run black

src/examples/scratch/run_convergence_scratch.py

@@ -9,27 +9,27 @@
 
 atlas_dir = "/Users/nathanielimel/uci/projects/sciterra/src/examples/scratch/outputs/atlas_s2-11-10-23_centered_hafenetal"
 
-def main():
 
-    atl = Atlas.load(atlas_dir)    
+def main():
+    atl = Atlas.load(atlas_dir)
 
-    kernels = atl.history['kernel_size']
+    kernels = atl.history["kernel_size"]
 
     con_d = 3
     kernel_size = 10
     converged_filter = kernels[:, -con_d] >= kernel_size
     ids = np.array(atl.projection.index_to_identifier)
     converged_pub_ids = ids[converged_filter]
 
-    crt = Cartographer(vectorizer=SciBERTVectorizer()) 
+    crt = Cartographer(vectorizer=SciBERTVectorizer())
 
     measurements = crt.measure_topography(
-        atl, 
+        atl,
         ids=converged_pub_ids,
-        metrics=["density", "edginess"], 
+        metrics=["density", "edginess"],
         kernel_size=10,
     )
 
 
 if __name__ == "__main__":
-    main()
+    main()

src/sciterra/mapping/atlas.py

@@ -56,7 +56,7 @@ def __getitem__(self, identifier: str) -> Publication:
         if identifier in self.publications:
             return self.publications[identifier]
         raise ValueError(f"Identifier {identifier} not in Atlas.")
-    
+
     def ids(self) -> list[str]:
         """Get a list of all the publication identifiers in the Atlas."""
         return list(self.publications.keys())

src/sciterra/mapping/cartography.py

@@ -197,9 +197,7 @@ def project(self, atl: Atlas, **kwargs) -> Atlas:
             for id, pub in atl_filtered.publications.items()
             if id in merged_projection.identifier_to_index
         }
-        assert not set(atl_filtered.ids()) - set(
-            embedded_publications.keys()
-        )
+        assert not set(atl_filtered.ids()) - set(embedded_publications.keys())
 
         # Overwrite atlas data
         atl_filtered.publications = embedded_publications
@@ -309,15 +307,15 @@ def filter_by_attributes(
             "abstract",
             "publication_date",
         ],
-        record_pubs_per_update = False,
+        record_pubs_per_update=False,
         **kwargs,
     ) -> Atlas:
         """Update an atlas by dropping publications (and corresponding data in projection) when certain fields are empty.
 
         Args:
             atl: the Atlas containing publications to filter
 
-            attributes: the list of attributes to filter publications from the atlas IF any of items are None for a publication. For example, if attributes = ["abstract"], then all publications `pub` such that `pub.abstract is None` is True will be removed from the atlas, along with the corresponding data in the projection. 
+            attributes: the list of attributes to filter publications from the atlas IF any of items are None for a publication. For example, if attributes = ["abstract"], then all publications `pub` such that `pub.abstract is None` is True will be removed from the atlas, along with the corresponding data in the projection.
 
             record_pubs_per_update: whether to track all the publications that exist in the resulting atlas to `self.pubs_per_update`. This should only be set to `True` when you need to later filter by degree of convergence of the atlas. This is an important parameter because `self.filter` is called in `self.project`, which typically is called after `self.expand`, where we pass in the same parameter.
 
@@ -341,7 +339,7 @@ def filter_by_attributes(
             self.pubs_per_update[-1] = atl_filtered.ids()
 
         return atl_filtered
-    
+
     def filter_by_ids(
         self,
         atl: Atlas,
@@ -357,15 +355,19 @@ def filter_by_ids(
 
             drop_ids: the list of publications to filter; all publications in `atl` matching one of these ids will be removed.
         """
-        
+
         if all(x is not None for x in [keep_ids, drop_ids]):
-            raise ValueError("You must pass exactly one of `keep_ids` or `drop_ids`, but both had a value that was not `None`.")
+            raise ValueError(
+                "You must pass exactly one of `keep_ids` or `drop_ids`, but both had a value that was not `None`."
+            )
         if keep_ids is not None:
             filter_ids = set([id for id in atl.ids() if id not in keep_ids])
         elif drop_ids is not None:
             filter_ids = set(drop_ids)
         else:
-            raise ValueError("You must pass exactly one of `keep_ids` or `drop_ids`, but both had value `None`.")
+            raise ValueError(
+                "You must pass exactly one of `keep_ids` or `drop_ids`, but both had value `None`."
+            )
 
