Simplify how obs and var names handled in ZarrAnnData #5
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* re-enable matrices with NAs tests in X and layers * one more * Ensure that matrices are never written as nullables Take care when using reticulate for testing: before writing, convert NA to NaN * Fix Windows writing NA error * Remove commented code since no longer needed * remove commented code (no longer needed) --------- Co-authored-by: Louise Deconinck <[email protected]>
* Update write_h5ad_categorical * fix styling * Update write_h5ad_categorical * Adjust H5AD categorical write test * Add write_h5ad_attributes function Replace repeated code in individual writers * ignore cyclomatic complexity warning for `write_h5ad_element` warning * formatting changes * in write_h5ad_attributes, allow file to be an open hdf5 file * Add write_h5ad_boolean_attribute() * Add write_h5ad_boolean_array() Helper function for writing ENUM boolean arrays * Remove compression argument from write_h5ad_boolean_array Don't think it is possible to write compressed data using the workaround and ENUM format should be fairly space efficient anyway * Correctly read categorical levels from H5AD Fixes array when there are more levels than values * Fix writing scalar H5AD attributes Correctly check the is_scalra argument * add lintr exceptions * fix nolint --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
* port rownames-related changes from scverse#166 and scverse#169 * run styler * fix test * style * style * fix docs * fix documentation * simplify helper functions * simplify test * add more documentation to AnnData * fix docs
* Update write_h5ad_categorical * fix styling * Update write_h5ad_categorical * Adjust H5AD categorical write test * Add write_h5ad_attributes function Replace repeated code in individual writers * ignore cyclomatic complexity warning for `write_h5ad_element` warning * formatting changes * in write_h5ad_attributes, allow file to be an open hdf5 file * wip * wip * substitute mentions of rhdf5 with hdf5r * strip obs_names and var_names from framework * update * fix tests and finalize * remove mentions of obs_names and var_names in the constructor * make sure filenames are always unique * add mode to various functions * manually close anndatas in tests (where needed) * only close when pointer is valid * move match * use $close() instead of $close_all() * switch to different branch * simplify test * gc afterclosing the adata in write_h5ad * guess the dtype and the space * update docs * use hhoeflin's remote * bugfix in hdf5r has been released * update: nevermind, the fix wasn't included in the release yet * minor fixes * bump version number * remove remotes * remove references to rhdf5 * fix attributes * style * fix write h5ad helpers * fix unit tests * fix linting issues * move hdf5 helpers * reuse existing functionality * add test (this seems to have been fixed at some point) * improve guessing of dtype when storing a logical vector * fix styling * reenable more tests --------- Co-authored-by: Luke Zappia <[email protected]>
* Tidy user interface Co-authored-by: Luke Zappia <[email protected]> * Update docs Co-authored-by: Luke Zappia <[email protected]> * update docs * fix linting issues --------- Co-authored-by: Luke Zappia <[email protected]>
…dataR into keller-mark/zarr
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I think I understand why you commented out this test, since read_*_mapping returns lists in different orders right :D anndataR/tests/testthat/test-h5ad-zarr.R Lines 98 to 103 in 8790715 |
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I would say one way to go around this problem is the define additional name indexing for zarr stores, to capture the initial ordering of groups/arrays within h5? |
…milar to HDF5AnnData
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I fixed a lot of tests and indexing bugs, all tests are now working and I have even replaced |
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Thank you very much for the improvements/ bug fixes and getting it up to date with the original repo. All of the changes look good to me and the tests are passing locally, I will merge this and then open a PR into the original scverse repo. |
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This PR is similar to the one in scverse#171 and includes other changes in scverse/anndataR@main too.
Some tests are currently still failing but starting this PR to check em out! @keller-mark also feel free to review!
UPDATE: We commited some test and _index fixes.