Bump minimum Python version to 3.8

.github/workflows/ci.yaml

@@ -35,39 +35,10 @@ jobs:
           - macos-latest
           - windows-latest
         python:
-          - '3.6'
-          - '3.7'
           - '3.8'
           - '3.9'
           - '3.10'
 
-        # Python 3.6 is not available on Ubuntu 22.04, which is what
-        # ubuntu-latest points to as of Q4 2022¹, so replace that job with 3.6
-        # on Ubuntu 20.04.
-        #   -trs, 22 Nov 2022
-        #
-        # ¹ <https://github.blog/changelog/2022-11-09-github-actions-ubuntu-latest-workflows-will-use-ubuntu-22-04/>
-        #
-        # A bodged https://github.com/actions/python-version build of 3.7.17
-        # for macOS mistakenly doesn't include the bz2 module of the stdlib¹,
-        # which breaks us because some of our deps (fsspec, at the least)
-        # assume bz2 is available² (though that will be fixed in its next
-        # release³).  Replace the 3.7 macOS job with a 3.7.16 job.
-        #   -trs, 22 June 2023
-        #
-        # ¹ <https://github.com/actions/setup-python/issues/682>
-        # ² <https://github.com/nextstrain/cli/pull/289#issuecomment-1595417903>
-        # ³ <https://github.com/fsspec/filesystem_spec/pull/1295>
-        exclude:
-          - os: ubuntu-latest
-            python: '3.6'
-          - os: macos-latest
-            python: '3.7'
-        include:
-          - os: ubuntu-20.04
-            python: '3.6'
-          - os: macos-latest
-            python: '3.7.16'
     runs-on: ${{ matrix.os }}
     defaults:
       run:
@@ -240,11 +211,9 @@ jobs:
           - macos-latest
           - windows-latest
         python:
-          - '3.6'
-          - '3.7'
           - '3.8'
           - '3.9'
-          # XXX TODO: Add 3.10 here once supported by Conda/Bioconda/Conda Forge.
+          - '3.10'
     runs-on: ${{ matrix.os }}
     defaults:
       run:

CHANGES.md

@@ -13,6 +13,9 @@ development source code and as such may not be routinely kept up to date.
 
 # __NEXT__
 
+This release drops support for Python versions 3.6 and 3.7.
+([#325](https://github.com/nextstrain/cli/pull/325))
+
 ## Improvements
 
 * `nextstrain remote upload` now skips gzip compression when uploading

doc/development.md

@@ -2,7 +2,7 @@
 
 Development of `nextstrain-cli` happens at <https://github.com/nextstrain/cli>.
 
-We currently target compatibility with Python 3.6 and higher.
+We currently target compatibility with Python 3.8 and higher.
 
 Versions for this project follow the [Semantic Versioning rules][].
 

doc/installation.rst

@@ -42,7 +42,7 @@ From PyPI
 ---------
 
 .. note::
-    Nextstrain CLI is written in Python 3 and requires at least Python 3.6.  There
+    Nextstrain CLI is written in Python 3 and requires at least Python 3.8.  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

mypy.ini

@@ -1,6 +1,6 @@
 [mypy]
-# We currently aim for compat with 3.6.
-python_version = 3.6
+# We currently aim for compat with 3.8.
+python_version = 3.8
 namespace_packages = True
 
 # Check function bodies which don't have a typed signature. This prevents a
@@ -31,9 +31,6 @@ ignore_missing_imports = True
 [mypy-importlib.metadata]
 ignore_missing_imports = True
 
-[mypy-importlib_metadata]
-ignore_missing_imports = True
-
 [mypy-importlib.resources]
 ignore_missing_imports = True
 

nextstrain/cli/__main__.py

@@ -13,41 +13,29 @@ def main():
     # rest of the codebase.  Avoids needing to instruct folks to set
     # PYTHONIOENCODING=UTF-8 or use Python's UTF-8 mode (-X utf8 or
     # PYTHONUTF8=1).
-    sys.stdout = reconfigure_stdio(sys.stdout) # type: ignore[arg-type]
-    sys.stderr = reconfigure_stdio(sys.stderr) # type: ignore[arg-type]
+    reconfigure_stdio(sys.stdout) # type: ignore[arg-type]
+    reconfigure_stdio(sys.stderr) # type: ignore[arg-type]
 
     return cli.run( argv[1:] )
 
 
-def reconfigure_stdio(stdio: TextIOWrapper) -> TextIOWrapper:
+def reconfigure_stdio(stdio: TextIOWrapper):
     """
     Reconfigure *stdio* to match the assumptions of this codebase.
 
