Merge branch 'develop' into petab_import_changes

CHANGELOG.rst

@@ -6,6 +6,25 @@ Release notes
 ..........
 
 
+0.3.3 (2023-10-19)
+-------------------
+
+* Visualize:
+    * Get optimization result by id (#1116)
+* Storage:
+    * allow "{id}" in history storage filename (#1118)
+* Objective:
+    * adjusted PEtab.jl syntax to new release (#1128, #1131)
+    * Documentation on PEtab importer updated (#1126)
+* Ensembles
+    * Additional option for cutoff calculation (#1124)
+    * Ensembles from optimization endpoints now only takes free parameters (#1130)
+* General
+    * Added How to Cite (#1125)
+    * Additional summary option (#1134)
+    * Speed up base tests (#1127)
+
+
 0.3.2 (2023-10-02)
 -------------------
 

pypesto/version.py

@@ -1 +1 @@
-__version__ = "0.3.2"
+__version__ = "0.3.3"

test/base/test_engine.py

@@ -36,12 +36,12 @@ def _test_basic(engine):
     optimizer = pypesto.optimize.ScipyOptimizer(options={'maxiter': 10})
     result = pypesto.optimize.minimize(
         problem=problem,
-        n_starts=5,
+        n_starts=2,
         engine=engine,
         optimizer=optimizer,
         progress_bar=False,
     )
-    assert len(result.optimize_result) == 5
+    assert len(result.optimize_result) == 2
 
 
 def test_petab():
@@ -59,7 +59,9 @@ def test_petab():
 def _test_petab(engine):
     petab_importer = pypesto.petab.PetabImporter.from_yaml(
         os.path.join(
-            models.MODELS_DIR, "Zheng_PNAS2012", "Zheng_PNAS2012.yaml"
+            models.MODELS_DIR,
+            "Boehm_JProteomeRes2014",
+            "Boehm_JProteomeRes2014.yaml",
         )
     )
     objective = petab_importer.create_objective()
@@ -79,7 +81,9 @@ def test_deepcopy_objective():
     """Test copying objectives (needed for MultiProcessEngine)."""
     petab_importer = pypesto.petab.PetabImporter.from_yaml(
         os.path.join(
-            models.MODELS_DIR, "Zheng_PNAS2012", "Zheng_PNAS2012.yaml"
+            models.MODELS_DIR,
+            "Boehm_JProteomeRes2014",
+            "Boehm_JProteomeRes2014.yaml",
         )
     )
     objective = petab_importer.create_objective()
@@ -114,7 +118,9 @@ def test_pickle_objective():
     """Test serializing objectives (needed for MultiThreadEngine)."""
     petab_importer = pypesto.petab.PetabImporter.from_yaml(
         os.path.join(
-            models.MODELS_DIR, "Zheng_PNAS2012", "Zheng_PNAS2012.yaml"
+            models.MODELS_DIR,
+            "Boehm_JProteomeRes2014",
+            "Boehm_JProteomeRes2014.yaml",
         )
     )
     objective = petab_importer.create_objective()

tox.ini

@@ -53,10 +53,10 @@ deps =
     git+https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git@master\#subdirectory=src/python
 commands =
     pytest --cov=pypesto --cov-report=xml --cov-append \
-        test/base \
-        test/profile \
-        test/sample \
-        test/visualize \
+        test/base --durations=0 \
+        test/profile --durations=0 \
+        test/sample --durations=0 \
+        test/visualize --durations=0 \
         -s
 description =
     Test basic functionality