Merge pull request #524: Bump minimum Python version to 3.10

victorlin · web-flow · commit fd4aafc22295 · 2026-05-04T15:09:31.000-07:00
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -35,8 +35,6 @@ jobs:
           - macos-latest
           - windows-latest
         python:
-          - '3.8'
-          - '3.9'
           - '3.10'
           - '3.11'
           - '3.12'
@@ -253,8 +251,6 @@ jobs:
           - macos-latest
           - windows-latest
         python:
-          - '3.8'
-          - '3.9'
           - '3.10'
           - '3.11'
           - '3.12'
@@ -274,12 +270,6 @@ jobs:
         with:
           python-version: ${{ matrix.python }}
 
-          # Skip ambient runtime testing on 3.8, as it forces an old version of
-          # Augur (26.2.0, last with 3.8 support) that is not compatible with
-          # Nextstrain CLI >10.3.0 installed in the same Python environment due
-          # to conflicting jsonschema dependencies.
-          ambient: ${{ matrix.python != '3.8' }}
-
       - uses: actions/download-artifact@v8
         with:
           name: dist
@@ -289,12 +279,6 @@ jobs:
         run: python3 -m pip install --upgrade dist/nextstrain_cli-*-py3-none-any.whl
 
       - uses: ./src/.github/actions/run-integration-tests
-        with:
-          # Skip ambient runtime testing on 3.8, as it forces an old version of
-          # Augur (26.2.0, last with 3.8 support) that is not compatible with
-          # Nextstrain CLI >10.3.0 installed in the same Python environment due
-          # to conflicting jsonschema dependencies.
-          ambient: ${{ matrix.python != '3.8' }}
 
   test-standalone:
     needs: build-standalone
@@ -336,7 +320,7 @@ jobs:
 
       - uses: ./src/.github/actions/setup-integration-tests
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       # Download and extract the installation archive.
       - uses: actions/download-artifact@v8
diff --git a/CHANGES.md b/CHANGES.md
@@ -13,6 +13,16 @@ development source code and as such may not be routinely kept up to date.
 
 # __NEXT__
 
+This release drops support for Python versions 3.8 and 3.9.
+
+Note that this Python version support only matters if you're installing
+Nextstrain CLI from PyPI or Bioconda
+([c.f.](https://docs.nextstrain.org/projects/cli/en/__NEXT__/installation/)).  It
+does not apply if you're installing Nextstrain CLI using the standalone
+installation method we recommend in the [Nextstrain installation
+documentation](https://docs.nextstrain.org/page/install.html).  In that case, a
+supported Python version is always bundled with `nextstrain`.
+
 ## Improvements
 
 * `nextstrain build` now runs Snakemake with the `--rerun-incomplete` option,
diff --git a/doc/changes.md b/doc/changes.md
@@ -16,6 +16,16 @@ development source code and as such may not be routinely kept up to date.
 (v-next)=
 ## __NEXT__
 
+This release drops support for Python versions 3.8 and 3.9.
+
+Note that this Python version support only matters if you're installing
+Nextstrain CLI from PyPI or Bioconda
+([c.f.](https://docs.nextstrain.org/projects/cli/en/__NEXT__/installation/)).  It
+does not apply if you're installing Nextstrain CLI using the standalone
+installation method we recommend in the [Nextstrain installation
+documentation](https://docs.nextstrain.org/page/install.html).  In that case, a
+supported Python version is always bundled with `nextstrain`.
+
 (v-next-improvements)=
 ### Improvements
 
diff --git a/doc/development.md b/doc/development.md
@@ -2,7 +2,7 @@
 
 Development of `nextstrain-cli` happens at <https://github.com/nextstrain/cli>.
 
-We currently target compatibility with Python 3.8 and higher.
+We currently target compatibility with Python 3.10 and higher.
 
 Versions for this project follow the [Semantic Versioning rules][].
 
@@ -176,9 +176,6 @@ During development you can run static type checks using [pyright][]:
 
 There are also many [editor integrations for Pyright][].
 
