git subrepo pull (merge) ingest/vendored

subrepo:
  subdir:   "ingest/vendored"
  merged:   "c0b4c6b"
upstream:
  origin:   "https://github.com/nextstrain/ingest"
  branch:   "main"
  commit:   "c0b4c6b"
git-subrepo:
  version:  "0.4.6"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "73a0129"

ingest/vendored/.github/dependabot.yml

@@ -0,0 +1,17 @@
+# Dependabot configuration file
+# <https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file>
+#
+# Each ecosystem is checked on a scheduled interval defined below.  To trigger
+# a check manually, go to
+#
+#   https://github.com/nextstrain/ingest/network/updates
+#
+# and look for a "Check for updates" button.  You may need to click around a
+# bit first.
+---
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

ingest/vendored/.github/workflows/ci.yaml

@@ -11,13 +11,13 @@ jobs:
   shellcheck:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: nextstrain/.github/actions/shellcheck@master
 
   cram:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - run: pip install cram
       - run: cram tests/

ingest/vendored/.gitrepo

@@ -6,7 +6,7 @@
 [subrepo]
 	remote = https://github.com/nextstrain/ingest
 	branch = main
-	commit = 7617c39fae05e5882c5e6c065c5b47d500c998af
-	parent = b0ee1497a4d1f471ec87529fd7913fb96fbdf032
+	commit = c0b4c6bb5e6ccbba86374d2c09b42077768aac23
+	parent = 28e9bc3cca47ecc42f032b7252672b2c7e74b8f4
 	method = merge
 	cmdver = 0.4.6

ingest/vendored/README.md

@@ -2,7 +2,7 @@
 
 Shared internal tooling for pathogen data ingest.  Used by our individual
 pathogen repos which produce Nextstrain builds.  Expected to be vendored by
-each pathogen repo using `git subtree`.
+each pathogen repo using `git subrepo`.
 
 Some tools may only live here temporarily before finding a permanent home in
 `augur curate` or Nextstrain CLI.  Others may happily live out their days here.
@@ -12,6 +12,9 @@ Some tools may only live here temporarily before finding a permanent home in
 Nextstrain maintained pathogen repos will use [`git subrepo`](https://github.com/ingydotnet/git-subrepo) to vendor ingest scripts.
 (See discussion on this decision in https://github.com/nextstrain/ingest/issues/3)
 
+For a list of Nextstrain repos that are currently using this method, use [this
+GitHub code search](https://github.com/search?type=code&q=org%3Anextstrain+subrepo+%22remote+%3D+https%3A%2F%2Fgithub.com%2Fnextstrain%2Fingest%22).
+
 If you don't already have `git subrepo` installed, follow the [git subrepo installation instructions](https://github.com/ingydotnet/git-subrepo#installation).
 Then add the latest ingest scripts to the pathogen repo by running:
 
@@ -54,14 +57,14 @@ commit hash if needed.
 
 Much of this tooling originated in
 [ncov-ingest](https://github.com/nextstrain/ncov-ingest) and was passaged thru
-[monkeypox's ingest/](https://github.com/nextstrain/monkeypox/tree/@/ingest/).
-It subsequently proliferated from [monkeypox][] to other pathogen repos
-([rsv][], [zika][], [dengue][], [hepatitisB][], [forecasts-ncov][]) primarily
-thru copying.  To [counter that
+[mpox's ingest/](https://github.com/nextstrain/mpox/tree/@/ingest/). It
+subsequently proliferated from [mpox][] to other pathogen repos ([rsv][],
+[zika][], [dengue][], [hepatitisB][], [forecasts-ncov][]) primarily thru
+copying.  To [counter that
 proliferation](https://bedfordlab.slack.com/archives/C7SDVPBLZ/p1688577879947079),
 this repo was made.
 
-[monkeypox]: https://github.com/nextstrain/monkeypox
+[mpox]: https://github.com/nextstrain/mpox
 [rsv]: https://github.com/nextstrain/rsv
 [zika]: https://github.com/nextstrain/zika/pull/24
 [dengue]: https://github.com/nextstrain/dengue/pull/10