v0.1.5

Updates and bug fixes

• Added a series of functions to guess the best format for locus as the previous try-except statements were not working.

• Added a few more tests - now code coverage is 70%!

• Added sanitize_dtype function so that saving and conversion of format with R/h5/h5ad works.

• Changed bool to str where possible so as not to intefere with saving in h5ad with h5py>=3.0.0.

• Minor annotation update: Using Optional instead of Union[None, whatever].

• Fix broken links in docs.

• Bug fixes for compatibility with: mouse #70 and TCR data #81.

  • Added a series to checks to switch the locus for TRAV/DV genes (scverse/scirpy#285)

• Some bug fixes to container script.

• Updated container definition:

  • Now will try to build R version >= 4.
  • Added a test suite in the container so that it automatically runs pytest after building.
  • Trying out whether appending the paths to SINGULARITY_ENVIRONMENT first helps with #79.

• Added pytest suite within the container. Now I can quickly test like as follows:

  # devel and testing
  sudo singularity build --notest sc-dandelion_dev.sif sc-dandelion_dev.def
  sudo singularity test --writable-tmpfs sc-dandelion_dev.sif
  
  # for release
  sudo singularity build --notest sc-dandelion.sif sc-dandelion.def
  sudo singularity test --writable-tmpfs sc-dandelion.sif
  singularity sign sc-dandelion.sif
  singularity verify sc-dandelion.sif
  singularity push sc-dandelion.sif library://kt16/default/sc-dandelion

  The test requires root access otherwise wouldn't be able to write into the container. Should look into whether sandbox/fakeroot modes works.

• Interactive shell session of the container should now work with singularity shell --writable-tmpfs sc-dandelion.sif.

Still needs work

#62 Streamline update_metadata
#63 Fix update_metadata to work with concat.
#64 Allow retrieve to work both ways
#68 Native implementation of function to count mutation
#69 Rescue contigs that fail germline reconstruction?