Fix all the build issues, test and verify all basic features and release a new version for monailabel

[SachidanandAlle]

• Fix build
• Drop python 3.9 version
• Verify all good (models, ohif, 3d slicer extensions etc..)
• Release new version to PIP

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Coding Plan

Approach

Fix build issues by removing Python 3.9 support and correcting CI/CD configuration, verify core functionality across models, OHIF viewer, and 3D Slicer extensions, then release a new version to PyPI.

Observations

MONAILabel is a medical imaging annotation platform with CI/CD managed through GitHub Actions workflows. The project uses Versioneer for Git tag-based versioning, supports radiology/pathology/endoscopy sample applications, and integrates with OHIF viewer and 3D Slicer via plugins. The setup.cfg already specifies python_requires = >= 3.10, but CI/CD workflows still test against Python 3.9, and pyproject.toml contains outdated Black formatter targets. The release process uses manual workflow dispatch to publish to Test PyPI and production PyPI.

Assumptions

Assumption 1: Version Number for Release

Options Considered:

1. Release as 0.7.0 (minor version bump for Python 3.9 deprecation and accumulated changes)
2. Release as 0.6.1 (patch version if only bug fixes)
3. Release as 1.0.0 (major version if breaking changes warrant it)

Chosen Option: 1

Rationale: Release as 0.7.0 - Dropping Python 3.9 support is a significant compatibility change warranting a minor version bump, and there are likely substantial unreleased changes since December 2022.

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Implementation Steps

Phase 1: Fix Build Configuration

This phase addresses all Python version-related configuration issues that are causing build problems or inconsistencies. All changes ensure alignment with the already-established Python >= 3.10 requirement in setup.cfg.

Task 1: Remove Python 3.9 from GitHub Actions Test Matrix

Remove Python 3.9 from all CI/CD workflow test matrices to align with the project's minimum Python version requirement.

• Update .github/workflows/pythonapp.yml to remove "3.9" from the python-version matrix in three locations: deps_check job, build job, and packaging job
• Change matrix from ["3.9", "3.10", "3.11", "3.12"] to ["3.10", "3.11", "3.12"]

Task 2: Update Black Formatter Target Versions

Update the Black formatter configuration to target currently supported Python versions instead of deprecated ones.

• Update pyproject.toml in the [tool.black] section to change target-version from ['py36', 'py37', 'py38'] to ['py310', 'py311', 'py312']

Task 3: Fix Unquoted Python Version Numbers in Workflows

Correct YAML parsing issues where unquoted Python version numbers may be misinterpreted (e.g., 3.10 parsed as 3.1).

• Update .github/workflows/docker-plugin.yml to quote the python-version value (change python-version: 3.10 to python-version: "3.10")
• Update .github/workflows/release.yml to quote the python-version value (change python-version: 3.10 to python-version: "3.10")

🤖 Prompt for AI agents

Fix Python version-related configuration issues to align with the Python >= 3.10
requirement already established in setup.cfg.

**Update GitHub Actions Test Matrix:**
- In `.github/workflows/pythonapp.yml`, locate the `python-version` matrix in
three jobs: `deps_check`, `build`, and `packaging`
- Remove `"3.9"` from each matrix, changing from `["3.9", "3.10", "3.11",
"3.12"]` to `["3.10", "3.11", "3.12"]`

**Update Black Formatter Configuration:**
- In `pyproject.toml`, locate the `[tool.black]` section
- Change `target-version` from `['py36', 'py37', 'py38']` to `['py310', 'py311',
'py312']`

**Fix YAML Version Number Quoting:**
- In `.github/workflows/docker-plugin.yml`, quote the `python-version` value:
change `python-version: 3.10` to `python-version: "3.10"`
- In `.github/workflows/release.yml`, quote the `python-version` value: change
`python-version: 3.10` to `python-version: "3.10"`

Phase 2: Verification

This phase validates that all core functionality works correctly after the configuration changes. Verification should be performed locally and through CI/CD pipeline runs.

