From bd91f61973305745ab23f22647fc51454c67ff4c Mon Sep 17 00:00:00 2001 From: Victor Lin <13424970+victorlin@users.noreply.github.com> Date: Wed, 26 Jul 2023 11:44:06 -0700 Subject: [PATCH] Add deprecation warning for export v1 --- augur/export_v1.py | 4 ++++ tests/builds/zika.t | 2 ++ 2 files changed, 6 insertions(+) diff --git a/augur/export_v1.py b/augur/export_v1.py index 70de3124b..8a1b7c87b 100644 --- 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: """, + 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 index 745ab7453..7f349333a 100644 --- 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: $ ${AUGUR} validate export-v1 "$TMP/out/v1_zika_meta.json" "$TMP/out/v1_zika_tree.json" > /dev/null