Feature: migrate v1 partner recipes (#207)

* [wip] debugging * fix v1 to v2 partners * delete the partners key if there is none * delete partners if there is none * correct tests * simplify * set binding_probability in v2 to v2.1 * migrate color to v2 recipes * fix test
mesoscope · Nov 6, 2023 · 2c5e04b · 2c5e04b
1 parent c176ac8
commit 2c5e04b
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Showing 4 changed files with 16 additions and 5 deletions.
diff --git a/cellpack/autopack/loaders/migrate_v1_to_v2.py b/cellpack/autopack/loaders/migrate_v1_to_v2.py
@@ -96,6 +96,8 @@ def migrate_ingredient(old_ingredient):
     new_ingredient["representations"] = get_representations(old_ingredient)
     if new_ingredient["type"] == INGREDIENT_TYPE.SINGLE_SPHERE:
         new_ingredient["radius"] = old_ingredient["radii"][0][0]
+    if "partners" in new_ingredient and not new_ingredient["partners"].get("names"):
+        del new_ingredient["partners"]
     return new_ingredient
 
 

diff --git a/cellpack/autopack/loaders/migrate_v2_to_v2_1.py b/cellpack/autopack/loaders/migrate_v2_to_v2_1.py
@@ -5,7 +5,7 @@
 
 def convert_partners(object_data):
     partners_list = []
-    if "names" not in "partners":
+    if "names" not in object_data["partners"]:
         return partners_list
     for index, name in enumerate(object_data["partners"]["names"]):
         positions = object_data["partners"]["positions"]
@@ -16,7 +16,10 @@ def convert_partners(object_data):
         binding_probability = 1.0
         if "probability_binding" in object_data["partners"]:
             binding_probability = object_data["partners"]["probability_binding"]
-        if "probability_repelled" in object_data["partners"]:
+        if (
+            "probability_repelled" in object_data["partners"]
+            and object_data["partners"]["probability_repelled"] < 0
+        ):
             binding_probability = -object_data["partners"]["probability_repelled"]
 
         partner = {

diff --git a/cellpack/autopack/loaders/v1_v2_attribute_changes.py b/cellpack/autopack/loaders/v1_v2_attribute_changes.py
@@ -2,6 +2,7 @@
 
 v1_to_v2_name_map = {
     "Type": "type",
+    "color": "color",
     "distExpression": "distance_expression",
     "distFunction": "distance_function",
     "isAttractor": "is_attractor",

diff --git a/cellpack/tests/test_recipe_version_migration.py b/cellpack/tests/test_recipe_version_migration.py
@@ -141,13 +141,13 @@ def test_create_packing_atomic_representation(
                 "encapsulatingRadius": 100,
                 "nbMol": 15,
                 "orientBiasRotRangeMax": 12,
+                "partners_name": [],
                 "proba_binding": 0.5,
                 "Type": "MultiSphere",
             },
             {
                 "count": 15,
                 "orient_bias_range": [-pi, 12],
-                "partners": {"probability_binding": 0.5},
                 "representations": RecipeLoader.default_values["representations"],
                 "type": INGREDIENT_TYPE.MULTI_SPHERE,
             },
@@ -179,7 +179,6 @@ def test_create_packing_atomic_representation(
             {
                 "count": 15,
                 "orient_bias_range": [6, 12],
-                "partners": {"probability_binding": 0.5},
                 "radius": 100,
                 "representations": RecipeLoader.default_values["representations"],
                 "type": INGREDIENT_TYPE.SINGLE_SPHERE,
@@ -275,7 +274,6 @@ def test_get_v1_ingredient():
                     "orient_bias_range": [6, pi],
                 },
                 "C": {
-                    "partners": {"probability_binding": 0.5},
                     "orient_bias_range": [-pi, 12],
                     "radius": 10,
                     "representations": {
@@ -400,6 +398,11 @@ def test_migrate_version_error():
                         "rotation_range": 6.2831,
                         "max_jitter": [1, 1, 0],
                         "perturb_axis_amplitude": 0.1,
+                        "color": [
+                            0.498,
+                            0.498,
+                            0.498,
+                        ],
                         "is_attractor": False,
                         "principal_vector": [1, 0, 0],
                         "packing_mode": "random",
@@ -430,6 +433,7 @@ def test_migrate_version_error():
                         "rotation_range": 6.2831,
                         "max_jitter": [1, 1, 0],
                         "perturb_axis_amplitude": 0.1,
+                        "color": [0.306, 0.45100001, 0.81599998],
                         "is_attractor": False,
                         "principal_vector": [1, 0, 0],
                         "packing_mode": "random",
@@ -449,6 +453,7 @@ def test_migrate_version_error():
                         "rotation_range": 6.2831,
                         "max_jitter": [1, 1, 0],
                         "perturb_axis_amplitude": 0.1,
+                        "color": [0.306, 0.45100001, 0.81599998],
                         "is_attractor": False,
                         "principal_vector": [1, 0, 0],
                         "packing_mode": "random",