Fix imports related to v1 subpackage (#293)

dweindl · web-flow · commit 7587278c26ca · 2024-07-01T13:56:39.000+02:00
Fix imports related to v1 subpackage; fix deprecation warnings
diff --git a/petab/__init__.py b/petab/__init__.py
@@ -14,6 +14,7 @@
         By default, all operations are performed sequentially.
 """
 import functools
+import inspect
 import sys
 import warnings
 from warnings import warn
@@ -62,13 +63,13 @@ def _deprecated_import_v1(module_name: str):
     x
     for x in dir(sys.modules[__name__])
     if not x.startswith("_")
-    and x not in {"sys", "warnings", "functools", "warn"}
+    and x not in {"sys", "warnings", "functools", "warn", "inspect"}
 ]
 
 
 # apply decorator to all functions in the module
 for name in __all__:
     obj = globals().get(name)
-    if callable(obj):
+    if callable(obj) and inspect.isfunction(obj):
         globals()[name] = _deprecated_v1(obj)
 del name, obj
diff --git a/petab/petablint.py b/petab/petablint.py
@@ -10,7 +10,7 @@
 from colorama import init as init_colorama
 from jsonschema.exceptions import ValidationError as SchemaValidationError
 
-import petab
+import petab.v1 as petab
 from petab.v1.C import FORMAT_VERSION
 from petab.v2.lint import lint_problem
 from petab.versions import get_major_version
diff --git a/petab/v1/calculate.py b/petab/v1/calculate.py
@@ -7,7 +7,7 @@
 import pandas as pd
 import sympy as sp
 
-import petab
+import petab.v1 as petab
 
 from .C import *
 from .math import sympify_petab
diff --git a/petab/v1/lint.py b/petab/v1/lint.py
@@ -12,7 +12,7 @@
 import pandas as pd
 import sympy as sp
 
-import petab
+import petab.v1 as petab
 
 from . import core, measurements, parameters
 from .C import *  # noqa: F403
@@ -986,7 +986,7 @@ def lint_problem(problem: "petab.Problem") -> bool:
 
     if problem.visualization_df is not None:
         logger.info("Checking visualization table...")
-        from petab.visualize.lint import validate_visualization_df
+        from petab.v1.visualize.lint import validate_visualization_df
 
         errors_occurred |= validate_visualization_df(problem)
     else:
diff --git a/petab/v1/parameter_mapping.py b/petab/v1/parameter_mapping.py
@@ -129,7 +129,7 @@ def get_optimization_to_simulation_parameter_mapping(
             DeprecationWarning,
             stacklevel=2,
         )
-        from petab.models.sbml_model import SbmlModel
+        from .models.sbml_model import SbmlModel
 
         if model:
             raise ValueError(
@@ -379,7 +379,7 @@ def get_parameter_mapping_for_condition(
             DeprecationWarning,
             stacklevel=2,
         )
-        from petab.models.sbml_model import SbmlModel
+        from .models.sbml_model import SbmlModel
 
         if model:
             raise ValueError(
diff --git a/petab/v1/parameters.py b/petab/v1/parameters.py
@@ -195,7 +195,7 @@ def create_parameter_df(
             DeprecationWarning,
             stacklevel=2,
         )
-        from petab.models.sbml_model import SbmlModel
+        from .models.sbml_model import SbmlModel
 
         if model:
             raise ValueError(
diff --git a/petab/v1/sbml.py b/petab/v1/sbml.py
@@ -9,7 +9,7 @@
 import libsbml
 from pandas.io.common import get_handle, is_file_like, is_url
 
-import petab
+import petab.v1 as petab
 
 logger = logging.getLogger(__name__)
 __all__ = [
diff --git a/petab/v1/simplify.py b/petab/v1/simplify.py
@@ -3,7 +3,7 @@
 
 import pandas as pd
 
-import petab
+import petab.v1 as petab
 
 from . import Problem
 from .C import *  # noqa: F403
diff --git a/petab/v1/simulate.py b/petab/v1/simulate.py
@@ -11,7 +11,7 @@
 import pandas as pd
 import sympy as sp
 
