Model file parameterization

inferelator/utils/loader.py

@@ -104,8 +104,11 @@ def load_data_h5ad(
             gene_name_column
         )
 
+        if use_layer is None:
+            use_layer = "X"
+
         # Make sure layer is in the anndata object
-        if use_layer is not None and use_layer not in data.layers:
+        if use_layer != "X" and use_layer not in data.layers:
             raise ValueError(
                 f"Layer {use_layer} is not in {h5ad_file}"
             )

inferelator/workflows/workflow_base.py

@@ -34,6 +34,7 @@
 
 _VALID_FILE_TYPES = [_TSV, _H5AD, _HDF5, _MTX, _TENX]
 
+
 class WorkflowBaseLoader(object):
     """
     WorkflowBaseLoader is the class to load raw data.
@@ -251,7 +252,13 @@ def set_expression_file(
         :type h5_layer: str, optional
         """
 
-        nones = [tsv is None, hdf5 is None, h5ad is None, tenx_path is None, mtx is None]
+        nones = [
+            tsv is None,
+            hdf5 is None,
+            h5ad is None,
+            tenx_path is None,
+            mtx is None
+        ]
 
         if all(nones):
             Debug.vprint("No file provided", level=0)
@@ -570,9 +577,11 @@ def append_to_path(
         """
         Add a string to an existing path variable
 
-        :param var_name: The name of the path variable (`input_dir` or `output_dir`)
+        :param var_name: The name of the path variable
+            (`input_dir` or `output_dir`)
         :type var_name: str
-        :param to_append: The path to join to the end of the existing path variable
+        :param to_append: The path to join to the end of
+            the existing path variable
         :type to_append: str
 
         """
@@ -756,7 +765,7 @@ def read_genes(self, file=None):
             assert genes.shape[1] == 1
             self.gene_names = genes.values.flatten().tolist()
 
-        # Use the gene names in the data file if no restrictive list is provided
+        # Use the gene names in the data file if no list is provided
         if self.gene_names is None and self.data is not None:
             self.gene_names = self.data.gene_names.copy()
 
@@ -1119,8 +1128,8 @@ def set_crossvalidation_parameters(
 
             if not self.split_gold_standard_for_crossvalidation:
                 warnings.warn(
-                    "The split_gold_standard_for_crossvalidation flag is not set. "
-                    "Other options may be ignored"
+                    "The split_gold_standard_for_crossvalidation "
+                    "flag is not set. Other options may be ignored."
                 )
 
     def set_shuffle_parameters(
@@ -1194,10 +1203,12 @@ def set_output_file_names(
         confidence_file_name="",
         nonzero_coefficient_file_name="",
         pdf_curve_file_name="",
-        curve_data_file_name=""
+        curve_data_file_name="",
+        model_h5_file_name=""
     ):
         """
         Set output file names. File names that end in '.gz' will be gzipped.
+        Set any file name to None to prevent it from being generated
 
         :param network_file_name: Long-format network TSV file with
             TF->Gene edge information.
@@ -1217,6 +1228,9 @@ def set_output_file_names(
         :param curve_data_file_name: TSV file with the data used to plot
             curves. Default is None (this file is not produced).
         :type curve_data_file_name: str
+        :param model_h5_file_name: H5 file with model priors, coefficients,
+            and run parameters saved
+        :type model_h5_file_name: str
         """
 
         if network_file_name != "":
@@ -1229,6 +1243,8 @@ def set_output_file_names(
             IR.curve_file_name = pdf_curve_file_name
         if curve_data_file_name != "":
             IR.curve_data_file_name = curve_data_file_name
+        if model_h5_file_name != "":
+            IR.model_file_name = model_h5_file_name
 
     def set_run_parameters(
         self,