Fix linting errors.

7 files changed, 19 insertions, 19 deletions

diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index d805af7..e5934b6 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -196,7 +196,7 @@ def compute_all_sample_correlation(this_trait,
 
     """
     this_trait_samples = this_trait["trait_sample_data"]
-    with Pool(processes=(cpu_count() - 1)) as pool:
+    with Pool(processes=cpu_count() - 1) as pool:
         return sorted(
             (
                 corr for corr in
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 6c53ecc..f07628f 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -41,12 +41,13 @@ def generate_pheno_txt_file(trait_filename: str,
 
 
 # pylint: disable=R0913
-def generate_gemma_cmd(gemma_cmd: str,
-                       output_dir: str,
-                       token: str,
-                       gemma_kwargs: Dict,
-                       gemma_wrapper_kwargs: Optional[Dict] = None,
-                       chromosomes: Optional[str] = None) -> Dict:
+def generate_gemma_cmd(# pylint: disable=[too-many-positional-arguments]
+        gemma_cmd: str,
+        output_dir: str,
+        token: str,
+        gemma_kwargs: Dict,
+        gemma_wrapper_kwargs: Optional[Dict] = None,
+        chromosomes: Optional[str] = None) -> Dict:
     """Compute k values"""
     _hash = get_hash_of_files(
         [v for k, v in gemma_kwargs.items() if k in ["g", "p", "a", "c"]])
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 6eee299..88c6f3b 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -209,7 +209,7 @@ def good_dataset_samples_indexes(
         samples_from_file.index(good) for good in
         set(samples).intersection(set(samples_from_file))))
 
-def partial_correlations_fast(# pylint: disable=[R0913, R0914]
+def partial_correlations_fast(# pylint: disable=[R0913, R0914, too-many-positional-arguments]
         samples, primary_vals, control_vals, database_filename,
         fetched_correlations, method: str, correlation_type: str) -> Generator:
     """
@@ -334,7 +334,7 @@ def compute_partial(
     This implementation reworks the child function `compute_partial` which will
     then be used in the place of `determinPartialsByR`.
     """
-    with Pool(processes=(cpu_count() - 1)) as pool:
+    with Pool(processes=cpu_count() - 1) as pool:
         return (
             result for result in (
                 pool.starmap(
@@ -345,7 +345,7 @@ def compute_partial(
                      for target in targets)))
         if result is not None)
 
-def partial_correlations_normal(# pylint: disable=R0913
+def partial_correlations_normal(# pylint: disable=[R0913, too-many-positional-arguments]
         primary_vals, control_vals, input_trait_gene_id, trait_database,
         data_start_pos: int, db_type: str, method: str) -> Generator:
     """
@@ -381,7 +381,7 @@ def partial_correlations_normal(# pylint: disable=R0913
 
     return all_correlations
 
-def partial_corrs(# pylint: disable=[R0913]
+def partial_corrs(# pylint: disable=[R0913, too-many-positional-arguments]
         conn, samples, primary_vals, control_vals, return_number, species,
         input_trait_geneid, input_trait_symbol, tissue_probeset_freeze_id,
         method, dataset, database_filename):
@@ -667,7 +667,7 @@ def check_for_common_errors(# pylint: disable=[R0914]
 
     return non_error_result
 
-def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911]
+def partial_correlations_with_target_db(# pylint: disable=[R0913, R0914, R0911 too-many-positional-arguments]
         conn: Any, primary_trait_name: str,
         control_trait_names: Tuple[str, ...], method: str,
         criteria: int, target_db_name: str) -> dict:
diff --git a/gn3/computations/pca.py b/gn3/computations/pca.py
index 35c9f03..4cc04a3 100644
--- a/gn3/computations/pca.py
+++ b/gn3/computations/pca.py
@@ -133,7 +133,7 @@ def generate_pca_temp_traits(
 
     """
 
-    # pylint: disable=too-many-arguments
+    # pylint: disable=[too-many-arguments, too-many-positional-arguments]
 
     pca_trait_dict = {}
 
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 08c387f..e0d9d0b 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -38,7 +38,7 @@ def create_output_directory(path: str):
         # If the directory already exists, do nothing.
         pass
 
-# pylint: disable=too-many-arguments
+# pylint: disable=[too-many-arguments, too-many-positional-arguments]
 def run_reaper(
         reaper_cmd: str,
         genotype_filename: str, traits_filename: str,
diff --git a/gn3/computations/rqtl2.py b/gn3/computations/rqtl2.py
index b482c47..e3a6446 100644
--- a/gn3/computations/rqtl2.py
+++ b/gn3/computations/rqtl2.py
@@ -57,9 +57,8 @@ def validate_required_keys(required_keys: list, data: dict) -> tuple[bool, str]:
     return True, ""
 
 
-def compose_rqtl2_cmd(rqtl_path, input_file,
-                      output_file, workspace_dir,
-                      data, config):
+def compose_rqtl2_cmd(# pylint: disable=[too-many-positional-arguments]
+        rqtl_path, input_file, output_file, workspace_dir, data, config):
     """Compose the command for running the R/QTL2 analysis."""
     # pylint: disable=R0913
     params = {
diff --git a/gn3/computations/rust_correlation.py b/gn3/computations/rust_correlation.py
index 5ce097d..69817d1 100644
--- a/gn3/computations/rust_correlation.py
+++ b/gn3/computations/rust_correlation.py
@@ -53,7 +53,7 @@ def run_correlation(
         corr_type: str = "sample", top_n: int = 500):
     """entry function to call rust correlation"""
 
-    # pylint: disable=too-many-arguments
+    # pylint: disable=[too-many-arguments, too-many-positional-arguments]
     correlation_command = current_app.config["CORRELATION_COMMAND"] # make arg?
     (tmp_dir, tmp_file) = generate_input_files(dataset)
     (output_file, json_file) = generate_json_file(
@@ -67,7 +67,7 @@ def run_correlation(
             os.readlink(correlation_command)
             if os.path.islink(correlation_command)
             else correlation_command)
-        raise Exception(command_list, actual_command, cpe.stdout) from cpe
+        raise Exception(command_list, actual_command, cpe.stdout) from cpe# pylint: disable=[broad-exception-raised]
 
     return parse_correlation_output(output_file, corr_type, top_n)