add new functions and rework github actions

[zktuong]

New features

• add two(three) new functions
  • tl.productive_ratio
    • Calculates a cell-level representation of productive vs non-productive contigs.
    • Plotting is achieved through pl.productive_ratio
  • tl.vj_usage_pca
    • Computes PCA on a cell-level representation of V/J gene usage across designated groupings
    • uses scanpy.pp.pca internally
    • Plotting can be achieved through scanpy.pl.pca

bug fixes

• check_contigs, find_clones and define_clones were removing non-productive contigs even though there's no need to.
• fix issue with min_size in network not behaving as intended. switch to using connected components to find which nodes to trim

other changes

• added a check files change step in the github actions workflow so that tests only run if certain conditions are met.
• removed a static devel branch as it's just duplication of effort to maintain it. Just treat master as the experimental/development and then whatever's released to pip will be stable.

[codecov]

Codecov Report

Merging #161 (28e6d99) into master (04586e2) will increase coverage by 0.77%.
The diff coverage is 91.86%.

@@            Coverage Diff             @@
##           master     #161      +/-   ##
==========================================
+ Coverage   81.29%   82.07%   +0.77%     
==========================================
  Files          46       47       +1     
  Lines        8452     8590     +138     
==========================================
+ Hits         6871     7050     +179     
+ Misses       1581     1540      -41     

Flag	Coverage Δ
unittests	82.07% <91.86%> (+0.77%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
dandelion/plotting/__init__.py	100.00% <ø> (ø)
dandelion/tools/__init__.py	100.00% <ø> (ø)
dandelion/preprocessing/_preprocessing.py	68.88% <82.35%> (+1.84%)	⬆️
dandelion/tools/_tools.py	85.94% <88.65%> (+1.17%)	⬆️
dandelion/plotting/_plotting.py	82.26% <100.00%> (+0.86%)	⬆️
dandelion/tools/_network.py	75.10% <100.00%> (+0.10%)	⬆️
tests/test_filter.py	100.00% <100.00%> (ø)
tests/test_load_data.py	100.00% <100.00%> (ø)
tests/test_productive.py	100.00% <100.00%> (ø)

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