v2.0: migrate template from environment.yml/micromamba to pixi#1
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Switch the template's dep-manifest from environment.yml/micromamba to
pixi.toml + pixi.lock. Lockfile is committed, pins linux-64 + osx-arm64 +
win-64. Channels: conda-forge + bioconda (snakemake is not on conda-forge).
Mechanics
- pixi.toml: workspace name {{REPO_NAME}}, dependencies mirror env.yml core,
feature.docs (mystmd) and feature.tests (pytest) split out, tasks for run /
book / lab. pixi accepts the {{REPO_NAME}} placeholder; /init-template
substitutes it.
- pixi.lock: 12k-line per-platform lockfile, 3 envs (default + docs + tests).
- environment.yml deleted; v1.0-environment-yml tag (pushed) preserves the
old flow for existing forks.
Build / CI
- Dockerfile: mambaorg/micromamba -> ghcr.io/prefix-dev/pixi:0.68.1, install
from pixi.lock, drop the micromamba entrypoint, CMD via pixi run.
- ci.yml + jupyter-book.yml: setup-micromamba -> prefix-dev/setup-pixi@v0.9
with locked + cache; all run steps become pixi run. jupyter-book.yml uses
the docs feature; setup-node + npm install -g mystmd is removed (mystmd
ships from conda-forge now).
- docker.yml: unchanged except its first-run guard now includes *.toml.
- All three workflow guards now scan *.toml so pixi.toml's {{REPO_NAME}}
placeholder is detected during scaffold runs.
Docs
- docs/cicd-conventions.md: major rewrite — "environment.yml is the single
source of truth" -> "pixi.toml is the single source of truth"; old
snakemake-via-pip workaround section dropped; all examples use pixi run.
Audit step adds a pixi.lock-staleness check.
- docs/fair4rs-checklist.md, ro-crate.md, verify-before-drafting.md,
nanopub-chain-discovery.md, domain-flavours/{_template, biodiversity-eo}.md:
references to environment.yml swapped to pixi.toml + pixi.lock.
- grid4earth-benchmark.md flavour deferred (separate release).
Operating manual
- CLAUDE.md, DOMAIN.md: I (Interoperable) evidence and Phase 2 + document map
point to pixi.toml + pixi.lock.
- .claude/settings.json: Bash(pixi *) added to allowlist.
- .claude/agents/replication-coder.md + .claude/skills/{replication-study,
init-template, import-from-nanopub}/SKILL.md: env.yml -> pixi.toml; starter
files for /import-from-nanopub now include pixi.toml + pixi.lock.
Repo metadata
- README.md, index.md, notebooks/README.md: quick-start uses pixi install +
pixi run snakemake; structure block names pixi.toml + pixi.lock.
- ro-crate-metadata.json: replaces environment.yml ConfigurationFile entry
with pixi.toml + pixi.lock (both ConfigurationFile; both Workflow inputs).
- scripts/import-nanopub-chain.py: STARTER_FILES enumeration now ships
pixi.toml + pixi.lock; user-facing merge instructions rewritten.
- .gitignore: ignore .pixi/ install cache and .snakemake/ run cache;
pixi.lock is NOT ignored.
Acceptance (osx-arm64)
- pixi install --locked: green; lockfile stable.
- pixi run snakemake --cores 1 -n: dry-run produces the scaffold DAG.
- pixi run -e docs myst build --html: builds the Jupyter Book to _build/html.
setup-pixi only publishes patch-level tags. CI failed at action resolution on first push. Pin to the current latest, v0.9.6.
The pre-existing v1 guards used `if ... | head -1 > /dev/null` which always returns 0 under bash without pipefail (the GH Actions default when shell is unspecified) — so the guard fired even when no placeholders remained. Rewrite each guard to capture the grep output into a variable and check it with `[ -n "$..." ]`. Also relax the init-template skill exclusion from `^./...` to a path-fragment match (`claude/skills/init-template/`) — strict `^./` anchor only matches when grep emits `./` prefix, which differs between greps. Also fix the pages_check guard in jupyter-book.yml the same way: `gh api ... | head -1 > /dev/null` always succeeds and flagged Pages as enabled on repos where it isn't, causing the deploy step to 404. Validated end-to-end on a trial substituted-state repo: - ci.yml ran setup-pixi + pixi install + pixi run snakemake green (41s). - jupyter-book.yml build step ran setup-pixi (docs env) + pixi run jupytext + pixi run jupyter execute + pixi run -e docs myst build green (1m01s).
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Summary
environment.yml+mamba-org/setup-micromamba@v3withpixi.toml+pixi.lock+prefix-dev/setup-pixi@v0.9. Lockfile is committed and pins linux-64 + osx-arm64 + win-64. Channels:conda-forge+bioconda(snakemake is not on conda-forge).v1.0-environment-ymlalready pushed for existing forks that need the old flow.ghcr.io/prefix-dev/pixi:0.68.1;jupyter-book.ymldropssetup-node+npm install -g mystmd(mystmd now ships from conda-forge viafeature.docs).docs/cicd-conventions.mdfor the rewritten conventions doc and the new audit step (pixi install --locked && git diff --exit-code pixi.lock).Deviations from the original migration plan
channels = ["conda-forge", "bioconda"], not["conda-forge"]alone — the plan assumed snakemake was on conda-forge; it is bioconda-only. Pixi handles the multi-channel solve cleanly.setup-pixi@v0.9(actual current major; plan said v0.8.x).ci.yml,jupyter-book.yml,docker.yml) now also scan*.tomlsopixi.toml's{{REPO_NAME}}placeholder triggers the scaffold-skip path..snakemake/added to.gitignorealongside.pixi/.Test plan
pixi install --lockedclean on osx-arm64 (all 3 envs: default, docs, tests).pixi run snakemake --cores 1 -nproduces the scaffold DAG.pixi run -e docs myst build --htmlwrites_build/html/.{{REPO_NAME}}inpixi.toml.ci.yml,jupyter-book.yml)./init-template, verify{{REPO_NAME}}substitutes inpixi.toml, CI stays green end-to-end.After merge
v2.0.0release with body: "Default dep manifest is nowpixi.toml+pixi.lock. For the previousenvironment.yml/micromamba flow, pin to tagv1.0-environment-yml."