Merge pull request #19 from nextstrain/remove-ncbi-virus

Remove NCBI Virus

.github/workflows/ci.yaml

@@ -1,21 +1,15 @@
 name: CI
 
 on:
-  - push
-  - pull_request
-  - workflow_dispatch
+  push:
+    branches:
+      - main
+  pull_request:
+  workflow_dispatch:
 
 jobs:
   shellcheck:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: nextstrain/.github/actions/shellcheck@master
-
-  cram:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
-      - run: pip install cram
-      - run: cram tests/

README.md

@@ -72,10 +72,9 @@ 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