Merge remote-tracking branch 'origin/develop' into fix_typehints

.github/workflows/ci.yml

@@ -3,12 +3,14 @@ name: CI
 # trigger
 on:
   push:
-    branches:
-    - main
   pull_request:
+    branches:
+      - main
   schedule:
     # run Tuesday and Friday at 02:00 UTC
     - cron: '00 2 * * TUE,FRI'
+  workflow_dispatch:
+  merge_group:
 
 jobs:
   base:

.pre-commit-config.yaml

@@ -5,12 +5,12 @@
 
 repos:
 - repo: https://github.com/psf/black
-  rev: 22.6.0
+  rev: 23.10.0
   hooks:
   - id: black
     description: The uncompromising code formatter
 - repo: https://github.com/pycqa/isort
-  rev: 5.10.1
+  rev: 5.12.0
   hooks:
   - id: isort
     name: isort (python)
@@ -21,14 +21,14 @@ repos:
     name: isort (pyi)
     types: [pyi]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.3.1
+  rev: 1.7.0
   hooks:
     - id: nbqa-black
     - id: nbqa-pyupgrade
       args: [--py36-plus]
     - id: nbqa-isort
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.3.0
+  rev: v4.5.0
   hooks:
   - id: check-yaml
     description: Check yaml files for parseable syntax

petab_select/candidate_space.py

@@ -4,7 +4,6 @@
 import copy
 import csv
 import logging
-import os.path
 import warnings
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Union, Type
@@ -27,7 +26,6 @@
     Method,
 )
 from .handlers import TYPE_LIMIT, LimitHandler
-from .misc import snake_case_to_camel_case
 from .model import Model, default_compare
 
 

petab_select/cli.py

@@ -1,18 +1,16 @@
 """The PEtab Select command-line interface."""
-import warnings
 from pathlib import Path
 from typing import Any, Dict, List
 
 import click
 import dill
 import numpy as np
 import pandas as pd
-import yaml
 from more_itertools import one
 
 from . import ui
-from .candidate_space import CandidateSpace, method_to_candidate_space_class
-from .constants import INITIAL_MODEL_METHODS, PETAB_YAML
+from .candidate_space import CandidateSpace
+from .constants import PETAB_YAML
 from .model import Model, models_from_yaml_list, models_to_yaml_list
 from .problem import Problem
 

petab_select/criteria.py

@@ -3,13 +3,9 @@
 import math
 
 import petab
-from petab.C import OBJECTIVE, OBJECTIVE_PRIOR_PARAMETERS, OBJECTIVE_PRIOR_TYPE
+from petab.C import OBJECTIVE_PRIOR_PARAMETERS, OBJECTIVE_PRIOR_TYPE
 
-from .constants import (  # LH,; LLH,; NLLH,
-    PETAB_PROBLEM,
-    TYPE_CRITERION,
-    Criterion,
-)
+from .constants import PETAB_PROBLEM, Criterion  # LH,; LLH,; NLLH,
 
 # from .model import Model
 

petab_select/handlers.py

@@ -1,7 +1,4 @@
-from pathlib import Path
-from typing import Any, Callable, List, Optional, Union
-
-import numpy as np
+from typing import Callable, Union
 
 # `float` for `np.inf`
 TYPE_LIMIT = Union[float, int]

petab_select/misc.py

@@ -1,7 +1,7 @@
 import hashlib
 
 # import json
-from typing import Any, Dict, List, Union
+from typing import Any, List, Union
 
 from .constants import (  # TYPE_PARAMETER_OPTIONS_DICT,
     ESTIMATE,

petab_select/model.py

@@ -1,11 +1,9 @@
 """The `Model` class."""
-import abc
 import warnings
 from os.path import relpath
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
 
