From a1cd0bdc03ef50a7120d63318c0d8f5372e8cc86 Mon Sep 17 00:00:00 2001
From: Nathaniel Imel <nathanielimel@Nathaniels-MacBook-Air.local>
Date: Sat, 30 Dec 2023 15:26:27 -0800
Subject: [PATCH] run black

---
 src/sciterra/mapping/cartography.py | 33 +++++++++++++++++------------
 src/sciterra/mapping/tracing.py     |  2 +-
 src/tests/test_cartography.py       |  6 +++++-
 3 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/src/sciterra/mapping/cartography.py b/src/sciterra/mapping/cartography.py
index a1dab43..f272a6c 100644
--- a/src/sciterra/mapping/cartography.py
+++ b/src/sciterra/mapping/cartography.py
@@ -57,22 +57,27 @@ def batch_cospsi_matrix(embeddings: np.ndarray) -> np.ndarray:
 
 # Helper function for filtering
 def pub_has_attributes(
-    pub: Publication, 
+    pub: Publication,
     attributes: list[str],
-    ) -> bool:
+) -> bool:
     """Return True if a publication has all `attributes`.
-    
-    Args: 
-        attributes: the list of attributes to check are not `None` for each publication from the atlas. 
+
+    Args:
+        attributes: the list of attributes to check are not `None` for each publication from the atlas.
     """
-    return pub is not None and all([getattr(pub, attr) is not None for attr in attributes])
+    return pub is not None and all(
+        [getattr(pub, attr) is not None for attr in attributes]
+    )
+
 
 def pub_has_fields_of_study(
     pub: Publication,
     fields_of_study: list[str],
 ) -> bool:
     """Return true if any of `pub.fields_of_study` are in passed `fields_of_study`."""
-    return pub is not None and any([field in fields_of_study for field in pub.fields_of_study])
+    return pub is not None and any(
+        [field in fields_of_study for field in pub.fields_of_study]
+    )
 
 
 ##############################################################################
@@ -348,10 +353,12 @@ def expand(
     def filter_by_func(
         self,
         atl: Atlas,
-        require_func: Callable[[Publication], bool] = lambda pub: pub_has_attributes(pub, attributes=[
-            "abstract",
-            "publication_date",
-            "fields_of_study",
+        require_func: Callable[[Publication], bool] = lambda pub: pub_has_attributes(
+            pub,
+            attributes=[
+                "abstract",
+                "publication_date",
+                "fields_of_study",
             ],
         ),
         record_pubs_per_update=False,
@@ -371,9 +378,7 @@ def filter_by_func(
         """
         # Filter publications
         invalid_pubs = {
-            id: pub
-            for id, pub in atl.publications.items()
-            if not require_func(pub)
+            id: pub for id, pub in atl.publications.items() if not require_func(pub)
         }
 
         # Do not update if unnecessary
diff --git a/src/sciterra/mapping/tracing.py b/src/sciterra/mapping/tracing.py
index 3f7b4b1..e2bce87 100644
--- a/src/sciterra/mapping/tracing.py
+++ b/src/sciterra/mapping/tracing.py
@@ -128,7 +128,7 @@ def __init__(
 
             vectorizer_name: a str name of a vectorizer, one of `vectorization.vectorizers.keys()`, e.g. 'BOW' or 'SciBERT'.
 
-            vectorizer_kwargs: keyword args propogated to a Vectorizer initialization; if values are `None` they will be omitted           
+            vectorizer_kwargs: keyword args propogated to a Vectorizer initialization; if values are `None` they will be omitted
         """
         ######################################################################
         # Initialize cartography tools
diff --git a/src/tests/test_cartography.py b/src/tests/test_cartography.py
index 824d904..e5ff61b 100644
--- a/src/tests/test_cartography.py
+++ b/src/tests/test_cartography.py
@@ -7,7 +7,11 @@
 from datetime import datetime
 
 from sciterra.mapping.atlas import Atlas
-from sciterra.mapping.cartography import Cartographer, pub_has_attributes, pub_has_fields_of_study
+from sciterra.mapping.cartography import (
+    Cartographer,
+    pub_has_attributes,
+    pub_has_fields_of_study,
+)
 from sciterra.librarians.s2librarian import SemanticScholarLibrarian
 from sciterra.mapping.publication import Publication
 from sciterra.vectorization import SciBERTVectorizer, Word2VecVectorizer