NEWS.md

zellkonverter 1.16.0

• Bioconductor 3.20, October 2024

zellkonverter 1.15.4 (2024-10-18)

• Fix correctly assign levels to factors in R reader with anndata v0.7 files (Fixes #122)
• Add environment for anndata v0.10.9
• Avoid deprecation warning due to setting dtype when creating Python AnnData objects
• Standardise code styling using {styler}

zellkonverter 1.15.3 (2024-10-04)

• Correctly assign levels to factors in R reader (Fixes #122)

zellkonverter 1.15.2 (2024-10-02)

• Correctly set filepath in the R reader with reading adata.raw with use_hdf5 = TRUE (PR #124 @GabrielHoffman, Fixes #123)

zellkonverter 1.15.1 (2024-06-21)

• Skip anndata v0.7.6 tests on Apple Silicon as Python 3.7 is not available
• Fix URL for GTEx 8 tissues dataset in long tests
• Add test using the more complete example H5AD file

zellkonverter 1.15.0 (2024-05-01)

• Bioconductor 3.20 devel

zellkonverter 1.14.0 (2024-05-01)

• Bioconductor 3.19, May 2023

zellkonverter 1.14.1 (2024-06-21)

• Skip anndata v0.7.6 tests on Apple Silicon as Python 3.7 is not available
• Fix URL for GTEx 8 tissues dataset in long tests
• Add test using the more complete example H5AD file

zellkonverter 1.13.4 (2024-04-26)

• Prepare NEWS for release

zellkonverter 1.13.3 (2024-03-25)

• Correctly handle use_backed = TRUE with newer anndata versions (Fixes #114)
• Improve warnings when converting matrices fails
• Add environment for anndata v0.10.6

zellkonverter 1.13.2 (2024-01-17)

• Minor change to writing DelayedArrays for compatibility with {HDF5Array} v1.31.1

zellkonverter 1.13.1 (2023-11-13)

• Fix the anndata v0.10.2 environment instantiation (Fixes #103)
• Fix a typo in the AnnData Conversion docs (Fixes #100)

zellkonverter 1.13.0 (2023-10-25)

• Bioconductor 3.19 devel

zellkonverter 1.12.0 (2023-10-25)

• Bioconductor 3.18, October 2023

zellkonverter 1.12.1 (2023-11-13)

• Fix the anndata v0.10.2 environment instantiation (Fixes #103)
• Fix a typo in the AnnData Conversion docs (Fixes #100)

zellkonverter 1.11.4 (2023-10-16)

• Add environment for anndata v0.10.2

zellkonverter 1.11.3 (2023-10-2)

• Add environment for anndata v0.9.2

zellkonverter 1.11.2 (2023-08-28)

• Changes for compatibility with {rhdf5} v2.45.1
  • Support for enum types that simplifies reading of nullable types in the native R reader

zellkonverter 1.11.1 (2023-05-23)

• Pass correct dimensions when converting raw (Fixes #96)
• Convert anndata backed sparse matrices in AnnData2SCE() (Fixes #96)

zellkonverter 1.11.0 (2023-04-26)

• Bioconductor 3.18 devel

zellkonverter 1.10.0 (2023-04-26)

• Bioconductor 3.17, April 2023

zellkonverter 1.10.1 (2023-05-23)

• Pass correct dimensions when converting raw (Fixes #96)
• Convert anndata backed sparse matrices in AnnData2SCE() (Fixes #96)

zellkonverter 1.9.3 (2023-04-06)

• Add functions for converting pandas arrays used by anndata when arrays have missing values (Fixes #87)
• Read the correct index names in the R reader (PR #93 mtmorgan)
• Adjust tests to match reader changes

zellkonverter 1.9.2 (2023-03-28)

• Add @rcannood as a contributor (PR #90 @rcannood, fixes #88)

zellkonverter 1.9.1 (2023-03-14)

• Add compatibility with the anndata v0.8 H5AD format to the the native R writer (PR #86 @jackkamm, fixes #78)

zellkonverter 1.9.0 (2022-11-02)