-import numpy as np
 import petab
 import yaml
 from more_itertools import one

petab_select/model_space.py

@@ -1,35 +1,20 @@
 """The `ModelSpace` class and related methods."""
-import abc
 import itertools
 import logging
 from pathlib import Path
 from tempfile import NamedTemporaryFile
-from typing import (
-    Any,
-    Callable,
-    Iterable,
-    List,
-    Optional,
-    TextIO,
-    Union,
-    get_args,
-)
+from typing import Any, Iterable, List, Optional, TextIO, Union, get_args
 
 import numpy as np
 import pandas as pd
-from more_itertools import nth
 
 from .candidate_space import CandidateSpace
 from .constants import (
-    ESTIMATE,
     HEADER_ROW,
-    MODEL_ID,
     MODEL_ID_COLUMN,
-    MODEL_SPACE_FILE_NON_PARAMETER_COLUMNS,
     MODEL_SUBSPACE_ID,
     PARAMETER_DEFINITIONS_START,
     PARAMETER_VALUE_DELIMITER,
-    PETAB_YAML,
     PETAB_YAML_COLUMN,
     TYPE_PATH,
 )

petab_select/model_subspace.py

@@ -1,27 +1,20 @@
 import math
 import warnings
-from itertools import chain, product
+from itertools import product
 from pathlib import Path
 from typing import Any, Dict, Iterable, Iterator, List, Optional, Union
 
 import numpy as np
 import pandas as pd
-import petab
-from more_itertools import one, powerset
-from petab.C import NOMINAL_VALUE
+from more_itertools import powerset
 
 from .candidate_space import CandidateSpace
 from .constants import (
-    CODE_DELIMITER,
     ESTIMATE,
     MODEL_SPACE_FILE_NON_PARAMETER_COLUMNS,
-    MODEL_SUBSPACE_ID,
     PARAMETER_VALUE_DELIMITER,
-    PETAB_ESTIMATE_FALSE,
-    PETAB_ESTIMATE_TRUE,
     PETAB_YAML,
     STEPWISE_METHODS,
-    TYPE_PARAMETER,
     TYPE_PARAMETER_DICT,
     TYPE_PARAMETER_OPTIONS,
     TYPE_PARAMETER_OPTIONS_DICT,

petab_select/petab.py

@@ -2,6 +2,7 @@
 from typing import List, Optional
 
 import petab
+from more_itertools import one
 from petab.C import ESTIMATE, NOMINAL_VALUE
 
 from .constants import PETAB_ESTIMATE_FALSE, TYPE_PARAMETER_DICT, TYPE_PATH

petab_select/problem.py

@@ -1,13 +1,12 @@
 """The model selection problem class."""
 import abc
 from functools import partial
-from itertools import chain
 from pathlib import Path
 from typing import Any, Callable, Dict, Iterable, Optional, Union
 
 import yaml
 
-from .candidate_space import CandidateSpace, method_to_candidate_space_class
+from .candidate_space import method_to_candidate_space_class
 from .constants import (
     CANDIDATE_SPACE_ARGUMENTS,
     CRITERION,

petab_select/ui.py

@@ -1,19 +1,11 @@
-import csv
-import os.path
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Union
 
 import numpy as np
 import petab
 
 from .candidate_space import CandidateSpace
-from .constants import (
-    ESTIMATE,
-    INITIAL_MODEL_METHODS,
-    TYPE_PATH,
-    Criterion,
-    Method,
-)
+from .constants import INITIAL_MODEL_METHODS, TYPE_PATH, Criterion, Method
 from .model import Model, default_compare
 from .problem import Problem
 

test/candidate_space/test_famos.py

@@ -76,6 +76,7 @@ def expected_progress_list():
     ]
 
 
+@pytest.mark.skip(reason="FIXME")
 def test_famos(
     petab_select_problem,
     expected_criterion_values,

test/pypesto/test_pypesto.py

@@ -46,6 +46,7 @@ def objective_customizer(obj):
     obj.amici_solver.setRelativeTolerance(1e-12)
 
 
+@pytest.mark.skip(reason="FIXME")
 def test_pypesto():
     for test_case_path in test_cases_path.glob('*'):
         if test_cases and test_case_path.stem not in test_cases: