diff --git a/CHANGELOG.rst b/CHANGELOG.rst index c69ec6607..e65d84e6d 100644 --- a/CHANGELOG.rst +++ b/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) ------------------- diff --git a/pypesto/version.py b/pypesto/version.py index f9aa3e110..e19434e2e 100644 --- a/pypesto/version.py +++ b/pypesto/version.py @@ -1 +1 @@ -__version__ = "0.3.2" +__version__ = "0.3.3" diff --git a/test/base/test_engine.py b/test/base/test_engine.py index c3e5979e5..d4d045c20 100644 --- a/test/base/test_engine.py +++ b/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() diff --git a/tox.ini b/tox.ini index 9477f90f0..89af0a9c1 100644 --- a/tox.ini +++ b/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