Task 1: Run CI/CD Pipeline Verification

Trigger the CI/CD pipeline to verify that all automated tests pass with the updated configuration.

• Push changes to a feature branch and create a pull request to trigger the pythonapp.yml workflow
• Verify the deps_check job passes on all Python versions (3.10, 3.11, 3.12)
• Verify the build job passes unit tests with coverage reporting
• Verify the packaging job successfully builds and validates packages
• Review any test failures and address them before proceeding

Task 2: Verify Model Functionality

Confirm that sample application models work correctly with the updated configuration.

• Run integration tests for radiology models: ./runtests.sh --net or execute tests in tests/integration/radiology/
• Run integration tests for pathology models using the pathology test suite
• Run integration tests for endoscopy and monaibundle applications
• Verify MONAI Bundle compatibility (requires MONAI >= 1.4.0)
• Note: vista2d app requires Python 3.10+ for SAM-2, which is now properly enforced

Task 3: Verify OHIF Viewer Integration

Confirm that OHIF viewer builds and integrates correctly with MONAILabel.

• Execute OHIF v2 build script (plugins/ohif/build.sh) and verify completion without errors
• Confirm static assets are generated in monailabel/endpoints/static/ohif/
• Optionally test OHIF v3 build (plugins/ohifv3/build.sh) if v3 support is actively used
• Verify the /ohif/ endpoint responds correctly when running the server

Task 4: Verify 3D Slicer Extension Compatibility

Confirm that the 3D Slicer plugin remains compatible with the updated Python requirements.

• Review plugins/slicer/ for any Python 3.9-specific code or dependencies
• Run existing MONAILabelReviewer unit tests in plugins/slicer/MONAILabelReviewer/UnitTests/
• Verify the plugin client library (MONAILabelLib/client.py) works with Python 3.10+
• Note: 3D Slicer 5.0+ uses Python 3.9, but 3D Slicer 5.2+ uses Python 3.10, so users may need to upgrade their Slicer installation

🤖 Prompt for AI agents

Validate that all core functionality works correctly after the Python version
configuration changes. Verification should be performed both locally and through
CI/CD pipeline runs.

**CI/CD Pipeline Verification:**
- Push changes to a feature branch and create a pull request to trigger the
`pythonapp.yml` workflow
- Verify the `deps_check` job passes on Python 3.10, 3.11, and 3.12
- Verify the `build` job passes unit tests with coverage reporting
- Verify the `packaging` job successfully builds and validates packages
- Review and address any test failures before proceeding

**Model Functionality Verification:**
- Run integration tests for radiology models using `./runtests.sh --net` or
tests in `tests/integration/radiology/`
- Run integration tests for pathology models
- Run integration tests for endoscopy and monaibundle applications
- Verify MONAI Bundle compatibility (requires MONAI >= 1.4.0)
- Note that vista2d app requires Python 3.10+ for SAM-2

**OHIF Viewer Integration:**
- Execute OHIF v2 build script at `plugins/ohif/build.sh` and verify completion
without errors
- Confirm static assets are generated in `monailabel/endpoints/static/ohif/`
- Optionally test OHIF v3 build at `plugins/ohifv3/build.sh` if actively used
- Verify the `/ohif/` endpoint responds correctly when running the server

**3D Slicer Extension Compatibility:**
- Review `plugins/slicer/` for any Python 3.9-specific code or dependencies
- Run MONAILabelReviewer unit tests in
`plugins/slicer/MONAILabelReviewer/UnitTests/`
- Verify the plugin client library at `MONAILabelLib/client.py` works with
Python 3.10+
- Note that 3D Slicer 5.2+ is required for Python 3.10 compatibility

Phase 3: Release Preparation and Publication

This phase prepares the release artifacts and publishes the new version to PyPI following the established release workflow.

