From 090a35eed9c09636f0eed601a9c0fd3848d439f2 Mon Sep 17 00:00:00 2001
From: John SJ Anderson <janders4@fredhutch.org>
Date: Fri, 31 May 2024 11:33:29 -0700
Subject: [PATCH] Refactor `pathogen-repo-ci` to be smarter [#89]

---
 .github/workflows/pathogen-repo-ci.yaml  | 74 +++++++++++++++++++++---
 actions/run-nextstrain-build/action.yaml | 38 ++++++++++++
 2 files changed, 104 insertions(+), 8 deletions(-)
 create mode 100644 actions/run-nextstrain-build/action.yaml

diff --git a/.github/workflows/pathogen-repo-ci.yaml b/.github/workflows/pathogen-repo-ci.yaml
index a8ce20e..45a7471 100644
--- a/.github/workflows/pathogen-repo-ci.yaml
+++ b/.github/workflows/pathogen-repo-ci.yaml
@@ -232,16 +232,74 @@ jobs:
         with:
           runtime: ${{ matrix.runtime }}
 
+      - name: Run ingest
+        uses: nextstrain/.github/actions/run-nextstrain-build@update-ci-89
+        with:
+          step: ingest
+
+      #   run: |
+      #     if [[ -f nextstrain-pathogen.yaml && -f ingest/Snakefile && -f ingest/build-configs/ci/config.yaml ]]; then
+      #       nextstrain build ingest --configfile build-configs/ci/config.yaml ${{ inputs.build-args }}
+      #     else
+      #       echo "Skipping ingest build due to one or more missing files."
+      #       for i in nextstrain-pathogen.yaml ingest/Snakefile ingest/build-configs/ci/config.yaml; do
+      #         ! test -f $i && echo missing $i
+      #       done
+      #     fi
+
+      # - name: Upload ingest artifact
+      #   if: always()
+      #   uses: actions/upload-artifact@v4
+      #   with:
+      #     name: ingest-${{ inputs.artifact-name }}-${{ matrix.runtime }}
+      #     path: |
+      #       ingest/results/
+      #       ingest/benchmarks/
+      #       ingest/logs/
+      #       ingest/.snakemake/log/
+
+      - name: Run phylogenetic
+        run: |
+          if [[ -f nextstrain-pathogen.yaml && -f phylogenetic/Snakefile && -f phylogenetic/build-configs/ci/config.yaml ]]; then
+            nextstrain build phylogenetic --configfile build-configs/ci/config.yaml ${{ inputs.build-args }}
+          else
+            echo "Skipping phylogenetic build due to one or more missing files."
+            for i in nextstrain-pathogen.yaml phylogenetic/Snakefile phylogenetic/build-configs/ci/config.yaml; do
+              ! test -f $i && echo missing $i
+            done
+          fi
 
-      - run: nextstrain build . ${{ inputs.build-args }}
+      - name: Upload phylogenetic artifact
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: phylogenetic-${{ inputs.artifact-name }}-${{ matrix.runtime }}
+          path: |
+            phylogenetic/auspice/
+            phylogenetic/results/
+            phylogenetic/benchmarks/
+            phylogenetic/logs/
+            phylogenetic/.snakemake/log/
+
+      - name: Run nextclade
+        run: |
+          if [[ -f nextstrain-pathogen.yaml && -f nextclade/Snakefile && -f nextclade/build-configs/ci/config.yaml ]]; then
+            nextstrain build nextclade --configfile build-configs/ci/config.yaml ${{ inputs.build-args }}
+          else
+            echo "Skipping nextclade build due to one or more missing files."
+            for i in nextstrain-pathogen.yaml nextclade/Snakefile nextclade/build-configs/ci/config.yaml; do
+              ! test -f $i && echo missing $i
+            done
+          fi
 
-      - if: always()
+      - name: Upload nextclade artifact
+        if: always()
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
+          name: nextclade-${{ inputs.artifact-name }}-${{ matrix.runtime }}
           path: |
-            auspice/
-            results/
-            benchmarks/
-            logs/
-            .snakemake/log/
+            nextclade/auspice/
+            nextclade/results/
+            nextclade/benchmarks/
+            nextclade/logs/
+            nextclade/.snakemake/log/
diff --git a/actions/run-nextstrain-build/action.yaml b/actions/run-nextstrain-build/action.yaml
new file mode 100644
index 0000000..14d54a8
--- /dev/null
+++ b/actions/run-nextstrain-build/action.yaml
@@ -0,0 +1,38 @@
+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:
+  steps:
+    - name: Run ${{ inputs.step }}
+      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
+
+    - name: Upload ${{ inputs.step }} 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/