Add explicit exports and sort with ruff --preview (#215)

This PR adds explicit `__all__` to some of the top level packages and runs ruff check with preview mode enabled to sort the `__all__` in existing modules
biopragmatics · Nov 17, 2024 · 41248d3 · 41248d3
1 parent da8ca39
commit 41248d3
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Showing 42 changed files with 279 additions and 126 deletions.
diff --git a/src/pyobo/__init__.py b/src/pyobo/__init__.py
@@ -1,6 +1,6 @@
 """A python package for handling and generating OBO."""
 
-from .api import (  # noqa: F401
+from .api import (
     get_alts_to_id,
     get_ancestors,
     get_children,
@@ -20,6 +20,7 @@
     get_id_synonyms_mapping,
     get_id_to_alts,
     get_ids,
+    get_metadata,
     get_name,
     get_name_by_curie,
     get_name_id_mapping,
@@ -43,26 +44,94 @@
     has_ancestor,
     is_descendent,
 )
-from .getters import get_ontology  # noqa: F401
-from .identifier_utils import normalize_curie  # noqa: F401
-from .normalizer import OboNormalizer, ground  # noqa: F401
-from .obographs import parse_results_from_obo  # noqa: F401
-from .plugins import (  # noqa: F401
+from .getters import get_ontology
+from .normalizer import OboNormalizer, ground
+from .obographs import parse_results_from_obo
+from .plugins import (
     has_nomenclature_plugin,
     iter_nomenclature_plugins,
     run_nomenclature_plugin,
 )
-from .reader import from_obo_path, from_obonet  # noqa: F401
-from .struct import Obo, Reference, Synonym, SynonymTypeDef, Term, TypeDef  # noqa: F401
-from .utils.path import ensure_path  # noqa: F401
-from .version import get_version  # noqa: F401
-from .xrefdb.canonicalizer import (  # noqa: F401
+from .reader import from_obo_path, from_obonet
+from .struct import Obo, Reference, Synonym, SynonymTypeDef, Term, TypeDef
+from .utils.path import ensure_path
+from .version import get_version
+from .xrefdb.canonicalizer import (
     Canonicalizer,
     get_equivalent,
     get_priority_curie,
 )
-from .xrefdb.sources import (  # noqa: F401
+from .xrefdb.sources import (
     has_xref_plugin,
     iter_xref_plugins,
     run_xref_plugin,
 )
+
+__all__ = [
+    "Canonicalizer",
+    "Obo",
+    "OboNormalizer",
+    "Reference",
+    "Synonym",
+    "SynonymTypeDef",
+    "Term",
+    "TypeDef",
+    "ensure_path",
+    "from_obo_path",
+    "from_obonet",
+    "get_alts_to_id",
+    "get_ancestors",
+    "get_children",
+    "get_definition",
+    "get_descendants",
+    "get_equivalent",
+    "get_filtered_properties_df",
+    "get_filtered_properties_mapping",
+    "get_filtered_properties_multimapping",
+    "get_filtered_relations_df",
+    "get_filtered_xrefs",
+    "get_graph",
+    "get_hierarchy",
+    "get_id_definition_mapping",
+    "get_id_multirelations_mapping",
+    "get_id_name_mapping",
+    "get_id_species_mapping",
+    "get_id_synonyms_mapping",
+    "get_id_to_alts",
+    "get_ids",
+    "get_metadata",
+    "get_name",
+    "get_name_by_curie",
+    "get_name_id_mapping",
+    "get_obsolete",
+    "get_ontology",
+    "get_primary_curie",
+    "get_primary_identifier",
+    "get_priority_curie",
+    "get_properties",
+    "get_properties_df",
+    "get_property",
+    "get_relation",
+    "get_relation_mapping",
+    "get_relations_df",
+    "get_species",
+    "get_sssom_df",
+    "get_subhierarchy",
+    "get_synonyms",
+    "get_typedef_df",
+    "get_version",
+    "get_xref",
+    "get_xrefs",
+    "get_xrefs_df",
+    "ground",
+    "ground",
+    "has_ancestor",
+    "has_nomenclature_plugin",
+    "has_xref_plugin",
+    "is_descendent",
+    "iter_nomenclature_plugins",
+    "iter_xref_plugins",
+    "parse_results_from_obo",
+    "run_nomenclature_plugin",
+    "run_xref_plugin",
+]
diff --git a/src/pyobo/api/__init__.py b/src/pyobo/api/__init__.py
@@ -1,12 +1,12 @@
 """High-level API for accessing content."""
 