Task 1: Update CHANGELOG

Document all changes since the last release (0.6.0) to maintain proper release documentation.

• Update CHANGELOG.md to create a new version section (e.g., ## [0.7.0] - YYYY-MM-DD)
• Move any items from the [Unreleased] section to the new version section
• Document the Python 3.9 deprecation as a breaking change or compatibility note
• Include any other significant changes that have accumulated since version 0.6.0
• Follow the Keep a Changelog format already established in the file

Task 2: Create Release Tag

Create a Git tag that Versioneer will use to determine the package version.

• Ensure all changes from Phase 1 and documentation from Task 3.1 are merged to main branch
• Create an annotated Git tag: git tag -a 0.7.0 -m "Release 0.7.0 - Drop Python 3.9 support"
• Push the tag to the repository: git push origin 0.7.0
• Versioneer will automatically compute the version from this tag during build

Task 3: Publish to Test PyPI

Validate the release package on Test PyPI before publishing to production.

• Navigate to GitHub Actions and trigger the release.yml workflow manually
• Set test_py: true and main_py: false for Test PyPI publication
• Wait for workflow completion and verify success
• Install from Test PyPI to verify: pip install -i https://test.pypi.org/simple/ monailabel==0.7.0
• Run basic smoke tests to confirm the package works correctly

Task 4: Publish to Production PyPI

Release the verified package to the production Python Package Index.

• After successful Test PyPI verification, trigger the release.yml workflow again
• Set test_py: false and main_py: true for production PyPI publication
• Wait for workflow completion and verify success
• Verify the release appears on https://pypi.org/project/monailabel/
• Test installation from production PyPI: pip install monailabel==0.7.0
• Optionally create a GitHub Release with release notes matching the CHANGELOG

🤖 Prompt for AI agents

Prepare release artifacts and publish version 0.7.0 to PyPI following the
established release workflow. The project uses Versioneer for Git tag-based
versioning.

**Update Release Documentation:**
- In `CHANGELOG.md`, create a new version section: `## [0.7.0] - YYYY-MM-DD`
- Move items from the `[Unreleased]` section to the new version section
- Document Python 3.9 deprecation as a breaking change or compatibility note
- Include other significant changes since version 0.6.0 (last release December
2022)
- Follow the Keep a Changelog format established in the file

**Create Git Tag:**
- Ensure all changes from Phase 1 and CHANGELOG updates are merged to main
branch
- Create annotated Git tag: `git tag -a 0.7.0 -m "Release 0.7.0 - Drop Python
3.9 support"`
- Push tag to repository: `git push origin 0.7.0`
- Versioneer will automatically compute the version from this tag during build

**Test PyPI Publication:**
- Navigate to GitHub Actions and manually trigger the `release.yml` workflow
- Set parameters: `test_py: true` and `main_py: false`
- Wait for workflow completion and verify success
- Install from Test PyPI: `pip install -i https://test.pypi.org/simple/
monailabel==0.7.0`
- Run basic smoke tests to validate the package

**Production PyPI Publication:**
- After successful Test PyPI verification, trigger `release.yml` workflow again
- Set parameters: `test_py: false` and `main_py: true`
- Wait for workflow completion and verify success
- Verify release appears on https://pypi.org/project/monailabel/
- Test installation: `pip install monailabel==0.7.0`
- Optionally create a GitHub Release with release notes matching the CHANGELOG

---

🚀 Next Steps

🤖 All AI agent prompts combined

Task: 1

Fix Python version-related configuration issues to align with the Python >= 3.10
requirement already established in setup.cfg.

