pathogen-repo-ci: Don't run workflow build steps if they're not going…

… to do anything

Instead of checking for whether to do anything or not _inside_ each
build step individually, move the check to the step's condition.  This
will make the logs a lot clearer and mean the GitHub workflow metadata
stays more in sync with reality.

I've used hashFiles() to check for file existence—it returns the empty
string, a falsey value, when there are no matching files—but we could
swap that out for using the output of a prior setup step that runs some
shell to determine what to run and what to skip.  Doing so might make
more sense if the conditional becomes more complicated or we want to do
more detailed reporting on _why_ steps were skipped or not.

With the changes, the internal-to-this-workflow action,
run-nextstrain-ci-build, is no longer that useful and so I've removed it
in favor of inlining things.  I think this is an improvement for
readability.

Related-to: <#95 (review)>

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

@@ -75,7 +75,7 @@ on:
       artifact-name:
         description: >-
           A base name to use for the uploaded artifacts from the
-          build. This will be concatenated with the directory name
+          build. This will be concatenated with the runtime name
           used to invoke the build to generate the full artifact file
           name.
 
@@ -252,35 +252,56 @@ jobs:
           runtime: ${{ matrix.runtime }}
 
       - name: Run ingest
+        if: hashFiles('ingest/Snakefile', 'ingest/build-configs/ci/config.yaml')
         id: ingest
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
-        with:
-          directory: ingest
-          runtime: ${{ matrix.runtime }}
-          artifact-name: ${{ inputs.artifact-name }}
+        run: nextstrain build ingest --configfile build-configs/ci/config.yaml
 
       - name: Run phylogenetic
+        if: hashFiles('phylogenetic/Snakefile', 'phylogenetic/build-configs/ci/config.yaml')
         id: phylogenetic
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
-        with:
-          directory: phylogenetic
-          runtime: ${{ matrix.runtime }}
-          artifact-name: ${{ inputs.artifact-name }}
+        run: nextstrain build phylogenetic --configfile build-configs/ci/config.yaml
 
       - name: Run nextclade
+        if: hashFiles('nextclade/Snakefile', 'nextclade/build-configs/ci/config.yaml')
         id: nextclade
-        uses: ./.git/nextstrain/.github/actions/run-nextstrain-ci-build
+        run: nextstrain build nextclade --configfile build-configs/ci/config.yaml
+
+      - if: always()
+        uses: actions/upload-artifact@v4
         with:
-          directory: nextclade
-          runtime: ${{ matrix.runtime }}
-          artifact-name: ${{ inputs.artifact-name }}
+          name: ${{ inputs.artifact-name }}-${{ inputs.runtime }}
+          if-no-files-found: ignore
+          # @actions/glob has no support for brace expansion. Hrumph.
+          path: |
+            ingest/.snakemake/log/
+            ingest/auspice/
+            ingest/benchmarks/
+            ingest/logs/
+            ingest/results/
+
+            phylogenetic/.snakemake/log/
+            phylogenetic/auspice/
+            phylogenetic/benchmarks/
+            phylogenetic/logs/
+            phylogenetic/results/
+
+            nextclade/.snakemake/log/
+            nextclade/auspice/
+            nextclade/benchmarks/
+            nextclade/logs/
+            nextclade/results/
 
       - name: Verify a workflow ran
+        env:
+          ingest: ${{ steps.ingest.conclusion }}
+          phylogenetic: ${{ steps.phylogenetic.conclusion }}
+          nextclade: ${{ steps.nextclade.conclusion }}
         run: |
-          # shellcheck disable=SC2242
+          # Show step conclusions.
+          echo "ingest        $ingest"
+          echo "phylogenetic  $phylogenetic"
+          echo "nextclade     $nextclade"
 
-          # if we see at least one success, we're good
-          echo "INGEST ATTEMPTED=${{ steps.ingest.outputs.run-attempted }}"
-          echo "PHYLOGENETIC ATTEMPTED=${{ steps.phylogenetic.outputs.run-attempted }}"
-          echo "NEXTCLADE ATTEMPTED=${{ steps.nextclade.outputs.run-attempted }}"
-          exit ${{ contains(steps.*.outputs.run-attempted, 'true') && '0' || '1' }}
+          # Assert status; if we see at least one attempt, regardless of
+          # success/failure, we're good.
+          [[ $ingest != skipped || $phylogenetic != skipped || $nextclade != skipped ]]

README.md

@@ -29,7 +29,6 @@ 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 CI Build](actions/run-nextstrain-ci-build/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