chore(deps): allow xopen major version 2

CHANGES.md

@@ -2,6 +2,11 @@
 
 ## __NEXT__
 
+### Features
+
+* Support xopen major version 2. Deprecate v1. Schedule for removal around November 2024. [#1532][] (@corneliusroemer)
+
+[#1532]: https://github.com/nextstrain/augur/pull/1532
 
 ## 25.0.0 (10 July 2024)
 

DEPRECATED.md

@@ -4,6 +4,10 @@ These features are deprecated, which means they are no longer maintained and
 will go away in a future major version of Augur. They are currently still
 available for backwards compatibility, but should not be used in new code.
 
+## `xopen` major version 1
+
+*Deprecated in version __NEXT__ (July 2024). Planned for removal at the earliest with major version 26 not before November 2024*
+
 ## `augur parse` preference of `name` over `strain` as the sequence ID field
 
 *Deprecated in February 2024. Planned to be reordered June 2024 or after.*

augur/io/file.py

@@ -2,9 +2,23 @@
 from contextlib import contextmanager
 from io import IOBase
 from textwrap import dedent
-from xopen import PipedCompressionReader, PipedCompressionWriter, xopen
+
+from xopen import xopen
+
 from augur.errors import AugurError
 
+# Workaround to maintain compatibility with both xopen v1 and v2
+# Around November 2024, we shall drop support for xopen v1
+# by removing the try-except block and using
+# _PipedCompressionProgram directly
+try:
+    from xopen import _PipedCompressionProgram as PipedCompressionReader
+    from xopen import _PipedCompressionProgram as PipedCompressionWriter
+except ImportError:
+    from xopen import (  # type: ignore[attr-defined, no-redef]  
+        PipedCompressionReader,
+        PipedCompressionWriter,
+    )
 
 ENCODING = "utf-8"
 

setup.py

@@ -65,7 +65,7 @@
         "phylo-treetime >=0.11.2, <0.12",
         "pyfastx >=1.0.0, <3.0",
         "scipy ==1.*",
-        "xopen[zstd] >=1.7.0, ==1.*"
+        "xopen[zstd] >=1.7.0, <3" # TODO: Deprecated, remove v1 support around November 2024
     ],
     extras_require = {
         'dev': [