git subrepo pull (merge) ingest/vendored

subrepo:
  subdir:   "ingest/vendored"
  merged:   "258ab8c"
upstream:
  origin:   "https://github.com/nextstrain/ingest"
  branch:   "main"
  commit:   "258ab8c"
git-subrepo:
  version:  "0.4.6"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "110b9eb"

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

@@ -13,11 +13,3 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - uses: nextstrain/.github/actions/shellcheck@master
-
-  cram:
-    runs-on: ubuntu-latest
-    steps:
-      - 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 = c94d78d1f38b99e893007a76526f3d3824ecded0
-	parent = ad0b045811bdd327a4caadf1f2ce9b94430dc4cb
+	commit = 258ab8ce898a88089bc88caee336f8d683a0e79a
+	parent = c839dc0c4c44805fd29e2437bd6199c9b8d64c5a
 	method = merge
 	cmdver = 0.4.6

ingest/vendored/README.md

@@ -117,15 +117,6 @@ Potential Nextstrain CLI scripts
 - [download-from-s3](download-from-s3) - Download file from AWS S3 bucket with decompression based on file extension in S3 URL.
   Skips download if the local file already exists and has a hash identical to the S3 object's metadata `sha256sum`.
 
-Potential augur curate scripts
-
-- [apply-geolocation-rules](apply-geolocation-rules) - Applies user curated geolocation rules to NDJSON records
-- [merge-user-metadata](merge-user-metadata) - Merges user annotations with NDJSON records
-- [transform-authors](transform-authors) - Abbreviates full author lists to '<first author> et al.'
-- [transform-field-names](transform-field-names) - Rename fields of NDJSON records
-- [transform-genbank-location](transform-genbank-location) - Parses `location` field with the expected pattern `"<country_value>[:<region>][, <locality>]"` based on [GenBank's country field](https://www.ncbi.nlm.nih.gov/genbank/collab/country/)
-- [transform-strain-names](transform-strain-names) - Ordered search for strain names across several fields.
-
 ## Software requirements
 
 Some scripts may require Bash ≥4. If you are running these scripts on macOS, the builtin Bash (`/bin/bash`) does not meet this requirement. You can install [Homebrew's Bash](https://formulae.brew.sh/formula/bash) which is more up to date.
@@ -134,11 +125,6 @@ Some scripts may require Bash ≥4. If you are running these scripts on macOS, t
 
 Most scripts are untested within this repo, relying on "testing in production". That is the only practical testing option for some scripts such as the ones interacting with S3 and Slack.
 
-For more locally testable scripts, Cram-style functional tests live in `tests` and are run as part of CI. To run these locally,
-
-1. Download Cram: `pip install cram`
-2. Run the tests: `cram tests/`
-
 ## Working on this repo
 
 This repo is configured to use [pre-commit](https://pre-commit.com),