♻️ Refactor/821 refactor model spec (#836)

* 🗑️ Deprecated {relations,constraints} -> {clp_relations,clp_constraints)
👌 Improved deprecation messages to users

* ♻️ Change relations -> clp_relations
🩹 Fixes glotaran/builtin/io/yml/test/test_model_parser.py::test_relations

* ♻️ Change constraints-> clp_constraints
🩹 Fixes glotaran/builtin/io/yml/test/test_model_parser.py::test_constraints

glotaran/analysis/test/test_constraints.py

@@ -15,7 +15,7 @@
 def test_constraint(index_dependent, grouped):
     model = deepcopy(suite.model)
     model.megacomplex["m1"].is_index_dependent = index_dependent
-    model.constraints.append(ZeroConstraint.from_dict({"target": "s2"}))
+    model.clp_constraints.append(ZeroConstraint.from_dict({"target": "s2"}))
 
     print("grouped", grouped, "index_dependent", index_dependent)
     dataset = simulate(

glotaran/analysis/test/test_relations.py

@@ -16,7 +16,9 @@
 def test_relations(index_dependent, grouped):
     model = deepcopy(suite.model)
     model.megacomplex["m1"].is_index_dependent = index_dependent
-    model.relations.append(Relation.from_dict({"source": "s1", "target": "s2", "parameter": "3"}))
+    model.clp_relations.append(
+        Relation.from_dict({"source": "s1", "target": "s2", "parameter": "3"})
+    )
     parameters = ParameterGroup.from_list([11e-4, 22e-5, 2])
 
     print("grouped", grouped, "index_dependent", index_dependent)

glotaran/analysis/util.py

@@ -113,12 +113,12 @@ def apply_constraints(
     index: Any | None,
 ) -> CalculatedMatrix:
 
-    if len(model.constraints) == 0:
+    if len(model.clp_constraints) == 0:
         return matrix
 
     clp_labels = matrix.clp_labels
     removed_clp_labels = [
-        c.target for c in model.constraints if c.target in clp_labels and c.applies(index)
+        c.target for c in model.clp_constraints if c.target in clp_labels and c.applies(index)
     ]
     reduced_clp_labels = [c for c in clp_labels if c not in removed_clp_labels]
     mask = [label in reduced_clp_labels for label in clp_labels]
@@ -133,14 +133,14 @@ def apply_relations(
     index: Any | None,
 ) -> CalculatedMatrix:
 
-    if len(model.relations) == 0:
+    if len(model.clp_relations) == 0:
         return matrix
 
     clp_labels = matrix.clp_labels
     relation_matrix = np.diagflat([1.0 for _ in clp_labels])
 
     idx_to_delete = []
-    for relation in model.relations:
+    for relation in model.clp_relations:
         if relation.target in clp_labels and relation.applies(index):
 
             if relation.source not in clp_labels:
@@ -166,7 +166,7 @@ def retrieve_clps(
     reduced_clps: xr.DataArray,
     index: Any | None,
 ) -> xr.DataArray:
-    if len(model.relations) == 0 and len(model.constraints) == 0:
+    if len(model.clp_relations) == 0 and len(model.clp_constraints) == 0:
         return reduced_clps
 
     clps = np.zeros(len(clp_labels))
@@ -175,7 +175,7 @@ def retrieve_clps(
         idx = clp_labels.index(label)
         clps[idx] = reduced_clps[i]
 
-    for relation in model.relations:
+    for relation in model.clp_relations:
         relation = relation.fill(model, parameters)
         if (
             relation.target in clp_labels

glotaran/builtin/io/yml/test/test_model_parser.py

@@ -61,15 +61,15 @@ def test_dataset(model):
 
 
 def test_constraints(model):
-    print(model.constraints)
-    assert len(model.constraints) == 2
+    print(model.clp_constraints)
+    assert len(model.clp_constraints) == 2
 
-    zero = model.constraints[0]
+    zero = model.clp_constraints[0]
     assert isinstance(zero, ZeroConstraint)
     assert zero.target == "s1"
     assert zero.interval == [[1, 100], [2, 200]]
 
-    only = model.constraints[1]
+    only = model.clp_constraints[1]
     assert isinstance(only, OnlyConstraint)
     assert only.target == "s1"
     assert only.interval == [[1, 100], [2, 200]]
@@ -88,10 +88,10 @@ def test_penalties(model):
 
 
 def test_relations(model):
-    print(model.relations)
-    assert len(model.relations) == 1
+    print(model.clp_relations)
+    assert len(model.clp_relations) == 1
 
-    rel = model.relations[0]
+    rel = model.clp_relations[0]
 
     assert rel.source == "s1"
     assert rel.target == "s2"

glotaran/builtin/io/yml/test/test_model_spec.yml

@@ -71,7 +71,7 @@ megacomplex:
       s1: shape1
       s2: shape2
 
-constraints:
+clp_constraints:
   - type: zero
     target: s1
     interval:
@@ -92,7 +92,7 @@ clp_area_penalties:
     parameter: 55
     weight: 0.0016
 
-relations:
+clp_relations:
   - source: s1
     target: s2
     parameter: 8

glotaran/deprecation/modules/builtin_io_yml.py

@@ -40,18 +40,27 @@ def model_spec_deprecations(spec: MutableMapping[Any, Any]) -> None:
     deprecate_dict_entry(
         dict_to_check=spec,
         deprecated_usage="spectral_relations",
-        new_usage="relations",
+        new_usage="clp_relations",
         to_be_removed_in_version="0.7.0",
-        swap_keys=("spectral_relations", "relations"),
+        swap_keys=("spectral_relations", "clp_relations"),
         stacklevel=load_model_stack_level,
     )
 
