Merge pull request #542 from nextstrain/migrate-shared-vendored

Migrate vendored/ to the shared/vendored git-subrepo

Author: trvrb

Snakefile

@@ -94,7 +94,7 @@ onstart:
         print(f"\t${{{var}}}: " + ("YES" if os.environ.get(var, "") else "NO") + f"({description})")
     if send_notifications:
         message="🥗 GISAID ingest" if database=="gisaid" else "🥣 GenBank ingest"
-        shell(f"./vendored/notify-on-job-start \"{message}\" nextstrain/ncov-ingest '.'")
+        shell(f"./shared/vendored/scripts/notify-on-job-start \"{message}\" nextstrain/ncov-ingest '.'")
 
 onsuccess:
     message = "✅ This pipeline has successfully finished 🎉"
@@ -106,7 +106,7 @@ onsuccess:
 onerror:
     print("Pipeline failed.")
     if send_notifications:
-        shell("./vendored/notify-on-job-fail Ingest nextstrain/ncov-ingest")
+        shell("./shared/vendored/scripts/notify-on-job-fail Ingest nextstrain/ncov-ingest")
     if not config.get("keep_all_files", False):
         print("Removing intermediate files (set config option keep_all_files to skip this)")
         shell("./bin/clean")

bin/archive-to-s3

@@ -23,7 +23,7 @@ main() {
     # Docker image being stuck on AWS CLI v1, but the chance of collision is
     # slim with the timestamped filenames.
     # <https://github.com/nextstrain/docker-base/issues/216>
-    "$(dirname "$0")/../vendored/upload-to-s3" --quiet "$src" "$dst"
+    "$(dirname "$0")/../shared/vendored/scripts/upload-to-s3" --quiet "$src" "$dst"
 }
 
 make_archive_filename() {

bin/generate-nextclade-version-json

@@ -2,7 +2,7 @@
 
 set -euo pipefail
 
-vendored="$(dirname "$0")"/../vendored
+vendored="$(dirname "$0")"/../shared/vendored/scripts
 
 
 nextclade="${1:?A path to the Nextclade executable is required as the first argument}"

bin/notify-on-additional-info-change

@@ -4,7 +4,7 @@ set -euo pipefail
 : "${SLACK_TOKEN:?The SLACK_TOKEN environment variable is required.}"
 : "${SLACK_CHANNELS:?The SLACK_CHANNELS environment variable is required.}"
 
-vendored="$(dirname "$0")"/../vendored
+vendored="$(dirname "$0")"/../shared/vendored/scripts
 
 src="${1:?A source additional info TSV file is required as the first argument.}"
 dst="${2:?A destination additional info TSV s3:// URL is required as the second argument.}"

bin/notify-on-duplicate-biosample-change

@@ -4,7 +4,7 @@ set -euo pipefail
 : "${SLACK_TOKEN:?The SLACK_TOKEN environment variable is required.}"
 : "${SLACK_CHANNELS:?The SLACK_CHANNELS environment variable is required.}"
 
-vendored="$(dirname "$0")"/../vendored
+vendored="$(dirname "$0")"/../shared/vendored/scripts
 
 src="${1:?A source duplicate BioSample txt file is required as the first argument.}"
 dst="${2:?A destination duplicate BioSample txt s3:// URL is required as the second argument.}"

bin/notify-on-problem-data

@@ -4,7 +4,7 @@ set -euo pipefail
 : "${SLACK_TOKEN:?The SLACK_TOKEN environment variable is required.}"
 : "${SLACK_CHANNELS:?The SLACK_CHANNELS environment variable is required.}"
 
-vendored="$(dirname "$0")"/../vendored
+vendored="$(dirname "$0")"/../shared/vendored/scripts
 
 problem_data="${1:?A problem data TSV file is required as the first argument.}"
 

bin/use-nextclade-cache

@@ -2,7 +2,7 @@
 set -euo pipefail
 
 bin="$(dirname "$0")"
-vendored="$bin"/../vendored
+vendored="$bin"/../shared/vendored/scripts
 
 main() {
     s3_dst="${1:?A destination s3:// URL where the renew file is hosted is required as the first argument.}"

vendored/.github/dependabot.yml shared/vendored/.github/dependabot.ymlvendored/.github/dependabot.yml renamed to shared/vendored/.github/dependabot.yml

@@ -4,7 +4,7 @@
 # Each ecosystem is checked on a scheduled interval defined below.  To trigger
 # a check manually, go to
 #
-#   https://github.com/nextstrain/ingest/network/updates
+#   https://github.com/nextstrain/shared/network/updates
 #
 # and look for a "Check for updates" button.  You may need to click around a
 # bit first.

vendored/.github/pull_request_template.md …endored/.github/pull_request_template.mdvendored/.github/pull_request_template.md renamed to shared/vendored/.github/pull_request_template.md vendored/.github/pull_request_template.md renamed to shared/vendored/.github/pull_request_template.md

@@ -11,5 +11,5 @@ jobs:
   shellcheck:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v7
       - uses: nextstrain/.github/actions/shellcheck@master