more ruff fixes 2

mdgo/coordination.py

@@ -1043,6 +1043,7 @@ def concat_coord_array(
             and the corresponding values are the selection language.
         run_start: Start frame of analysis.
         run_end: End frame of analysis.
+        kwargs: Keyword arguments in the func.
 
     Returns:
         A diction containing the coordination number sequence of each specified neighbor species

mdgo/msd.py

@@ -285,7 +285,7 @@ def parse_msd_type(msd_type: DIM) -> list[int]:
         dim = keys[msd_type_str]
     except KeyError:
         raise ValueError(
-            f"invalid msd_type: {msd_type_str} specified, please specify one of xyz, " "xy, xz, yz, x, y, z"
+            f"invalid msd_type: {msd_type_str} specified, please specify one of xyz, xy, xz, yz, x, y, z"
         )
     return dim
 

mdgo/residence_time.py

@@ -125,9 +125,9 @@ def calc_neigh_corr(
 
     Args:
         nvt_run: An MDAnalysis ``Universe``.
-        distance_dict:
-        select_dict:
-        time_step:
+        distance_dict: A dict of coordination cutoff distance of the neighbor species.
+        select_dict: A dictionary of atom species selection.
+        time_step: Timestep between each frame, in ps.
         run_start: Start frame of analysis.
         run_end: End frame of analysis.
         center_atom: The center atom to calculate the ACF for. Default to "cation".
@@ -158,8 +158,7 @@ def calc_neigh_corr(
                 run_end,
             )
             acfs = calc_acf(adjacency_matrix)
-            for acf in acfs:
-                acf_all.append(acf)
+            acf_all.extend(list(acfs))
         acf_avg[kw] = np.mean(acf_all, axis=0)
     return times, acf_avg
 

tasks.py

@@ -1,5 +1,8 @@
 """
 Pyinvoke tasks.py file for automating releases and admin stuff.
+
+To cut a new mdgo release, use `invoke update-changelog` followed by `invoke release`.
+
 Author: Tingzheng Hou
 """
 from __future__ import annotations
@@ -179,8 +182,8 @@ def update_changelog(ctx, version, sim=False):
     output = subprocess.check_output(["git", "log", "--pretty=format:%s", "v%s..HEAD" % CURRENT_VER])
     lines = []
     misc = []
-    for l in output.decode("utf-8").strip().split("\n"):
-        m = re.match(r"Merge pull request \#(\d+) from (.*)", l)
+    for line in output.decode("utf-8").strip().split("\n"):
+        m = re.match(r"Merge pull request \#(\d+) from (.*)", line)
         if m:
             pr_number = m.group(1)
             contrib, pr_name = m.group(2).split("/", 1)
@@ -191,22 +194,22 @@ def update_changelog(ctx, version, sim=False):
                     ll = ll.strip()
                     if ll in ["", "## Summary"]:
                         continue
-                    elif ll.startswith(("## Checklist", "## TODO")):
+                    if ll.startswith(("## Checklist", "## TODO")):
                         break
                     lines.append(f"    {ll}")
-        misc.append(l)
+        misc.append(line)
     with open("CHANGES.rst") as f:
         contents = f.read()
-    l = "=========="
-    toks = contents.split(l)
+    line = "=========="
+    toks = contents.split(line)
     head = "\n\nv%s\n" % version + "-" * (len(version) + 1) + "\n"
     toks.insert(-1, head + "\n".join(lines))
     if not sim:
         with open("CHANGES.rst", "w") as f:
-            f.write(toks[0] + l + "".join(toks[1:]))
+            f.write(toks[0] + line + "".join(toks[1:]))
         ctx.run("open CHANGES.rst")
     else:
-        print(toks[0] + l + "".join(toks[1:]))
+        print(toks[0] + line + "".join(toks[1:]))
     print("The following commit messages were not included...")
     print("\n".join(misc))