-from .alts import (  # noqa: F401
+from .alts import (
     get_alts_to_id,
     get_id_to_alts,
     get_primary_curie,
     get_primary_identifier,
 )
-from .hierarchy import (  # noqa: F401
+from .hierarchy import (
     get_ancestors,
     get_children,
     get_descendants,
@@ -15,8 +15,8 @@
     has_ancestor,
     is_descendent,
 )
-from .metadata import get_metadata  # noqa: F401
-from .names import (  # noqa: F401
+from .metadata import get_metadata
+from .names import (
     get_definition,
     get_id_definition_mapping,
     get_id_name_mapping,
@@ -28,28 +28,77 @@
     get_obsolete,
     get_synonyms,
 )
-from .properties import (  # noqa: F401
+from .properties import (
     get_filtered_properties_df,
     get_filtered_properties_mapping,
     get_filtered_properties_multimapping,
     get_properties,
     get_properties_df,
     get_property,
 )
-from .relations import (  # noqa: F401
+from .relations import (
     get_filtered_relations_df,
     get_graph,
     get_id_multirelations_mapping,
     get_relation,
     get_relation_mapping,
     get_relations_df,
 )
-from .species import get_id_species_mapping, get_species  # noqa: F401
-from .typedefs import get_typedef_df  # noqa: F401
-from .xrefs import (  # noqa: F401
+from .species import get_id_species_mapping, get_species
+from .typedefs import get_typedef_df
+from .xrefs import (
     get_filtered_xrefs,
     get_sssom_df,
     get_xref,
     get_xrefs,
     get_xrefs_df,
 )
+
+__all__ = [
+    "get_alts_to_id",
+    "get_ancestors",
+    "get_children",
+    "get_definition",
+    "get_descendants",
+    "get_equivalent",
+    "get_filtered_properties_df",
+    "get_filtered_properties_mapping",
+    "get_filtered_properties_multimapping",
+    "get_filtered_relations_df",
+    "get_filtered_xrefs",
+    "get_graph",
+    "get_hierarchy",
+    "get_id_definition_mapping",
+    "get_id_multirelations_mapping",
+    "get_id_name_mapping",
+    "get_id_species_mapping",
+    "get_id_synonyms_mapping",
+    "get_id_to_alts",
+    "get_ids",
+    "get_metadata",
+    "get_name",
+    "get_name_by_curie",
+    "get_name_id_mapping",
+    "get_obsolete",
+    "get_ontology",
+    "get_primary_curie",
+    "get_primary_identifier",
+    "get_priority_curie",
+    "get_properties",
+    "get_properties_df",
+    "get_property",
+    "get_relation",
+    "get_relation_mapping",
+    "get_relations_df",
+    "get_species",
+    "get_sssom_df",
+    "get_subhierarchy",
+    "get_synonyms",
+    "get_typedef_df",
+    "get_version",
+    "get_xref",
+    "get_xrefs",
+    "get_xrefs_df",
+    "has_ancestor",
+    "is_descendent",
+]
diff --git a/src/pyobo/api/alts.py b/src/pyobo/api/alts.py
@@ -11,8 +11,8 @@
 from ..utils.path import prefix_cache_join
 
 __all__ = [
-    "get_id_to_alts",
     "get_alts_to_id",
+    "get_id_to_alts",
     "get_primary_curie",
     "get_primary_identifier",
 ]

diff --git a/src/pyobo/api/hierarchy.py b/src/pyobo/api/hierarchy.py
@@ -14,13 +14,13 @@
 from ..struct.reference import Reference
 
 __all__ = [
+    "get_ancestors",
+    "get_children",
+    "get_descendants",
     "get_hierarchy",
     "get_subhierarchy",
-    "get_descendants",
-    "get_ancestors",
     "has_ancestor",
     "is_descendent",
-    "get_children",
 ]
 