         # Keep track of the bad identifiers to skip them in future expansions
         new_bad_ids = atl.bad_ids.union(filter_ids)
@@ -410,7 +412,6 @@ def filter_by_ids(
 
         return atl_filtered
 
-
     ########################################################################
     # Record Atlas history
     ########################################################################
@@ -581,14 +582,12 @@ def measure_topography(
             ids = atl.ids()
         else:
             ids = list(ids)
-        
+
         if not ids:
             raise Exception("No publications to measure topography of.")
 
         # Get publication dates, for filtering
-        dates = np.array([
-            atl[identifier].publication_date for identifier in ids
-        ])
+        dates = np.array([atl[identifier].publication_date for identifier in ids])
 
         # Get pairwise cosine similarities for ids
         embeddings = atl.projection.identifiers_to_embeddings(ids)
@@ -720,8 +719,8 @@ def iterate_expand(
 
         # Obtain document embeddings for all new abstracts.
         atl = crt.project(
-            atl, 
-            verbose=True, 
+            atl,
+            verbose=True,
             record_pubs_per_update=record_pubs_per_update,
         )
         print_progress(atl)

src/sciterra/vectorization/projection.py

@@ -33,12 +33,14 @@ def identifiers_to_embeddings(self, identifiers: list[str]) -> np.ndarray:
         return self.embeddings[self.identifiers_to_indices(identifiers)]
 
     # def identifier_to_embedding(self, identifier: str) -> np.ndarray:
-        # """Retrieve the document embedding of a Publication."""
-        # return self.embeddings[self.identifier_to_index[identifier]]
-    
+    # """Retrieve the document embedding of a Publication."""
+    # return self.embeddings[self.identifier_to_index[identifier]]
+
     def identifiers_to_indices(self, identifiers: list[str]) -> np.ndarray:
         """Retrieve the embedding indices for a list of identifiers."""
-        return np.array([self.identifier_to_index[identifier] for identifier in identifiers])
+        return np.array(
+            [self.identifier_to_index[identifier] for identifier in identifiers]
+        )
 
     def __len__(self) -> int:
         return len(self.identifier_to_index)

src/tests/test_cartography.py

@@ -214,7 +214,8 @@ def test_project_correct_number(self, tmp_path):
         # 1. Simulate first part of project
         # 'only project publications that have abstracts'
         atl_filtered = TestS2SBProjection.crt.filter_by_attributes(
-            atl_exp_double, attributes=["abstract"],
+            atl_exp_double,
+            attributes=["abstract"],
         )
 
         # 'get only embeddings for publications not already projected in atlas'
@@ -337,7 +338,7 @@ class TestTopography:
 
     def test_measure_topography_full(self):
         bibtex_fp = ten_pub_bibtex_fp
-        atl = TestTopography.crt.bibtex_to_atlas(bibtex_fp)        
+        atl = TestTopography.crt.bibtex_to_atlas(bibtex_fp)
         atl = TestTopography.crt.project(atl)
         metrics = [
             "density",
@@ -395,7 +396,7 @@ def test_measure_topography_realistic(self):
             ids=ids,
             metrics=metrics,
         )
-        assert measurements.shape == tuple((len(atl), len(metrics)))          
+        assert measurements.shape == tuple((len(atl), len(metrics)))
 
 
 class TestConvergence:
@@ -585,5 +586,3 @@ def test_iterate_expand(self, tmp_path):
             n_sources_max=None,
             record_pubs_per_update=True,
         )
-
-