Drop Python 3.9 support, require Python 3.10+

[yarikoptic]

Labeling to release to test docker container generation

[gemini-code-assist]

Summary of Changes

Hello @yarikoptic, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request updates the project's Python compatibility, moving to a minimum requirement of Python 3.10. This change streamlines development by leveraging newer language features and ensures alignment with current Python ecosystem standards. All references and configurations across the codebase, documentation, and build processes have been adjusted to reflect this updated dependency.

Highlights

• Python Version Update: The project now officially requires Python 3.10 or newer, dropping support for Python 3.9.
• Dockerfile Base Image: The Dockerfile base image has been updated from python:3.9-alpine to python:3.10-alpine.
• Documentation Updates: All relevant documentation and examples have been updated to reflect the new Python 3.10 requirement.
• Project Configuration: The pyproject.toml file has been adjusted to remove Python 3.9 classifiers, update the requires-python constraint, and set the black formatter target to py310.

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Changelog

• Dockerfile
  • Updated the base Python image from 3.9-alpine to 3.10-alpine.
• docs/user_guide/installation.rst
  • Updated the minimum Python version requirement in the installation guide from 3.7 to 3.10.
  • Modified the conda create command example to use python=3.10.
• docs/user_guide/quickstart.rst
  • Updated the docker run command example to use python:3.10-slim.
• neurodocker/cli/generate.py
  • Updated an example string for conda_install to python=3.10.
• neurodocker/cli/minify/trace.py
  • Updated the docker run command example in the minify documentation to use python:3.10-slim.
• pyproject.toml
  • Removed the Programming Language :: Python :: 3.9 classifier.
  • Updated the requires-python field from >=3.9 to >=3.10.
  • Changed the black formatter target-version from py39 to py310.

Ignored Files

• Ignored by pattern: .github/workflows/** (2)
  • .github/workflows/pull-request.yml
  • .github/workflows/type_checks.yml

Activity

• The pull request was labeled to facilitate testing of docker container generation.

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[gemini-code-assist]

Code Review

This pull request correctly drops support for Python 3.9 and sets the minimum required version to 3.10. All related changes in the Dockerfile, documentation, and pyproject.toml are consistent with this goal. I have one suggestion for a potential follow-up improvement related to this version bump.

[gemini-code-assist]

With Python 3.10 as the new minimum version, it's a good opportunity to review the usage of the typing-extensions dependency. Some features provided by typing-extensions for older Python versions (like TypeGuard and ParamSpec) are available in the standard typing module in Python 3.10. You might be able to simplify your code by using the native implementations and potentially remove the typing-extensions dependency if it's no longer providing unique functionality for your project.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.02%. Comparing base (41a3eef) to head (353f745).
⚠️ Report is 89 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #698      +/-   ##
==========================================
- Coverage   88.06%   88.02%   -0.04%     
==========================================
  Files          11       11              
  Lines        1039     1044       +5     
==========================================
+ Hits          915      919       +4     
- Misses        124      125       +1     

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[yarikoptic]

precommit was broken elsewhere but let's fix here since it is minor.

[yarikoptic]

pre commit is happy now