🎨 Improve from_source docstrings for entities

bionty/_shared_docstrings.py

@@ -0,0 +1,4 @@
+doc_from_source = """\
+source: Optional Source record to use
+        mute: Whether to suppress logging
+"""

bionty/base/dev/_doc_util.py

@@ -0,0 +1,14 @@
+from textwrap import dedent
+
+
+def _doc_params(**kwds):  # pragma: no cover
+    r"""\
+    Docstrings should start with "\" in the first line for proper formatting.
+    """
+
+    def dec(obj):
+        obj.__orig_doc__ = obj.__doc__
+        obj.__doc__ = dedent(obj.__doc__).format_map(kwds)
+        return obj
+
+    return dec

bionty/base/dev/_io.py

@@ -10,9 +10,7 @@
 from bionty.base._settings import settings
 
 
-def load_yaml(
-    filename: Union[str, Path], convert_dates: bool = True
-):  # pragma: no cover
+def load_yaml(filename: Union[str, Path]):  # pragma: no cover
     with open(filename) as f:
         return yaml.safe_load(f)
 

bionty/base/entities/_bfxpipeline.py

@@ -3,9 +3,10 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 from bionty.base.dev._io import s3_bionty_assets
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_biosample.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_cellline.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_cellmarker.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_celltype.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_developmentalstage.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_disease.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_drug.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_ethnicity.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_experimentalfactor.py

@@ -7,7 +7,8 @@
 
 from bionty.base._ontology import Ontology
 from bionty.base._public_ontology import PublicOntology
-from bionty.base.entities._shared_docstrings import _doc_params, organism_removed
+from bionty.base.dev._doc_util import _doc_params
+from bionty.base.entities._shared_docstrings import organism_removed
 
 
 @_doc_params(doc_entities=organism_removed)

bionty/base/entities/_gene.py

@@ -1,16 +1,17 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Literal, NamedTuple
+from typing import TYPE_CHECKING, Literal, NamedTuple, overload
 
 import pandas as pd
 from lamin_utils import logger
 
 from bionty.base._public_ontology import PublicOntology
 from bionty.base._settings import settings
+from bionty.base.dev._doc_util import _doc_params
 from bionty.base.dev._io import s3_bionty_assets
 
 from ._organism import Organism
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 if TYPE_CHECKING:
     from collections.abc import Iterable

bionty/base/entities/_organism.py

@@ -5,8 +5,9 @@
 import pandas as pd
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 from bionty.base.dev._io import s3_bionty_assets
-from bionty.base.entities._shared_docstrings import _doc_params, organism_removed
+from bionty.base.entities._shared_docstrings import organism_removed
 
 
 @_doc_params(doc_entities=organism_removed)

bionty/base/entities/_pathway.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_phenotype.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_protein.py

@@ -3,8 +3,9 @@
 from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)

bionty/base/entities/_shared_docstrings.py

@@ -1,19 +1,3 @@
-from textwrap import dedent
-
-
-def _doc_params(**kwds):  # pragma: no cover
-    r"""\
-    Docstrings should start with "\" in the first line for proper formatting.
-    """
-
-    def dec(obj):
-        obj.__orig_doc__ = obj.__doc__
-        obj.__doc__ = dedent(obj.__doc__).format_map(kwds)
-        return obj
-
-    return dec
-
-
 doc_entites = """\
 organism: `name` of `Organism` entity.
         source: The key of the source in the local.yml versions file.

bionty/base/entities/_tissue.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 
-from typing import Literal, Optional
+from typing import Literal
 
 from bionty.base._public_ontology import PublicOntology
+from bionty.base.dev._doc_util import _doc_params
 
-from ._shared_docstrings import _doc_params, doc_entites
+from ._shared_docstrings import doc_entites
 
 
 @_doc_params(doc_entities=doc_entites)