sphinx fixes

petab/__init__.py

@@ -9,6 +9,7 @@
         By default, all operations are performed sequentially.
 """
 import functools
+import sys
 import warnings
 from warnings import warn
 
@@ -57,3 +58,11 @@ def _deprecated_import_v1(module_name: str):
     obj = globals().get(name)
     if callable(obj):
         globals()[name] = _deprecated_v1(obj)
+del name, obj
+
+__all__ = [
+    x
+    for x in dir(sys.modules[__name__])
+    if not x.startswith("_")
+    and x not in {"sys", "warnings", "functools", "warn"}
+]

petab/v1/C.py

@@ -2,8 +2,8 @@
 """
 This file contains constant definitions.
 """
-
 import math as _math
+import sys
 
 # MEASUREMENTS
 
@@ -363,3 +363,10 @@
 
 # separator for multiple parameter values (bounds, observableParameters, ...)
 PARAMETER_SEPARATOR = ";"
+
+
+__all__ = [
+    x
+    for x in dir(sys.modules[__name__])
+    if not x.startswith("_") and x not in {"sys", "math"}
+]

petab/v1/models/__init__.py

@@ -7,3 +7,5 @@
 }
 
 from .model import Model  # noqa F401
+
+__all__ = ["MODEL_TYPE_SBML", "MODEL_TYPE_PYSB", "known_model_types", "Model"]

petab/v1/models/model.py

@@ -6,6 +6,8 @@
 from pathlib import Path
 from typing import Any
 
+__all__ = ["Model"]
+
 
 class Model(abc.ABC):
     """Base class for wrappers for any PEtab-supported model type"""
@@ -78,8 +80,9 @@ def has_entity_with_id(self, entity_id) -> bool:
         """Check if there is a model entity with the given ID
 
         :param entity_id: ID to check for
-        :returns: ``True``, if there is an entity with the given ID,
-        ``False`` otherwise
+        :returns:
+            ``True``, if there is an entity with the given ID,
+            ``False`` otherwise
         """
         ...
 
@@ -114,8 +117,9 @@ def symbol_allowed_in_observable_formula(self, id_: str) -> bool:
     def is_valid(self) -> bool:
         """Validate this model
 
-        :returns: `True` if the model is valid, `False` if there are errors in
-        this model
+        :returns:
+            `True` if the model is valid, `False` if there are errors in
+            this model
         """
         ...
 

petab/v1/models/pysb_model.py

@@ -12,6 +12,8 @@
 from . import MODEL_TYPE_PYSB
 from .model import Model
 
+__all__ = ["PySBModel", "parse_species_name", "pattern_from_string"]
+
 
 def _pysb_model_from_path(pysb_model_file: str | Path) -> pysb.Model:
     """Load a pysb model module and return the :class:`pysb.Model` instance

petab/v1/models/sbml_model.py

@@ -17,6 +17,8 @@
 from . import MODEL_TYPE_SBML
 from .model import Model
 
+__all__ = ["SbmlModel"]
+
 
 class SbmlModel(Model):
     """PEtab wrapper for SBML models"""

petab/v1/problem.py

@@ -50,7 +50,7 @@ class Problem:
 
     Optionally it may contain visualization tables.
 
-    Attributes:
+    Parameters:
         condition_df: PEtab condition table
         measurement_df: PEtab measurement table
         parameter_df: PEtab parameter table

petab/v1/visualize/cli.py

@@ -7,6 +7,8 @@
 from .. import Problem, get_simulation_df, get_visualization_df
 from .plot_data_and_simulation import plot_problem
 
+__all__ = []
+
 
 def _parse_cli_args():
     """Parse command-line arguments."""

petab/v1/visualize/lint.py

@@ -1,4 +1,6 @@
 """Validation of PEtab visualization files"""
+from __future__ import annotations
+
 import logging
 
 import pandas as pd
@@ -8,6 +10,8 @@
 
 logger = logging.getLogger(__name__)
 
+__all__ = ["validate_visualization_df"]
+
 
 def validate_visualization_df(problem: Problem) -> bool:
     """Validate visualization table