-    if "relations" in spec:
-        for relation in spec["relations"]:
+    deprecate_dict_entry(
+        dict_to_check=spec,
+        deprecated_usage="relations",
+        new_usage="clp_relations",
+        to_be_removed_in_version="0.7.0",
+        swap_keys=("relations", "clp_relations"),
+        stacklevel=load_model_stack_level,
+    )
+
+    if "clp_relations" in spec:
+        for relation in spec["clp_relations"]:
             deprecate_dict_entry(
                 dict_to_check=relation,
-                deprecated_usage="compartment",
-                new_usage="source",
+                deprecated_usage="clp_relations:\n - compartment",
+                new_usage="clp_relations:\n - source",
                 to_be_removed_in_version="0.7.0",
                 swap_keys=("compartment", "source"),
                 stacklevel=load_model_stack_level,
@@ -60,18 +69,27 @@ def model_spec_deprecations(spec: MutableMapping[Any, Any]) -> None:
     deprecate_dict_entry(
         dict_to_check=spec,
         deprecated_usage="spectral_constraints",
-        new_usage="constraints",
+        new_usage="clp_constraints",
+        to_be_removed_in_version="0.7.0",
+        swap_keys=("spectral_constraints", "clp_constraints"),
+        stacklevel=load_model_stack_level,
+    )
+
+    deprecate_dict_entry(
+        dict_to_check=spec,
+        deprecated_usage="constraints",
+        new_usage="clp_constraints",
         to_be_removed_in_version="0.7.0",
-        swap_keys=("spectral_constraints", "constraints"),
+        swap_keys=("constraints", "clp_constraints"),
         stacklevel=load_model_stack_level,
     )
 
-    if "constraints" in spec:
-        for constraint in spec["constraints"]:
+    if "clp_constraints" in spec:
+        for constraint in spec["clp_constraints"]:
             deprecate_dict_entry(
                 dict_to_check=constraint,
-                deprecated_usage="constraint.compartment",
-                new_usage="constraint.target",
+                deprecated_usage="clp_constraints:\n - compartment",
+                new_usage="clp_constraints:\n - target",
                 to_be_removed_in_version="0.7.0",
                 swap_keys=("compartment", "target"),
                 stacklevel=load_model_stack_level,

glotaran/deprecation/modules/test/test_builtin_io_yml.py

@@ -29,7 +29,19 @@
                 """
             ),
             3,
-            "relations",
+            "clp_relations",
+            [{"source": "s1"}, {"source": "s2"}],
+        ),
+        (
+            dedent(
+                """
+                relations:
+                    - compartment: s1
+                    - compartment: s2
+                """
+            ),
+            3,
+            "clp_relations",
             [{"source": "s1"}, {"source": "s2"}],
         ),
         (
@@ -41,7 +53,19 @@
                 """
             ),
             3,
-            "constraints",
+            "clp_constraints",
+            [{"target": "s1"}, {"target": "s2"}],
+        ),
+        (
+            dedent(
+                """
+                constraints:
+                    - compartment: s1
+                    - compartment: s2
+                """
+            ),
+            3,
+            "clp_constraints",
             [{"target": "s1"}, {"target": "s2"}],
         ),
         (
@@ -86,7 +110,9 @@
         "type: kinetic-spectrum",
         "type: spectrum",
         "spectral_relations",
+        "relations",
         "spectral_constraints",
+        "constraints",
         "equal_area_penalties",
         "center_dispersion",
         "width_dispersion",

glotaran/model/model.py

@@ -24,8 +24,8 @@
 
 default_model_items = {
     "clp_area_penalties": EqualAreaPenalty,
-    "constraints": Constraint,
-    "relations": Relation,
+    "clp_constraints": Constraint,
+    "clp_relations": Relation,
     "weights": Weight,
 }
 
@@ -254,8 +254,8 @@ def global_megacomplex(self) -> dict[str, Megacomplex]:
         return self.megacomplex
 
     def need_index_dependent(self) -> bool:
-        """Returns true if e.g. relations with intervals are present."""
-        return any(i.interval is not None for i in self.constraints + self.relations)
+        """Returns true if e.g. clp_relations with intervals are present."""
+        return any(i.interval is not None for i in self.clp_constraints + self.clp_relations)
 
     def is_groupable(self, parameters: ParameterGroup, data: dict[str, xr.DataArray]) -> bool:
         if any(d.has_global_model() for d in self.dataset.values()):

glotaran/model/test/test_model.py

@@ -227,15 +227,15 @@ def test_model_init():
     assert "clp_area_penalties" in model._model_items
     assert issubclass(model._model_items["clp_area_penalties"], EqualAreaPenalty)
 
-    assert hasattr(model, "constraints")
-    assert isinstance(model.constraints, list)
-    assert "constraints" in model._model_items
-    assert issubclass(model._model_items["constraints"], Constraint)
-
-    assert hasattr(model, "relations")
-    assert isinstance(model.relations, list)
-    assert "relations" in model._model_items
-    assert issubclass(model._model_items["relations"], Relation)
+    assert hasattr(model, "clp_constraints")
+    assert isinstance(model.clp_constraints, list)
+    assert "clp_constraints" in model._model_items
+    assert issubclass(model._model_items["clp_constraints"], Constraint)
+
+    assert hasattr(model, "clp_relations")
+    assert isinstance(model.clp_relations, list)
+    assert "clp_relations" in model._model_items
+    assert issubclass(model._model_items["clp_relations"], Relation)
 
     assert hasattr(model, "weights")
     assert isinstance(model.weights, list)