 

diff --git a/src/pyobo/api/names.py b/src/pyobo/api/names.py
@@ -18,16 +18,16 @@
 from ..utils.path import prefix_cache_join
 
 __all__ = [
-    "get_name",
-    "get_name_by_curie",
-    "get_ids",
-    "get_id_name_mapping",
-    "get_name_id_mapping",
     "get_definition",
     "get_id_definition_mapping",
-    "get_synonyms",
+    "get_id_name_mapping",
     "get_id_synonyms_mapping",
+    "get_ids",
+    "get_name",
+    "get_name_by_curie",
+    "get_name_id_mapping",
     "get_obsolete",
+    "get_synonyms",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/pyobo/api/properties.py b/src/pyobo/api/properties.py
@@ -15,12 +15,12 @@
 from ..utils.path import prefix_cache_join
 
 __all__ = [
-    "get_properties_df",
     "get_filtered_properties_df",
     "get_filtered_properties_mapping",
     "get_filtered_properties_multimapping",
-    "get_property",
     "get_properties",
+    "get_properties_df",
+    "get_property",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/pyobo/api/relations.py b/src/pyobo/api/relations.py
@@ -25,12 +25,12 @@
 from ..utils.path import prefix_cache_join
 
 __all__ = [
-    "get_relations_df",
     "get_filtered_relations_df",
+    "get_graph",
     "get_id_multirelations_mapping",
-    "get_relation_mapping",
     "get_relation",
-    "get_graph",
+    "get_relation_mapping",
+    "get_relations_df",
 ]
 
 # TODO get_relation, get_relations

diff --git a/src/pyobo/api/utils.py b/src/pyobo/api/utils.py
@@ -10,10 +10,10 @@
 from ..utils.path import prefix_directory_join
 
 __all__ = [
-    "safe_get_version",
+    "VersionError",
     "get_version",
     "get_version_pins",
-    "VersionError",
+    "safe_get_version",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/pyobo/api/xrefs.py b/src/pyobo/api/xrefs.py
@@ -17,11 +17,11 @@
 from ..utils.path import prefix_cache_join
 
 __all__ = [
-    "get_xrefs_df",
     "get_filtered_xrefs",
+    "get_sssom_df",
     "get_xref",
     "get_xrefs",
-    "get_sssom_df",
+    "get_xrefs_df",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/pyobo/aws.py b/src/pyobo/aws.py
@@ -24,9 +24,9 @@
 
 __all__ = [
     "download_artifacts",
+    "list_artifacts",
     "upload_artifacts",
     "upload_artifacts_for_prefix",
-    "list_artifacts",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/pyobo/cli/utils.py b/src/pyobo/cli/utils.py
@@ -9,12 +9,12 @@
 from ..constants import DATABASE_DIRECTORY
 
 __all__ = [
-    "echo_df",
     "directory_option",
-    "zenodo_option",
+    "echo_df",
     "force_option",
-    "prefix_argument",
     "no_strict_option",
+    "prefix_argument",
+    "zenodo_option",
 ]
 
 

diff --git a/src/pyobo/constants.py b/src/pyobo/constants.py
@@ -8,8 +8,8 @@
 import pystow
 
 __all__ = [
-    "RAW_DIRECTORY",
     "DATABASE_DIRECTORY",
+    "RAW_DIRECTORY",
     "SPECIES_REMAPPING",
 ]
 

diff --git a/src/pyobo/getters.py b/src/pyobo/getters.py
@@ -29,8 +29,8 @@
 from .version import get_git_hash, get_version
 
 __all__ = [
-    "get_ontology",
     "NoBuildError",
+    "get_ontology",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/pyobo/gilda_utils.py b/src/pyobo/gilda_utils.py
@@ -26,9 +26,9 @@
 from pyobo.utils.io import multidict
 
 __all__ = [
-    "iter_gilda_prediction_tuples",
-    "get_grounder",
     "get_gilda_terms",
+    "get_grounder",
+    "iter_gilda_prediction_tuples",
 ]
 
 logger = logging.getLogger(__name__)