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Merge pull request #232 from CovertLab/basic_docs
More Jenkins tests
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from typing import Any, TYPE_CHECKING | ||
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if TYPE_CHECKING: | ||
from reconstruction.ecoli.simulation_data import SimulationDataEcoli | ||
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def apply_variant( | ||
sim_data: "SimulationDataEcoli", params: dict[str, Any] | ||
) -> "SimulationDataEcoli": | ||
""" | ||
Modify sim_data to environmental condition from condition_defs.tsv. | ||
Args: | ||
sim_data: Simulation data to modify | ||
params: Parameter dictionary of the following format:: | ||
{ | ||
# Environmental condition: "basal", "with_aa", "acetate", | ||
# "succinate", "no_oxygen" | ||
"condition": str, | ||
} | ||
Returns: | ||
Simulation data with the following attributes modified:: | ||
sim_data.condition | ||
sim_data.external_state.current_timeline_id | ||
""" | ||
# Set media condition | ||
sim_data.condition = params["condition"] | ||
sim_data.external_state.current_timeline_id = params["condition"] | ||
sim_data.external_state.saved_timelines[params["condition"]] = [ | ||
(0, sim_data.conditions[params["condition"]]["nutrients"]) | ||
] | ||
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return sim_data |
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{ | ||
"experiment_id": "Daily with AA", | ||
"single_daughters": true, | ||
"generations": 8, | ||
"fail_at_total_time": true, | ||
"trna_attenuation": false, | ||
"ppgpp_regulation": false, | ||
"mechanistic_translation_supply": false, | ||
"mechanistic_aa_transport": false, | ||
"aa_supply_in_charging": false, | ||
"d_period_division": false, | ||
"mechanistic_replisome": true, | ||
"mass_distribution": false, | ||
"emitter" : { | ||
"type": "parquet", | ||
"config": { | ||
"out_dir": "/scratch/groups/mcovert/vecoli" | ||
} | ||
}, | ||
"analysis_options": { | ||
"single": {"mass_fraction_summary": {}} | ||
}, | ||
"variants": { | ||
"condition": {"condition": "no_oxygen"} | ||
} | ||
} |
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{ | ||
"experiment_id": "Daily new gene GFP", | ||
"single_daughters": true, | ||
"generations": 4, | ||
"fail_at_total_time": true, | ||
"emitter" : { | ||
"type": "parquet", | ||
"config": { | ||
"out_dir": "/scratch/groups/mcovert/vecoli" | ||
} | ||
}, | ||
"parca_options": { | ||
"new_genes": "gfp" | ||
}, | ||
"analysis_options": { | ||
"single": {"mass_fraction_summary": {}} | ||
}, | ||
"variants": { | ||
"new_gene_internal_shift": { | ||
"condition": {"value": ["basal"]}, | ||
"induction_gen": {"value": [1]}, | ||
"knockout_gen": {"value": [-1]}, | ||
"exp_trl_eff": { | ||
"nested": { | ||
"exp": { | ||
"logspace": { | ||
"start": 7, | ||
"stop": 8, | ||
"num": 1 | ||
} | ||
}, | ||
"trl_eff": {"value": [1.0]}, | ||
"op": "zip" | ||
} | ||
}, | ||
"op": "zip" | ||
} | ||
} | ||
} |
22 changes: 22 additions & 0 deletions
22
runscripts/jenkins/configs/ecoli-no-growth-rate-control.json
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{ | ||
"experiment_id": "Daily no growth rate control", | ||
"single_daughters": true, | ||
"generations": 4, | ||
"fail_at_total_time": true, | ||
"trna_attenuation": false, | ||
"ppgpp_regulation": false, | ||
"mechanistic_translation_supply": false, | ||
"mechanistic_aa_transport": false, | ||
"aa_supply_in_charging": false, | ||
"d_period_division": false, | ||
"mechanistic_replisome": true, | ||
"emitter" : { | ||
"type": "parquet", | ||
"config": { | ||
"out_dir": "/scratch/groups/mcovert/vecoli" | ||
} | ||
}, | ||
"analysis_options": { | ||
"single": {"mass_fraction_summary": {}} | ||
} | ||
} |
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{ | ||
"experiment_id": "Daily no operons", | ||
"single_daughters": true, | ||
"generations": 4, | ||
"fail_at_total_time": true, | ||
"emitter" : { | ||
"type": "parquet", | ||
"config": { | ||
"out_dir": "/scratch/groups/mcovert/vecoli" | ||
} | ||
}, | ||
"parca_options": { | ||
"operons": false | ||
}, | ||
"analysis_options": { | ||
"single": {"mass_fraction_summary": {}} | ||
} | ||
} |
16 changes: 16 additions & 0 deletions
16
runscripts/jenkins/configs/ecoli-superhelical-density.json
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{ | ||
"experiment_id": "Daily superhelical density", | ||
"single_daughters": true, | ||
"generations": 4, | ||
"fail_at_total_time": true, | ||
"superhelical_density": true, | ||
"emitter" : { | ||
"type": "parquet", | ||
"config": { | ||
"out_dir": "/scratch/groups/mcovert/vecoli" | ||
} | ||
}, | ||
"analysis_options": { | ||
"single": {"mass_fraction_summary": {}} | ||
} | ||
} |
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{ | ||
"experiment_id": "Daily with AA", | ||
"single_daughters": true, | ||
"generations": 8, | ||
"fail_at_total_time": true, | ||
"emitter" : { | ||
"type": "parquet", | ||
"config": { | ||
"out_dir": "/scratch/groups/mcovert/vecoli" | ||
} | ||
}, | ||
"analysis_options": { | ||
"single": {"mass_fraction_summary": {}} | ||
}, | ||
"variants": { | ||
"condition": {"condition": "with_aa"} | ||
} | ||
} |
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pipeline { | ||
agent any | ||
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stages { | ||
stage('Test Reproducibility') { | ||
steps { | ||
script { | ||
sh "bash runscripts/jenkins/check-reproducibility.sh" | ||
} | ||
} | ||
} | ||
} | ||
} |
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pipeline { | ||
agent any | ||
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stages { | ||
stage('Test 2 Generations') { | ||
steps { | ||
script { | ||
sh "bash runscripts/jenkins/workflow.sh runscripts/jenkins/configs/two-generations.json" | ||
} | ||
} | ||
} | ||
} | ||
} |