• Bioconductor 3.17 devel

zellkonverter 1.8.0 (2022-11-02)

• Bioconductor 3.16, November 2022

zellkonverter 1.7.8 (2022-10-04)

• Improve compatibility with the R {anndata} package (PR #76 @rcannood, fixes #75)
  • Python objects are now explicitly converted rather than relying on automatic conversion
  • Other minor modifications for compatibility
• Added support for numpy recarrays (dtype number 20) (PR #81, fixes #45, #28)
  • Added a new py_to_r.numpy.ndarray() function which extends the default {reticulate} function
• Improvements to warnings
• Improvements and updates to tests

zellkonverter 1.7.7 (2022-10-04)

• Pin python version to 3.7.10 in anndata v0.7.6 environment (3.7.12 was not compatible with other dependencies)

zellkonverter 1.7.6 (2022-09-29)

• Pin python version to 3.7.12 in anndata v0.7.6 environment to match {basilisk} changes

zellkonverter 1.7.5 (2022-09-13)

• Minor changes for compatibility with {cli} v3.4.0
  • Added tests for verbose=TRUE

zellkonverter 1.7.4 (2022-08-17)

• Minor changes for compatibility with the upcoming {Matrix} 1.4-2 release

zellkonverter 1.7.3 (2022-06-23)

• Move verbose from zellkonverterAnnDataEnv() (Fixes #66)

zellkonverter 1.7.2 (2022-06-09)

• Instantiate environments for basilisk::configureBasiliskEnv() (Fixes #66)
• Allow missing obs/var names when use_hdf5 = TRUE (Fixes #65)

zellkonverter 1.7.1 (2022-05-17)

• Fix bug in long tests

zellkonverter 1.7.0 (2022-04-27)

• Bioconductor 3.16 devel

zellkonverter 1.6.0 (2022-04-27)

• Bioconductor 3.15, April 2022

zellkonverter 1.6.5 (2022-09-13)

• Minor changes for compatibility with {cli} v3.4.0
  • Added tests for verbose=TRUE

zellkonverter 1.6.4 (2022-08-17)

• Minor changes for compatibility with the upcoming {Matrix} 1.4-2 release

zellkonverter 1.6.3 (2022-06-23)

• Move verbose from zellkonverterAnnDataEnv() (Fixes #66)

zellkonverter 1.6.2 (2022-06-09)

• Instantiate environments for basilisk::configureBasiliskEnv() (Fixes #66)
• Allow missing obs/var names when use_hdf5 = TRUE (Fixes #65)

zellkonverter 1.6.1 (2022-05-17)

• Fix bug in long tests

zellkonverter 1.5.4 (2022-04-25)

• Fix progress messages in .convert_anndata_df()
• Allow data.frames in varm in SCE2AnnData()
• Standardise uns names to match R conventions in AnnData2SCE()
• Adjust long tests

zellkonverter 1.5.3 (2022-04-19)

• Reduce scipy version to 1.7.3
  • scipy >= 1.8.0 is incompatible with {reticulate} <= 1.24 (see rstudio/reticulate#1173)
• Add GTEX 8 tissues dataset to long tests (see #58)

zellkonverter 1.5.2 (2022-04-17)

• Update the default Python environment to use anndata v0.8.0
  • anndata 0.8.0
  • h5py 3.6.0
  • hdf5 1.12.1
  • natsort 8.1.0
  • numpy 1.22.3
  • packaging 21.3
  • pandas 1.4.2
  • python 3.8.13
  • scipy 1.8.0
  • sqlite 3.38.2
• Add options to choose Python environments with different versions of anndata
  • To facilitate this zellkonverterAnnDataEnv() and AnnDataDependencies() are new functions rather than variables
  • Added a new .AnnDataVersions variable which stores the available anndata versions
  • Updates to the vignette and function documentation explaining this option

zellkonverter 1.5.1 (2022-03-21)

• Modify how Pandas DataFrames are converted to R
  • Columns should now use R approved names with a warning when changes are made

zellkonverter 1.5.0 (2021-10-27)

