Merge pull request #523 from joaomcteixeira/minorlints2

Corrects minor lint issues

examples/compare_runs.py

@@ -266,7 +266,7 @@ def error_1(l1, l2):
     is_in_l1 = set(l1).difference(set(l2))
     is_in_l2 = set(l2).difference(set(l1))
 
-    if not(is_in_l1) and not(is_in_l2):
+    if not is_in_l1 and not is_in_l2:
         raise AssertionError(
             "BUG FOUND: at least one of these sets should have values"
             )

src/haddock/clis/cli_dmn.py

@@ -66,8 +66,8 @@
     )
 
 ap.add_argument(
-    '--short-first',
-    dest='short_first',
+    '--sort-first',
+    dest='sort_first',
     help=(
         'Sort jobs by size in ascending order. If not given jobs are order by '
         'size in descending order: the biggest first.'
@@ -242,7 +242,7 @@ def main(
         job_limit=10,
         manager='slurm',
         restart=False,
-        short_first=False,
+        sort_first=False,
         ):
     """
     Execute the benchmark daemon.
@@ -274,9 +274,9 @@ def main(
         Whether to restart the `RUNNING` jobs that might have been halted
         in previous daemon runs. Defaults to False.
 
-    short_first : bool
+    sort_first : bool
         Whether to sort jobs by their size in ascending manner. That is,
-        the shorted jobs first. Defaults to False, the longer first.
+        the sorted jobs first. Defaults to False, the longer first.
     """
     # lists of all the job files in the benchmark_path folder
     job_list = list(benchmark_path.glob('*/jobs/*.job'))
@@ -286,7 +286,7 @@ def main(
         sys.exit('+ ERROR! No jobs found in folder: {str(benchmark_path)!r}')
 
     # sorts the job list
-    job_list.sort(key=calc_size, reverse=not(short_first))
+    job_list.sort(key=calc_size, reverse=not(sort_first))  # noqa: E275
 
     # create the job objects according to the queue managing systme
     _jobsys = workload_manager_launch[manager]

src/haddock/gear/prepare_run.py

@@ -728,7 +728,7 @@ def populate_topology_molecule_params(topoaa):
     # well. `prot_segid` is the only one differing per molecule.
     for i in range(1, len(topoaa["molecules"]) + 1):
         mol = f"mol{i}"
-        if not(mol in topoaa and "prot_segid" in topoaa[mol]):
+        if not (mol in topoaa and "prot_segid" in topoaa[mol]):
             topoaa_dft["mol1"]["prot_segid"] = uppers.pop()
 
         topoaa[mol] = recursive_dict_update(