v2.0.0 — pixi-based template

The default dep manifest for this template is now pixi.toml + pixi.lock (the lockfile pins every package to an exact per-platform build). CI installs via prefix-dev/setup-pixi@v0.9.6; the Docker image is built from ghcr.io/prefix-dev/pixi:0.68.1 with pixi install --locked. Jupyter Book builds use a dedicated docs pixi feature.

This release also fixes a pre-existing CI guard logic bug (if grep | head -1 > /dev/null always passed under bash without pipefail) that prevented the workflows from running once the template was actually substituted.

For new replications

gh repo create my-replication --template ScienceLiveHub/forrt-replication-template --public --clone
cd my-replication
# inside Claude Code:
/init-template
pixi install
pixi run snakemake --cores 1

For existing forks built from v1

The previous flow (environment.yml + micromamba) is preserved at tag v1.0-environment-yml. Forks that need the old flow can pin to that tag.

To migrate an existing fork to v2.0: copy pixi.toml from this release, run pixi install locally to generate your own pixi.lock, commit both, then update .github/workflows/{ci,jupyter-book}.yml and Dockerfile per the v2.0 diff.

What's new

• pixi.toml + pixi.lock (per-platform: linux-64 + osx-arm64 + win-64)
• prefix-dev/setup-pixi@v0.9.6 in both CI workflows
• ghcr.io/prefix-dev/pixi:0.68.1 Docker base
• mystmd ships from conda-forge via the docs pixi feature (no more setup-node + npm install -g)
• Channels: conda-forge + bioconda (snakemake)
• CI guard logic fix (substituted state now actually runs)
• Major rewrite of docs/cicd-conventions.md; tool-agnostic content elsewhere is preserved