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chore: remove legacy shell scripts, add pre-commit hooks, drop Python 3.9
Removes unused and outdated shell scripts and legacy build utilities superseded by the new Python build system. Adds pre-commit hooks with linting applied across the codebase. Drops Python 3.9 support as it is EOL. Includes README and documentation updates for the new build workflow.
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‎.gitattributes‎

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# SCM syntax highlighting & preventing 3-way merges
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pixi.lock merge=binary linguist-language=YAML linguist-generated=true

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Something is broken in the build or packaging pipeline
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title: "fix: "
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labels: bug
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assignees: ""
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---
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## Environment
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- **OS / Platform**: <!-- e.g. Ubuntu 22.04 x86_64, macOS 14 arm64, Windows Server 2022 -->
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- **Python version**: <!-- e.g. 3.11.9 -->
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- **ITK version / branch**: <!-- e.g. v5.4.0, or commit hash -->
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- **Script / entry point used**: <!-- e.g. scripts/build_wheels.py, dockcross-manylinux-build-wheels.sh -->
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## Steps to Reproduce
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## Expected Behavior
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<!-- What should happen. -->
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## Actual Behavior
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<!-- What actually happens. Paste relevant log output below. -->
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<details>
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<summary>Log output</summary>
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```
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```
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</details>
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## Additional Context
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<!-- build_report.json contents, Docker image tag, CMake args, etc. -->

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: true
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contact_links:
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- name: ITK Discourse (questions & support)
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url: https://discourse.itk.org
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about: For build questions or general ITK support, please use the ITK Discourse forum.
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- name: ITK Documentation
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url: https://itkpythonpackage.readthedocs.io
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about: Check the docs before filing an issue.

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest a new capability or improvement to the build/packaging pipeline
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title: "feat: "
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labels: enhancement
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assignees: ""
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---
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## Problem / Motivation
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<!-- What limitation or pain point does this address? -->
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## Proposed Solution
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<!-- Describe what you'd like to see added or changed. -->
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## Alternatives Considered
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<!-- Any other approaches you've thought about? -->
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## Additional Context
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<!-- Platform relevance, ITK module context, links, etc. -->

‎.github/pull_request_template.md‎

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## Summary
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<!-- One or two sentences describing what this PR does and why. -->
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## Type of Change
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- [ ] Bug fix
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- [ ] New feature / enhancement
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- [ ] Refactor / cleanup
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- [ ] Docs / CI only
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## Checklist
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- [ ] Pre-commit hooks pass locally (`pre-commit run --all-files`)
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- [ ] Tested wheel build on affected platform(s) (Linux / macOS / Windows)
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- [ ] Docs updated if behavior changed (`docs/`)
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- [ ] Commit messages follow Conventional Commits (`feat:`, `fix:`, `chore:`, etc.)
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## Platform(s) Tested
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<!-- Check all that apply, or note "untested" where applicable. -->
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- [ ] Linux x86_64 (manylinux)
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- [ ] Linux aarch64 (manylinux)
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- [ ] macOS x86_64
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- [ ] macOS arm64
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- [ ] Windows x86_64
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## Related Issues
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<!-- Closes #... -->

‎.github/workflows/pre-commit.yaml‎

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name: pre-commit
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on:
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pull_request:
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push:
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branches: [main]
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jobs:
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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- uses: pre-commit/action@v3.0.1

‎.gitignore‎

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lib64
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MANIFEST
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oneTBB-prefix/
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pyproject.toml
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# Installer logs
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pip-log.txt
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# IDE junk
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.idea/*
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*.swp
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/itkVersion.py
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# pixi environments
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.pixi/*
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!.pixi/config.toml

‎.pre-commit-config.yaml‎

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# Pre-commit configuration for ITKPythonPackage
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# Run `pre-commit install` to install git hooks locally
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# Run `pre-commit run --all-files` to check all files
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# Run `pre-commit autoupdate` to update hook versions
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# Exclude generated/vendored directories from all hooks
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exclude: ^(\.pixi|build|pixi.lock|docs)/
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repos:
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# General file hygiene
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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stages: [pre-commit]
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- id: end-of-file-fixer
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stages: [pre-commit]
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- id: check-yaml
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stages: [pre-commit]
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- id: check-toml
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stages: [pre-commit]
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- id: check-merge-conflict
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stages: [pre-commit]
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- id: check-added-large-files
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args: [--maxkb=500]
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stages: [pre-commit]
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# Enforce LF line endings everywhere except Windows PowerShell scripts
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- id: mixed-line-ending
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args: [--fix=lf]
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exclude: \.ps1$
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stages: [pre-commit]
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# Python: formatting
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- repo: https://github.com/psf/black
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rev: 24.10.0
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hooks:
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- id: black
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stages: [pre-commit]
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# Python: linting + import sorting
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.8.6
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hooks:
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- id: ruff
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args: [--fix]
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stages: [pre-commit]
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# Shell: linting
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- repo: https://github.com/shellcheck-py/shellcheck-py
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rev: v0.10.0.1
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hooks:
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- id: shellcheck
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stages: [pre-commit]
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# Shell: formatting
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- repo: https://github.com/scop/pre-commit-shfmt
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rev: v3.12.0-2
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hooks:
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- id: shfmt
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args: [-i, "2", -w]
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stages: [pre-commit]
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- repo: https://github.com/commitizen-tools/commitizen
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rev: "v4.13.0"
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hooks:
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- id: commitizen
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stages: [commit-msg]
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# TOML: formatting
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- repo: https://github.com/ComPWA/taplo-pre-commit
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rev: v0.9.3
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hooks:
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- id: taplo-format
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stages: [pre-commit]

‎.travis.yml‎

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