Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add H5AD read/write helpers #88

Merged
merged 10 commits into from
Sep 4, 2023
Merged

Add H5AD read/write helpers #88

merged 10 commits into from
Sep 4, 2023

Commits on Jul 6, 2023

  1. Add read_h5ad function

    lazappi committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    66ad104 View commit details
    Browse the repository at this point in the history
  2. Add read_h5ad tests

    lazappi committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    6fe52e0 View commit details
    Browse the repository at this point in the history
  3. Add write_h5ad function

    lazappi committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    d2eddea View commit details
    Browse the repository at this point in the history
  4. Move test dummy helper to main function

    Makes it possible to use for examples. Also add SingleCellExperiment and
    Seurat dummy functions.
    lazappi committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    eb68d02 View commit details
    Browse the repository at this point in the history
  5. Refactor dummy datasets into a single function

    Needs to be exported for examples
    lazappi committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    278ecf3 View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    aea2b96 View commit details
    Browse the repository at this point in the history
  7. Style and lint

    lazappi committed Jul 6, 2023
    Configuration menu
    Copy the full SHA
    989e125 View commit details
    Browse the repository at this point in the history

Commits on Jul 21, 2023

  1. Configuration menu
    Copy the full SHA
    15f5b6f View commit details
    Browse the repository at this point in the history

Commits on Aug 31, 2023

  1. H5ad helpers ++ (#89)

    * Remove temporary workaround
    
    * use `inherits()` instead of `is()`
    
    * Add HDF5AnnData and InMemoryAnnData to `read_h5ad()`
    
    * fix incorrect merge
    
    * try to fix error in R devel
    
    * fix docs
    
    * add terminal newline
    
    * remove conditions
    
    * undo previous commit
    rcannood authored Aug 31, 2023
    Configuration menu
    Copy the full SHA
    f10b77f View commit details
    Browse the repository at this point in the history

Commits on Sep 1, 2023

  1. H5ad helpers with pr83 (#90)

    * support rhdf5 nullable vector and boolean enum implementation
    
    - use `as.vector()` to reduce code duplication when reading
      nullable vectors
    - closes #82
    
    * implement and use read_h5ad_attributes
    
    - 'quietly' to suppress warnings; set to TRUE when relevant warnings
      are handled by calling code
    
    * use 'anndataR-category-unknown' as a class of warning
    
    - versions of rhdf5 that don't support ENUM; more user-friendly message
    - use to suppress irrelevant warnings in unit tests
    
    * Tidy after merge and style
    
    * More tidying...
    
    * Roxygenise
    
    * Fix namespace
    
    ---------
    
    Co-authored-by: Martin Morgan <[email protected]>
    Co-authored-by: Luke Zappia <[email protected]>
    3 people authored Sep 1, 2023
    Configuration menu
    Copy the full SHA
    d8445a6 View commit details
    Browse the repository at this point in the history