From 26e4cbe81c6e6baac2a4ea8a8561ffb26a415b20 Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Fri, 1 Sep 2023 22:32:40 +0200
Subject: [PATCH 1/5] chore(ci): prevent ci loops

---
 scripts/rebuild_v3 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/rebuild_v3 b/scripts/rebuild_v3
index 14e9d1b6d..1ffa943ab 100755
--- a/scripts/rebuild_v3
+++ b/scripts/rebuild_v3
@@ -285,7 +285,7 @@ def aggregate_release_notes(release_infos):
 def commit_changes(args, tag, release_infos):
   l.info(f"Commiting changes for '{tag}'")
 
-  commit_message = "chore: rebuild"
+  commit_message = "chore: rebuild [skip ci]"
   if args.release:
     dataset_names = format_list(
       unique([get_dataset_name(release_info["dataset"]) for release_info in release_infos]),

From 6c2d1b90836be80d9561a4e581be6895fd437903 Mon Sep 17 00:00:00 2001
From: nextstrain-bot <hello@nextstrain.org>
Date: Fri, 1 Sep 2023 20:34:26 +0000
Subject: [PATCH 2/5] chore: rebuild [skip ci]

---
 data_output/index.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data_output/index.json b/data_output/index.json
index 94fee2061..a0c6369bf 100644
--- a/data_output/index.json
+++ b/data_output/index.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": "3.0.0",
-  "updatedAt": "2023-08-31T11:28:52Z",
+  "updatedAt": "2023-09-01T20:34:20Z",
   "collections": [
     {
       "meta": {

From 8d7da2369b439b7c721b4e2f3f897769cfc49c4a Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Fri, 1 Sep 2023 22:36:44 +0200
Subject: [PATCH 3/5] chore(ci): avoid duplicated ci runs on push and
 pull_request events

---
 .github/workflows/build-and-deploy.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/build-and-deploy.yml b/.github/workflows/build-and-deploy.yml
index c97c027ae..35621986d 100644
--- a/.github/workflows/build-and-deploy.yml
+++ b/.github/workflows/build-and-deploy.yml
@@ -1,5 +1,9 @@
 on:
   push:
+    branches:
+      - master
+      - staging
+      - release
   pull_request:
   repository_dispatch:
     types: build-and-deploy

From a48c57f992ea5d514f51a600cb03a6772b5f9f2a Mon Sep 17 00:00:00 2001
From: nextstrain-bot <hello@nextstrain.org>
Date: Fri, 1 Sep 2023 20:39:23 +0000
Subject: [PATCH 4/5] chore: rebuild [skip ci]

---
 data_output/index.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data_output/index.json b/data_output/index.json
index a0c6369bf..a5e6c5515 100644
--- a/data_output/index.json
+++ b/data_output/index.json
@@ -1,6 +1,6 @@
 {
   "schemaVersion": "3.0.0",
-  "updatedAt": "2023-09-01T20:34:20Z",
+  "updatedAt": "2023-09-01T20:39:16Z",
   "collections": [
     {
       "meta": {

From ae96eb6a9a9d5d901a71079cceb2d747db5ef955 Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Mon, 4 Sep 2023 15:06:14 +0200
Subject: [PATCH 5/5] chore(ci): ensure a branch is checked out even in
 pull_request runs

---
 .github/workflows/build-and-deploy.yml | 37 ++++++++++++++++----------
 1 file changed, 23 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/build-and-deploy.yml b/.github/workflows/build-and-deploy.yml
index 35621986d..237f0f237 100644
--- a/.github/workflows/build-and-deploy.yml
+++ b/.github/workflows/build-and-deploy.yml
@@ -42,22 +42,9 @@ jobs:
       - name: "Checkout code"
         uses: actions/checkout@v3
         with:
-          fetch-depth: 50
+          fetch-depth: 0
           submodules: true
 
-      - name: "Install system dependencies"
-        run: |
-          sudo apt-get install brotli pigz parallel rename --yes -qq >/dev/null
-
-      - name: "Install awscli"
-        run: |
-          pushd /tmp >/dev/null
-            curl -fsSL "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
-            unzip -oqq awscliv2.zip
-            sudo ./aws/install --update
-          popd >/dev/null
-          aws --version
-
       - name: "Authenticate git"
         run: |
           export GITHUB_TOKEN="${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_REPO }}"
@@ -73,6 +60,28 @@ jobs:
 
           gh auth setup-git >/dev/null
 
+      - name: "Extract branch name"
+        run: |
+          echo "current_branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+        id: branch-name
+
+      - name: "Checkout branch"
+        run: |
+          git checkout ${{ steps.branch-name.outputs.current_branch }}
+
+      - name: "Install system dependencies"
+        run: |
+          sudo apt-get install brotli pigz parallel rename --yes -qq >/dev/null
+
+      - name: "Install awscli"
+        run: |
+          pushd /tmp >/dev/null
+            curl -fsSL "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
+            unzip -oqq awscliv2.zip
+            sudo ./aws/install --update
+          popd >/dev/null
+          aws --version
+
       - name: "Rebuild, commit and push datasets"
         if: github.ref != 'refs/heads/release'
         run: |