Defaults for all repos.
See also GitHub's documentation on community health files.
Defaults for all repos.
See also GitHub's documentation on issue and PR templates.
Invoked by our GitHub Actions workflows, including the reusable workflows below.
- Setup Nextstrain CLI
- shellcheck
- Setup SSH access to runner machine (README)
- Setup debugger for interactive debugging of workflow jobs (README)
- Workflow context
See also GitHub's documentation on creating custom actions.
Invoked by other repos.
-
CI for pathogen repos (workflow source, workflow compiled)
-
CI for docs (workflow)
-
Sync RTD redirects (workflow)
-
Pathogen repo build (workflow source, workflow compiled)
See also GitHub's documentation on reusing workflows.
aka "starter" workflows
Used to setup other repos.
-
CI for pathogen repos (template, properties)
-
CI for docs (template, properties)
-
Sync RTD redirects (template, properties)
-
shellcheck (template, properties)
-
Debugging runner: Launch a runner for ad-hoc interactive debugging over SSH using
setup-sshabove. Only for use in private repositories! (template, properties) -
Pathogen repo build (template, properties)
See also GitHub's documentation on starter workflows.
- CI tests for the actions and reusable workflows above (workflow)
Executable scripts that are used in our workflows.
Text templates for messages and summaries in our workflows.
-
Linting to ensure the README stays complete (devel/check-readme)
-
Pre-processing of YAML to satisfy the requirements of GitHub Actions (Makefile, devel/regenerate-workflow, devel/explode-yaml)
-
Git pre-commit hook for keeping generated files in sync every commit (devel/pre-commit)
-
Per-file Git attributes (.gitattributes)