-The [`typing_extensions`][] module should be used for features not yet available
-in the the standard `typings` module of supported Python versions.
-
 We also use [Flake8][] for some static analysis checks focusing on runtime
 safety and correctness.  You can run them like this:
 
@@ -238,7 +235,6 @@ environmental factors.
 [type annotations]: https://www.python.org/dev/peps/pep-0484/
 [pyright]: https://github.com/microsoft/pyright
 [editor integrations for Pyright]: https://microsoft.github.io/pyright/#/installation
-[`typing_extensions`]: https://pypi.org/project/typing-extensions
 [Flake8]: https://flake8.pycqa.org
 [post-release version]: https://peps.python.org/pep-0440/#post-releases
 [autobump PR]: https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Apr+author%3Abiocondabot+nextstrain-cli
diff --git a/doc/installation.rst b/doc/installation.rst
@@ -42,11 +42,11 @@ From PyPI
 ---------
 
 .. note::
-    Nextstrain CLI is written in Python 3 and requires at least Python 3.8.  There
+    Nextstrain CLI is written in Python 3 and requires at least Python 3.10.  There
     are many ways to install Python 3 on Windows, macOS, or Linux, including the
     `official packages`_, `Homebrew`_ for macOS, and the `Anaconda Distribution`_.
     Details are beyond the scope of this guide, but make sure you install Python
-    3.8 or higher. You may already have Python 3 installed, especially if you're on
+    3.10 or higher. You may already have Python 3 installed, especially if you're on
     Linux. Check by running ``python --version`` or ``python3 --version``.
 
     .. _official packages: https://www.python.org/downloads/
diff --git a/nextstrain/cli/argparse.py b/nextstrain/cli/argparse.py
@@ -2,7 +2,6 @@
 Custom helpers for extending the behaviour of argparse standard library.
 """
 import os
-import sys
 from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser, ArgumentTypeError, SUPPRESS, _SubParsersAction # pyright: ignore[reportPrivateUsage]
 from itertools import chain, takewhile
 from pathlib import Path
@@ -15,10 +14,7 @@
 from .util import format_usage, runner_module
 
 
-# The standard argument group title for non-positional arguments.  See
-# <https://github.com/python/cpython/pull/23858> and
-# <https://bugs.python.org/issue9694>.
-OPTIONS_TITLE = "options" if sys.version_info >= (3, 10) else "optional arguments"
+OPTIONS_TITLE = "options"
 
 
 # Include this in an argument help string to suppress the automatic appending
diff --git a/nextstrain/cli/authn/session.py b/nextstrain/cli/authn/session.py
@@ -2,18 +2,8 @@
 Authentication sessions.
 """
 import boto3
-import warnings
-
-# Ignore noisy warning from cryptography 47.0.0 about deprecated support for Python 3.8
-with warnings.catch_warnings():
-    warnings.filterwarnings(
-        "ignore",
-        message = "Python 3\\.8 is no longer supported by the Python core team and support for it is deprecated",
-        category = UserWarning
-    )
-    import jwt
-    import jwt.exceptions
-
+import jwt
+import jwt.exceptions
 import secrets
 
 from base64 import b64encode
diff --git a/nextstrain/cli/command/shell.py b/nextstrain/cli/command/shell.py
@@ -10,7 +10,7 @@
 from ..argparse import add_extended_help_flags
 from ..paths import SHELL_HISTORY
 from ..runner import docker, conda, singularity
-from ..util import colored, remove_prefix, runner_name
+from ..util import colored, runner_name
 from ..volume import NamedVolume
 from .build import assert_overlay_volumes_support, pathogen_volumes
 
@@ -113,7 +113,7 @@ def fg(color: str) -> str: return r'\[\e[38;2;{};{};{}m\]'.format(*rgb(color))
     def bg(color: str) -> str: return r'\[\e[48;2;{};{};{}m\]'.format(*rgb(color))
 
     def rgb(color: str) -> Tuple[int, int, int]:
-        color = remove_prefix("#", color)
+        color = color.removeprefix("#")
         r,g,b = (int(c, 16) for c in (color[0:2], color[2:4], color[4:6]))
         return r,g,b
 
diff --git a/nextstrain/cli/command/view.py b/nextstrain/cli/command/view.py
@@ -59,7 +59,7 @@
 from ..argparse import add_extended_help_flags, SUPPRESS, SKIP_AUTO_DEFAULT_IN_HELP
 from ..browser import BROWSER, open_browser as __open_browser
 from ..runner import docker, ambient, conda, singularity
-from ..util import colored, remove_suffix, warn
+from ..util import colored, warn
 from ..volume import NamedVolume
 
