v0.2.1

What's Changed

• Update documentation by @zktuong in #142
• Add google colab button by @zktuong in #143
• Fix pytest issue on macos by @zktuong in #144
• v0.2.1 by @zktuong in #147
  • minor QoL changes
  • remove skbio from dependencies

Full Changelog: v0.2.0...v0.2.1

0.2.0

What's Changed

• add hiconf to pipeline by @ktpolanski in #130
• Singularity ci by @zktuong in #131
• v0.1.13 by @zktuong in #132
• add db-all file by @zktuong in #134
• fix bcr strict option by @zktuong in #136
• clarify and add new detail by @ktpolanski in #137
• fix container workflow by @zktuong in #138
• Internal external preprocessing steps (igblastn, blastn) and Query classes are also simplified/sped up.
• AIRR format sanitisation is also enforced to prevent issues during I/O.
• Full distance slot is no longer automatically saved to reduce I/O times

Full Changelog: v0.1.12...v0.2.0

v0.1.12

What's Changed

• update flexibility of singularity container by @zktuong in #122
• Update find clones by @zktuong in #124

Full Changelog: v0.1.11...v0.1.12

v0.1.11

What's Changed

• added airr compliant badge by @zktuong in #118
• fixed notebook from crashing readthedocs.

Full Changelog: v0.1.10...v0.1.11

v0.1.10

Fix minor bug in TCR preprocessing.
Fix documentation building script.
Add logging in singularity container.
Also testing an automated build test for creating singularity container that seems to be working:
https://github.com/zktuong/github-ci
Added support statement in readme.

v0.1.9

• bug fix for numeric dtypes being converted incorrectly during saving, resulting in empty columns.
• Adjustment to Query to return numerical queries properly.

v0.1.8

• Much required speed upgrade for the following newly added functions to be fully usable:
  • Refactored filter_contigs/FilterContigs/FilterContigLite. Solves #92
    • Reworked into a tree format where it iterates the rows to form cells (~1k iter/s), and then iterate through the cells (~150 iter/s) compared to previous 3-4 iter/s.
    • Adjusted small bug where the duplicate_counts were not adding up
  • Refactored Query.
    • Now does the __init__ method preloads the required fields as a tree and a separate retrieve method and access the dictionaries much faster. Same method as above.
  • read_10x_vdj
    • Refactored parse_annotation which was slowing everything down.
    • Similar method to above
  • sanitize_data
    • Use airr.RearrangementSchema to match the dtype to deal with missing values. Also speed up some steps to make the validation faster.
    • Also bug fix causing float columns to be unintentially converted to integers e.g. mu_freq columns should hopefully now return properly.
• Added write_airr function that basically calls airr.create_rearrangement
• Adjusted quantify_mutations to hopefully return the right dtypes now.
• Added option to filter_contigs to run without anndata.
• Bug fix to dandelion_preprocessing.py to let it run quantify_mutations based on the args.file_prefix.

v0.1.7

• Refactored the now depreicated retrieve_metadata which is now a new internal Query class.
• Bug fix for sanitization of Dandelion object.
• No longer require to split locus when initializing. Dandelion should now parse everything.
  • find_clones still require locus of either ig or tr to be specified.
• Largely addressed:
  • #62
  • #63

v0.1.6

• bug fix when sanitizing dtypes and validating airr columns.
• Switch from enforcing pd.Int64Dtype to just switch to np.float64 if there is missing info.
• speed up sanitization steps.

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?