Add local fork of pathogen-repo-ci to test refactor [#8]

This modifies `pathogen-repo-ci` to allow the injection of a build
target.

.github/workflows/ci.yaml

@@ -11,6 +11,19 @@ jobs:
     #     runtime: [docker, conda]
     # permissions:
     #   id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master
+    name: nextstrain build ingest
+    uses: ./.github/workflows/pathogen-repo-ci.yaml
     with:
-      build-args: ingest --config '[viruses="hku1"]'
+      artifact-name: ingest
+      build-target: ingest
+      build-args: --config viruses="hku1"
+  phylogenetic:
+    name: nextstrain build phylogenetic
+    needs: ingest
+    uses: ./.github/workflows/pathogen-repo-ci.yaml
+    with:
+      artifact-name: phylogenetic
+      build-target: phylogenetic
+      build-args: --config viruses="hku1"
+      download-previous-artifact: true
+      previous-artifact-name: ingest

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

@@ -0,0 +1,276 @@
+# This workflow is intended to be called by workflows in our various pathogen
+# build repos.  See workflow-templates/pathogen-repo-ci.yaml (a "starter"
+# workflow) in this repo for an example of what the caller workflow looks like.
+name: CI-upstream
+
+on:
+  workflow_call:
+    inputs:
+      build-target:
+        description: >-
+          The build directory to provide as the first argument to `nextstrain build`. Defaults to ".".
+        type: string
+        default: "."
+        required: false
+
+      build-args:
+        description: >-
+          Additional command-line arguments to pass to `nextstrain build` after the build directory (e.g. to Snakemake).
+        type: string
+        default: ""
+        required: false
+
+      repo:
+        description: >-
+          Repository name with owner (e.g. nextstrain/zika).  Defaults to the repository of the caller workflow.
+        type: string
+        default: ${{ github.repository }}
+        required: false
+
+      env:
+        description: >-
+          Additional environment variables to set before the build, as a string containing YAML.  This is easily produced,
+          for example, by pretending you're writing normal nested YAML within a literal multi-line block scalar (introduced
+          by "|"): #magic___^_^___line
+            with:
+              env: |
+                FOO: bar
+                I_CANT_BELIEVE: "it's not YAML"
+                would_you_believe: |
+                  it's
+                  not
+                  yaml
+
+          Do not use for secrets!  Instead, pass them via GitHub Action's dedicated secrets mechanism.
+        type: string
+        default: ""
+        required: false
+
+      runtimes:
+        description: >-
+          List of Nextstrain runtimes under which to run the build, as a string containing YAML.  This is easily produced,
+          for example, by pretending you're writing normal nested YAML within a literal multi-line block scalar (introduced
+          by "|"):
+
+            with:
+              runtimes: |
+                - docker
+                - conda
+
+          Defaults to "docker" and "conda".  One job per runtime will be run.
+        type: string
+        default: |
+          - docker
+          - conda
+        required: false
+
+      artifact-name:
+        description: >-
+          Name to use for build results artifact uploaded at the end of the workflow.  This name will be suffixed with other
+          information from the workflow job matrix to distinguish each artifact in a workflow run.
+
+          If you're invoking this workflow multiple times from the same calling workflow, you should set this.  Otherwise,
+          the default of "outputs" is probably fine.
+        type: string
+        default: outputs
+        required: false
+
+      download-previous-artifact:
+        description: >-
+          Boolean indicating whether to try to download a build artifact from a previous stage.
+        type: boolean
+        default: false
+        required: false
+
+      previous-artifact-name:
+        description: >-
+          Name to use for previous artifact file, when downloading previous artifact.
+
+          If you're downloading the previous step's artifact, you should set `artifact-name` to something in that step's config,
+          then use that same name here.
+        type: string
+        default: outputs
+        required: false
+
+      continue-on-error:
+        description: >-
+          Pass thru for <https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idcontinue-on-error>.
+        type: boolean
+        default: false
+        required: false
+
+permissions:
+  contents: read
+  packages: read
+
+jobs:
+  configuration:
+    runs-on: ubuntu-latest
+    steps:
+      - id: inputs
+        env:
+          runtimes: ${{ inputs.runtimes }}
+        shell: bash
+        run: |
+          runtimes="$(yq --output-format=json --indent=0 . <<<"$runtimes")"
+          echo runtimes="$runtimes" | tee -a "$GITHUB_OUTPUT"
+    outputs:
+      runtimes: ${{ steps.inputs.outputs.runtimes }}
+
+  build:
+    needs: configuration
+    strategy:
+      fail-fast: false
+      matrix:
+        runtime: ${{ fromJSON(needs.configuration.outputs.runtimes) }}
+    name: build (${{ matrix.runtime }})
+    runs-on: ubuntu-latest
+    continue-on-error: ${{ inputs.continue-on-error }}
+    steps:
+      # Log in, if possible, to docker.io (Docker Hub), since authenticated
+      # requests get higher rate limits (e.g. for image pulls).  Our org-level
+      # secret DOCKER_TOKEN_PUBLIC_READ_ONLY is available to all our public
