Merge pull request #499: Update dependencies

Author: victorlin

CHANGES.md

@@ -41,6 +41,15 @@ development source code and as such may not be routinely kept up to date.
   existing `--resources` given to Snakemake.
   ([#514](https://github.com/nextstrain/cli/pull/514))
 
+## Bug fixes
+
+* Updated code to support the latest version of `wrapt`, used to show
+  `--dry-run` outputs.
+  ([#499](https://github.com/nextstrain/cli/pull/499))
+* Updated the dependency list to explicitly include `boto3`, used for various
+  commands.
+  ([#499](https://github.com/nextstrain/cli/pull/499))
+
 # 10.4.2 (7 January 2026)
 
 ## Improvements

doc/changes.md

@@ -47,6 +47,16 @@ development source code and as such may not be routinely kept up to date.
   existing `--resources` given to Snakemake.
   ([#514](https://github.com/nextstrain/cli/pull/514))
 
+(v-next-bug-fixes)=
+### Bug fixes
+
+* Updated code to support the latest version of `wrapt`, used to show
+  `--dry-run` outputs.
+  ([#499](https://github.com/nextstrain/cli/pull/499))
+* Updated the dependency list to explicitly include `boto3`, used for various
+  commands.
+  ([#499](https://github.com/nextstrain/cli/pull/499))
+
 (v10-4-2)=
 ## 10.4.2 (7 January 2026)
 

nextstrain/cli/console.py

@@ -6,7 +6,7 @@
 from contextlib import contextmanager, ExitStack, redirect_stdout, redirect_stderr
 from functools import wraps
 from typing import Callable, TextIO
-from wrapt import ObjectProxy
+from wrapt import BaseObjectProxy # pyright: ignore[reportAttributeAccessIssue]
 
 
 def auto_dry_run_indicator(getter: Callable[..., bool] = lambda opts, *args, **kwargs: opts.dry_run):
@@ -83,7 +83,7 @@ def dry_run_indicator(dry_run: bool = False):
         yield dry_run
 
 
-class LinePrefixer(ObjectProxy): # pyright: ignore[reportUntypedBaseClass]
+class LinePrefixer(BaseObjectProxy): # pyright: ignore[reportUntypedBaseClass]
     """
     Add *prefix* to every line written to *file*.
 

setup.py

@@ -102,7 +102,7 @@ def find_namespaced_packages(namespace):
         "requests",
         "typing_extensions >=3.7.4",
         "wcmatch >=6.0",
-        "wrapt",
+        "wrapt >=2.0.0",
 
         # We use fsspec's S3 support, which has a runtime dep on s3fs.  s3fs
         # itself requires aiobotocore, which in turn requires very specific
@@ -112,33 +112,18 @@ def find_namespaced_packages(namespace):
         # versions closely matching the boto3 version (they're released in near
         # lock step).
         #
-        # If we declare a dep on boto3 directly, this leads to conflicts during
-        # dependency resolution when a newer boto3 (from our declaration here)
-        # requires a newer botocore than is supported by s3fs → aiobotocore's
-        # declarations.
-        #
-        # Resolve the issue by using a specially-provided package extra from
-        # s3fs (first introduced with 2021.4.0, removed in 2025.12.0) which
-        # causes them to declare an explicit dependency on aiobotocore's
-        # specially-provided package extra on boto3 so that dependency resolver
-        # can figure it out properly.
-        #
-        # Note that the upper limit is not future-proof and will likely cause
-        # issues down the road. There may be a better combination to use here,
-        # but that needs extra digging.
+        # boto3 must be unconstrained.  Adding any constraint causes pip to lock
+        # the boto3/botocore version early in resolution, often resulting in a
+        # version newer than what aiobotocore supports.
         #
         # More background:
-        # <https://github.com/dask/s3fs/issues/357>
-        # <https://github.com/nextstrain/cli/issues/133>
-        # <https://github.com/fsspec/s3fs/issues/994>
-        #
-        # What a mess.
-        #
+        # <https://github.com/nextstrain/cli/issues/496>
+        "boto3",
+
         # Avoiding 2023.9.1 due to change in `auto_mkdir` parameter in
         # https://github.com/fsspec/filesystem_spec/pull/1358 that causes the
         # error described in https://github.com/fsspec/s3fs/issues/790
-        "fsspec !=2023.9.1",
-        "s3fs[boto3] >=2021.04.0, !=2023.9.1, <2025.12.0",
+        "fsspec[s3] !=2023.9.1",
 
         # From 2.0.0 onwards, urllib3 is better typed, but not usable (given
         # our dep tree) on 3.8 and 3.9 so we use types-urllib3 there (see