Merge pull request #1367 from nextstrain/james/treetime-exit-code

Exit code 2 if TreeTimeError encountered
nextstrain · Dec 20, 2023 · 52a0366 · 52a0366
2 parents 7474a2d + e98f088
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diff --git a/CHANGES.md b/CHANGES.md
@@ -27,12 +27,14 @@
     * `--tree` and `--ancestral-sequences` are now required arguments.
     * separate VCF-only arguments into their own group
 * translate: Fixes a bug in the parsing behaviour of GFF files whereby the presence of the `--genes` command line argument would change how we read individual GFF lines. Issue [#1349][], PR [#1351][] (@jameshadfield)
+* If `TreeTimeError` is encountered Augur now exits with code 2 rather than 0. (This restores the original behaviour.) [#1367][] (@jameshadfield)
 
 
 [#1344]: https://github.com/nextstrain/augur/pull/1344
 [#1348]: https://github.com/nextstrain/augur/pull/1348
 [#1351]: https://github.com/nextstrain/augur/pull/1351
 [#1349]: https://github.com/nextstrain/augur/issues/1349
+[#1367]: https://github.com/nextstrain/augur/pull/1367
 
 ## 23.1.1 (7 November 2023)
 

diff --git a/augur/__init__.py b/augur/__init__.py
@@ -87,6 +87,7 @@ def run(argv):
             Please check your input data and try again. If you continue to have problems, please open a new issue including
             the original command and the error above:  <https://github.com/nextstrain/augur/issues/new/choose>
             """))
+        sys.exit(2)
     except Exception:
         traceback.print_exc(file=sys.stderr)
         print_err("\n")