docs: fix missing pixi -e flags in CONTRIBUTING.md - #1541
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Every quickstart command (`pixi run test`, `test-cov`, `pre-commit ...`) omitted `-e <environment>`, so it resolved to the `default` pixi environment, which only installs bare `datajoint` — no pytest or pre-commit. Following the doc verbatim on a clean clone fails with `pytest: command not found` / `pre-commit: command not found`. Add `-e test` to the test/test-cov invocations and `-e dev` to the pre-commit invocations, matching the already-correct `-e test` usage further down in the same doc and how CI itself invokes pixi (.github/workflows/test.yaml).
dimitri-yatsenko
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Aug 14, 2026
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Verified against pyproject.toml: test/test-cov are global [tool.pixi.tasks], so a bare pixi run test runs in the default environment, whose base deps are just editable datajoint — pytest/pre-commit are in the test/dev features only. So bare pixi run test does fail with pytest: command not found, and the fix matches CI (pixi run -e <env> …). Correctly adds -e test to the test tasks and -e dev to pre-commit (pre-commit is in the dev feature), and only touches the bare commands. Clean doc fix — thanks @gtouloumes!
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Why
Every top-level
pixi runcommand in the Quick Start and "Before Submittinga PR" sections (
pixi run test,pixi run test-cov,pixi run pre-commit ...) omits-e <environment>. Without it, pixi resolves the task againstthe
defaultenvironment, which only installs the baredatajointpackage(
[tool.pixi.pypi-dependencies]) — pytest and pre-commit only exist in thetest/devfeature environments. Following the Quick Start verbatim on aclean clone fails on the very first command:
This also left the doc inconsistent with itself (the finer-grained examples
a few lines down already use
-e test, e.g.pixi run -e test pytest tests/unit/) and with CI, which always callspixi run -e <env> ...(.github/workflows/test.yaml:55,70), never a bare
pixi run <task>.What
pixi run test/test-cov→pixi run -e test test/test-cov(Quick Start, Running Tests, External Containers, Before Submitting a PR)
pixi run pre-commit ...→pixi run -e dev pre-commit ...(Quick Start, Pre-commit Hooks, Before Submitting a PR)
Test plan
pixi run -e test pytest --versionresolves (barepixi run testpreviously failed with
pytest: command not found)pixi run -e dev pre-commit --versionresolvespixi run -e test testruns the full suite successfully (994 passed, 14 skipped)