More Jenkins tests

ecoli/variants/condition.py

@@ -0,0 +1,35 @@
+from typing import Any, TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from reconstruction.ecoli.simulation_data import SimulationDataEcoli
+
+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"])
+    ]
+
+    return sim_data

ecoli/variants/new_gene_internal_shift.py

@@ -1,5 +1,7 @@
 from typing import Any, TYPE_CHECKING
 
+from ecoli.variants.condition import apply_variant as condition_variant
+
 if TYPE_CHECKING:
     from reconstruction.ecoli.simulation_data import SimulationDataEcoli
 
@@ -125,11 +127,7 @@ def apply_variant(
 
     """
     # 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"])
-    ]
+    sim_data = condition_variant(sim_data, params)
 
     # Initialize internal shift dictionary
     sim_data.internal_shift_dict = {}  # type: ignore[attr-defined]

runscripts/jenkins/configs/ecoli-anaerobic.json

@@ -0,0 +1,26 @@
+{
+    "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"}
+    }
+}

runscripts/jenkins/configs/ecoli-new-gene-gfp.json

@@ -0,0 +1,39 @@
+{
+    "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"
+        }
+    }
+}

runscripts/jenkins/configs/ecoli-no-growth-rate-control.json

@@ -0,0 +1,22 @@
+{
+    "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": {}}
+    }
+}

runscripts/jenkins/configs/ecoli-no-operons.json

@@ -0,0 +1,18 @@
+{
+    "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": {}}
+    }
+}

runscripts/jenkins/configs/ecoli-superhelical-density.json

@@ -0,0 +1,16 @@
+{
+    "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": {}}
+    }
+}

runscripts/jenkins/configs/ecoli-with-aa.json

@@ -0,0 +1,18 @@
+{
+    "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"}
+    }
+}

runscripts/jenkins/reproducibility

@@ -0,0 +1,13 @@
+pipeline {
+    agent any
+
+    stages {
+        stage('Test Reproducibility') {
+            steps {
+                script {
+                    sh "bash runscripts/jenkins/check-reproducibility.sh"
+                }
+            }
+        }
+    }
+}

runscripts/jenkins/two-generations

@@ -0,0 +1,13 @@
+pipeline {
+    agent any
+
+    stages {
+        stage('Test 2 Generations') {
+            steps {
+                script {
+                    sh "bash runscripts/jenkins/workflow.sh runscripts/jenkins/configs/two-generations.json"
+                }
+            }
+        }
+    }
+}