Deprecate petab_yaml properly; move pypesto test to pyPESTO (#145)

PEtab-dev · Jan 8, 2025 · 23cae9c · 23cae9c
1 parent 404af84
commit 23cae9c
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Showing 6 changed files with 10 additions and 346 deletions.
diff --git a/petab_select/model_subspace.py b/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()

diff --git a/pyproject.toml b/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 = [

diff --git a/test/pypesto/__init__.py b/test/pypesto/__init__.py
diff --git a/test/pypesto/generate_expected_models.py b/test/pypesto/generate_expected_models.py
diff --git a/test/pypesto/regenerate_model_hashes.py b/test/pypesto/regenerate_model_hashes.py
diff --git a/test/pypesto/test_pypesto.py b/test/pypesto/test_pypesto.py