-import petab
+import petab.v1 as petab
 
 __all__ = ["Simulator", "sample_noise"]
 
diff --git a/petab/v1/visualize/data_overview.py b/petab/v1/visualize/data_overview.py
@@ -7,8 +7,13 @@
 
 import pandas as pd
 
-import petab
-from petab.C import *
+import petab.v1 as petab
+from petab.v1.C import (
+    MEASUREMENT,
+    OBSERVABLE_ID,
+    PREEQUILIBRATION_CONDITION_ID,
+    SIMULATION_CONDITION_ID,
+)
 
 __all__ = ["create_report"]
 
diff --git a/petab/v1/yaml.py b/petab/v1/yaml.py
@@ -122,7 +122,7 @@ def _check_file(_filename: str, _field: str):
         # the simplest check is just trying to load the respective table or
         # sbml model
         if _field == SBML_FILES:
-            from ..models.sbml_model import SbmlModel
+            from .models.sbml_model import SbmlModel
 
             try:
                 SbmlModel.from_file(_filename)
diff --git a/petab/v2/lint.py b/petab/v2/lint.py
@@ -10,14 +10,15 @@
 import numpy as np
 import pandas as pd
 
-from petab.C import NOISE_PARAMETERS, OBSERVABLE_PARAMETERS
 from petab.v1 import (
     assert_model_parameters_in_condition_or_parameter_table,
 )
 from petab.v1.C import (
     ESTIMATE,
     MODEL_ENTITY_ID,
+    NOISE_PARAMETERS,
     NOMINAL_VALUE,
+    OBSERVABLE_PARAMETERS,
     PARAMETER_DF_REQUIRED_COLS,
     PARAMETER_ID,
 )
@@ -40,6 +41,7 @@
 from petab.v1.parameters import (
     get_valid_parameters_for_parameter_table,
 )
+from petab.v1.visualize.lint import validate_visualization_df
 
 from ..v1 import (
     assert_measurement_conditions_present_in_condition_table,
@@ -449,8 +451,6 @@ def run(self, problem: Problem) -> ValidationIssue | None:
         if problem.visualization_df is None:
             return
 
-        from petab.visualize.lint import validate_visualization_df
-
         if validate_visualization_df(problem):
             return ValidationIssue(
                 level=ValidationIssueSeverity.ERROR,
diff --git a/petab/v2/petab1to2.py b/petab/v2/petab1to2.py
@@ -5,14 +5,15 @@
 
 from pandas.io.common import get_handle, is_url
 
-import petab.C
+import petab.v1.C as C
 from petab.models import MODEL_TYPE_SBML
+from petab.v1 import Problem as ProblemV1
 from petab.v2.lint import lint_problem as lint_v2_problem
 from petab.yaml import get_path_prefix
 
-from .. import lint_problem as lint_v1_problem
+from ..v1 import lint_problem as lint_v1_problem
+from ..v1.yaml import load_yaml, validate, write_yaml
 from ..versions import get_major_version
-from ..yaml import load_yaml, validate, write_yaml
 
 __all__ = ["petab1to2"]
 
@@ -58,7 +59,7 @@ def petab1to2(yaml_config: Path | str, output_dir: Path | str = None):
     validate(yaml_config, path_prefix=path_prefix)
     if get_major_version(yaml_config) != 1:
         raise ValueError("PEtab problem is not version 1.")
-    petab_problem = petab.Problem.from_yaml(yaml_file or yaml_config)
+    petab_problem = ProblemV1.from_yaml(yaml_file or yaml_config)
     if lint_v1_problem(petab_problem):
         raise ValueError("PEtab problem does not pass linting.")
 
