Release 1.3.1

.github/workflows/tests.yml

@@ -35,7 +35,7 @@ jobs:
           python3 -m pip install .[test]
       - name: Run tests
         run: |
-          coverage run --omit=tests/*,*/_*.py -m pytest
+          coverage run --omit=tests/*,*/_*.py -m pytest --doctest-modules
           coverage xml
       - name: Upload to codecov
         uses: codecov/codecov-action@v3

CHANGELOG.md

@@ -2,6 +2,24 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.3.1] - 2025-01-31
+
+### Bug Fixes
+
+- `get_named_params()` returns only named params and doesn't raise an error anymore.
+- Add deleter to `named_params` property.
+
+### Change
+
+- Move `named_params` stuff from dedicated mixin to `types.Model`.
+- Raise explicit invalid param name error.\
+  This ensures that e.g. during sampling, the likelihood does not simply
+  return `-np.inf` because it sees a `ValueError`.
+- Call `set_named_params()` in likelihoods.\
+  This ensures that a model definition is respected during inference and
+  also when reloading sampled parameters. In case no `named_params` are
+  provided, this will simply behave as `set_params()`.
+
 ## [1.3.0] - 2025-01-29
 
 ### Bug Fixes
@@ -819,10 +837,11 @@ Almost the entire API has changed. I'd therefore recommend to have a look at the
 - fix pyproject.toml typo
 - add pre-commit hook to check commit msg
 
+[1.3.1]: https://github.com/rmnldwg/lymph/compare/1.3.0...1.3.1
 [1.3.0]: https://github.com/rmnldwg/lymph/compare/1.2.3...1.3.0
 [1.2.3]: https://github.com/rmnldwg/lymph/compare/1.2.2...1.2.3
 [1.2.2]: https://github.com/rmnldwg/lymph/compare/1.2.1...1.2.2
-[1.2.1]: https://github.com/rmnldwg/lymph/compare/1.1.0...1.2.1
+[1.2.1]: https://github.com/rmnldwg/lymph/compare/1.2.0...1.2.1
 [1.2.0]: https://github.com/rmnldwg/lymph/compare/1.1.0...1.2.0
 [1.1.0]: https://github.com/rmnldwg/lymph/compare/1.0.0...1.1.0
 [1.0.0]: https://github.com/rmnldwg/lymph/compare/1.0.0.rc2...1.0.0

lymph/models/bilateral.py

@@ -10,7 +10,7 @@
 import numpy as np
 import pandas as pd
 
-from lymph import diagnosis_times, matrix, mixins, modalities, models, types, utils
+from lymph import diagnosis_times, matrix, modalities, models, types, utils
 
 warnings.filterwarnings("ignore", category=pd.errors.PerformanceWarning)
 logger = logging.getLogger(__name__)
@@ -19,7 +19,6 @@
 class Bilateral(
     diagnosis_times.Composite,
     modalities.Composite,
-    mixins.NamedParamsMixin,
     types.Model,
 ):
     """Class that models metastatic progression in a bilateral lymphatic system.

lymph/models/hpv.py

@@ -11,7 +11,7 @@
 import numpy as np
 import pandas as pd
 
-from lymph import diagnosis_times, mixins, modalities, models, types, utils
+from lymph import diagnosis_times, modalities, models, types, utils
 
 warnings.filterwarnings("ignore", category=pd.errors.PerformanceWarning)
 logger = logging.getLogger(__name__)
@@ -34,7 +34,6 @@ def wrapper(self, *args, hpv_status: bool | None = None, **kwargs):
 class HPVUnilateral(
     diagnosis_times.Composite,
     modalities.Composite,
-    mixins.NamedParamsMixin,
     types.Model,
 ):
     """Class that models metastatic progression in HPV and non HPV lymphatic systems.

lymph/models/midline.py

@@ -10,7 +10,7 @@
 import numpy as np
 import pandas as pd
 
-from lymph import diagnosis_times, matrix, mixins, modalities, models, types, utils
+from lymph import diagnosis_times, matrix, modalities, models, types, utils
 
 warnings.filterwarnings("ignore", category=pd.errors.PerformanceWarning)
 logger = logging.getLogger(__name__)
@@ -23,7 +23,6 @@
 class Midline(
     diagnosis_times.Composite,
     modalities.Composite,
-    mixins.NamedParamsMixin,
     types.Model,
 ):
     r"""Models metastatic progression bilaterally with tumor lateralization.

lymph/models/unilateral.py

@@ -11,10 +11,8 @@
 import pandas as pd
 from cachetools import LRUCache
 
-from lymph import diagnosis_times, graph, matrix, mixins, modalities, types, utils
-
-# pylint: disable=unused-import
-from lymph.utils import (  # nopycln: import
+from lymph import diagnosis_times, graph, matrix, modalities, types, utils
+from lymph.utils import (
     add_or_mult,
     dict_to_func,  # noqa: F401
     draw_diagnosis,  # noqa: F401
@@ -34,7 +32,6 @@
 class Unilateral(
     diagnosis_times.Composite,
     modalities.Composite,
-    mixins.NamedParamsMixin,
     types.Model,
 ):
     """Class that models metastatic progression in a unilateral lymphatic system.
@@ -938,10 +935,8 @@ def draw_patients(
                 Method to draw individual diagnosis.
             :py:meth:`lymph.models.Bilateral.draw_patients`
                 The corresponding bilateral method.
-
         """
-        if rng is None:
-            rng = np.random.default_rng(seed)
+        rng = rng or np.random.default_rng(seed)
 
         if sum(stage_dist) != 1.0:
             warnings.warn("Sum of stage distribution is not 1. Renormalizing.")