GitHub organization support files

Community health

Defaults for all repos.

• Code of conduct
• Contributing guidelines
• How to get support

See also GitHub's documentation on community health files.

Issue and PR templates

Defaults for all repos.

• Bug report template

• Documentation issue template

• Feature request template

• New issue config

• Pull request template

See also GitHub's documentation on issue and PR templates.

Actions

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.

Reusable workflows

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.

Workflow templates

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-ssh above. Only for use in private repositories! (template, properties)

• Pathogen repo build (template, properties)

See also GitHub's documentation on starter workflows.

Workflows for this repo itself

• CI tests for the actions and reusable workflows above (workflow)

Workflow scripts

Executable scripts that are used in our workflows.

• interpolate-env
• json-to-envvars
• write-envdir
• yaml-to-envvars

Workflow text templates

Text templates for messages and summaries in our workflows.

• attach-aws-batch
• pathogen-repo-ci

Development tools for this repo itself

• 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)

Configuration for this repo itself

• Per-file Git attributes (.gitattributes)

• Dependabot configuration