Add and rename significance thresholds

[LuisHeinzlmeier]

• closes Add a signifiance threshold for plot_fold_change() #967
• replaces common significance threshold terms like alpha, thres, etc. with consistent parameter names, where appropriate
• adds a warning filter to _pydeseq2.py and _milo.py because lazy loading of packages (probably PyDESeq2) pre-appends ignoring all future warnings (also the scverse_misc warnings from pertpy)
• remove warning of plot_fold_change() by adding .copy()

[codecov-commenter]

Codecov Report

❌ Patch coverage is 90.90909% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 77.76%. Comparing base (12897e1) to head (c934878).
⚠️ Report is 81 commits behind head on main.

Files with missing lines	Patch %	Lines
pertpy/tools/_enrichment.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #974      +/-   ##
==========================================
+ Coverage   73.54%   77.76%   +4.21%     
==========================================
  Files          48       48              
  Lines        5613     6372     +759     
==========================================
+ Hits         4128     4955     +827     
+ Misses       1485     1417      -68     

Files with missing lines	Coverage Δ
...ertpy/tools/_differential_gene_expression/_base.py	90.58% <100.00%> (+1.56%)	⬆️
...y/tools/_differential_gene_expression/_pydeseq2.py	90.90% <100.00%> (-0.99%)	⬇️
pertpy/tools/_milo.py	71.91% <100.00%> (-8.75%)	⬇️
pertpy/tools/_enrichment.py	66.38% <80.00%> (+0.29%)	⬆️

... and 8 files with indirect coverage changes

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[LuisHeinzlmeier]

@Zethson, this is still work in progress for #967, but before I try to harmonize all threshold naming:

• Are you happy with the names?
• Are you happy with how I handle backward compatibility?

[Zethson]

2x yes. But you may also introduce scverse-misc and use https://scverse-misc.readthedocs.io/stable/generated/scverse_misc.deprecated_arg.html

[LuisHeinzlmeier]

Manual testing

enrichment
hypergeometric():

dge
plot_fold_change():
Only top log-fold changes that pass the padj_threshold are plotted. For example, PDGFRL is not plotted because 0.0135 > 0.01.

plot_volcano():

milo
milo_de.plot_de_nhood_graph():
Now, padj_threshold is used for the significance of SpatialFDR and alpha is passed to matplotlib.pyplot.scatter() of scanpy.pl.embedding() and changes the transparency of the dots.

plot_da_beeswarm():

milo.plot_nhood_graph()

[LuisHeinzlmeier]

Ready for a review! I also updated the notebooks, but couldn't push them into this PR because I am working on a forked repo. This time, I will create a separate PR in pertpy-tutorials (see here).