[bot] Update shared/vendored

shared/vendored/.github/workflows/update-downstream-repos.yaml

@@ -5,6 +5,12 @@ on:
     branches:
       - main
   workflow_dispatch:
+    inputs:
+      force:
+        description: 'Pass --force to git subrepo pull'
+        type: boolean
+        required: false
+        default: false
 
 concurrency:
   group: ${{ github.workflow }}
@@ -106,7 +112,7 @@ jobs:
             git switch -c "$branch"
           fi
 
-          git subrepo pull "$VENDORED_PATH"
+          git subrepo pull "$VENDORED_PATH" ${{ inputs.force && '--force' || '' }}
 
           # Check for changes to determine if we need to create/update PRs
           changes=$(git rev-list --count "$parent".."$branch")
@@ -124,6 +130,8 @@ jobs:
             Subrepo changes may break workflows and require manual updates to
             fix errors. It is safe to add manual updates directly to this PR
             since they will not be overwritten by future automatic updates.
+
+            ${{ inputs.force && 'Subrepo updates were made with the `--force` flag so it overwrites any local changes in the subrepo.' || '' }}
         run: |
           if [[ "$changes" == "1" ]]; then
             git push origin HEAD

shared/vendored/.gitrepo

@@ -6,7 +6,7 @@
 [subrepo]
 	remote = https://github.com/nextstrain/shared
 	branch = main
-	commit = 0fb80b17054fdd283d35a6c4c00e3cab810a5781
-	parent = 75428af330b0ec08ebcbe764fe53d9bf6e2b1f63
+	commit = 9b91ad2885963b5596ef80f78db12c1f1f7577b7
+	parent = 35f06c363137ee08a2ff2e184cd5cb433aedf6e4
 	method = merge
 	cmdver = 0.4.9

shared/vendored/README.md

@@ -125,6 +125,7 @@ Snakemake workflow functions that are shared across many pathogen workflows that
 
 - [config.smk](snakemake/config.smk) - Shared functions for handling workflow configs.
 - [remote_files.smk](snakemake/remote_files.smk) - Exposes the `path_or_url` function which will use Snakemake's storage plugins to download/upload files to remote providers as needed.
+- [dependencies.py](./snakemake/dependencies.py) - Helper functions for checking dependency versions.
 
 
 ## Software requirements

shared/vendored/snakemake/config.smk

@@ -2,6 +2,9 @@
 Shared functions to be used within a Snakemake workflow for handling
 workflow configs.
 """
+from dependencies import set_min_augur_version
+set_min_augur_version("34.1.0")
+
 import os
 import sys
 import yaml

shared/vendored/snakemake/dependencies.py

@@ -0,0 +1,10 @@
+from packaging import version
+from augur.__version__ import __version__ as augur_version
+import sys
+
+
+def set_min_augur_version(min_augur_version: str):
+    if version.parse(augur_version) < version.parse(min_augur_version):
+      print("This pipeline needs a newer version of augur than you currently have...")
+      print(f"Current augur version: {augur_version}. Minimum required: {min_augur_version}")
+      sys.exit(1)