Migrate project configuration and CI/CD workflows from Poetry to Pixi#104
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MrTomRod wants to merge 3 commits into
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Migrate project configuration and CI/CD workflows from Poetry to Pixi#104MrTomRod wants to merge 3 commits into
MrTomRod wants to merge 3 commits into
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- Replace `[tool.poetry]` configuration in `pyproject.toml` with PEP 621 standard metadata. - Switch the build backend to `hatchling.build`. - Configure Pixi workspace environments (`default`, `dev`) and features (`test`, `lint`) utilizing `conda-forge` and `bioconda` channels. - Add Pixi tasks mapping to code development commands (restricted to `src` and `tests` directories). - Update `justfile` targets to run commands using `pixi run`. - Delete `poetry.lock` (replaced by `pixi.lock`) and add `.pixi/` to `.gitignore`.
Author
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build seems to have crashed because i didn't push the changes that |
Owner
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Hi @MrTomRod - thanks for this, a nice improvement over poetry. I’ll work on merging it in once I integrate my substantive changes on the dev branch george |
gbouras13
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Jun 30, 2026
Documents `pixi global install dnaapler` as a recommended installation method (alongside conda and pip), following #104. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Owner
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Incorporated a bunch of these changes in #106 |
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Description
This pull request transitions the repository's development environment, dependency management, and CI/CD pipelines from Poetry to Pixi.
Why Pixi is a better, imo:
dnaaplerrelies on binary utilities likeMMseqs2, developers previously had to manage non-Python tools out-of-band. Pixi bridges this gap by integrating both PyPI and Conda channels (conda-forge&bioconda) directly intopyproject.toml.mmseqs2,just, andripgrepdirectly inside the isolated workspace environment. Setup is now a single, reproducible command:pixi install.hatchlingand standard[project]metadata, making it fully portable and compatible with standard python packaging and bioconda feedstocks.Summary of Changes:
pyproject.toml: Replaced proprietary[tool.poetry]blocks with standard[project]metadata, changed the build backend tohatchling, and added Pixi workspace/environment configuration.justfile: Updated command invocations to usepixi run. (We could also delete the justfile because pixi also contains these features.)ci.yaml&release.yaml): Swapped outconda-incubator/setup-minicondafor the officialprefix-dev/setup-pixiGitHub Action, which speeds up CI builds and ensures CI runs the exact same tasks as local development.requirements.txt,poetry.lock, andbuild/environment.yamlfiles.Verification and Testing
pixi run fmt,pixi run lint, and the full unit test suite locally. All 99 tests passed successfully..github/workflows/ci.yamllocally usinggh act -j testsinside Docker. The setup, formatting check, linting, and tests all completed and passed successfully.