v0.3.0

Added

• Support more AnnData fields, additional API for accessing, modifying and deleting fields: layers, obsm, varm, obsp, varp was added.(#22, #26)
• String representation for CapAnnData objects. (#24)
• Deprecation warnings for read_directly function. (#25). It is recommended to use read_h5ad instead.

Changed

• Dependencies updated in setup.py and requirements.txt to relax version constraints. (#23)
• Internal implementation CapAnnDataUns was renamed to CapAnnDataDict.

Fixed

• Empty raw layer fix. The situation when raw h5py.Group exists in the .h5ad file but is empty is recognized as no raw layer exists. (#27)

Full Changelog: v.0.2.2...v0.3.0

v0.2.2

Added

• compression option in overwrite method to allow using different compression algorithms. Note: lzf is still default (#20).

Changed

• requirements.txt updated to freeze package versions. Possible incompatibility with numpy v2+ was displayed. (#20)

Full Changelog: v0.2.1...v.0.2.2

v0.2.1

Fixed

• Python 3.9 Compatibility: Fixed type notation in CapAnnDataDF. (#16 )

Full Changelog: v0.2.0...v0.2.1

v0.2.0

Added

• Reader Module: Introduced reader.py with context manager read_h5ad and function read_directly for reading AnnData files.
• Join and Merge Methods: Enhanced methods for joining and merging dataframes in CapAnnDataDF.
• New Methods for Accessing Keys: Added obs_keys and var_keys methods to CapAnnData for retrieving column keys without load content of .h5ad file to memory.
• Append columns from disc: Added the possibility to join the new column from disc to in-memory DataFrame. Previously, it was only possible to read new DataFrame from disc inplace of in-memory one.
• DataFrame Setters: Added validation in DataFrame setters to ensure correct data types and shapes.

Changed

• Refactored CapAnnData Class:
  • Moved RawLayer to a separate class.
  • Introduced BaseLayerMatrixAndDf as a base class for CapAnnData and RawLayer.
  • Simplified read_obs, read_var, and overwrite methods.
  • Enhanced _read_df to handle column order and in-memory DataFrame updates.
  • Replaced read_obs and read_var methods to support resetting DataFrames and incremental reads.

Fixed

• Empty Column Order Handling: Fixed issue with empty column order attribute in CapAnnDataDF.
• Overwrite Method: Corrected handling of column order in the overwrite method to avoid type mismatches.

Removed

• Context Manager for AnnData Files: Removed context manager method read_anndata_file from CapAnnData.

Full Changelog: v0.1.1...v0.2.0

v0.1.1

Fixed

• Bug in overwrite method for empty obs/var sections by ensuring that the column_order attribute is always of type object (#5 ).

Full Changelog: v0.1.0...v0.1.1

v0.1.0

Added

• Initial release of CAP-AnnData.
• Introduced the CapAnnData class for managing AnnData files, with functionalities to:
  • Read and write specific columns of obs and var.
  • Handle the X and raw.X matrices efficiently.
  • Link and manage obsm and uns sections lazily, loading them only when accessed.
• Included the CapAnnDataDF class to extend pandas.DataFrame for handling partial reads and writes, with additional methods for renaming and removing columns.
• Provided the CapAnnDataDict class to manage the uns section of AnnData files, tracking keys to remove upon overwrite.
• Implemented methods to facilitate in-memory modifications and saving changes back to the file, including the overwrite method to selectively update sections of the AnnData file.

Full Changelog: https://github.com/cellannotation/cap-anndata/commits/v0.1.0