Release v0.3.4 · zktuong/dandelion

Summary

Speed up network generation in generate_network
Add soft filtering and normalisation to vdj_psuedobulk functions - @ktpolanski
Created a new column in .data (extra) to flag if contig is considered extra.
New clone id definition to insert VDJ and VJ to the id to reduce ambiguity - need to check if it does it properly for cells with no clone ids. This also means that now clone ids can be created for orphan chains.
New to_scirpy/from_scirpy functions that will now convert them to the new scverse airr formats - @amoschoomy
Container build is now simplified and uses mamba to manage all the dependencies.
New option to run preprocessing with ogrdb references in both the base package and the container.
New reference download function in the container folder to ensure the latest references are pulled for every new iteration of the container.
Deprecate support for python3.7 tests.

create a remove_malformed option by @zktuong in #315
fix future warning for multimappers by @zktuong in #316
fix cleaning up step in the singularity image by @zktuong in #317
Speed up network generation by @zktuong in #319
remove d gene VJ columns by @zktuong in #320
Running palantir by @zktuong in #321
update workflow dependencies by @zktuong in #323
Fix #325 by @zktuong in #326
add concat in tutorial by @zktuong in #327
Update 3_dandelion_findingclones-10x_data.ipynb by @tnieuwe in #328
disable 3.7 tests by @zktuong in #330
add logic to deal with contigs with no clone id during network generation step by @zktuong in #335
Soft filtering in setup_vdj_pseudobulk() by @ktpolanski in #334
attempting to reduce code bloat for find_clones by @zktuong in #329
fix bug with check contigs by @zktuong in #341
add an option to the singularity container to skip tigger step. by @zktuong in #343
add new option to check contigs by @zktuong in #344
simplify build container by @zktuong in #346
Awkward to pandas by @amoschoomy in #342
Fix yml by @zktuong in #349
fix container build definition file by @zktuong in #348

pip prod(deps): update pandas requirement from <=2.1.0,>=1.0.3 to >=1.0.3,<=2.1.1 by @dependabot in #314
pip dev(deps-dev): update readthedocs-sphinx-ext requirement from <=2.2.2 to <=2.2.3 by @dependabot in #318
pip prod(deps): update pandas requirement from <=2.1.1,>=1.0.3 to >=1.0.3,<=2.1.2 by @dependabot in #324
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=1.24.0 to <=1.24.1 by @dependabot in #331
pip prod(deps): update pandas requirement from <=2.1.2,>=1.0.3 to >=1.0.3,<=2.1.3 by @dependabot in #332
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=1.24.1 to <=1.25.2 by @dependabot in #333
pip dev(deps-dev): update sphinx-rtd-theme requirement from <=1.2.2 to <=2.0.0 by @dependabot in #338
pip prod(deps): update pandas requirement from <=2.1.3,>=1.0.3 to >=1.0.3,<=2.1.4 by @dependabot in #339
pip dev(deps-dev): update readthedocs-sphinx-ext requirement from <=2.2.3 to <=2.2.4 by @dependabot in #340
pip dev(deps-dev): update readthedocs-sphinx-ext requirement from <=2.2.4 to <=2.2.5 by @dependabot in #345
Bump tj-actions/changed-files from 35 to 41 in /.github/workflows by @dependabot in #347

Full Changelog: v0.3.3...v0.3.4