Refactored test cases

[anushka255]

• Refactored test cases to use .npz files mostly.
• Consolidated tests/data/input and tests/data/output directories to a single one tests/data.
• Upgraded numpy to be greater than version 2.0.
• The docs are failing in this PR because, one of the docs dependency squidpy is not compatible with numpy of version greater than 2.0. Removed squidpy as docs dependency; using scanpy instead #99 deals with this issue.

[vineetbansal]

If I understand correctly, the tests in this PR are passing with numpy<2 (the pinned workflows) and also numpy>2 (unpinned workflows). Given that this is the case, and we're not explicitly using any features exclusive to numpy 2 and above, why don't we just unpin numpy's version from our requirements completely? We should also update our pinned workflows to whatever latest versions seem to be working on the CI.

[anushka255]

Unpinned everything in pyproject.toml and updated requirements.txt to pin the latest versions of the packages that work.