Miscellaneous

[thalassemia]

• Use uv for Python package management and installation of the model
  • This resulted in a much simpler and more reproducible installation process
  • Update all containerized workflows (Google Cloud, Sherlock) to use uv
  • Update all packages to latest compatible versions and use Python 3.12
• Move required data files out of data into reconstruction/ecoli/flat
• Exclude data (now only required for testing) and other large folders like .git, notebooks, reconstruction/sim_data, and reconstruction/ecoli/scripts from container images for faster builds and leaner images
• Try Altair plotting backend instead of hvplot, which requires hundreds of MBs in dependencies
• Use Autograd instead of Jax for much lighter install, saving hundreds of MBs
• Reformulate RNA degradation Km optimization as a minimization problem (see benchmarks here)
• Go back to 4-core ParCa job that is submitted to SLURM queue on Sherlock (faster now that I've specified that jobs can run on the dev and normal partitions in addition to mcovert and owners)
• Use a different seed for rich media Jenkins test because of numerical instability with default seed 0
• Fix unique index generation so there is not even a slim chance of conflicts unless you generate more than 2**59 of a single unique molecule

TODO:

• Wait for PR on stochastic-arrow to be merged and new wheels published
• Try to fix migration tests. If too difficult, can get rid of them
• Clean up repository. Now that the ParCa is fully functional, it is about time to scrub the pickle files that are adding a lot of bloat to the repo.

[github-actions]

Package	Line Rate	Complexity	Health
.	30%	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	35%	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	35%	0	❌
io	52%	0	➖
library	47%	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% (8451 / 30006)	0	❌