src(gates): Use cattrs + attrs

[gegnew]

• deps(munch): remove
• src(gates): use cattrs for Gate
• beh(gate): Remove parent_population_id (closes gate.parentPopulationId has been removed from the API #125 )

Depends on #128 , #133 (will break until 128 is merged)
Fixes #118, #130
Supersedes #131 , since the underlying code changes quite a bit

[zbjornson]

TODO: update the docs to show the correct/simplest usage pattern sometime.

[zbjornson]

Quick scan to start. Can you rebase next time you push please?

[zbjornson]

Sorry for being so slow!

Looking good, almost ready to land.

[zbjornson]

Much improved interface. A few more questions on it though.

[zbjornson]

Would it work to keep all of the named args and pass all of them to RectangleGate.create()? Know it's a lot of code, but it would make type info work.

[gegnew]

The args/kwargs, not the docstring, right? We certainly can, but it means we have to maintain them in two places.

The type info actually works for me; this is the hint I get:

def create_rectangle_gate(self, x_channel: str, y_channel: str, name: str, x1: float, x2: float, y1: float, y2: float, label: List[float]=[], gid: Optional[str]=None, locked: bool=False, tailored_per_file: bool=False, fcs_file_id: Optional[str]=None, fcs_file: Optional[str]=None, parent_population_id: str=None, /, *, create_population=True, x_channel: str, y_channel: str, name: str, x1: float, x2: float, y1: float, y2: float, label: List[float]=[], gid: Optional[str]=None, locked: bool=False, tailored_per_file: bool=False, fcs_file_id: Optional[str]=None, fcs_file: Optional[str]=None, parent_population_id: str=None) -> RectangleGate

Let me know what you think

[zbjornson]

This won't be a breaking change if we change it later to include all the args here. What tool is giving you that type hint? VSCode/Pylance is just giving me this:

[codecov-commenter]

Codecov Report

Merging #136 (7c59370) into master (0791214) will decrease coverage by 0.79%.
The diff coverage is 87.50%.

@@            Coverage Diff             @@
##           master     #136      +/-   ##
==========================================
- Coverage   93.63%   92.83%   -0.80%     
==========================================
  Files          67       60       -7     
  Lines        2906     3084     +178     
==========================================
+ Hits         2721     2863     +142     
- Misses        185      221      +36     

Flag	Coverage Δ
unittests	92.83% <87.50%> (-0.80%)	⬇️

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

Impacted Files	Coverage Δ
cellengine/resources/fcs_file.py	89.18% <ø> (ø)
setup.py	0.00% <ø> (ø)
cellengine/resources/experiment.py	79.47% <62.79%> (-8.36%)	⬇️
cellengine/utils/api_client/APIClient.py	82.89% <64.81%> (-1.38%)	⬇️
cellengine/resources/gate.py	88.68% <87.80%> (+8.29%)	⬆️
cellengine/utils/helpers.py	75.67% <94.73%> (-9.08%)	⬇️
cellengine/resources/scaleset.py	92.15% <100.00%> (+0.49%)	⬆️
cellengine/utils/__init__.py	100.00% <100.00%> (ø)
cellengine/utils/api_client/BaseAPIClient.py	86.15% <100.00%> (ø)
cellengine/utils/parse_fcs_file_args.py	100.00% <100.00%> (ø)
... and 6 more

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[zbjornson]

RectangleGate is almost there. These comments apply to the other gate classes, but I didn't read through them yet.

[zbjornson]

Just one last suggestion and a typo.

[zbjornson]

I fixed up a bunch of stuff and pointed out a few of the changes below. All of gate.py has no type errors and all of the integration tests pass now. https://github.com/primitybio/cellengine-python-toolkit/compare/d672d65..8c957bb

(Saving test responses was a bad idea of mine here and in the R toolkit -- too much work to keep up with the changes and we don't catch errors when API changes break the toolkit. I just added GitHub action secrets for CellEngine credentials to let us run integration tests against the real API.)