From 7628a9f16616ea9673e43ce2e7497b4b871e295e Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Tue, 16 Jul 2024 15:23:42 -0700
Subject: [PATCH 1/2] CI: Switch CI to `pathogen-repo-ci` workflow

See https://github.com/nextstrain/.github/issues/94 for context
---
 .github/workflows/ci.yaml | 30 +++++++-----------------------
 1 file changed, 7 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 7cc7827..520a4ae 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -1,28 +1,12 @@
 name: CI
 
 on:
-  - push
-  - pull_request
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
 
 jobs:
-  pathogen-ci:
-    strategy:
-      matrix:
-        runtime: [docker, conda]
-    permissions:
-      id-token: write
-    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
-    secrets: inherit
-    with:
-      runtime: ${{ matrix.runtime }}
-      run: |
-        nextstrain build \
-          phylogenetic \
-          --configfile build-configs/ci/config.yaml
-      artifact-name: output-${{ matrix.runtime }}
-      artifact-paths: |
-        phylogenetic/auspice/
-        phylogenetic/results/
-        phylogenetic/benchmarks/
-        phylogenetic/logs/
-        phylogenetic/.snakemake/log/
\ No newline at end of file
+  ci:
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-ci.yaml@master

From fdf1b705fd0a83b97d01d58938e9ecdcc6e042be Mon Sep 17 00:00:00 2001
From: Jover Lee <joverlee521@gmail.com>
Date: Tue, 16 Jul 2024 15:23:57 -0700
Subject: [PATCH 2/2] ingest: Add CI build config

The ingest workflow current runs in <2 minutes so I figured it'd be nice
to add as an additional check in the GH Action CI workflow.

Copied change made in zika
<https://github.com/nextstrain/zika/commit/44f27a5670e391b4a5df93ba56d08e2d99fa415c>
---
 ingest/build-configs/ci/config.yaml | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 ingest/build-configs/ci/config.yaml

diff --git a/ingest/build-configs/ci/config.yaml b/ingest/build-configs/ci/config.yaml
new file mode 100644
index 0000000..4b15515
--- /dev/null
+++ b/ingest/build-configs/ci/config.yaml
@@ -0,0 +1,6 @@
+# TODO: If the ingest workflow ever runs too long, we should figure out a way
+# to subset the ingest data. Currently, the CI just runs the default ingest workflow.
+
+# Snakemake requires at least one top level key in a config file, so including
+# a bogus key here that should not be used anywhere in the Snakemake workflow
+bogus_ci_config: "bogus_ci_config"