diff --git a/.pylintrc b/.pylintrc index 2ab69e7..a62b978 100644 --- a/.pylintrc +++ b/.pylintrc @@ -1,5 +1,5 @@ [MESSAGES CONTROL] -disable=fixme,invalid-name,len-as-condition,no-else-return,eval-used,unspecified-encoding,empty-docstring,broad-exception-raised,wrong-import-position,pointless-string-statement +disable=fixme,invalid-name,len-as-condition,no-else-return,eval-used,unspecified-encoding,empty-docstring,broad-exception-raised,wrong-import-position,pointless-string-statement,possibly-used-before-assignment [FORMAT] # Regexp for a line that is allowed to be longer than the limit. diff --git a/emodel_generalisation/cli.py b/emodel_generalisation/cli.py index a4451d8..3c439d9 100644 --- a/emodel_generalisation/cli.py +++ b/emodel_generalisation/cli.py @@ -340,6 +340,7 @@ def plot_evaluation(cells_df, access_point, main_path="analysis_plot", clip=5, f @click.option("--with-model-management", is_flag=True) @click.option("--evaluate-all", is_flag=True) @click.option("--mech-path", default=None, type=str) +@click.option("--no-reuse", is_flag=True) def evaluate( input_path, population_name, @@ -360,6 +361,7 @@ def evaluate( with_model_management, evaluate_all, mech_path, + no_reuse, ): """Evaluate models from a circuit.""" load_mechanisms(mech_path) @@ -407,7 +409,7 @@ def evaluate( L.info("Nothing to compute, only placeholder models found.") return - with Reuse(output_path, index=False) as reuse: + with Reuse(output_path, index=False, disable=no_reuse) as reuse: cells_df = reuse( feature_evaluation, cells_df, @@ -431,7 +433,9 @@ def evaluate( exemplar_df.loc[gid, "path"] = morph["path"] exemplar_df.loc[gid, "name"] = morph["name"] - with Reuse(str(Path(output_path).with_suffix("")) + "_exemplar.csv") as reuse: + with Reuse( + str(Path(output_path).with_suffix("")) + "_exemplar.csv", disable=no_reuse + ) as reuse: exemplar_df = reuse( feature_evaluation, exemplar_df, @@ -601,6 +605,7 @@ def assign_emodel(row): @click.option("--min-scale", default=0.8, type=float) @click.option("--max-scale", default=1.2, type=float) @click.option("--mech-path", default=None, type=str) +@click.option("--no-reuse", is_flag=True) def adapt( input_node_path, population_name, @@ -618,6 +623,7 @@ def adapt( min_scale, max_scale, mech_path, + no_reuse, ): """Adapt cells from a circuit with rho factors. @@ -697,7 +703,7 @@ def _get_exemplar_data(exemplar_df): return dict(exemplar_data) - with Reuse(local_dir / "exemplar_data.yaml") as reuse: + with Reuse(local_dir / "exemplar_data.yaml", disable=no_reuse) as reuse: exemplar_data = reuse(_get_exemplar_data, exemplar_df) L.info("Compute exemplar rho factors...") @@ -714,7 +720,7 @@ def _get_exemplar_data(exemplar_df): n_placeholders = len(cells_df.emodel.unique()) - len(placeholder_mask) n_emodels = len(exemplar_df) L.info("We found %s placeholders models out of %s models.", n_placeholders, n_emodels) - with Reuse(local_dir / "exemplar_rho.csv", index=False) as reuse: + with Reuse(local_dir / "exemplar_rho.csv", index=False, disable=no_reuse) as reuse: data = reuse( evaluate_rho, exemplar_df.loc[placeholder_mask], @@ -728,7 +734,7 @@ def _get_exemplar_data(exemplar_df): exemplar_df[col] = None exemplar_df.loc[placeholder_mask, col] = data[col].to_list() - with Reuse(local_dir / "exemplar_rho_axon.csv", index=False) as reuse: + with Reuse(local_dir / "exemplar_rho_axon.csv", index=False, disable=no_reuse) as reuse: data = reuse( evaluate_rho_axon, exemplar_df.loc[placeholder_mask], @@ -754,7 +760,7 @@ def _get_resistance_models(exemplar_df, exemplar_data, scales_params): ) return models - with Reuse(local_dir / "resistance_models.yaml") as reuse: + with Reuse(local_dir / "resistance_models.yaml", disable=no_reuse) as reuse: resistance_models = reuse( _get_resistance_models, exemplar_df.loc[placeholder_mask], exemplar_data, scales_params ) @@ -805,7 +811,7 @@ def _adapt(): return cells_df - with Reuse(local_dir / "adapt_df.csv") as reuse: + with Reuse(local_dir / "adapt_df.csv", disable=no_reuse) as reuse: cells_df = reuse(_adapt) # finally save a node.h5 file