Skip to content

Add make linkcheck step, to check external links [#29] #528

Add make linkcheck step, to check external links [#29]

Add make linkcheck step, to check external links [#29] #528

Workflow file for this run

name: CI
on:
push:
branches:
- master
pull_request:
workflow_dispatch:
jobs:
test-setup-nextstrain-cli:
name: test-setup-nextstrain-cli (os=${{ matrix.os }})
strategy:
fail-fast: false
matrix:
os:
- ubuntu-latest
- macos-latest
- windows-latest
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
- uses: ./actions/setup-nextstrain-cli
- run: nextstrain version --verbose
test-pathogen-repo-ci:
uses: ./.github/workflows/pathogen-repo-ci.yaml
with:
repo: nextstrain/zika
artifact-name: outputs-test-pathogen-repo-ci
secrets: inherit
test-docs-ci-conda:
uses: ./.github/workflows/docs-ci.yaml
with:
repo: nextstrain/docs.nextstrain.org
docs-directory: .
environment-file: conda.yml
test-docs-ci-pip:
uses: ./.github/workflows/docs-ci.yaml
with:
repo: nextstrain/augur
docs-directory: docs/
pip-install-target: .[dev]
test-pathogen-repo-build:
permissions:
id-token: write
strategy:
matrix:
runtime: [docker, conda]
uses: ./.github/workflows/pathogen-repo-build.yaml
with:
repo: nextstrain/zika-tutorial
runtime: ${{ matrix.runtime }}
run: nextstrain build --env BOGUS_ENVVAR .
artifact-name: build-output-${{ matrix.runtime }}
env: |
BOGUS_ENVVAR: BOGUS_ENVVAR
secrets: inherit
# This job has to be separate from the matrix above because we want
# to check the aws-batch-job-id output from the workflow but matrix outputs
# currently will overwrite each other.
# See <https://github.com/orgs/community/discussions/26639>
test-pathogen-repo-build-aws-batch:
permissions:
id-token: write
uses: ./.github/workflows/pathogen-repo-build.yaml
with:
repo: nextstrain/zika-tutorial
runtime: aws-batch
run: nextstrain build --env BOGUS_ENVVAR .
artifact-name: build-output-aws-batch
env: |
BOGUS_ENVVAR: BOGUS_ENVVAR
secrets: inherit
test-pathogen-repo-build-aws-batch-id-output:
needs: [test-pathogen-repo-build-aws-batch]
permissions:
id-token: write
uses: ./.github/workflows/pathogen-repo-build.yaml
with:
repo: nextstrain/zika-tutorial
runtime: aws-batch
run: nextstrain build --attach "$AWS_BATCH_JOB_ID" .
artifact-name: build-output-aws-batch-reattached
env: |
AWS_BATCH_JOB_ID: ${{ needs.test-pathogen-repo-build-aws-batch.outputs.aws-batch-job-id }}
secrets: inherit
lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- run: make check
- run: ./devel/check-readme
- uses: ./actions/shellcheck