[phylo github actions] add summary message

The `pathogen-repo-build` reusable action adds an extremely helpful summary describing the AWS run. This adds some similarly helpful info which should make it much simpler to check the results of a phylo run.
nextstrain · Jul 16, 2024 · 5f67e06 · 5f67e06
1 parent 736b114
commit 5f67e06
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diff --git a/.github/workflows/phylogenetic-fauna.yaml b/.github/workflows/phylogenetic-fauna.yaml
@@ -25,6 +25,46 @@ on:
         type: string
 
 jobs:
+  summary:
+    runs-on: ubuntu-latest
+    steps:
+      - name: summary_step
+        run: |
+          URL_A="avian-flu/h5n1/ha/2y"
+          URL_B="avian-flu/h9n2/pb2/all-time"
+          if [[ "$TRIAL_NAME" ]]; then
+              echo "### Trial Build URLs" >> $GITHUB_STEP_SUMMARY
+              URL_BASE="https://nextstrain.org/staging/avian-flu/trials"
+              TRIAL_NAME_URL=$( echo "$TRIAL_NAME" | sed "s|_|/|g" )
+              echo "" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_BASE}/${TRIAL_NAME_URL}/${URL_A}" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_BASE}/${TRIAL_NAME_URL}/${URL_B}" >> $GITHUB_STEP_SUMMARY
+              echo "  * etc" >> $GITHUB_STEP_SUMMARY
+          else
+              echo "### Canonical URLs will be updated by this run" >> $GITHUB_STEP_SUMMARY
+              URL_BASE="https://nextstrain.org"
+              echo "" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_BASE}/${URL_A}" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_BASE}/${URL_B}" >> $GITHUB_STEP_SUMMARY
+              echo "  * etc" >> $GITHUB_STEP_SUMMARY
+          fi;
+          echo "" >> $GITHUB_STEP_SUMMARY
+          NOTE="NOTE: These URL paths may be incorrect if you've changed the  "
+          NOTE+="snakemake targets in 'config/gisaid.yaml' as part of this PR. "
+          NOTE+="Please update this GitHub Action if so!"
+          echo "> $NOTE" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "### Build (meta-)environment"  >> $GITHUB_STEP_SUMMARY
+          if [[ "$NEXTSTRAIN_DOCKER_IMAGE" ]]; then
+              echo "  * Docker image: $NEXTSTRAIN_DOCKER_IMAGE" >> $GITHUB_STEP_SUMMARY
+          else
+              echo "  * Docker image: default (latest)" >> $GITHUB_STEP_SUMMARY
+          fi;
+          echo "  * Git Branch: `${BRANCH_NAME}`" >> $GITHUB_STEP_SUMMARY
+    env:
+      NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
+      TRIAL_NAME: ${{ inputs.trial-name }}
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }} 
   phylogenetic:
     permissions:
       id-token: write

diff --git a/.github/workflows/phylogenetic-ncbi.yaml b/.github/workflows/phylogenetic-ncbi.yaml
@@ -32,6 +32,46 @@ on:
         type: string
 
 jobs:
+  summary:
+    runs-on: ubuntu-latest
+    steps:
+      - name: summary_step
+        run: |
+          URL_A="avian-flu/h5n1-cattle-outbreak/genome"
+          URL_B="avian-flu/h5n1-cattle-outbreak/ha"
+          if [[ "$TRIAL_NAME" ]]; then
+              echo "### Trial Build URLs" >> $GITHUB_STEP_SUMMARY
+              URL_BASE="https://nextstrain.org/staging/avian-flu/trials"
+              TRIAL_NAME_URL=$( echo "$TRIAL_NAME" | sed "s|_|/|g" )
+              echo "" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_BASE}/${TRIAL_NAME_URL}/${URL_A}" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_BASE}/${TRIAL_NAME_URL}/${URL_B}" >> $GITHUB_STEP_SUMMARY
+              echo "  * etc" >> $GITHUB_STEP_SUMMARY
+          else
+              echo "### Canonical URLs will be updated by this run" >> $GITHUB_STEP_SUMMARY
+              URL_BASE="https://nextstrain.org"
+              echo "" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_BASE}/${URL_A}" >> $GITHUB_STEP_SUMMARY
+              echo "  * ${URL_BASE}/${URL_B}" >> $GITHUB_STEP_SUMMARY
+              echo "  * etc" >> $GITHUB_STEP_SUMMARY
+          fi;
+          echo "" >> $GITHUB_STEP_SUMMARY
+          NOTE="NOTE: These URL paths may be incorrect if you've changed the  "
+          NOTE+="snakemake targets in 'config/gisaid.yaml' as part of this PR. "
+          NOTE+="Please update this GitHub Action if so!"
+          echo "> $NOTE" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "### Build (meta-)environment"  >> $GITHUB_STEP_SUMMARY
+          if [[ "$NEXTSTRAIN_DOCKER_IMAGE" ]]; then
+              echo "  * Docker image: $NEXTSTRAIN_DOCKER_IMAGE" >> $GITHUB_STEP_SUMMARY
+          else
+              echo "  * Docker image: default (latest)" >> $GITHUB_STEP_SUMMARY
+          fi;
+          echo "  * Git Branch: `${BRANCH_NAME}`" >> $GITHUB_STEP_SUMMARY
+    env:
+      NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
+      TRIAL_NAME: ${{ inputs.trial-name }}
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }} 
   phylogenetic:
     permissions:
       id-token: write