Fix a myriad of linter issues

* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes

2 files changed, 17 insertions, 14 deletions

diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py
index 3633a59..f7ddfd0 100644
--- a/gn3/computations/partial_correlations.py
+++ b/gn3/computations/partial_correlations.py
@@ -141,7 +141,7 @@ def find_identical_traits(
         return acc + ident[1]
 
     def __dictify_controls__(acc, control_item):
-        ckey = tuple("{:.3f}".format(item) for item in control_item[0])
+        ckey = tuple("{item:.3f}" for item in control_item[0])
         return {**acc, ckey: acc.get(ckey, tuple()) + (control_item[1],)}
 
     return (reduce(## for identical control traits
@@ -181,8 +181,8 @@ def tissue_correlation(
     assert len(primary_trait_values) == len(target_trait_values), (
         "The lengths of the `primary_trait_values` and `target_trait_values` "
         "must be equal")
-    assert method in method_fns.keys(), (
-        "Method must be one of: {}".format(",".join(method_fns.keys())))
+    assert method in method_fns, (
+        "Method must be one of: {','.join(method_fns.keys())}")
 
     corr, pvalue = method_fns[method](primary_trait_values, target_trait_values)
     return (corr, pvalue)
@@ -241,7 +241,7 @@ def partial_correlations_fast(# pylint: disable=[R0913, R0914]
     function in GeneNetwork1.
     """
     assert method in ("spearman", "pearson")
-    with open(database_filename, "r") as dataset_file:
+    with open(database_filename, "r") as dataset_file: # pytest: disable=[W1514]
         dataset = tuple(dataset_file.readlines())
 
     good_dataset_samples = good_dataset_samples_indexes(
@@ -290,12 +290,15 @@ def build_data_frame(
     if isinstance(zdata[0], float):
         return x_y_df.join(pandas.DataFrame({"z": zdata}))
     interm_df = x_y_df.join(pandas.DataFrame(
-        {"z{}".format(i): val for i, val in enumerate(zdata)}))
+        {f"z{i}": val for i, val in enumerate(zdata)}))
     if interm_df.shape[1] == 3:
         return interm_df.rename(columns={"z0": "z"})
     return interm_df
 
 def compute_trait_info(primary_vals, control_vals, target, method):
+    """
+    Compute the correlation values for the given arguments.
+    """
     targ_vals = target[0]
     targ_name = target[1]
     primary = [
@@ -629,7 +632,7 @@ def partial_correlations_entry(# pylint: disable=[R0913, R0914, R0911]
             "status": "not-found",
             "message": "None of the requested control traits were found."}
     for trait in cntrl_traits:
-        if trait["haveinfo"] == False:
+        if trait["haveinfo"] is False:
             warnings.warn(
                 (f"Control traits {trait['trait_fullname']} was not found "
                  "- continuing without it."),
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index d1ff4ac..b61bdae 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -27,7 +27,7 @@ def generate_traits_file(samples, trait_values, traits_filename):
         ["{}\t{}".format(
             len(trait_values), "\t".join([str(i) for i in t]))
          for t in trait_values[-1:]])
-    with open(traits_filename, "w") as outfile:
+    with open(traits_filename, "w", encoding="utf8") as outfile:
         outfile.writelines(data)
 
 def create_output_directory(path: str):
@@ -68,13 +68,13 @@ def run_reaper(
     The function will raise a `subprocess.CalledProcessError` exception in case
     of any errors running the `qtlreaper` command.
     """
-    create_output_directory("{}/qtlreaper".format(output_dir))
-    output_filename = "{}/qtlreaper/main_output_{}.txt".format(
-        output_dir, random_string(10))
+    create_output_directory(f"{output_dir}/qtlreaper")
+    output_filename = (
+        f"{output_dir}/qtlreaper/main_output_{random_string(10)}.txt")
     output_list = ["--main_output", output_filename]
     if separate_nperm_output:
-        permu_output_filename: Union[None, str] = "{}/qtlreaper/permu_output_{}.txt".format(
-            output_dir, random_string(10))
+        permu_output_filename: Union[None, str] = (
+            f"{output_dir}/qtlreaper/permu_output_{random_string(10)}.txt")
         output_list = output_list + [
             "--permu_output", permu_output_filename] # type: ignore[list-item]
     else:
@@ -135,7 +135,7 @@ def parse_reaper_main_results(results_file):
     """
     Parse the results file of running QTLReaper into a list of dicts.
     """
-    with open(results_file, "r") as infile:
+    with open(results_file, "r", encoding="utf8") as infile:
         lines = infile.readlines()
 
     def __parse_column_float_value(value):
@@ -164,7 +164,7 @@ def parse_reaper_permutation_results(results_file):
     """
     Parse the results QTLReaper permutations into a list of values.
     """
-    with open(results_file, "r") as infile:
+    with open(results_file, "r", encoding="utf8") as infile:
         lines = infile.readlines()
 
     return [float(line.strip()) for line in lines]