• Bioconductor 3.15 devel

zellkonverter 1.4.0 (2021-10-27)

• Bioconductor 3.14, October 2021

zellkonverter 1.3.3 (2021-10-20)

• Add progress messages to various functions
  • Can be controlled by function arguments or a global variable
• Split konverter.R into two files (AnnData2SCE.R and SCE2AnnData.R)
• Add arguments to control how slots are converted in AnnData2SCE() and SCE2AnnData() (Fixes #47)
  • Each slot can now be fully converted, skipped entirely or only selected items converted.
• Add support for converting the raw slot to an altExp in AnnData2SCE() (Fixes #53, fixes #57)

zellkonverter 1.3.2 (2021-09-09)

• Add recursive conversion of lists in AnnData2SCE()
• Correctly handle DataFrame objects stored in adata.obsm
• Remove pandas indexes from converted DataFrame objects
• Add functions for validating SingleCellExperiment objects (for testing)
• Add long tests for various public datasets

zellkonverter 1.3.1 (2021-06-22)

• Fix bug in converting dgRMatrix sparse matrices (Fixes #55)

zellkonverter 1.3.0 (2021-05-20)

• Bioconductor 3.14 devel

zellkonverter 1.2.0 (2021-05-20)

• Bioconductor 3.13, May 2021

zellkonverter 1.2.1 (2021-06-22)

• Fix bug in converting dgRMatrix sparse matrices (Fixes #55)

zellkonverter 1.1.11 (2021-05-19)

• Add experimental native R reader to readH5AD()

zellkonverter 1.1.10 (2021-05-18)

• Update NEWS for release

zellkonverter 1.1.9 (2021-05-12)

• AnnData2SCE() no longer returns dgRMatrix sparse matrices (Fixes #34)

zellkonverter 1.1.8 (2021-05-03)

• Add conversion checks to all slots in AnnData2SCE() (See #45)
• Enable return conversion of varm in SCE2AnnData() (Fixes #43)
• Store X_name in AnnData2SCE() for use by SCE2AnnData() and add an X_name argument to AnnData2SCE() and readH5AD() (Fixes #7)

zellkonverter 1.1.7 (2021-04-30)

• Add compression argument to writeH5AD() (Fixes #49)
• Update anndata Python dependencies, now using anndata v0.7.6

zellkonverter 1.1.6 (2021-04-27)

• Adapt to changes in HDF5Array::HDF5Array()

zellkonverter 1.1.5 (2021-03-05)

• Better support for anndata SparseDataset arrays (PR #41, Fixes #37, Fixes #42)
• More consistent conversion of metadata to uns in SCE2AnnData() (Fixes #40)
• Add handling of list columns in colData and rowData in SCE2AnnData() (Fixes #26)
• Export zellkonverterAnnDataEnv (Fixes #38)

zellkonverter 1.1.4 (2021-02-18)

• Handle writing DelayedArray assays on the R side in writeH5AD() (PR #35, Fixes #32)

zellkonverter 1.1.3 (2021-01-22)

• Adjust SCE2AnnData() example (Fixes #31)

zellkonverter 1.1.2 (2020-12-19)

• Improved support for HDF5 backed conversion (PR #29, fixes #13)

zellkonverter 1.1.1 (2020-12-03)

• Add example_anndata.h5ad file to inst/extdata/ and creation script to inst/scripts/
• Improve conversion checks when converting .uns to metadata
• Avoid converting obsp and varp to dense matrices

zellkonverter 1.1.0 (2020-10-28)

• Bioconductor 3.13 devel

zellkonverter 1.0.0 (2020-10-28)

• Bioconductor 3.12, October 2020

zellkonverter 1.0.3 (2021-03-08)

• Avoid converting obsp and varp to dense matrices

zellkonverter 1.0.2 (2021-01-28)

• Merge remaining commits for HDF5 conversion (fixes #33)

zellkonverter 1.0.1 (2021-01-26)

• Improved support for HDF5 backed conversion (PR #29, fixes #13, fixes #33)

zellkonverter 0.99.7 (2020-10-16)