     Suitable only for output streams (e.g. stdout, stderr), as reconfiguring an
     input stream is more complicated.
     """
-    # XXX TODO: When we drop Python 3.6 support, most of this function can be
-    # replaced by stdio.reconfigure().
-    #   -trs, 6 June 2022
-
-    # Flush any pending output under old configuration.
-    stdio.flush()
 
     # Configure new text stream on the same underlying buffered byte stream.
-    return TextIOWrapper(
-        stdio.buffer,
-
+    stdio.reconfigure(
         # Always use UTF-8 and be more lenient on stderr so even mangled error
         # messages make it out.
         encoding = "UTF-8",
         errors = "backslashreplace" if stdio is sys.stderr else "strict",
 
         # Explicitly enable universal newlines mode so we do the right thing.
-        newline = None,
-
-        # Preserve line buffering which is set at process start dynamically
-        # depending on what the stdio is actually attached to.
-        line_buffering = stdio.line_buffering)
+        newline = None)
 
 
 # Run when called as `python -m nextstrain.cli`, here for good measure.

nextstrain/cli/aws/cognito/__init__.py

@@ -2,17 +2,8 @@
 AWS Cognito helpers.
 """
 import boto3
-import warnings
-
-# Ignore noisy warning from cryptography 37.0.0 and 39.0.0 about deprecated support for Python 3.6.
-with warnings.catch_warnings():
-    warnings.filterwarnings(
-        "ignore",
-        message  = "Python 3\\.6 is no longer supported by the Python core team\\. Therefore, support for it is deprecated in cryptography",
-        category = UserWarning)
-
-    import jwt
-    import jwt.exceptions
+import jwt
+import jwt.exceptions
 
 from .srp import CognitoSRP, NewPasswordRequiredError # noqa: F401 (NewPasswordRequiredError is for re-export)
 

nextstrain/cli/command/build.py

@@ -253,10 +253,6 @@ def parse_snakemake_args(args):
     >>> sorted(parse_snakemake_args([]).items())
     [('--cores', []), ('--resources', [])]
     """
-    # XXX TODO: Consider using a small ArgumentParser() for this in the
-    # future, when we can require Python 3.7 and use parse_intermixed_args().
-    #   -trs, 20 May 2020
-
     opts = {
         "-j" if re.search(r"^-j\d+$", arg) else arg
             for arg in map(lambda arg: arg.split("=", 1)[0], args)

nextstrain/cli/util.py

@@ -1,8 +1,3 @@
-try:
-    from importlib.metadata import distribution as distribution_info, PackageNotFoundError
-except ModuleNotFoundError:
-    from importlib_metadata import distribution as distribution_info, PackageNotFoundError
-
 import os
 import platform
 import re
@@ -11,6 +6,7 @@
 import subprocess
 import sys
 from functools import partial
+from importlib.metadata import distribution as distribution_info, PackageNotFoundError
 from typing import Any, Callable, Iterable, Mapping, List, Optional, Sequence, Tuple, Union, overload
 # TODO: Use typing.Literal once Python 3.8 is the minimum supported version.
 from typing_extensions import Literal
@@ -271,10 +267,6 @@ def capture_output(argv, extra_env: Mapping = {}):
     Run the command specified by the argument list and return a list of output
     lines.
 
-    This wrapper around subprocess.run() exists because its own capture_output
-    parameter wasn't added until Python 3.7 and we aim for compat with 3.6.
-    When we bump our minimum Python version, we can remove this wrapper.
-
     If an *extra_env* mapping is passed, the provided keys and values are
     overlayed onto the current environment.  Keys with a value of ``None`` are
     removed from the current environment (i.e. like ``del os.environ[key]``).

pyrightconfig.json

@@ -1,5 +1,5 @@
 {
-  "pythonVersion": "3.6",
+  "pythonVersion": "3.8",
   "include": ["nextstrain"],
   "ignore": [
     "nextstrain/cli/markdown.py",

setup.py

@@ -70,7 +70,9 @@ def find_namespaced_packages(namespace):
 
         # Python 3 only
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
     ],
 
     # Install a "nextstrain" program which calls nextstrain.cli.__main__.main()
@@ -81,13 +83,11 @@ def find_namespaced_packages(namespace):
         ],
     },
 
-    python_requires = '>=3.6',
+    python_requires = '>=3.8',
 
     install_requires = [
-        "dataclasses; python_version < '3.7'",
         "docutils",
         "fasteners",
-        "importlib_metadata; python_version < '3.8'",
         "importlib_resources >=5.3.0; python_version < '3.11'",
         "packaging",
         "pyjwt[crypto] >=2.0.0",