**Update GitHub Actions Test Matrix:**
- In `.github/workflows/pythonapp.yml`, locate the `python-version` matrix in
three jobs: `deps_check`, `build`, and `packaging`
- Remove `"3.9"` from each matrix, changing from `["3.9", "3.10", "3.11",
"3.12"]` to `["3.10", "3.11", "3.12"]`

**Update Black Formatter Configuration:**
- In `pyproject.toml`, locate the `[tool.black]` section
- Change `target-version` from `['py36', 'py37', 'py38']` to `['py310', 'py311',
'py312']`

**Fix YAML Version Number Quoting:**
- In `.github/workflows/docker-plugin.yml`, quote the `python-version` value:
change `python-version: 3.10` to `python-version: "3.10"`
- In `.github/workflows/release.yml`, quote the `python-version` value: change
`python-version: 3.10` to `python-version: "3.10"`
===============================================================================

Task: 2

Validate that all core functionality works correctly after the Python version
configuration changes. Verification should be performed both locally and through
CI/CD pipeline runs.

**CI/CD Pipeline Verification:**
- Push changes to a feature branch and create a pull request to trigger the
`pythonapp.yml` workflow
- Verify the `deps_check` job passes on Python 3.10, 3.11, and 3.12
- Verify the `build` job passes unit tests with coverage reporting
- Verify the `packaging` job successfully builds and validates packages
- Review and address any test failures before proceeding

**Model Functionality Verification:**
- Run integration tests for radiology models using `./runtests.sh --net` or
tests in `tests/integration/radiology/`
- Run integration tests for pathology models
- Run integration tests for endoscopy and monaibundle applications
- Verify MONAI Bundle compatibility (requires MONAI >= 1.4.0)
- Note that vista2d app requires Python 3.10+ for SAM-2

**OHIF Viewer Integration:**
- Execute OHIF v2 build script at `plugins/ohif/build.sh` and verify completion
without errors
- Confirm static assets are generated in `monailabel/endpoints/static/ohif/`
- Optionally test OHIF v3 build at `plugins/ohifv3/build.sh` if actively used
- Verify the `/ohif/` endpoint responds correctly when running the server

**3D Slicer Extension Compatibility:**
- Review `plugins/slicer/` for any Python 3.9-specific code or dependencies
- Run MONAILabelReviewer unit tests in
`plugins/slicer/MONAILabelReviewer/UnitTests/`
- Verify the plugin client library at `MONAILabelLib/client.py` works with
Python 3.10+
- Note that 3D Slicer 5.2+ is required for Python 3.10 compatibility
===============================================================================

Task: 3

Prepare release artifacts and publish version 0.7.0 to PyPI following the
established release workflow. The project uses Versioneer for Git tag-based
versioning.

**Update Release Documentation:**
- In `CHANGELOG.md`, create a new version section: `## [0.7.0] - YYYY-MM-DD`
- Move items from the `[Unreleased]` section to the new version section
- Document Python 3.9 deprecation as a breaking change or compatibility note
- Include other significant changes since version 0.6.0 (last release December
2022)
- Follow the Keep a Changelog format established in the file

**Create Git Tag:**
- Ensure all changes from Phase 1 and CHANGELOG updates are merged to main
branch
- Create annotated Git tag: `git tag -a 0.7.0 -m "Release 0.7.0 - Drop Python
3.9 support"`
- Push tag to repository: `git push origin 0.7.0`
- Versioneer will automatically compute the version from this tag during build

**Test PyPI Publication:**
- Navigate to GitHub Actions and manually trigger the `release.yml` workflow
- Set parameters: `test_py: true` and `main_py: false`
- Wait for workflow completion and verify success
- Install from Test PyPI: `pip install -i https://test.pypi.org/simple/
monailabel==0.7.0`
- Run basic smoke tests to validate the package

**Production PyPI Publication:**
- After successful Test PyPI verification, trigger `release.yml` workflow again
- Set parameters: `test_py: false` and `main_py: true`
- Wait for workflow completion and verify success
- Verify release appears on https://pypi.org/project/monailabel/
- Test installation: `pip install monailabel==0.7.0`
- Optionally create a GitHub Release with release notes matching the CHANGELOG

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Example Feedback
- `@coderabbitai` You can skip phase 3. Add a simple unit test case for phase 2.
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