From 920cb9f8174c5421dffdea6cdd0f0783c1a950ca Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Fri, 12 Jul 2024 00:29:35 +0200
Subject: [PATCH] chore(deps): allow xopen major version 2 (#1532)

See xopen changelog: https://github.com/pycompression/xopen/blob/main/README.rst#v200-2024-03-26

Maintain compatibility with v1 and v2, deprecate v1 with period of 4 months and requiring major version bump

---------

Co-authored-by: Victor Lin <13424970+victorlin@users.noreply.github.com>
---
 CHANGES.md       |  5 +++++
 DEPRECATED.md    |  4 ++++
 augur/io/file.py | 14 +++++++++++++-
 setup.py         |  2 +-
 4 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index b78fdeecd..e0ecf7ea6 100644
--- a/CHANGES.md
+++ b/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)
 
diff --git a/DEPRECATED.md b/DEPRECATED.md
index 772b428c0..090326fe8 100644
--- a/DEPRECATED.md
+++ b/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@@ -4,6 +4,10 @@ These features are deprecated, which means they are no longer maintained and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.*
diff --git a/augur/io/file.py b/augur/io/file.py
index 5b8a7bc13..1aa5f59af 100644
--- a/augur/io/file.py
+++ b/augur/io/file.py
@@ -2,9 +2,21 @@
 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"
 
diff --git a/setup.py b/setup.py
index efc46cd06..14ca3ee5e 100644
--- a/setup.py
+++ b/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': [