+      # repos on GitHub but only available here to this reusable workflow when
+      # called with "secrets: inherit".  On Docker Hub, the token is granted
+      # "public read-only" access.
+      #
+      # The secrets context is not allowed in "if:" conditions, so we must
+      # launder it thru env.
+      - if: env.token-available == 'true'
+        env:
+          token-available: ${{ secrets.DOCKER_TOKEN_PUBLIC_READ_ONLY != '' }}
+        name: Log in to docker.io
+        uses: docker/login-action@v3
+        with:
+          registry: docker.io
+          username: nextstrainbot
+          password: ${{ secrets.DOCKER_TOKEN_PUBLIC_READ_ONLY }}
+        continue-on-error: true
+
+      # Log in, if possible, to ghcr.io which we use for staging images in
+      # nextstrain/docker-base.  The automatic GITHUB_TOKEN is restricted to
+      # read-only access by the "permissions:" block above.
+      - name: Log in to ghcr.io
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+        continue-on-error: true
+
+      # Transforms the inputs.env *string* containing YAML like this:
+      #
+      #   FOO: bar
+      #   I_CANT_BELIEVE: "it's not YAML"
+      #   would_you_believe: |
+      #     it's
+      #     not
+      #     yaml
+      #
+      # first into the equivalent JSON (with yq) and then into text (with jq)
+      # like this:
+      #
+      #   FOO=<<__EOF__
+      #   bar
+      #   __EOF__
+      #   I_CANT_BELIEVE<<__EOF__
+      #   it's not YAML
+      #   __EOF__
+      #   would_you_believe<<__EOF__
+      #   it's
+      #   not
+      #   yaml
+      #   __EOF__
+      #
+      # which is suitable for appending to the $GITHUB_ENV file in order to set
+      # the environment variables for subsequent steps.
+      #
+      # See the GitHub docs for more info on this heredoc-like syntax¹, which I
+      # use here to avoid quoting issues in arbitrary env var values.
+      #
+      # By doing this slightly-convoluted conversion here, callers can use the
+      # familiar env: block syntax almost without change and avoid paying much
+      # in accidental complexity.  We box it up here and let callers focus on
+      # their essential complexity.
+      #   -trs, 23 May 2022
+      #
+      # ¹ https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#multiline-strings
+      #
+      - if: inputs.env
+        name: Set environment variables
+        env:
+          env: ${{ inputs.env }}
+        run: >
+          # shellcheck disable=SC2154
+
+          echo "$env" | yq --output-format json . | jq --raw-output '
+              to_entries
+            | map("\(.key)<<__EOF__\n\(.value)\n__EOF__")
+            | join("\n")
+          ' | tee -a "$GITHUB_ENV"
+
+      - uses: actions/checkout@v4
+        with:
+          repository: ${{ inputs.repo }}
+
+      - name: Download previous step artifact
+        if: inputs.download-previous-artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: ${{ inputs.previous-artifact-name }}-${{ matrix.runtime }}
+          path: ${{ inputs.previous-artifact-name }}
+      # - name: expand archive
+      #   run: |
+      #     unzip -of ${{ github.repository }}/outputs-conda.zip 'results/*' -d ingest
+      #     rm ${{ github.repository }}/outputs-conda.zip
+      # XXX TODO: It would be better for this to call setup-nextstrain-cli
+      # using the same ref that this workflow was called with (e.g. if this
+      # workflow was invoked by the caller workflow with @foo than we invoke
+      # the action with @foo too), but it's not currently possible to figure
+      # out that ref.  See discussion around this (including results of some
+      # investigation I did):
+      #
+      #   - https://github.community/t/reusable-workflows-get-the-ref-inside-the-called-workflow/224109
+      #   - https://github.community/t/ref-head-in-reusable-workflows/203690/92
+      #
+      # Once we can figure out that ref, then we can actions/checkout our
+      # nextstrain/.github repo at that ref as a sidecar path somewhere and
+      # then invoke the setup-nextstrain-cli action using a local file path
+      # instead of a remote owner/repo path.  This separate checkout will be
+      # necessary since the "uses:" key can't be interpolated (${{…}}) with
+      # context vars.
+      #
+      # For now, update the hardcoded ref (e.g. @90af34…) below when you make
+      # future changes to setup-nextstrain-cli.
+      #
+      # [ Update 16 Feb 2024: We solved this for pathogen-repo-build.yaml, but
+      #   because it required a new permission on the GitHub tokens (id-token:
+      #   write) we decided not to update this workflow (yet?) to use the same
+      #   approach. -trs ]
+      #
+      #   -trs, 28 April 2022
+      - uses: nextstrain/.github/actions/setup-nextstrain-cli@c1191de9d5e1a30e91d70b0fd1041d97ed1b2496
+        with:
+          runtime: ${{ matrix.runtime }}
+
+      - name: Copy example data
+        run: |
+          if [[ -d example_data ]]; then
+            mkdir -p data/
+            cp -r -v example_data/* data/
+          else
+            echo No example data to copy.
+          fi
+
+      - run: nextstrain build ${{ inputs.build-target }} ${{ inputs.build-args }}
+
+      - if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ inputs.artifact-name }}-${{ matrix.runtime }}
+          path: |
+            ${{ inputs.build-target }}/auspice/
+            ${{ inputs.build-target }}/results/
+            ${{ inputs.build-target }}/benchmarks/
+            ${{ inputs.build-target }}/logs/
+            ${{ inputs.build-target }}/.snakemake/log/