Add parse growth file task

[Isabelle-C]

Resolves #13

[codecov-commenter]

Codecov Report

Merging #14 (5968462) into main (7aa5dfe) will increase coverage by 24.14%.
The diff coverage is 81.35%.

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@@            Coverage Diff             @@
##            main      #14       +/-   ##
==========================================
+ Coverage   0.00%   24.14%   +24.14%     
==========================================
  Files         13       15        +2     
  Lines        293      352       +59     
==========================================
+ Hits           0       85       +85     
+ Misses       293      267       -26     

Impacted Files	Coverage Δ
src/arcade_collection/output/parse_params_file.py	38.88% <38.88%> (ø)
src/arcade_collection/output/__init__.py	100.00% <100.00%> (+100.00%)	⬆️
src/arcade_collection/output/parse_growth_file.py	100.00% <100.00%> (ø)

... and 5 files with indirect coverage changes

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[Isabelle-C]

Hi @jessicasyu, I completed the parse_growth_file and the corresponding test. Please only review these two.

A few things I would like to mention:

1. I edited the __init__ in src/output/ so I added some code for parse_param_file.py to prevent errors. I think it's better if I complete parse_param_file after you review this round since it is very similar to parse_growth_file. The lint is not passing because parse_param_file is incomplete.
2. There are two functions: convert_state_to_string and parse_growth_timepoint that I use in parse_growth_file. I am not sure if the tests of those are needed.
3. I modified the tox.ini to accommodate my local testing environment. I will revert to the original python version later.

Thank you so much!

[jessicasyu]

Good start! The structure of the repo has changed so you'll need to fix merge conflicts. In particular, revisit how the __init__.py is handled.

[jessicasyu]

@Isabelle-C This version is pretty far behind main at this point, I would merge main into this branch and fix any merge conflicts/linting errors (I think there are a couple mypy issues). It might make sense to have this PR just be for the parse growth file task, and put the parse params file task into a different PR.

[Isabelle-C]

@jessicasyu Sounds great! I merged main, fixed and mypy error, and deleted the parse param. Once this PR is finished, I will open a new one for the parse param.

I was wondering in the src/arcade_collection/output/__init__.py, there is a block with things like parse_cells_file = task(parse_cells_file). I tried to do the same for parse growth, but the pytest does not work. There is a TypeError: module, class, method, function, traceback, frame, or code object was expected, got Task for pytest. I did attempt to resolve this, but couldn't. Thank you!