code cleanup and lint

setup.py

@@ -42,7 +42,7 @@
     "vivarium_medyan @ git+https://github.com/vivarium-collective/vivarium-MEDYAN.git",
     "vivarium_cytosim @ git+https://github.com/vivarium-collective/vivarium-cytosim.git",
     "simularium_readdy_models @ git+https://github.com/simularium/readdy-models.git",
-    "simulariumio>=1.5.0",
+    "simulariumio",
 ]
 
 extra_requirements = {

vivarium_models/__init__.py

@@ -14,7 +14,8 @@ def get_module_version():
 
 
 from .processes import ReaddyActinProcess  # noqa: F401
-from vivarium.core.registry import emitter_registry  # noqa: F401
 from .processes.simularium_emitter import SimulariumEmitter  # noqa: F401
 
+from vivarium.core.registry import emitter_registry
+
 emitter_registry.register("simularium", SimulariumEmitter)

vivarium_models/composites/actin_fiber.py

@@ -81,7 +81,7 @@ def generate_topology(self, config):
         }
 
 
-def test_actin_fiber():
+def run_actin_fiber():
     initial_state = centered_initial_fibers()
     initial_state["choices"] = {"medyan_active": True, "readdy_active": False}
     medyan_config = {
@@ -100,8 +100,8 @@ def test_actin_fiber():
         emit_processes=True,
     )
     engine.update(5)
-    engine.emitter.get_data()
+    return engine.emitter.get_data()
 
 
 if __name__ == "__main__":
-    test_actin_fiber()
+    run_actin_fiber()

vivarium_models/composites/filament_alternatives.py

@@ -61,7 +61,7 @@ def generate_topology(self, config):
         }
 
 
-def test_filament_alternatives():
+def run_filament_alternatives():
     initial_state = centered_initial_fibers()
     initial_state["choices"] = {"medyan_active": False, "cytosim_active": True}
     medyan_config = {
@@ -87,8 +87,8 @@ def test_filament_alternatives():
         emit_processes=True,
     )
     engine.update(6)
-    engine.emitter.get_data()
+    return engine.emitter.get_data()
 
 
 if __name__ == "__main__":
-    test_filament_alternatives()
+    run_filament_alternatives()

vivarium_models/composites/moving_anchor.py

@@ -48,13 +48,8 @@ def next_update(self, timestep, state):
         anchor_moved = anchor + np.array(self.parameters["movement_vector"])
         points[self.parameters["point_index"]] = anchor_moved
 
-        return {
-            "fibers": {
-                self.parameters["fiber_id"]: {
-                    "points": points
-                }
-            }
-        }
+        return {"fibers": {self.parameters["fiber_id"]: {"points": points}}}
+
 
 class AnchorMoverCytosim(CytosimProcess):
     new_defaults = {
@@ -76,13 +71,12 @@ def next_update(self, timestep, state):
         update = super().next_update(timestep, state)
         return update
 
+
 class BucklingSqueeze(Composer):
     defaults = {
-        "periodic_event": {
-            "periods": [1.0]
-        },
+        "periodic_event": {"periods": [1.0]},
         "cytosim_anchor_mover_squeeze": {
-            'model_name': 'buckling_squeeze',
+            "model_name": "buckling_squeeze",
             "movement_vector": [5, 0, 0],
             "fiber_id": "1",
         },
@@ -102,13 +96,15 @@ def generate_processes(self, config):
         periodic_event = PeriodicEvent(config["periodic_event"])
         # cytosim_squeeze = CytosimProcess(config['cytosim_squeeze'])
         # anchor_mover = AnchorMover(config["anchor_mover"])
-        cytosim_anchor_mover_squeeze = AnchorMoverCytosim(config["cytosim_anchor_mover_squeeze"])
+        cytosim_anchor_mover_squeeze = AnchorMoverCytosim(
+            config["cytosim_anchor_mover_squeeze"]
+        )
 
         return {
             "periodic_event": periodic_event,
             # 'cytosim_squeeze': cytosim_squeeze,
             # "anchor_mover": anchor_mover,
-            "cytosim_anchor_mover_squeeze": cytosim_anchor_mover_squeeze
+            "cytosim_anchor_mover_squeeze": cytosim_anchor_mover_squeeze,
         }
 
     def generate_topology(self, config):
@@ -131,16 +127,17 @@ def generate_topology(self, config):
         }
 
 
-def test_buckling_squeeze():
+def run_buckling_squeeze():
     initial_state = single_fiber()
-    initial_state['choices'] = 'N/A'
+    initial_state["choices"] = "N/A"
     cytosim_config = {
-        'actin_segmentation': 0.005,
+        "actin_segmentation": 0.005,
         "timestep": 5,
-        "template_directory": "vivarium_models/templates/"}
+        "template_directory": "vivarium_models/templates/",
+    }
     buckling_squeeze_config = {
         # "cytosim_squeeze": cytosim_config
-         "cytosim_anchor_mover_squeeze": cytosim_config
+        "cytosim_anchor_mover_squeeze": cytosim_config
     }
     buckling_squeeze = BucklingSqueeze(buckling_squeeze_config)
     composite = buckling_squeeze.generate()
@@ -153,11 +150,8 @@ def test_buckling_squeeze():
         emit_processes=True,
     )
     engine.update(100)
-
-    output = engine.emitter.get_data()
-    # import ipdb; ipdb.set_trace()
-
+    return engine.emitter.get_data()
 
 
 if __name__ == "__main__":
-    test_buckling_squeeze()
+    run_buckling_squeeze()

vivarium_models/data/fibers.py

@@ -228,13 +228,14 @@ def centered_initial_fibers():
             )
     return result
 
