Create package (#359)

* convert to pypi package, init

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* reorg package struckure to match standard

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Fix incomplete import migration from src to claymodel

- Update trainer.py imports to use claymodel instead of src
- Fix all notebook files to use claymodel imports
- Fix circular import in claymodel/callbacks_wandb.py
- Add pip installation instructions to README
- All import paths now consistently use claymodel package

Resolves the ModuleNotFoundError issues and makes the package
properly installable via pip.

* Enhance package configuration and initialization

- Improve pyproject.toml with proper metadata, license, and flexible dependencies
- Add comprehensive package documentation and usage examples
- Create structured __init__.py files for better package organization
- Update dependency versions to use >= for better compatibility
- Add proper package metadata for PyPI publication

The package now has professional-grade configuration suitable for
distribution while maintaining all functionality.

* Complete import migration for all example scripts

- Fix remaining finetune imports in classify.py, segment.py, regression.py
- Update internal imports in model files (eurosat_model.py, etc.)
- All scripts now use claymodel.finetune.* imports consistently
- Ready for full testing in proper environment

All import migration work completed:
✅ trainer.py fixed
✅ All 12 notebooks updated
✅ All finetune example scripts fixed
✅ Internal cross-module imports updated

* Add comprehensive testing status documentation

- Documents all completed import migration work
- Lists all fixed files (6 Python scripts + 12 notebooks)
- Provides testing checklist for clean environment
- Ready for validation in proper PyTorch environment

* Add minimum version constraints for better dependency resolution

- Add lightning>=2.0.0 to ensure compatibility
- Add timm>=0.6.0 for stable API
- Maintain flexible upper bounds for PyTorch ecosystem

This ensures users get compatible versions while allowing
for future updates. The flexible bounds prevent the version
conflicts we encountered in testing environments.

* Remove outdated testing status documentation

- Delete the TESTING_STATUS.md file as it is no longer relevant
- This file contained information on completed import migration and testing status
- The removal reflects the transition to a new testing framework or documentation approach

This change simplifies the repository by eliminating obsolete documentation, ensuring that only current and relevant information is maintained.

* """
Update documentation and .gitignore for improved usability

- Add new entries to .gitignore to exclude checkpoint files (*.ckpt) from version control
- Enhance documentation by adding a Quick Start guide and a Migration guide to facilitate user onboarding
- Update installation instructions to reflect the new pip-installable package structure
- Include detailed examples for generating embeddings and using pretrained models

These changes aim to streamline the user experience, making it easier for new users to get started with the Clay Foundation Model while ensuring that unnecessary files are not tracked in the repository.
"""

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* make ruff happy

* ruff-ing

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Refactor function and condition checks for clarity

- Corrected the type check in `initialize_weights` method to use a tuple for `isinstance`, ensuring proper evaluation of both `nn.Linear` and `nn.Conv2d`.
- Fixed a typo in the function name `list_uniqe_ids` to `list_unique_ids` for consistency and accuracy in `preprocess_data.py`.
- Updated the call to the corrected function name in the `process` function.

These changes enhance code readability and maintainability by ensuring correct type checks and function naming conventions.

* Refactor tutorial notebook for clarity and error handling

- Removed unnecessary output cells from the `tutorial_digital_earth_pacific_patch_level.ipynb` notebook, which included warnings and installation logs that cluttered the output.
- Updated the execution count for code cells to `null` to reset the notebook state, ensuring a clean slate for users running the tutorial.
- This refactoring enhances the user experience by providing a cleaner and more focused tutorial without extraneous information.

These changes aim to improve the clarity and usability of the tutorial notebook, making it easier for users to follow along without distractions.

* Update docs/index.md

Co-authored-by: Copilot <[email protected]>

---------

Co-authored-by: Romeo Kienzler <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Copilot <[email protected]>

Segmentation on Clay (#257)

- Add segmentation support for Clay
- Add preprocessing script for Chesapeake Bay dataset

Changelog entry for v0.0.1 (#113)

First release of Clay Foundation Model.