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Per recent discussion, as well as various legacy conversations here, here, and here, we want to update the pathogen-repo-ci GitHub Action to a "strict" version that can be used across all of our "modern" pathogen repos with zero configuration on the consuming repo side.
Description
Update the pathogen-repo-ci workflow so that:
For each build-name (i.e., each of ingest, phylogenetic, and nextclade):
a. If the repo contains a <build-name>/Snakefile file and a <build-name>/build-configs/ci/config.yaml file
b. Run nextstrain build <build-name> --configfile build-configs/ci/config.yaml
The consuming repo will be responsible for providing an appropriate config file that either sets up appropriate example data or results in a subset of a full workflow being run, so as to validate that the repo workflows have not been broken by a change.
Examples
This workflow, plus the appropriate build-config files, should be sufficient to enable CI for a pathogen repo:
name: CI
on:
- push
jobs:
ci:
name: CI
uses: nextstrain/.github/workflows/pathogen-repo-ci.yaml
The text was updated successfully, but these errors were encountered:
This was opened in the wrong repo, and is being closed in favor of nextstrain/.github#89, which has the supreme advantage of being in the correct repo.
Context
Per recent discussion, as well as various legacy conversations here, here, and here, we want to update the
pathogen-repo-ci
GitHub Action to a "strict" version that can be used across all of our "modern" pathogen repos with zero configuration on the consuming repo side.Description
Update the
pathogen-repo-ci
workflow so that:ingest
,phylogenetic
, andnextclade
):a. If the repo contains a
<build-name>/Snakefile
file and a<build-name>/build-configs/ci/config.yaml
fileb. Run
nextstrain build <build-name> --configfile build-configs/ci/config.yaml
The consuming repo will be responsible for providing an appropriate config file that either sets up appropriate example data or results in a subset of a full workflow being run, so as to validate that the repo workflows have not been broken by a change.
Examples
This workflow, plus the appropriate build-config files, should be sufficient to enable CI for a pathogen repo:
The text was updated successfully, but these errors were encountered: