Removed Generator and project

glotaran · Sep 17, 2021 · 9d61605 · 9d61605
1 parent 968ebb8
commit 9d61605
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Showing 5 changed files with 60 additions and 579 deletions.
diff --git a/glotaran/examples/sequential.py b/glotaran/examples/sequential.py
@@ -3,12 +3,8 @@
 from glotaran.analysis.simulation import simulate
 from glotaran.builtin.megacomplexes.decay import DecayMegacomplex
 from glotaran.builtin.megacomplexes.spectral import SpectralMegacomplex
-from glotaran.io import load_model
-from glotaran.io import load_parameters
 from glotaran.model import Model
 from glotaran.parameter import ParameterGroup
-from glotaran.project import Scheme
-from glotaran.project.generators.generator import generate_model_yml
 
 sim_model = Model.from_dict(
     {
@@ -92,6 +88,21 @@
     }
 )
 
+parameter = ParameterGroup.from_dict(
+    {
+        "j": [
+            ["1", 1, {"vary": False, "non-negative": False}],
+            ["0", 0, {"vary": False, "non-negative": False}],
+        ],
+        "kinetic": [
+            ["1", 0.5],
+            ["2", 0.3],
+            ["3", 0.1],
+        ],
+        "irf": [["center", 0.3], ["width", 0.1]],
+    }
+)
+
 _time = np.arange(-1, 20, 0.01)
 _spectral = np.arange(600, 700, 1.4)
 
@@ -104,28 +115,36 @@
     noise_std_dev=1e-2,
 )
 
-parameter_yml = """
-initial_concentration:
-  - ["1", 1]
-  - ["0", 0]
-  - {"vary": False, "non-negative": False}
-
-decay:
-  - [species_1, 0.5]
-  - [species_2, 0.3]
-  - [species_3, 0.1]
-
-irf:
-  - [center, 0.3]
-  - [width, 0.1]
-"""
-parameter = load_parameters(parameter_yml, format_name="yml_str")
-
-model_yml = generate_model_yml("decay-sequential", nr_species=3, irf=True)
-model = load_model(model_yml, format_name="yml_str")
-
-scheme = Scheme(
-    model=model,
-    parameters=parameter,
-    data={"dataset_1": dataset},
+model = Model.from_dict(
+    {
+        "initial_concentration": {
+            "j1": {"compartments": ["s1", "s2", "s3"], "parameters": ["j.1", "j.0", "j.0"]},
+        },
+        "k_matrix": {
+            "k1": {
+                "matrix": {
+                    ("s2", "s1"): "kinetic.1",
+                    ("s3", "s2"): "kinetic.2",
+                    ("s3", "s3"): "kinetic.3",
+                }
+            }
+        },
+        "megacomplex": {
+            "m1": {
+                "type": "decay",
+                "k_matrix": ["k1"],
+            }
+        },
+        "irf": {
+            "irf1": {"type": "gaussian", "center": "irf.center", "width": "irf.width"},
+        },
+        "dataset": {
+            "dataset1": {
+                "initial_concentration": "j1",
+                "megacomplex": ["m1"],
+                "irf": "irf1",
+            }
+        },
+    },
+    megacomplex_types={"decay": DecayMegacomplex},
 )
diff --git a/glotaran/io/interface.py b/glotaran/io/interface.py
@@ -22,8 +22,8 @@
 
     from glotaran.model import Model
     from glotaran.parameter import ParameterGroup
+    from glotaran.plugin_system.project_io_registration import SavingOptions
     from glotaran.project import Result
-    from glotaran.project import SavingOptions
     from glotaran.project import Scheme
 
     DataLoader = Callable[[str], Union[xr.Dataset, xr.DataArray]]