 
@@ -324,7 +324,7 @@ def sidecar_file(path):
 
     # v1: All *_tree.json files with corresponding *_meta.json files.
     def meta_exists(path):
-        return path.with_name(remove_suffix("_tree.json", path.name) + "_meta.json").exists()
+        return path.with_name(path.name.removesuffix("_tree.json") + "_meta.json").exists()
 
     datasets_v1 = set(
         re.sub(r"_tree$", "", path.stem).replace("_", "/")
diff --git a/nextstrain/cli/console.py b/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 BaseObjectProxy # pyright: ignore[reportAttributeAccessIssue]
+from wrapt import BaseObjectProxy
 
 
 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(BaseObjectProxy): # pyright: ignore[reportUntypedBaseClass]
+class LinePrefixer(BaseObjectProxy):
     """
     Add *prefix* to every line written to *file*.
 
@@ -147,3 +147,8 @@ def write(self, s) -> int:
         s_ += re.sub(r'(?<=\n)(?!\Z)', self.__prefix, s)
 
         return self.__wrapped__.write(s_)
+
+    # BaseObjectProxy forwards this at runtime, but Pyright is not aware of that
+    # when checking redirect_stdout()/redirect_stderr().
+    def flush(self) -> None:
+        self.__wrapped__.flush()
diff --git a/nextstrain/cli/pathogens.py b/nextstrain/cli/pathogens.py
@@ -390,11 +390,7 @@ def workflow_path(self, name: str) -> Path:
             resolved_pathogen_path = self.path.resolve()
             resolved_workflow_path = (resolved_pathogen_path / path).resolve()
 
-            # Path.is_relative_to() was added in Python 3.9, so implement it
-            # ourselves around .relative_to().
-            try:
-                resolved_workflow_path.relative_to(resolved_pathogen_path)
-            except ValueError:
+            if not resolved_workflow_path.is_relative_to(resolved_pathogen_path):
                 raise UserError(f"""
                     The {self.registration_path.name} file for {str(self)!r}
                     registers an out-of-bounds path for the workflow {name!r}:
diff --git a/nextstrain/cli/remote/nextstrain_dot_org.py b/nextstrain/cli/remote/nextstrain_dot_org.py
@@ -86,7 +86,7 @@
 from ..gzip import GzipCompressingReader
 from ..net import is_loopback
 from ..url import URL, Origin
-from ..util import remove_prefix, glob_matcher, glob_match
+from ..util import glob_matcher, glob_match
 
 
 # Default to embedding images, but allow it to be turned off as an escape
@@ -971,7 +971,7 @@ def authn_challenge(response: requests.Response) -> Optional[Dict[str, str]]:
     if not challenge or not challenge.startswith("Bearer "):
         return None
 
-    challenge_params = remove_prefix("Bearer ", challenge).lstrip(" ")
+    challenge_params = challenge.removeprefix("Bearer ").lstrip(" ")
 
     return requests.utils.parse_dict_header(challenge_params)
 
diff --git a/nextstrain/cli/remote/s3.py b/nextstrain/cli/remote/s3.py
@@ -51,7 +51,7 @@
 from ..aws.s3 import split_url
 from ..authn import User
 from ..gzip import GzipCompressingReader, ContentDecodingWriter
-from ..util import warn, remove_prefix
+from ..util import warn
 from ..errors import UserError
 from ..types import S3Object
 from ..url import URL, Origin
@@ -454,4 +454,4 @@ def remove_origin_path(origin: dict, prefix: str) -> str:
     """
     Return the given prefix stripped of any implicit distribution origin path.
     """
-    return remove_prefix(origin["OriginPath"].lstrip("/"), prefix)
+    return prefix.removeprefix(origin["OriginPath"].lstrip("/"))
diff --git a/nextstrain/cli/resources/__init__.py b/nextstrain/cli/resources/__init__.py
@@ -6,7 +6,7 @@
 # backwards compatible with importers only providing the original path() /
 # ResourceReader API.  The PyPI backport, on the other hand, contains the full
 # adapter since 5.3.0, which we declare as our minimum version in setup.py, so
-# we use that even on 3.9 and 3.10.
+# we use that even on 3.10.
 #
 # We're using the new API at all because the original one is being deprecated
 # and we want to avoid warnings both from the stdlib implementation on 3.11 and
diff --git a/nextstrain/cli/rst/__init__.py b/nextstrain/cli/rst/__init__.py
@@ -24,7 +24,6 @@
 from docutils.parsers.rst.roles import register_local_role
 from docutils.utils import unescape
 from ..__version__ import __version__ as cli_version
-from ..util import remove_suffix
 from .sphinx import TextWriter
 