@@ -74,21 +75,19 @@ def petab1to2(yaml_config: Path | str, output_dir: Path | str = None):
     # Update tables
     # condition tables, observable tables, SBML files, parameter table:
     #  no changes - just copy
-    file = yaml_config[petab.C.PARAMETER_FILE]
+    file = yaml_config[C.PARAMETER_FILE]
     _copy_file(get_src_path(file), get_dest_path(file))
 
-    for problem_config in yaml_config[petab.C.PROBLEMS]:
+    for problem_config in yaml_config[C.PROBLEMS]:
         for file in chain(
-            problem_config.get(petab.C.CONDITION_FILES, []),
-            problem_config.get(petab.C.OBSERVABLE_FILES, []),
+            problem_config.get(C.CONDITION_FILES, []),
+            problem_config.get(C.OBSERVABLE_FILES, []),
             (
-                model[petab.C.MODEL_LOCATION]
-                for model in problem_config.get(
-                    petab.C.MODEL_FILES, {}
-                ).values()
+                model[C.MODEL_LOCATION]
+                for model in problem_config.get(C.MODEL_FILES, {}).values()
             ),
-            problem_config.get(petab.C.MEASUREMENT_FILES, []),
-            problem_config.get(petab.C.VISUALIZATION_FILES, []),
+            problem_config.get(C.MEASUREMENT_FILES, []),
+            problem_config.get(C.VISUALIZATION_FILES, []),
         ):
             _copy_file(get_src_path(file), get_dest_path(file))
 
@@ -111,23 +110,23 @@ def _update_yaml(yaml_config: dict) -> dict:
     yaml_config = yaml_config.copy()
 
     # Update format_version
-    yaml_config[petab.C.FORMAT_VERSION] = "2.0.0"
+    yaml_config[C.FORMAT_VERSION] = "2.0.0"
 
     # Add extensions
-    yaml_config[petab.C.EXTENSIONS] = []
+    yaml_config[C.EXTENSIONS] = []
 
     # Move models and set IDs (filename for now)
-    for problem in yaml_config[petab.C.PROBLEMS]:
-        problem[petab.C.MODEL_FILES] = {}
-        models = problem[petab.C.MODEL_FILES]
-        for sbml_file in problem[petab.C.SBML_FILES]:
+    for problem in yaml_config[C.PROBLEMS]:
+        problem[C.MODEL_FILES] = {}
+        models = problem[C.MODEL_FILES]
+        for sbml_file in problem[C.SBML_FILES]:
             model_id = sbml_file.split("/")[-1].split(".")[0]
             models[model_id] = {
-                petab.C.MODEL_LANGUAGE: MODEL_TYPE_SBML,
-                petab.C.MODEL_LOCATION: sbml_file,
+                C.MODEL_LANGUAGE: MODEL_TYPE_SBML,
+                C.MODEL_LOCATION: sbml_file,
             }
-            problem[petab.C.MODEL_FILES] = problem.get(petab.C.MODEL_FILES, {})
-        del problem[petab.C.SBML_FILES]
+            problem[C.MODEL_FILES] = problem.get(C.MODEL_FILES, {})
+        del problem[C.SBML_FILES]
 
     return yaml_config
 
diff --git a/petab/v2/problem.py b/petab/v2/problem.py
@@ -10,7 +10,6 @@
 
 import pandas as pd
 
-from ..C import *  # noqa: F403
 from ..v1 import (
     conditions,
     core,
@@ -22,6 +21,7 @@
     sampling,
     yaml,
 )
+from ..v1.C import *  # noqa: F403
 from ..v1.models.model import Model, model_factory
 from ..v1.yaml import get_path_prefix
 
diff --git a/tests/v1/test_lint.py b/tests/v1/test_lint.py
@@ -38,7 +38,7 @@ def test_assert_measured_observables_present():
 
 def test_condition_table_is_parameter_free():
     with patch(
-        "petab.get_parametric_overrides"
+        "petab.v1.get_parametric_overrides"
     ) as mock_get_parametric_overrides:
         mock_get_parametric_overrides.return_value = []
         assert lint.condition_table_is_parameter_free(pd.DataFrame()) is True

Original file line number	Diff line number	Diff line change
`@@ -195,7 +195,7 @@ def create_parameter_df(`
`195`	`195`	`DeprecationWarning,`
`196`	`196`	`stacklevel=2,`
`197`	`197`	`)`
`198`		`- from petab.models.sbml_model import SbmlModel`
	`198`	`+ from .models.sbml_model import SbmlModel`
`199`	`199`
`200`	`200`	`if model:`
`201`	`201`	`raise ValueError(`