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Update dependencies #499

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16d4fb7
Use fsspec[s3] extra, declare dependency on boto3
victorlin Dec 30, 2025
d0aa9f7
Pin wrapt to version 1
victorlin Dec 30, 2025
a4fea46
Bump wrapt to version 2
victorlin Dec 30, 2025
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9 changes: 6 additions & 3 deletions CHANGES.md
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Original file line number Diff line number Diff line change
Expand Up @@ -15,9 +15,12 @@ development source code and as such may not be routinely kept up to date.

## Bug fixes

* Updated the s3fs dependency to avoid versions starting with 2025.12.0. This
maintains a dependency on `boto3` which is used for various commands.
([#495](https://github.com/nextstrain/cli/pull/495))
* Updated the dependency list to explicitly include `boto3`, used for various
commands.
([#499](https://github.com/nextstrain/cli/pull/499))
* Updated code to support the latest version of `wrapt`, used to show
`--dry-run` outputs.
([#499](https://github.com/nextstrain/cli/pull/499))

# 10.4.1 (14 October 2025)

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9 changes: 6 additions & 3 deletions doc/changes.md
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Expand Up @@ -19,9 +19,12 @@ development source code and as such may not be routinely kept up to date.
(v-next-bug-fixes)=
### Bug fixes

* Updated the s3fs dependency to avoid versions starting with 2025.12.0. This
maintains a dependency on `boto3` which is used for various commands.
([#495](https://github.com/nextstrain/cli/pull/495))
* Updated the dependency list to explicitly include `boto3`, used for various
commands.
([#499](https://github.com/nextstrain/cli/pull/499))
* Updated code to support the latest version of `wrapt`, used to show
`--dry-run` outputs.
([#499](https://github.com/nextstrain/cli/pull/499))

(v10-4-1)=
## 10.4.1 (14 October 2025)
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4 changes: 2 additions & 2 deletions nextstrain/cli/console.py
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Expand Up @@ -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):
Expand Down Expand Up @@ -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*.

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38 changes: 4 additions & 34 deletions setup.py
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Expand Up @@ -90,6 +90,7 @@ def find_namespaced_packages(namespace):
python_requires = '>=3.8',

install_requires = [
"boto3 ==1.*",
"certifi",
"docutils",
"fasteners",
Expand All @@ -102,43 +103,12 @@ def find_namespaced_packages(namespace):
"requests",
"typing_extensions >=3.7.4",
"wcmatch >=6.0",
"wrapt",

# We use fsspec's S3 support, which has a runtime dep on s3fs. s3fs
# itself requires aiobotocore, which in turn requires very specific
# versions of botocore (because aiobotocore is a giant monkey-patch).
#
# We also use boto3, which also requires botocore, usually with minimum
# 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.
#
# 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.
#
"wrapt >=2.0.0",

# 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
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