git subrepo pull (merge) vendored

subrepo:
  subdir:   "vendored"
  merged:   "7617c39"
upstream:
  origin:   "https://github.com/nextstrain/ingest"
  branch:   "main"
  commit:   "7617c39"
git-subrepo:
  version:  "0.4.6"
  origin:   "https://github.com/ingydotnet/git-subrepo"
  commit:   "110b9eb"

vendored/.github/workflows/ci.yaml

@@ -1,9 +1,11 @@
 name: CI
 
 on:
-  - push
-  - pull_request
-  - workflow_dispatch
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
 
 jobs:
   shellcheck:
@@ -18,4 +20,4 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
       - run: pip install cram
-      - run: cram tests/
+      - run: cram tests/

vendored/.gitrepo

@@ -6,7 +6,7 @@
 [subrepo]
 	remote = https://github.com/nextstrain/ingest
 	branch = main
-	commit = c97df238518171c2b1574bec0349a55855d1e7a7
-	parent = 6ef4dc097df037130845d002e54eb4b7338e3d5b
+	commit = 7617c39fae05e5882c5e6c065c5b47d500c998af
+	parent = 6c0a9cc7a1c3cfc6a055707a0eb661af56befeb6
 	method = merge
 	cmdver = 0.4.6

vendored/README.md

@@ -25,6 +25,31 @@ Any future updates of ingest scripts can be pulled in with:
 git subrepo pull ingest/vendored
 ```
 
+If you run into merge conflicts and would like to pull in a fresh copy of the
+latest ingest scripts, pull with the `--force` flag:
+
+```
+git subrepo pull ingest/vendored --force
+```
+
+> **Warning**
+> Beware of rebasing/dropping the parent commit of a `git subrepo` update
+
+`git subrepo` relies on metadata in the `ingest/vendored/.gitrepo` file,
+which includes the hash for the parent commit in the pathogen repos.
+If this hash no longer exists in the commit history, there will be errors when
+running future `git subrepo pull` commands.
+
+If you run into an error similar to the following:
+```
+$ git subrepo pull ingest/vendored
+git-subrepo: Command failed: 'git branch subrepo/ingest/vendored '.
+fatal: not a valid object name: ''
+```
+Check the parent commit hash in the `ingest/vendored/.gitrepo` file and make
+sure the commit exists in the commit history. Update to the appropriate parent
+commit hash if needed.
+
 ## History
 
 Much of this tooling originated in
@@ -72,10 +97,9 @@ Scripts for supporting ingest workflow automation that don’t really belong in
 NCBI interaction scripts that are useful for fetching public metadata and sequences.
 
 - [fetch-from-ncbi-entrez](fetch-from-ncbi-entrez) - Fetch metadata and nucleotide sequences from [NCBI Entrez](https://www.ncbi.nlm.nih.gov/books/NBK25501/) and output to a GenBank file.
-  Useful for pathogens with metadata and annotations in custom fields that are not part of the standard [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/) or [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/) outputs.
-- [fetch-from-ncbi-virus](fetch-from-ncbi-virus) - Fetch metadata and nucleotide sequences from [NCBI Virus](https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/) and output NDJSON records to stdout.
-- [ncbi-virus-url](ncbi-virus-url) - Generates the URL to download metadata and sequences from NCBI Virus as a single CSV file.
-- [csv-to-ndjson](csv-to-ndjson) - Converts CSV file to NDJSON file with a hard-coded 200MiB field size limit to accommodate sequences in the NCBI Virus download.
+  Useful for pathogens with metadata and annotations in custom fields that are not part of the standard [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/) outputs.
+
+Historically, some pathogen repos used the undocumented NCBI Virus API through [fetch-from-ncbi-virus](https://github.com/nextstrain/ingest/blob/c97df238518171c2b1574bec0349a55855d1e7a7/fetch-from-ncbi-virus) to fetch data. However we've opted to drop the NCBI Virus scripts due to https://github.com/nextstrain/ingest/issues/18.
 
 Potential Nextstrain CLI scripts
 
@@ -97,6 +121,7 @@ Potential augur curate scripts
 - [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