[r/python] R/Python feature-gap analysis (high-level/parent issue)

[maniarathi]

Analyze the Python and R tiledbsoma packages to ensure that the APIs are at parity and document any gaps.

---

• Foundational types
  • SOMADataFrame
    • create: spec, R
      • Needs to take args for platform_config and context [r] Platform config #735
    • read: spec, R
      • Needs full argument support [r] Platform config #735
    • write: spec, R
      • Needs platform_config support [r] Platform config #735
      • Only supports Arrow Table while Python supports Arrow RecordBatch or Table [r] Let SOMADataFrame.write accept Arrow RecordBatch in addition to Arrow Table #939
    • schema: spec, R [r] Return schema information as an Arrow schema #978
    • index_column_names accessor: spec, [R] -- [r] Implement a read-accessor for SOMADataFrame$index_column_names #1006
  • SOMASparseNDArray
    • create: spec, R
      • Needs to take args for platform_config and context [r] Platform config #735
      • Needs factory-method approach [r] Make create and open into non-instance factory methods #1008
    • read: spec, R read_arrow_table, R read_sparse_matrix
      • Needs batch_size and partitions [r] Add batch_size and partitions to read_arrow_table and read_sparse_matrix #1005
    • shape: spec, [R] ... [r] Implement shape, nnz, and ndim accessors #940
    • nnz: spec, [R] ... [r] Implement shape, nnz, and ndim accessors #940
    • ndim: spec, [R] ... [r] Implement shape, nnz, and ndim accessors #940
    • schema: spec, [R] [r] Return schema information as an Arrow schema #978
    • write: spec, R: data argument should be values [r] Make SparseNDArray$write arg name match Python/spec #1004
  • SOMADenseNDArray
    • read: spec, R read_arrow_table, R read_dense_matrix
      • Needs platform_config, partitions, result_order [r] Platform config #735
    • shape: spec, [R] ... [r] Implement shape, nnz, and ndim accessors #940
    • ndim: spec, [R] ... [r] Implement shape, nnz, and ndim accessors #940
    • schema: spec, [R] [r] Return schema information as an Arrow schema #978
    • write: spec, R
      • Needs to take platform_config [r] Platform config #735
• Composed types
  • Shared code
    • create: spec, R -- needs factory-method approach [r] Make create and open into non-instance factory methods #1008
    • open: spec, R -- needs factory-method approach [r] Make create and open into non-instance factory methods #1008
    • close: spec, [R] needs to be public: [r] Make close methods public #1010
    • context accessor: spec, [R] [r] Add a context accessor #1011, with [r] Platform config #735 as prerequisite
    • uri accessor: spec, R
    • metadata accessor: spec; R arrays, R groups
  • SOMACollection
    • add_new_collection: spec, [R] ... [r] Implement add_new_* #938
    • add_new_dataframe: spec, [R] ... [r] Implement add_new_* #938
    • add_new_dense_ndarray: spec, [R] ... [r] Implement add_new_* #938
    • add_new_sparse_ndarray: spec, [R] ... [r] Implement add_new_* #938
    • set mutator: spec, R
  • SOMAExperiment
    • Class: spec, R
      • Full parity except for axis_query
      • [R] Use Futures library to accelerate [r] Use Futures library to accelerate ExperimentQuery #943
    • axis_query -- convenience method on SOMAExperiment to create one spec, [R] ... [r] Experiment-query API #736
    • AxisQuery class: spec, [R] ... [r] Experiment-query API #736
  • SOMAMeasurement
    • Class: spec, R -- full parity
  • Ephemeral -- more analysis pending until R's ExperimentQuery is merged
    • uri: spec, [R] [r] Port ephemeral classes from Python to R #1022
    • metadata: spec, [R] [r] Port ephemeral classes from Python to R #1022
    • open: spec, [R] [r] Port ephemeral classes from Python to R #1022
    • create: spec, [R] [r] Port ephemeral classes from Python to R #1022
    • add_new_collection: spec, [R] [r] Implement add_new_* #938
    • set: spec, [R] [r] Port ephemeral classes from Python to R #1022
• Options
  • Class: spec, [R] ...
• To be filed
  • coos: spec, [R] [r] Implement read return types tables, record_batches, coos, dense_tensors for SOMASparseNDArray #1007
  • dense_tensors: spec, [R] [r] Implement read return types tables, record_batches, coos, dense_tensors for SOMASparseNDArray #1007
  • record_batches: spec, [R] [r] Implement read return types tables, record_batches, coos, dense_tensors for SOMASparseNDArray #1007
  • tables: spec, [R] [r] Implement read return types tables, record_batches, coos, dense_tensors for SOMASparseNDArray #1007
• To/from Seurat matching Python's soma.io
  • to_seurat [r] Implement to_seurat #941
  • from_seurat [r] Implement to_seurat #941
• Other
  • nnz when allow_duplicates=True [c++] Support nnz when allow_duplicates=True #989 [r] Handle empty matrices when creating SOMA from Seurat #990 [r] Unit-test accesses of nnz when allow_duplicates=True #991
  • Appendability of SparseNDArray [python] Fix non-appendability of SparseNDArray #931 [r] Fix non-appendability of SparseNDArray #972

[johnkerl]

It looks like a merge of #963 auto-closed this parent task; GH automation overstep 😁

[eddelbuettel]

My bad. I put the wrong ticket into the PR. Should have been #963, typed #863. Whoops. Get me one of those 'do what I mean not do as I say' computers, please.

[johnkerl]

Everything here has been split out into separate tracking issues. Closing this issue.