Rework Documentation

[thalassemia]

Completely rework documentation hosted at https://covertlab.github.io/vEcoli/.

• Remove outdated tutorial notebooks from notebooks folder
• Add pages describing stores, processes, composites, experiments, workflows, and simulation output in the docs folder
• Fix variable time stepping (not implemented yet)
• Add GitHub Actions tasks to test reproducibility and two generation workflows
• Update Python library versions used to build documentation
• Update all run scripts to accept command-line arguments with underscores instead of dashes
• Fix a bunch of existing Sphinx automatically generated API documentation issues
• Update all run scripts to accept configuration JSON using --config command-line argument
• Import biology module before nextflow for Sherlock Jenkins tests
• Update runscripts/analysis.py to run all analysis scripts of all types specified in input configuration JSON on all possible filtered subsets of data for each analysis script type (e.g. run all single analysis scripts on all single cells included in dataset filtered by --experiment_id, etc)

[github-actions]

Package	Line Rate	Complexity	Health
.	31%	0	❌
analysis	100%	0	✔
analysis.antibiotics_colony	11%	0	❌
analysis.antibiotics_colony.subgen_gene_plots	20%	0	❌
analysis.causality_network	18%	0	❌
analysis.colony	11%	0	❌
analysis.multidaughter	100%	0	✔
analysis.multiexperiment	100%	0	✔
analysis.multigeneration	23%	0	❌
analysis.multiseed	17%	0	❌
analysis.multivariant	17%	0	❌
analysis.single	15%	0	❌
composites	34%	0	❌
composites.ecoli_configs	90%	0	✔
composites.environment	26%	0	❌
debug	17%	0	❌
ecoli	9%	0	❌
ecoli.compendium	18%	0	❌
ecoli.dataclasses	31%	0	❌
ecoli.dataclasses.process	22%	0	❌
ecoli.dataclasses.state	32%	0	❌
ecoli.scripts	43%	0	❌
ecoli.scripts.fold_changes	15%	0	❌
ecoli.scripts.metabolism_kinetics	36%	0	❌
ecoli.scripts.metabolite_concentrations	26%	0	❌
ecoli.scripts.nca	10%	0	❌
ecoli.scripts.protein_half_lives	29%	0	❌
ecoli.scripts.rna_half_lives	21%	0	❌
experiments	37%	0	❌
io	52%	0	➖
library	48%	0	❌
library.cell_wall	14%	0	❌
processes	43%	0	❌
processes.antibiotics	27%	0	❌
processes.chemotaxis	14%	0	❌
processes.environment	29%	0	❌
processes.listeners	78%	0	✔
processes.membrane	27%	0	❌
processes.spatiality	19%	0	❌
processes.stubs	45%	0	❌
tests	22%	0	❌
tests.io	24%	0	❌
tests.utils	25%	0	❌
utils	28%	0	❌
utils._netflow	45%	0	❌
variants	36%	0	❌
Summary	28% (8433 / 29891)	0	❌