• Update Python dependencies
  • numpy 1.18.5 -> 1.19.1
  • pandas 1.0.4 -> 1.1.2
  • scipy 1.4.1 -> 1.5.2
  • sqlite 3.30.1 -> 3.33.0

zellkonverter 0.99.6 (2020-10-12)

• Document character to factor coercion in writeH5ad() (Fixes #6)
• Add X_name argument to writeH5AD() (Fixes #23)

zellkonverter 0.99.5 (2020-09-28)

• Tidy NEWS files for Bioconductor release

zellkonverter 0.99.4 (2020-08-28)

• Bump anndata version to 0.7.4

zellkonverter 0.99.3 (2020-08-21)

• Document the krumsiek11.h5ad file
• Remove the internal keyword from the zellkonverter-package documentation

zellkonverter 0.99.2 (2020-08-21)

• Update .gitignore

zellkonverter 0.99.1 (2020-07-15)

• Fix SCE to AnnData map figure in PDF manual
• Use expect_equal() instead of expect_identical() in writeH5AD() sparse matrices test
• Edit package title and description

zellkonverter 0.99.0 (2020-07-10)

• Initial Bioconductor submission

zellkonverter 0.0.0 (early development version)

zellkonverter 0.0.0.9017 (2020-07-10)

• Add biocViews to DESCRIPTION
• Edit package description
• Tidy code
• Replace 1:... with seq_len()

zellkonverter 0.0.0.9016 (2020-07-10)

• Add check for scRNAseq in examples (Fixes #18)

zellkonverter 0.0.0.9015 (2020-07-02)

• Skip AnnData matrices without a transposable R counterpart
• Only replace skipped matrices when use_hdf5 = TRUE in readH5AD() (Fixes #12)
• Additional tests for sparse matrices

zellkonverter 0.0.0.9014 (2020-06-30)

• Allow assay skipping when converting from SingleCellExperiment to AnnData
• Allow skipping of assays that aren't numpy friendly in writeH5AD()
• Wait for basilisk process shutdown to release .h5ad file
• Updates to documentation and tests

zellkonverter 0.0.0.9013 (2020-06-25)

• Improve conversion between SingleCellExperiment and AnnData (See #8)
  • Convert between metadata and uns (where objects are compatible)
  • Convert between rowPairs and varp
  • Convert between colPairs and obsp
  • Convert from varm to rowData (but not in reverse)
• Add mapping table to docs

zellkonverter 0.0.0.9012 (2020-06-19)

• Tidy documentation and code
• Tidy vignette

zellkonverter 0.0.0.9011 (2020-06-18)

• Support for HDF5Array outputs in readH5AD() (Fixes #4)

zellkonverter 0.0.0.9010 (2020-06-17)

• Avoid checking column names for colData and rowData in SCE2AnnData()
• Make sure that all matrices passes to {reticulate} are numpy friendly
• Add more tests
• Update vignette front matter

zellkonverter 0.0.0.9009 (2020-06-15)

• Add vignette

zellkonverter 0.0.0.9008 (2020-06-12)

• Add examples and improve documentation
• Export .AnnDataDependencies for external use

zellkonverter 0.0.0.9007 (2020-06-11)

• Add SCE2AnnData() function
• Add writeH5AD() function

zellkonverter 0.0.0.9006 (2020-06-11)

• Use internal function in readH5AD()

zellkonverter 0.0.0.9005 (2020-06-09)

• Rename adata2SCE() to AnnData2SCE()
• Remove {basilisk} context from AnnData2SCE() (See #1)
  • Now uses the calling context

zellkonverter 0.0.0.9004 (2020-06-09)

• Pin more AnnData dependencies (See #1)

zellkonverter 0.0.0.9003 (2020-06-08)

• Add test .h5ad file
• Add test for readH5AD()
• Add package man page

zellkonverter 0.0.0.9002 (2020-06-08)

• Add adata2SCE() function
• Add readH5AD() function

zellkonverter 0.0.0.9001 (2020-06-08)

• Add {basilisk} infrastructure

zellkonverter 0.0.0.9000 (2020-06-08)

• Set up package