Merge pull request #1290: Configure output streams to support non-Uni…

…code encodings

CHANGES.md

@@ -5,8 +5,10 @@
 ### Bug fixes
 
 * distance: Improve documentation by describing how gaps get treated as indels and how users can ignore specific characters in distance calculations. [#1285][] (@huddlej)
+* Fix help output compatibility with non-Unicode streams. [#1290][] (@victorlin)
 
 [#1285]: https://github.com/nextstrain/augur/pull/1285
+[#1290]: https://github.com/nextstrain/augur/pull/1290
 
 ## 22.3.0 (14 August 2023)
 

augur/__main__.py

@@ -2,11 +2,25 @@
 Stub function and module used as a setuptools entry point.
 """
 
+import sys
 import augur
 from sys import argv, exit
 
 # Entry point for setuptools-installed script and bin/augur dev wrapper.
 def main():
+    sys.stdout.reconfigure(
+        # Support non-Unicode encodings by replacing Unicode characters instead of erroring.
+        errors="backslashreplace",
+
+        # Explicitly enable universal newlines mode so we do the right thing.
+        newline=None,
+    )
+    # Apply the above to stderr as well.
+    sys.stderr.reconfigure(
+        errors="backslashreplace",
+        newline=None,
+    )
+
     return augur.run( argv[1:] )
 
 # Run when called as `python -m augur`, here for good measure.