Package UELer as a pip package

[yulewu]

UELer will be prepared for distribution on PyPI. The codebase will be packaged following Python best practices to allow users to install UELer via pip.

Tasks include:

• Adding a setup.py and necessary packaging files.
• Writing or updating the README.md with pip installation instructions.
• Ensuring that dependencies are specified and handled properly.
• Testing the package installation process locally and from PyPI.

This will enhance the usability and accessibility of UELer for the community.

[yulewu]

Update Summary: pip packaging cleanup (#79) (commit 9985621)

Cleaned up the project structure so that pip install -e . works correctly with only ueler/ as the package root.

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Actions Taken

• Deleted stale top-level viewer/ directory:
  Removed all files under viewer/ (including plugin/ and images/ subdirectories). The canonical versions live in ueler/viewer/.
• Deleted stale root-level module files:
  Removed constants.py, data_loader.py, image_utils.py, and __init__.py from the repo root, whose content has been migrated into ueler/.
• Rewrote pyproject.toml:
  Updated to the full dependency list (scikit-image, dask, ipydatagrid, opencv-python, jupyter-scatter, etc.), added ark and dev optional-dependency groups, restricted [tool.setuptools.packages.find] to ueler and ueler.* only (removing viewer and viewer.*), removed py-modules for the deleted root modules, and added [tool.setuptools.package-data] for ueler.viewer/images/*. Also normalised the version from "v0.3.1" to "0.3.1" (PEP 440).
• Fixed stale imports:
  Updated all from viewer.* / from data_loader import / from viewer import references in ueler/, ueler/viewer/, and the test suite to use the correct ueler.* paths.

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Files Changed

• pyproject.toml — rewrote with full dependency list and corrected package discovery config.
• viewer/ (deleted) — removed stale top-level copy of viewer modules.
• constants.py, data_loader.py, image_utils.py, __init__.py (deleted from root) — removed stale root-level modules.
• ueler/__init__.py — fixed TYPE_CHECKING import of viewer → ueler.viewer.
• ueler/viewer/__init__.py — fixed TYPE_CHECKING import of viewer → ueler.viewer.
• tests/test_annotation_palettes.py — fixed from data_loader import and from viewer.* imports.
• tests/test_scatter_widget_dependencies.py — fixed from viewer.plugin.scatter_widget import.
• tests/test_mask_color_sets.py — fixed from viewer.plugin.mask_painter import.
• tests/bootstrap.py — fixed from viewer.plugin import heatmap* imports.
• tests/test_wide_plugin_panel.py — fixed from viewer.ui_components and viewer.plugin.plugin_base imports.
• tests/test_chart_footer_behavior.py — fixed three from viewer.* imports.
• tests/test_roi_manager_tags.py — fixed from viewer.plugin.roi_manager_plugin import.

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Tests

python -m pip install -e ".[dev]" --dry-run

• ✅ Dry-run completed successfully; all dependencies resolved for ueler==0.3.1.