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Changelog

Source: NEWS.md

dbMatrix 0.0.0.9023 (2024-09-18)

Breaking Changes

  • dbMatrix summary methods now return dbDenseMatrix objects instead of in-memory vectors.

  • Removed colTypes from castNumeric.

  • Removed @name check in initialize.

Features

  • New compute method for saving dbMatrix objects. This writes the dbMatrix object to a table in the database along with its row and column names (e.g. ‘dbMatrixname_rownames’).

  • New load method for loading computed dbMatrix objects. The dbMatrix::compute() method must be called before loading the object.

  • Updated .check_overwrite to allow for passing overwrite arg.

  • New internal function write_dimnames to enable saving dbMatrix objects.

  • New sum method for dbMatrix objects.

  • Improvements to precomputed table: Use existing precomputed table in db if available.

  • Improvements to precomputed table: Transpose precomputed table of sufficient dimensions if it exists instead of creating a new one. This is done via a TEMPORARY VIEW to avoid writing to disk and modifying existing precomputed table which may be referenced by other tables.

  • Custom SQL statement for todbDense conversion creates a TEMPORARY VIEW with name dbDenseMatrix_hash.

Chore

  • Update whitespace.

  • Update dbMatrix constructor roxygen.

  • Update roxygen in toDbDense.

Docs

  • Update reference page.

  • Update mean documentation.

  • Update log documentation.

  • Update roxygen.

Bug fixes

  • Do not recycle matrix if not needed.

dbMatrix 0.0.0.9022 (2024-08-14)

Breaking changes

Features

  • Add more tests for dbMatrix and dbDenseMatrix.

  • Add internal function map_ijx_dimnames.

  • Add internal function dbMatrix_from_tbl.

  • Extract now constructs unique temporary virtual tables in the arrow schema.

Chore

  • Document pkgdown website.

  • Add cli to imports.

  • Update generics.

Bug fixes

  • Be more explicit about non-supported Arith and Ops operations.

  • Fix show() method for dbDenseMatrix objects.

dbMatrix 0.0.0.9021 (2024-07-05)

Bug fixes

  • Improve show function for dbDenseMatrix.

  • Updated simulate functions to include overwrite param.

  • Update .check_overwrite() internal function to avoid bug in overwritting passed table.

dbMatrix 0.0.0.9020 (2024-07-05)

Features

  • Add initial support for reading in .mtx files and creating dbMatrix objects.

Bug fixes

  • Update check_overwrite input validation

Chore

  • Update Royxgen

dbMatrix 0.0.0.9019 (2024-03-18)

Features

  • Add new precompute function to speed up matrix densification.

  • Add new show function for dbDenseMatrix with pretty color and better spacing.

  • Add new save function to save a dbMatrix.

  • Add new input validation functions.

Chore

  • Update docs.

  • Update imports to include glue, bit64 and crayon.

dbMatrix 0.0.0.9018 (2024-02-12)

Bug fixes

  • Update constructor calls in sim functions.

  • Remove redundant con from constructor.

  • Remove db_path from constructor.

  • Constructor db_path arg change to con object.

Features

  • Add dgTMatrix to in-memory matrix types supported in dbMatrix constructor.

Chore

  • Set :memory: to default db_path in constructor.

  • Update createDBMatrix docs.

Documentation

  • Spacing.

  • Update after constructor fix.

  • Remove :temp: in place of :memory:.

dbMatrix 0.0.0.9017 (2024-02-07)

Bug fixes

  • Remove “:temp:” from tests.

  • Replace ‘:temp:’ with ‘:memory:’.

  • Add matrix in addition to dgCMatrix in as_ijx().

Features

  • Add unit tests for scalar arith.

  • Add unit tests for names.R.

Chore

  • Remove random browser() call.

  • Add MatrixGenerics to deps.

  • Update gitignore.

dbMatrix 0.0.0.9016 (2024-01-23)

Features

  • Add boolean indexing tests to test-extract.R.

  • Add as_ijx() convenience function.

  • Update createDBMatrix() to use dplyr::copy_to().

  • Update as_matrix() convenience function.

  • Add unit tests for extract methods.

dbMatrix 0.0.0.9015 (2024-01-22)

Features

  • Add log().

  • Update toDbDense to use dplyr instead of SQL.

Chore

  • Update DESCRIPTION to include testthat.

  • Update docs.

dbMatrix 0.0.0.9014 (2024-01-19)

Features

  • update dbIndex superclass

  • update as_matrix()

dbMatrix 0.0.0.9013 (2024-01-18)

Bug fixes

  • Rename and update dbIndex superclass to fix indexing bugs.

Features

  • Add experimental as_matrix() convenience function.

Chore

  • Update docs.

  • Migrate site link to drieslab.

  • Move {Matrix} to Imports.

Documentation

  • Update overview.Rmd.

  • Update operations vignette.

dbMatrix 0.0.0.9012 (2023-12-08)

Bug fixes

  • Only densify if necessary. != 0, +/-.

  • toDbDense() previously updated table by value. change to update by reference via VIEW creation of table named ‘dense’.

Features

  • Add dbListTables().

Chore

  • Update docs.

  • Update gitignore.

dbMatrix 0.0.0.9011 (2023-12-08)

Bug fixes

  • Fix incorrect aggregate operations.

  • Fixes after con slot removal.

Features

  • Add get_con().

  • Add dbDisconnect() generic.

  • Update accessors.

Chore

  • Update vignettes.

  • Update README.

  • Update gitignore.

  • Update docs.

  • Update NEWS.

dbMatrix 0.0.0.9010 (2023-11-25)

Breaking changes

  • migrate to |> pipe, remove %>%, update deps.

Chore

  • Update docs.

dbMatrix 0.0.0.9009 (2023-11-20)

Bug fixes

  • Mean generic for dbDenseMatrix.

Chore

  • Update docs.

  • Update site.

  • Update gitignore.

dbMatrix 0.0.0.9008 (2023-11-17)

Bug fixes

  • Updates to dbSparseMatrix rowMeans, colMeans.

  • Updates to colSums and rowSums for dbSparseMatrix.

  • Update dbMatrix constructor dimnames issues.

Chore

  • Update DESCRIPTION, remove redundant Matrix import, dep.

  • Update docs.

  • Update roxygen for operations.

dbMatrix 0.0.0.9007 (2023-11-09)

Features

  • Add Matrix as dep.

dbMatrix 0.0.0.9006 (2023-11-09)

Bug fixes

  • Methods::as scope correction.

Features

  • Add methods to deps.

Chore

  • Update .gitignore.

dbMatrix 0.0.0.9005 (2023-11-09)

Feat

  • Add Matrix as pkg dep

dbMatrix 0.0.0.9004 (2023-11-09)

Bug fixes

  • Missing Matrix:: scope call.

Chore

  • Update docs.

dbMatrix 0.0.0.9003 (2023-11-07)

Fix

  • dims and dim_names in createDBMatrix() retained from in-memory matrix or Matrix object

Chore

  • Update docs for dbMatrix input checks

dbMatrix 0.0.0.9002 (2023-11-07)

Feat

  • Specify checks for ‘name’ param in createDBMatrix()

Chore

  • Update docs.

  • Add docs.

dbMatrix 0.0.0.9001 (2023-11-04)

Chore

  • Update docs and DESCRIPTION.

  • Migration dbMatrix.