fix(tasks): update args and examples for summarize dataset

Signed-off-by: Cameron Smith <cameron.ray.smith@gmail.com>

src/pyrovelocity/tasks/summarize.py

@@ -9,17 +9,18 @@
 from pyrovelocity.analysis.analyze import pareto_frontier_genes
 from pyrovelocity.io import CompressedPickle
 from pyrovelocity.logging import configure_logging
-from pyrovelocity.plots import cluster_violin_plots
-from pyrovelocity.plots import plot_gene_ranking
-from pyrovelocity.plots import plot_gene_selection_summary
-from pyrovelocity.plots import plot_parameter_posterior_distributions
-from pyrovelocity.plots import plot_shared_time_uncertainty
-from pyrovelocity.plots import plot_vector_field_summary
-from pyrovelocity.plots import posterior_curve
-from pyrovelocity.plots import rainbowplot
+from pyrovelocity.plots import (
+    cluster_violin_plots,
+    plot_gene_ranking,
+    plot_gene_selection_summary,
+    plot_parameter_posterior_distributions,
+    plot_shared_time_uncertainty,
+    plot_vector_field_summary,
+    posterior_curve,
+    rainbowplot,
+)
 from pyrovelocity.utils import save_anndata_counts_to_dataframe
 
-
 __all__ = ["summarize_dataset"]
 
 logger = configure_logging(__name__)
@@ -43,6 +44,8 @@ def summarize_dataset(
     Args:
         data_model (str): string containing the data set and model identifier,
             e.g. simulated_model1
+        data_model_path (str | Path):
+            path to a model trained on a particualar data set,
         model_path (str | Path): path to the model,
             e.g. models/simulated_model1/model
         pyrovelocity_data_path (str | Path): path to the pyrovelocity data,
@@ -54,23 +57,25 @@ def summarize_dataset(
         vector_field_basis (str): string containing the vector field basis
             identifier, e.g. umap
         reports_path (str | Path): path to the reports, e.g. reports
+        enable_experimental_plots (bool): flag to enable experimental plots
 
     Returns:
         Path: Top-level path to reports outputs for the data model combination,
             e.g. reports/simulated_model1
 
     Examples:
-        >>> from pyrovelocity.tasks.summarize import summarize_dataset # xdoctest: +SKIP
-        >>> tmp = getfixture("tmp_path") # xdoctest: +SKIP
+        >>> # xdoctest: +SKIP
+        >>> from pyrovelocity.tasks.summarize import summarize_dataset
+        >>> tmp = getfixture("tmp_path")
         >>> summarize_dataset(
-        ...     "simulated_model1",
-        ...     "models/simulated_model1",
-        ...     "models/simulated_model1/model",
-        ...     "models/simulated_model1/pyrovelocity.pkl.zst",
-        ...     "models/simulated_model1/postprocessed.h5ad",
-        ...     "leiden",
-        ...     "umap",
-        ... ) # xdoctest: +SKIP
+        ...     data_model="simulated_model1",
+        ...     data_model_path="models/simulated_model1",
+        ...     model_path="models/simulated_model1/model",
+        ...     pyrovelocity_data_path="models/simulated_model1/pyrovelocity.pkl.zst",
+        ...     postprocessed_data_path="models/simulated_model1/postprocessed.h5ad",
+        ...     cell_state="leiden",
+        ...     vector_field_basis="umap",
+        ... )
     """
 
     logger.info(f"\n\nPlotting summary figure(s) in: {data_model}\n\n")