 
@@ -225,7 +224,7 @@ def doc_url(target: str) -> str:
 
     if path.endswith("/index"):
         # a/b/index → a/b/ (e.g. implicitly a/b/index.html)
-        path_url = remove_suffix("index", path)
+        path_url = path.removesuffix("index")
     else:
         path_url = path + (suffix or "")
 
diff --git a/nextstrain/cli/runner/__init__.py b/nextstrain/cli/runner/__init__.py
@@ -1,9 +1,7 @@
 import argparse
 import os
 from argparse import ArgumentParser, ArgumentTypeError
-from typing import List, Union
-# TODO: Use typing.TypeAlias once Python 3.10 is the minimum supported version.
-from typing_extensions import TypeAlias
+from typing import List, TypeAlias, Union
 from . import docker, conda, singularity, ambient, aws_batch
 from .. import config, env, hostenv
 from ..argparse import DirectoryPath, SKIP_AUTO_DEFAULT_IN_HELP
diff --git a/nextstrain/cli/runner/conda.py b/nextstrain/cli/runner/conda.py
@@ -464,14 +464,7 @@ def which_finds_our(cmd) -> bool:
         if not found:
             return False
 
-        # Path.is_relative_to() was added in Python 3.9, so implement it
-        # ourselves around .relative_to().
-        try:
-            Path(found).relative_to(PREFIX_BIN)
-        except ValueError:
-            return False
-        else:
-            return True
+        return Path(found).is_relative_to(PREFIX_BIN)
 
 
     def runnable(*argv) -> bool:
diff --git a/nextstrain/cli/types.py b/nextstrain/cli/types.py
@@ -3,12 +3,8 @@
 """
 
 import argparse
-import builtins
-import sys
 from pathlib import Path
-from typing import Any, Callable, Iterable, List, Mapping, Optional, Protocol, Tuple, Union, TYPE_CHECKING, runtime_checkable
-# TODO: Use typing.TypeAlias once Python 3.10 is the minimum supported version.
-from typing_extensions import TypeAlias
+from typing import Any, Callable, Iterable, List, Mapping, Optional, Protocol, Tuple, TypeAlias, Union, TYPE_CHECKING, runtime_checkable
 
 # Import concrete types from our other modules only during type checking to
 # avoid import cycles during runtime.
@@ -17,11 +13,7 @@
     from .volume import NamedVolume
     from .url import URL, Origin
 
-# Re-export EllipsisType so we can paper over its absence from older Pythons
-if sys.version_info >= (3, 10):
-    from types import EllipsisType
-else:
-    EllipsisType: TypeAlias = 'builtins.ellipsis'
+from types import EllipsisType
 
 """
 An immutable mapping of (*name*, *value*) pairs representing a set of
diff --git a/nextstrain/cli/util.py b/nextstrain/cli/util.py
@@ -64,14 +64,6 @@ def colored(color, text):
     )
 
 
-# TODO: Use str.removeprefix/removesuffix once Python 3.9 is the minimum supported version.
-def remove_prefix(prefix, string):
-    return re.sub('^' + re.escape(prefix), '', string)
-
-def remove_suffix(suffix, string):
-    return re.sub(re.escape(suffix) + '$', '', string)
-
-
 class NewVersionCheckResult(NamedTuple):
     newer_version: Optional[str]
     status_message: Optional[str]
@@ -724,7 +716,7 @@ def print_and_check_setup_tests(tests: SetupTestResults) -> bool:
         # Indent subsequent lines of any multi-line descriptions so it
         # lines up under the status marker.
         formatted_description = \
-            remove_prefix("  ", indent(description, "  "))
+            indent(description, "  ").removeprefix("  ")
 
         results.append((description, result))
 
diff --git a/pyrightconfig.json b/pyrightconfig.json
@@ -1,5 +1,5 @@
 {
-  "pythonVersion": "3.8",
+  "pythonVersion": "3.10",
   "include": ["nextstrain"],
   "ignore": [
     "nextstrain/cli/markdown.py",
diff --git a/setup.py b/setup.py
