Skip to content

Latest commit

 

History

History
513 lines (317 loc) · 14 KB

NEWS.md

File metadata and controls

513 lines (317 loc) · 14 KB
Raw

zellkonverter 1.18.0

  • Bioconductor 3.21, May 2025

zellkonverter 1.17.0 (2024-10-30)

  • Bioconductor 3.21 devel

zellkonverter 1.16.0 (2024-10-30)

  • 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
  • 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