edit docstring codeblock highlighting

geneformer/emb_extractor.py

@@ -397,12 +397,12 @@ class EmbExtractor:
 
         **Parameters:**
 
-        model_type : {"Pretrained","GeneClassifier","CellClassifier"}
+        model_type : {"Pretrained", "GeneClassifier", "CellClassifier"}
             | Whether model is the pretrained Geneformer or a fine-tuned gene or cell classifier.
         num_classes : int
             | If model is a gene or cell classifier, specify number of classes it was trained to classify.
             | For the pretrained Geneformer model, number of classes is 0 as it is not a classifier.
-        emb_mode : {"cell","gene"}
+        emb_mode : {"cell", "gene"}
             | Whether to output cell or gene embeddings.
         cell_emb_style : "mean_pool"
             | Method for summarizing cell embeddings.
@@ -448,15 +448,14 @@ class EmbExtractor:
 
             >>> from geneformer import EmbExtractor
             >>> embex = EmbExtractor(model_type="CellClassifier",
-                ...    num_classes=3,
-                ...    emb_mode="cell",
-                ...    filter_data={"cell_type":["cardiomyocyte"]},
-                ...    max_ncells=1000,
-                ...    max_ncells_to_plot=1000,
-                ...    emb_layer=-1,
-                ...    emb_label=["disease","cell_type"],
-                ...    labels_to_plot=["disease","cell_type"],
-                ... )
+            ...         num_classes=3,
+            ...         emb_mode="cell",
+            ...         filter_data={"cell_type":["cardiomyocyte"]},
+            ...         max_ncells=1000,
+            ...         max_ncells_to_plot=1000,
+            ...         emb_layer=-1,
+            ...         emb_label=["disease", "cell_type"],
+            ...         labels_to_plot=["disease", "cell_type"])
 
         """
 
@@ -552,10 +551,9 @@ class EmbExtractor:
         .. code-block :: python
 
             >>> embs = embex.extract_embs("path/to/model",
-                ...    "path/to/input_data",
-                ...    "path/to/output_directory",
-                ...    "output_prefix",
-                ... )
+            ...                           "path/to/input_data",
+            ...                           "path/to/output_directory",
+            ...                           "output_prefix")
 
         """
 
@@ -741,10 +739,9 @@ class EmbExtractor:
         .. code-block :: python
 
             >>> embex.plot_embs(embs=embs,
-                ...    plot_style="heatmap",
-                ...    output_directory="path/to/output_directory",
-                ...    output_prefix="output_prefix",
-                ... )
+            ...                 plot_style="heatmap",
+            ...                 output_directory="path/to/output_directory",
+            ...                 output_prefix="output_prefix")
 
         """
 

geneformer/in_silico_perturber.py

@@ -7,22 +7,22 @@ Geneformer in silico perturber.
 
     >>> from geneformer import InSilicoPerturber
     >>> isp = InSilicoPerturber(perturb_type="delete",
-        ...                     perturb_rank_shift=None,
-        ...                     genes_to_perturb="all",
-        ...                     model_type="CellClassifier",
-        ...                     num_classes=0,
-        ...                     emb_mode="cell",
-        ...                     filter_data={"cell_type":["cardiomyocyte"]},
-        ...                     cell_states_to_model={"state_key": "disease", "start_state": "dcm", "goal_state": "nf", "alt_states": ["hcm", "other1", "other2"]},
-        ...                     state_embs_dict ={"nf": emb_nf, "hcm": emb_hcm, "dcm": emb_dcm, "other1": emb_other1, "other2": emb_other2},
-        ...                     max_ncells=None,
-        ...                     emb_layer=0,
-        ...                     forward_batch_size=100,
-        ...                     nproc=16)
+    ...                         perturb_rank_shift=None,
+    ...                         genes_to_perturb="all",
+    ...                         model_type="CellClassifier",
+    ...                         num_classes=0,
+    ...                         emb_mode="cell",
+    ...                         filter_data={"cell_type":["cardiomyocyte"]},
+    ...                         cell_states_to_model={"state_key": "disease", "start_state": "dcm", "goal_state": "nf", "alt_states": ["hcm", "other1", "other2"]},
+    ...                         state_embs_dict ={"nf": emb_nf, "hcm": emb_hcm, "dcm": emb_dcm, "other1": emb_other1, "other2": emb_other2},
+    ...                         max_ncells=None,
+    ...                         emb_layer=0,
+    ...                         forward_batch_size=100,
+    ...                         nproc=16)
     >>> isp.perturb_data("path/to/model",
-        ...              "path/to/input_data",
-        ...              "path/to/output_directory",
-        ...              "output_prefix")
+    ...                  "path/to/input_data",
+    ...                  "path/to/output_directory",
+    ...                  "output_prefix")
 
 **Description:**
 

geneformer/in_silico_perturber_stats.py

@@ -7,15 +7,14 @@ Geneformer in silico perturber stats generator.
 
     >>> from geneformer import InSilicoPerturberStats
     >>> ispstats = InSilicoPerturberStats(mode="goal_state_shift",
-        ...    cell_states_to_model={"state_key": "disease",
-        ...                          "start_state": "dcm",
-        ...                          "goal_state": "nf",
-        ...                          "alt_states": ["hcm", "other1", "other2"]})
-        ... )
+    ...    cell_states_to_model={"state_key": "disease",
+    ...                          "start_state": "dcm",
+    ...                          "goal_state": "nf",
+    ...                          "alt_states": ["hcm", "other1", "other2"]})
     >>> ispstats.get_stats("path/to/input_data",
-        ...                None,
-        ...                "path/to/output_directory",
-        ...                "output_prefix")
+    ...                    None,
+    ...                    "path/to/output_directory",
+    ...                    "output_prefix")
 
 **Description:**