Set `__all__

1. Avoids littering the namespace on star imports more than necessary
2. Simplifies cross-references to documentation,
   e.g., in addition to `petab_select.problem.Problem`, we can also
   now reference `petab_select.Problem`. This wasn't possible before.

petab_select/__init__.py

@@ -1,5 +1,7 @@
 """Model selection extension for PEtab."""
 
+import sys
+
 from .candidate_space import *
 from .constants import *
 from .criteria import *
@@ -9,3 +11,9 @@
 from .model_subspace import *
 from .problem import *
 from .ui import *
+
+__all__ = [
+    x
+    for x in dir(sys.modules[__name__])
+    if not x.startswith('_') or x == 'sys'
+]

petab_select/candidate_space.py

@@ -28,6 +28,17 @@
 from .handlers import TYPE_LIMIT, LimitHandler
 from .model import Model, default_compare
 
+__all__ = [
+    'BackwardCandidateSpace',
+    'BidirectionalCandidateSpace',
+    'BruteForceCandidateSpace',
+    'CandidateSpace',
+    'FamosCandidateSpace',
+    'ForwardAndBackwardCandidateSpace',
+    'ForwardCandidateSpace',
+    'LateralCandidateSpace',
+]
+
 
 class CandidateSpace(abc.ABC):
     """A base class for collecting candidate models.

petab_select/constants.py

@@ -1,4 +1,5 @@
 """Constants for the PEtab Select package."""
+import sys
 from enum import Enum
 from pathlib import Path
 from typing import Dict, List, Literal, Union
@@ -164,3 +165,11 @@ class Criterion(str, Enum):
     Method.FORWARD,
     Method.FORWARD_AND_BACKWARD,
 ]
+
+
+__all__ = [
+    x
+    for x in dir(sys.modules[__name__])
+    if not x.startswith('_')
+    or x in ('sys', "Enum", "Path", "Dict", "List", "Literal", "Union")
+]

petab_select/criteria.py

@@ -9,7 +9,12 @@
 
 from .constants import PETAB_PROBLEM, Criterion  # LH,; LLH,; NLLH,
 
-# from .model import Model
+__all__ = [
+    'calculate_aic',
+    'calculate_aicc',
+    'calculate_bic',
+    'CriterionComputer',
+]
 
 
 # use as attribute e.g. `Model.criterion_computer`?

petab_select/misc.py

@@ -9,6 +9,16 @@
     TYPE_PARAMETER_OPTIONS,
 )
 
+__all__ = [
+    'hashify',
+    'hash_parameter_dict',
+    'hash_parameter_options',
+    'hash_str',
+    'hash_list',
+    'snake_case_to_camel_case',
+    'parameter_string_to_value',
+]
+
 
 def hashify(x: Any) -> str:
     """Generate a hash.

petab_select/model.py

@@ -36,6 +36,13 @@
 )
 from .petab import PetabMixin
 
+__all__ = [
+    'Model',
+    'default_compare',
+    'models_from_yaml_list',
+    'models_to_yaml_list',
+]
+
 
 class Model(PetabMixin):
     """A (possibly uncalibrated) model.

petab_select/model_space.py

@@ -21,6 +21,13 @@
 from .model import Model
 from .model_subspace import ModelSubspace
 
+__all__ = [
+    "ModelSpace",
+    "get_model_space_df",
+    "read_model_space_file",
+    "write_model_space_df",
+]
+
 
 def read_model_space_file(filename: str) -> TextIO:
     """Read a model space file.

petab_select/model_subspace.py

@@ -26,6 +26,10 @@
 from .model import Model
 from .petab import PetabMixin
 
+__all__ = [
+    'ModelSubspace',
+]
+
 
 class ModelSubspace(PetabMixin):
     """Efficient representation of exponentially large model subspaces.

petab_select/petab.py

@@ -7,6 +7,10 @@
 
 from .constants import PETAB_ESTIMATE_FALSE, TYPE_PARAMETER_DICT, TYPE_PATH
 
+__all__ = [
+    'PetabMixin',
+]
+
 
 class PetabMixin:
     """Useful things for classes that contain a PEtab problem.

petab_select/problem.py

@@ -20,6 +20,10 @@
 from .model import Model, default_compare
 from .model_space import ModelSpace
 
+__all__ = [
+    'Problem',
+]
+
 
 class Problem(abc.ABC):
     """Handle everything related to the model selection problem.

petab_select/ui.py

@@ -9,6 +9,14 @@
 from .model import Model, default_compare
 from .problem import Problem
 
+__all__ = [
+    'candidates',
+    'model_to_petab',
+    'models_to_petab',
+    'best',
+    'write_summary_tsv',
+]
+
 
 def candidates(
     problem: Problem,