ci: Test pathogen repo CI builds with the final packages

[ Commit message based on that of 12000a20 in nextstrain/docker-base.¹
  Code changes also based on that commit, plus subsequent commits.² ]

A useful check for if new packages will break our pathogen builds.

I included all pathogen repos that already use our pathogen-repo-ci
reusable workflow.  It should be minimal effort to maintain this list
over time—I expect it to only grow—but perhaps in the future we will
want to abstract it out into a shared list of known pathogen repos.

I don't like that we have to copy the build-args for a few of the repos
here since it'll be easy for this copy to diverge from the repo's
authoritative build-args, but it's necessary for now.  Over time as we
work towards increased automation of pathogen builds, I think we can get
rid of this build-args copy by further standardizing how each repo
configures itself for automation.  For example, instead of specifying
build-args in a repo's CI workflow, the args for CI could be stored in a
broader workflow metadata file (e.g. nextstrain-workflow.yaml) read by
pathogen-repo-ci, or defined by some other convention.

An alternative to directly running pathogen-repo-ci against each repo
here would be instead triggering the CI workflows themselves within each
repo.  The downside to that is it would divorce the outcomes of those
workflows from this one and render them not visible from PRs in this
repo.  It would also require updates to each repo to support triggering
and passing in of additional parameters (i.e. for the package).  And
finally those CI workflows sometimes run other jobs, like linting and
other integration tests (e.g. with Cram), that aren't always necessary
to run with a new package.

Related-to: <nextstrain/docker-base#148>
Related-to: <nextstrain/docker-base#150>
Related-to: <nextstrain/docker-base#151>

¹ <nextstrain/docker-base@12000a20>
² <nextstrain/docker-base@bc22a0bc>
  <nextstrain/docker-base@0a20a474>
  <nextstrain/docker-base@75254e92>

.github/workflows/ci.yaml

@@ -18,10 +18,13 @@ jobs:
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v3
-      - id: set-version
-        run: echo "version=$(./devel/generate-version)" | tee -a "$GITHUB_OUTPUT"
+      - id: set
+        run: |
+          echo "version=$(./devel/generate-version)" | tee -a "$GITHUB_OUTPUT"
+          echo "label=$(./devel/label-for-ref "$GITHUB_REF")" | tee -a "$GITHUB_OUTPUT"
     outputs:
-      version: ${{ steps.set-version.outputs.version }}
+      version: ${{ steps.set.outputs.version }}
+      label: ${{ steps.set.outputs.label }}
 
   build-and-test:
     needs: generate-version
@@ -78,8 +81,6 @@ jobs:
           ./devel/diff-pkgs nextstrain-base-*.conda build/locked/*/nextstrain-base-*.conda \
             > "$GITHUB_STEP_SUMMARY"
 
-      # XXX TODO: Install Nextstrain CLI (standalone), then run test build.
-
   release:
     needs:
       - generate-version
@@ -98,12 +99,10 @@ jobs:
 
       - run: ./devel/setup
 
-      - name: Set LABEL
-        run: echo LABEL="$(./devel/label-for-ref "$GITHUB_REF")" | tee -a "$GITHUB_ENV"
-
       - run: ./devel/upload
         env:
           ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+          LABEL: ${{ needs.generate-version.outputs.label }}
 
       - name: Generate summary
         run: |
@@ -113,3 +112,34 @@ jobs:
             > "$GITHUB_STEP_SUMMARY"
         env:
           VERSION: ${{ needs.generate-version.outputs.version }}
+          LABEL: ${{ needs.generate-version.outputs.label }}
+
+  # Run pathogen repo CI builds with the final packages
+  test-pathogen-repo-ci:
+    needs:
+      - generate-version
+      - release
+    strategy:
+      # XXX TODO: Test on multiple platforms (os, maybe arch) via the matrix too
+      matrix:
+        include:
+          - { pathogen: avian-flu,       build-args: auspice/flu_avian_h5n1_ha.json }
+          - { pathogen: ebola }
+          - { pathogen: lassa }
+          - { pathogen: monkeypox }
+          - { pathogen: mumps }
+          - { pathogen: ncov,            build-args: all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci }
+          - { pathogen: seasonal-flu,    build-args: --configfile profiles/ci/builds.yaml -p }
+          - { pathogen: zika }
+    name: test-pathogen-repo-ci (${{ matrix.pathogen }})
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
+    with:
+      repo: nextstrain/${{ matrix.pathogen }}
+      build-args: ${{ matrix.build-args }}
+      runtimes: |
+        - conda
+      env: |
+        NEXTSTRAIN_CONDA_CHANNEL: nextstrain/label/${{ needs.generate-version.outputs.label }}
+        NEXTSTRAIN_CONDA_BASE_PACKAGE: nextstrain-base ==${{ needs.generate-version.outputs.version }}
+      artifact-name: ${{ matrix.pathogen }}-outputs
+      continue-on-error: true