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@zktuong zktuong released this 15 May 10:46
· 1128 commits to master since this release
v0.1.1.post1
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Learn about vigilant mode.

Bug fixes and updates:

  • versioning
    Changed versioning strategy to now use setuptools_scm to pull the version and predict next update version number.
    Note to self: From now on, any major updates just requires a new tag. For example:
    After the merge of the pull request, set a new tag and push
git tag -a v0.1.1
git push --tags

  • filter_bcr
    A minor edit, but decided to switching the fold-change cut off back to 2 to fit with the original filtering strategy.

  • setting up container
    Related to #51, to create a preprocessing wrapper, we will add in an option to export the plots generated during pre-processing.
    Simple addition of a boolean save_plot option to:

  • reassign_allele

  • reassign_alleles

  • assign_isotype

  • assign_isotypes

Still needs work

#51 Preprocessing wrapper for singularity container
#54 Check productive_only option in filter_bcr
#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?
#70 Check for compatibilty with mouse data

New features:

  • scirpy interopertability
    Now fully works with scirpy's tool to transfer the data format.

  • singularity container
    Singularity container recipe/image created.

ls
# database  environment.yml  ncbi-blast-2.10.1+  ncbi-igblast-1.15.0  sc-dandelion.def
singularity build --fakeroot sc-dandelion.sif sc-dandelion.def
singularity sign sc-dandelion.sif
singularity verify sc-dandelion.sif
singularity push sc-dandelion.sif library://kt16/default/sc-dandelion:latest 

To download and use:

singularity pull library://kt16/default/sc-dandelion:latest
singularity shell sc-dandelion.sif


- **pre-processing plots saving**
Meant to be used primarily for the container, but now specifiying `save_plot` into `reassign_alleles` and `assign_isotypes` will save the plots from pre-processing accordingly.

## Depreciated:

I should start using depreciation decorators but only one major change: `reassign_alleles_` no longer used/available.
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