (micro)mamba (less relevant now that conda uses the libmamba solver by default)

Note

For now I recommend setting up a development environment using:

uv pip install -e ".[dev]"

rather than:

uv sync --extra dev

While uv sync enforces lockfile-based reproducibility, it currently struggles with platform-specific Qt backend dependencies (e.g. PyQt5), which can cause installation failures on some systems:

• Bug Report: uv sync Fails to Install PyQt5 on Windows astral-sh/uv#11865
• uv add pyqt5 error astral-sh/uv#7005
• uv lock/add selects package versions not available for current platform astral-sh/uv#8603
• resolver: requiring PyQt5 produces non-portable locks astral-sh/uv#9907

Using uv pip installs only what’s needed for the local platform, keeping contributors unblocked while retaining the familiar editable-install workflow. We may revisit uv sync once our GUI dependency setup is more consistently cross-platform (e.g. if/when we migrate from PyQt5 to PySide6).

These changes also pave the way toward switching our CI to uv, but that will be pursued separately as it may require updates to our GitHub Actions.

References

Closes #524.

Related to #125

How has this PR been tested?

• Running tox locally on macOS Apple Silicon passes
• CI passes across all OS platforms
• uv run --python 3.13 --isolated --with-editable '.[dev]' pytest passes (after a one-off uv cache prune)

Is this a breaking change?

No, in the sense that conda-forge installation should still work.

Does this PR require an update to the documentation?

The installation and contributing guides have been updated.

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (560c325) to head (98f429e).

Additional details and impacted files

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  Coverage   100.00%   100.00%           
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  Files           34        34           
  Lines         1997      1997           
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  Hits          1997      1997           

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud