Release 0.3.2

Author: dilpath

doc/problem_definition.rst

@@ -109,7 +109,7 @@ can be specified like
    :header-rows: 1
 
    * - model_subspace_id
-     - petab_yaml
+     - model_subspace_petab_yaml
      - p1
      - p2
    * - subspace1
@@ -156,7 +156,7 @@ Brief format description
 - ``model_subspace_indices``: The indices that locate this model in its model subspace.
 - ``criteria``: The value of the criterion by which model selection was performed, at least. Optionally, other criterion values too.
 - ``model_hash``: The model hash, generated by the PEtab Select library. The format is ``[MODEL_SUBSPACE_ID]-[MODEL_SUBSPACE_INDICES_HASH]``. If all parameters are in the model are defined like ``0;estimate``, then the hash is a string of ``1`` and ``0``, for parameters that are estimated or not, respectively.
-- ``model_subspace_petab_yaml``: Same as in model space files (see ``petab_yaml``).
+- ``model_subspace_petab_yaml``: Same as in model space files.
 - ``estimated_parameters``: Parameter estimates, including all estimated parameters that are not in the model selection problem; i.e., parameters that are set to be estimated in the model subspace PEtab problem but don't appear in the column header of the model space file.
 - ``iteration``: The iteration of model selection in which this model appeared.
 - ``model_id``: The model ID.

petab_select/model_subspace.py

@@ -733,7 +733,16 @@ def from_definition(
             The model subspace.
         """
         model_subspace_id = definition.pop(MODEL_SUBSPACE_ID)
-        petab_yaml = definition.pop(MODEL_SUBSPACE_PETAB_YAML)
+        if "petab_yaml" in definition:
+            petab_yaml = definition.pop("petab_yaml")
+            warnings.warn(
+                "Change the `petab_yaml` column to "
+                "`model_subspace_petab_yaml`, in the model space TSV.",
+                DeprecationWarning,
+                stacklevel=1,
+            )
+        else:
+            petab_yaml = definition.pop(MODEL_SUBSPACE_PETAB_YAML)
         parameters = {
             column_id: decompress_parameter_values(value)
             for column_id, value in definition.items()

pyproject.toml

@@ -34,10 +34,6 @@ plot = [
 test = [
     "pytest >= 5.4.3",
     "pytest-cov >= 2.10.0",
-    "amici >= 0.11.25",
-    "fides >= 0.7.5",
-    "pypesto >= 0.5.4",
-    #"pypesto @ git+https://github.com/ICB-DCM/pyPESTO.git@select_mkstd#egg=pypesto",
     "tox >= 3.12.4",
 ]
 doc = [