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fix(docs): add pip install -e ".[dev,test]" support and update macOS setup guide#1205

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jhhornn:GH1204-add-pip-optional-deps
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fix(docs): add pip install -e ".[dev,test]" support and update macOS setup guide#1205
jhhornn wants to merge 5 commits intomalariagen:masterfrom
jhhornn:GH1204-add-pip-optional-deps

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@jhhornn jhhornn commented Mar 23, 2026

Fixes #1204

What problem does this solve?

Currently, the project's optional dependency groups (dev, test, docs) are only defined under [tool.poetry.group.*.dependencies], which means they are only installable via Poetry. Contributors or users who prefer plain pip cannot install these groups with pip install -e ".[dev,test]" because the standard [project.optional-dependencies] table is missing from pyproject.toml.

Additionally, the macOS setup guide (MACOS_SETUP.md) references the outdated command pip install -e ".[dev]", which omits the test dependency group.

How does it solve it?

pyproject.toml

  • Adds a [project] table with name and dynamic = ["version"].
  • Adds [project.optional-dependencies] with dev, test, and docs groups mirroring the existing Poetry dependency groups. This enables pip install -e ".[dev,test,docs]" for contributors who don't use Poetry.

MACOS_SETUP.md

  • Replaces pip install -e ".[dev]" with pip install -e ".[dev,test]" and adds a dedicated "Install the package and its dependencies" section.
  • Renumbers subsequent sections accordingly.

Testing done

  • Verified pip install -e ".[dev,test]" resolves and installs all expected packages.
  • Existing poetry install --with dev,test,docs continues to work as before.
  • Pre-commit hooks pass (pre-commit run --all-files).

Breaking changes

None. This is a purely additive change — existing Poetry-based workflows are unaffected.

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Fix macOS setup: pip extras not defined, dev dependencies not installed

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