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Add DEFAULT_AUGUR_RECURSION_LIMIT=10000
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We've had to use the `AUGUR_RECURSION_LIMIT` environment variable to
bump the recursion limit for SARS-CoV-2 builds¹, mpox builds², and
our `nextstrain-jobs` definition in AWS Batch. From a general search of
the envvar across GitHub³, 10,000 looks like the default that others use
as well (although this may be influenced by our discussions⁴).

¹ nextstrain/ncov#690
² nextstrain/mpox#150
³ https://cs.github.com/?scopeName=All+repos&scope=&q=AUGUR_RECURSION_LIMIT%3D#328
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joverlee521 committed Apr 14, 2023
1 parent f643bb8 commit 238b086
Showing 1 changed file with 2 additions and 3 deletions.
5 changes: 2 additions & 3 deletions augur/__init__.py
Expand Up @@ -15,9 +15,8 @@
from .io.print import print_err
from .argparse_ import add_command_subparsers, add_default_command

recursion_limit = os.environ.get("AUGUR_RECURSION_LIMIT")
if recursion_limit:
sys.setrecursionlimit(int(recursion_limit))
DEFAULT_AUGUR_RECURSION_LIMIT = 10000
sys.setrecursionlimit(int(os.environ.get("AUGUR_RECURSION_LIMIT", DEFAULT_AUGUR_RECURSION_LIMIT)))

command_strings = [
"parse",
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