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Exit code 2 if TreeTimeError encountered #1367

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Dec 20, 2023
Merged

Exit code 2 if TreeTimeError encountered #1367

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2 changes: 2 additions & 0 deletions CHANGES.md
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Expand Up @@ -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)

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1 change: 1 addition & 0 deletions augur/__init__.py
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Expand Up @@ -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")
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