From 5e3528cabf10083d0aa14b243a094b1bf9a915d8 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 22 Dec 2023 14:52:42 -0800
Subject: [PATCH 1/2] Enable pathogen-repo-ci for rsv
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

nextclade3 is now available in nextstrain-base.¹

¹ <https://github.com/nextstrain/conda-base/commit/b6834ea0c46ee2eff0a28696de1c13ab5ecfd7dc>
---
 .github/workflows/ci.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index c0b82a2c8..5900be45a 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -95,9 +95,7 @@ jobs:
               pathogen: ncov,
               build-args: all_regions -j 2 --profile nextstrain_profiles/nextstrain-ci,
             }
-          # Disable rsv CI until Nextclade v3 is available on Conda.
-          # See issue https://github.com/nextstrain/private/issues/97
-          # - { pathogen: rsv }
+          - { pathogen: rsv }
           - {
               pathogen: seasonal-flu,
               build-args: --configfile profiles/ci/builds.yaml -p,

From 31f01d838e5d3f094a02843e176f095f17c4db87 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 22 Dec 2023 15:09:54 -0800
Subject: [PATCH 2/2] setup-micromamba: Invalidate cache daily

The default cache key is dependent on changes in usage of this action,
and does not invalidate based on time. Since we don't change usage of
this action often, this leads to long cache times, which are not
desirable.

Defining a time-based cache expiry can be subjective, but I'll start
with daily - this is the easy to implement, and only results in one
longer running CI workflow per day.
---
 .github/workflows/ci.yaml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 5900be45a..f16612954 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -111,6 +111,10 @@ jobs:
         with:
           path: ./augur
 
+      - name: Set cache key
+        id: cache-key
+        run: echo "DATE=$(date +'%Y-%m-%d')" >> "$GITHUB_ENV"
+
       - uses: mamba-org/setup-micromamba@v1
         with:
           create-args: nextstrain-base
@@ -121,6 +125,7 @@ jobs:
               - bioconda
             channel_priority: strict
           cache-environment: true
+          cache-environment-key: ${{ env.DATE }}
           environment-name: augur
 
       - run: pip install ./augur