Add deprecation warning for export v1

nextstrain · Jul 26, 2023 · bd91f61 · bd91f61
1 parent da6a9f2
commit bd91f61
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diff --git a/augur/export_v1.py b/augur/export_v1.py
@@ -345,6 +345,10 @@ def register_parser(parent_subparsers):
 
 
 def run(args):
+    print("""DEPRECATION WARNING: augur export v1 will be removed in a future release.
+          Read more on how to migrate to export v2: <https://docs.nextstrain.org/projects/augur/en/22.1.0/releases/migrating-v5-v6.html>""",
+          file=sys.stderr)
+
     T = Phylo.read(args.tree, 'newick')
     node_data = read_node_data(args.node_data) # args.node_data is an array of multiple files (or a single file)
     nodes = node_data["nodes"] # this is the per-node metadata produced by various augur modules

diff --git a/tests/builds/zika.t b/tests/builds/zika.t
@@ -164,6 +164,8 @@ Export JSON files as v1 auspice outputs.
   >  --output-tree "$TMP/out/v1_zika_tree.json" \
   >  --output-meta "$TMP/out/v1_zika_meta.json" \
   >  --output-sequence "$TMP/out/v1_zika_seq.json" > /dev/null
+  DEPRECATION WARNING: augur export v1 will be removed in a future release.
+            Read more on how to migrate to export v2: <https://docs.nextstrain.org/projects/augur/en/22.1.0/releases/migrating-v5-v6.html>
 
   $ ${AUGUR} validate export-v1 "$TMP/out/v1_zika_meta.json" "$TMP/out/v1_zika_tree.json" > /dev/null