Changelog

Source: NEWS.md

dafr 0.1.0

Breaking Changes

Updated to DataAxesFormats.jl v0.2.0 API

• Renamed query operations to match v0.2.0 naming:
  • Lookup -> LookupVector
  • And -> AndMask
  • AndNot -> AndNegatedMask
  • Or -> OrMask
  • OrNot -> OrNegatedMask
  • Xor -> XorMask
  • XorNot -> XorNegatedMask
  • SquareMaskColumn -> SquareColumnIs
  • SquareMaskRow -> SquareRowIs
• Removed Fetch and MaskSlice (deprecated wrappers still provided for backwards compatibility)
• Deprecated wrappers provided for all renamed functions with deprecation warnings

Parameter Changes

• Names: removed kind parameter
• IfMissing: missing_value renamed to default_value, type parameter removed
• Axis: now optional in queries

New Features

New Query Operations

• Added LookupScalar for looking up scalar data
• Added LookupMatrix for looking up matrix data
• Added BeginMask for starting a mask combination
• Added BeginNegatedMask for starting a negated mask combination
• Added EndMask for ending a mask combination
• Added GroupColumnsBy for grouping columns
• Added GroupRowsBy for grouping rows
• Added ReduceToColumn for reducing matrix to a column vector
• Added ReduceToRow for reducing matrix to a row vector

New Functions

• Added complete_path for constructing complete paths to Daf data
• Added complete_chain for opening complete chain Daf repositories

Documentation

• All documentation URLs updated to DataAxesFormats.jl v0.2.0

dafr 0.0.3

New Functions

New Operations

• Added Count() for counting non-zero elements, with optional type parameter
• Added GeoMean() for geometric mean reduction, with optional type and eps parameters
• Added Mode() for most common value reduction

Query Utilities

• Added escape_value() for escaping special characters in query strings
• Added unescape_value() for reversing escape_value()
• Added query_requires_relayout() to check if a query needs data relayout

Empty Data Functions

• Added get_empty_dense_vector() for getting empty dense vectors for in-place filling
• Added get_empty_sparse_vector() for getting empty sparse vectors for in-place filling
• Added get_empty_dense_matrix() for getting empty dense matrices for in-place filling
• Added get_empty_sparse_matrix() for getting empty sparse matrices for in-place filling
• Added filled_empty_sparse_vector() for committing filled sparse vectors back to Daf
• Added filled_empty_sparse_matrix() for committing filled sparse matrices back to Daf
• Exported get_frame() for direct use

Enhanced Parameters

• Added type parameter to all reduction operations (Abs, Sum, Mean, Median, Quantile, Var, VarN, Std, StdN, Min, Max, Count, Fraction, Round, Clamp, Log)
• Added eps parameter to VarN, StdN, GeoMean
• Added type and insist parameters to copy_scalar()
• Added eltype, bestify, min_sparse_saving_fraction, and insist parameters to copy_vector()
• Added eltype, bestify, min_sparse_saving_fraction, and insist parameters to copy_matrix()
• Added relayout, bestify, min_sparse_saving_fraction parameters to copy_tensor()
• Added X_eltype parameter to daf_as_h5ad()

CI/CD

• Added GitHub Actions workflows for R CMD check, conda build, and pkgdown site deployment
• Added conda recipe for building and distributing conda packages
• Fixed CI test execution to properly install package before running testthat tests

Tests

• Added comprehensive tests for all new functions and parameters
• New test files: test-operations.R, test-copies.R, test-data-writers.R, test-queries.R, test-anndata_format.R

dafr 0.0.2

New Features

Contract System

• Added create_contract() for defining data contracts with axes and data specifications
• Added axis_contract(), scalar_contract(), vector_contract(), matrix_contract() for specifying contract requirements
• Added tensor_contract() for 3D tensor specifications
• Added verify_contract(), verify_input(), verify_output() for validating Daf objects against contracts
• Added contractor() for creating contract-aware Daf wrappers
• Added contract_docs() for generating markdown/text documentation from contracts
• Added expectation types: RequiredInput, OptionalInput, GuaranteedOutput, OptionalOutput

Group Functions

• Added group_names() for generating unique deterministic names for groups based on members
• Added collect_group_members() for converting group indices to member lists
• Added compact_groups() for compacting non-consecutive group indices to 1..N

View Constants

• Added VIEW_ALL_AXES, VIEW_ALL_SCALARS, VIEW_ALL_VECTORS, VIEW_ALL_MATRICES, VIEW_ALL_DATA constants for creating views of complete data

Query Utilities

• Added is_axis_query() to check if a query targets only axes
• Added query_axis_name() to extract axis name from axis-only queries

Version Counters

• Added axis_version_counter(), vector_version_counter(), matrix_version_counter() for tracking data modifications

Complete/Open Functions

• Added complete_daf() for opening complete chains of Daf repositories
• Added open_daf() for smart opening of files-based or HDF5-based Daf

Example Data

• Added example_chain_daf() for creating example chain data

Improvements

• Added tensors parameter to description() function
• Fixed issue with error when returning only names (#6)
• Improved test coverage with 1201 tests (up from baseline)

dafr 0.0.1

• Initial WIP