+
 def map_fibers(f, initial_fibers):
     result = copy.deepcopy(initial_fibers)
     for fiber_id in initial_fibers["fibers"]:
         fiber_points = initial_fibers["fibers"][fiber_id]["points"]
         for point_index in range(len(fiber_points)):
-            result["fibers"][fiber_id]["points"][point_index] = (
-                f(fiber_points[point_index], initial_fibers["fibers_box_extent"])
+            result["fibers"][fiber_id]["points"][point_index] = f(
+                fiber_points[point_index], initial_fibers["fibers_box_extent"]
             )
     return result
 
@@ -243,7 +244,7 @@ def single_fiber():
     fiber = {
         "fibers_box_extent": np.array([4000.0, 2000.0, 2000.0]),
         "fibers": {
-            '1': {
+            "1": {
                 "type_name": "Actin-Polymer",
                 "points": [
                     np.array([-0.250, 0.000, 0.000]),
@@ -297,14 +298,15 @@ def single_fiber():
                     np.array([0.230, 0.000, 0.000]),
                     np.array([0.240, 0.000, 0.000]),
                     np.array([0.250, 0.000, 0.000]),
-                ]}}}
+                ],
+            }
+        },
+    }
 
-    scaled = map_fibers(
-        lambda fiber_points, box_extent: fiber_points * 1000,
-        fiber)
+    scaled = map_fibers(lambda fiber_points, box_extent: fiber_points * 1000, fiber)
 
     return scaled
 
-if __name__ == '__main__':
-    fiber = single_fiber()
-    import ipdb; ipdb.set_trace()
+
+if __name__ == "__main__":
+    single_fiber()

vivarium_models/processes/fiber_to_monomer.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from vivarium.core.process import Deriver
-from vivarium.core.engine import Engine, pf
+from vivarium.core.engine import Engine
 
 from simularium_readdy_models.actin import ActinGenerator, ActinTestData, FiberData
 from ..util import create_monomer_update
@@ -114,7 +114,7 @@ def get_initial_fiber_data():
     return fibers_dict
 
 
-def test_fiber_to_monomer():
+def run_fiber_to_monomer():
     fiber_data = get_initial_fiber_data()
     fiber_to_monomer = FiberToMonomer()
 
@@ -132,10 +132,8 @@ def test_fiber_to_monomer():
     )
 
     engine.update(1.0)
-
-    output = engine.emitter.get_data()
-    print(pf(output))
+    return engine.emitter.get_data()
 
 
 if __name__ == "__main__":
-    test_fiber_to_monomer()
+    run_fiber_to_monomer()

vivarium_models/processes/monomer_to_fiber.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from vivarium.core.process import Deriver
-from vivarium.core.engine import Engine, pf
+from vivarium.core.engine import Engine
 from simularium_readdy_models.actin import ActinUtil, ActinTestData
 
 from ..util import agents_update
@@ -184,7 +184,7 @@ def generate_fibers_from_monomers(monomers, box_size=500.0):
         return result
 
 
-def test_fiber_to_monomer():
+def run_fiber_to_monomer():
     monomer_data = ActinTestData.linear_actin_monomers()
     monomer_to_fiber = MonomerToFiber()
 
@@ -202,10 +202,8 @@ def test_fiber_to_monomer():
     )
 
     engine.update(1.0)
-
-    output = engine.emitter.get_data()
-    print(pf(output))
+    return engine.emitter.get_data()
 
 
 if __name__ == "__main__":
-    test_fiber_to_monomer()
+    run_fiber_to_monomer()

vivarium_models/processes/readdy_actin_process.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 from vivarium.core.process import Process
-from vivarium.core.engine import Engine, pf
+from vivarium.core.engine import Engine
 from vivarium.core.control import run_library_cli
 
 from tqdm import tqdm
@@ -208,7 +208,7 @@ def get_monomer_data():
     return {"monomers": monomer_data}
 
 
-def test_readdy_actin_process():
+def run_readdy_actin_process():
     monomer_data = get_monomer_data()
     readdy_actin_process = ReaddyActinProcess()
 
@@ -225,12 +225,10 @@ def test_readdy_actin_process():
     )
 
     engine.update(0.0000001)  # 1e3 steps
+    return engine.emitter.get_data()
 
-    output = engine.emitter.get_data()
-    print(pf(output))
 
-
-def test_scan_readdy():
+def run_scan_readdy():
     monomer_data = get_monomer_data()
 
     parameters = {
@@ -354,10 +352,10 @@ def filament_straightness(results):
 
     scan = Scan(parameters, ReaddyActinProcess, 0.0000001, metrics=metrics)
     results = scan.run_scan()
-    print(results)
+    return results
 
 
-library = {"0": test_readdy_actin_process, "1": test_scan_readdy}
+library = {"0": run_readdy_actin_process, "1": run_scan_readdy}
 
 
 if __name__ == "__main__":