All notable changes to this project will be documented in this file.

• New validation error AnnDataMultipleOntologyIDs, which requires each ontology term ID to be a single term.
• New validation error AnnDataInvalidDiseaseOntologyForHuman, which requires the use of MONDO: and PATO: disease ontology terms for Homo sapiens datasets.

• Minor changes in error message formatting

• More dynamic error messages added.

• New genes were added to Gene Map file for Homo Sapiens
• New error message was added for CSC matrices in adata.X or adata.raw.X

• New genes were added to Gene Map file for Homo Sapiens

• New find_missing_genes()->pd.DataFrame function was added to UploadValidator to help users identify missing genes in their AnnData files.
• More gene ids were added to Homo Sapiens Gene Map to cover missing genes reported by users from outdated ensembl releases.

• Gene Map file for Homo Sapiens was updated to support some outdated ENSEMBL ids from the Issue

• Gene Map file for Homo Sapiens was updated from GENCODE Release 49
• Gene Map file for Mus Musculus was updated from GENCODE Release M38

• Added gene validation for cases when organisms are specified using ontology term IDs instead of names.

• New exception AnnDataNoneInGeneralMetadata to handle cases where required metadata fields contain None or empty values.

• General metadata check in UploadValidator now checks if any of general metadata or its ontology term ID exists in the obs dataframe. For example, the validator will pass if either tissue or tissue_ontology_term_id exists and non empty. Otherwise, the validator will raise AnnDataMissingObsColumns.

• Strict requirement to have dense matrix with embeddings in obsm. Data Frames and sparse matrices will be ignored.

• CLI interface

• UploadValidator class to validate AnnData files
• Gene mapping support for Homo sapiens and Mus musculus
• Custom error handling with CapMultiException
• Basic unit tests for core functionality

• This is the first public version of the package.