Refactor pathogen-repo-ci to be smarter [#89]

.github/workflows/pathogen-repo-ci.yaml

@@ -3,6 +3,15 @@
 # workflow) in this repo for an example of what the caller workflow looks like.
 name: CI
 
+defaults:
+  run:
+    # This is the same as GitHub Action's `bash` keyword as of 20 June 2023:
+    # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell
+    #
+    # Completely spelling it out here so that GitHub can't change it out from under us
+    # and we don't have to refer to the docs to know the expected behavior.
+    shell: bash --noprofile --norc -eo pipefail {0}
+
 on:
   workflow_call:
     inputs:
@@ -232,16 +241,17 @@ jobs:
         with:
           runtime: ${{ matrix.runtime }}
 
+      - name: Run ingest
+        uses: nextstrain/.github/actions/run-nextstrain-build@update-ci-89
+        with:
+          step: ingest
 
-      - run: nextstrain build . ${{ inputs.build-args }}
+      - name: Run phylogenetic
+        uses: nextstrain/.github/actions/run-nextstrain-build@update-ci-89
+        with:
+          step: phylogenetic
 
-      - if: always()
-        uses: actions/upload-artifact@v4
+      - name: Run nextclade
+        uses: nextstrain/.github/actions/run-nextstrain-build@update-ci-89
         with:
-          name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
-          path: |
-            auspice/
-            results/
-            benchmarks/
-            logs/
-            .snakemake/log/
+          step: nextclade

README.md

@@ -29,6 +29,7 @@ See also GitHub's [documentation on issue and PR templates](https://docs.github.
 
 Invoked by our GitHub Actions workflows, including the reusable workflows below.
 
+- [Run Nextstrain Build Step](actions/run-nextstrain-build-step/action.yaml)
 - [Setup Nextstrain CLI](actions/setup-nextstrain-cli/action.yaml)
 - [shellcheck](actions/shellcheck/action.yaml)
 - [Setup SSH](actions/setup-ssh/action.yaml) access to runner machine

actions/run-nextstrain-build-step/action.yaml

@@ -0,0 +1,39 @@
+name: run-nextstrain-build
+description: >-
+  Runs a single `nextstrain build` command in a given sub-directory of
+  a pathogen repo. Must be provided with the name of the
+  sub-directory.
+
+inputs:
+  step:
+    description: The name of the sub-directory to run the build from
+    type: string
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - id: run-build
+      env:
+        STEP: ${{ inputs.step }}
+      run: |
+        if [[ -f nextstrain-pathogen.yaml && -f $STEP/Snakefile && -f $STEP/build-configs/ci/config.yaml ]]; then
+          nextstrain build $STEP --configfile build-configs/ci/config.yaml
+        else
+          echo "Skipping $STEP build due to one or more missing files."
+          for i in nextstrain-pathogen.yaml $STEP/Snakefile $STEP/build-configs/ci/config.yaml; do
+            ! test -f $i && echo missing $i
+          done
+        fi
+      shell: bash
+
+    - id: upload-artifact
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{inputs.step }}-outputs-${{ matrix.runtime }}
+        path: |
+          ${{ inputs.step }}/results/
+          ${{ inputs.step }}/benchmarks/
+          ${{ inputs.step }}/logs/
+          ${{ inputs.step }}/.snakemake/log/