Use Apptainer containers on Sherlock

[thalassemia]

For better reproducibility, workflows are now run using Apptainer (formerly Singularity) containers on Sherlock. In light of the fact that containers are now used on Sherlock and Google Cloud, I added a script and accompanying documentation to assist with debugging and interacting with vEcoli inside an interactive container.

Now, if Apptainer is installed (true for most HPC clusters), Nextflow and PyArrow are the only requirements to run a workflow using python runscripts/workflow.py on an HPC cluster. This all but eliminates the difficulty of setting up and maintaining a complete installation (Python environment, system libraries, etc.).

Miscellaneous

• Increased the fitness threshold for ParCa from 1e-8 to 1e-7 because of failures to converge on Sherlock

[github-actions]

Package	Line Rate	Complexity	Health
.	29%	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	36%	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% (8446 / 30037)	0	❌