fix: max line-length of 79

.pre-commit-config.yaml

@@ -11,8 +11,9 @@ repos:
     hooks:
       - id: isort
         name: isort (python)
-        args: ["--profile", "black"]
+        args: ["--profile", "black", "--line-length", "79"]
 -   repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
     -   id: black
+        args: [--line-length=79]

doc/source/conf.py

@@ -175,7 +175,9 @@ def sort_authors(filename):
 html_favicon = "_static/logos/mdanalysis-logo.ico"
 html_logo = "_static/logos/user_guide.png"
 
-html_context = {"versions_json_url": "https://userguide.mdanalysis.org/versions.json"}
+html_context = {
+    "versions_json_url": "https://userguide.mdanalysis.org/versions.json"
+}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

doc/source/scripts/base.py

@@ -88,12 +88,16 @@ def write_table(self):
     @staticmethod
     def sphinx_class(klass, tilde=True):
         prefix = "~" if tilde else ""
-        return ":class:`{}{}.{}`".format(prefix, klass.__module__, klass.__name__)
+        return ":class:`{}{}.{}`".format(
+            prefix, klass.__module__, klass.__name__
+        )
 
     @staticmethod
     def sphinx_meth(meth, tilde=True):
         prefix = "~" if tilde else ""
-        return ":meth:`{}{}.{}`".format(prefix, meth.__module__, meth.__qualname__)
+        return ":meth:`{}{}.{}`".format(
+            prefix, meth.__module__, meth.__qualname__
+        )
 
     @staticmethod
     def sphinx_ref(txt: str, label: str = None, suffix: str = "") -> str:

doc/source/scripts/clean_example_notebooks.py

@@ -116,9 +116,9 @@ class JupyterCell:
     time_fmt = "%b %d, %Y"
     tag = "a"
     close_tag = "</{}>".format(tag)
-    tagline = ('<{} data-cite="{{key}}" ' 'href="{{url}}">{{authors}}</{}>').format(
-        tag, tag
-    )
+    tagline = (
+        '<{} data-cite="{{key}}" ' 'href="{{url}}">{{authors}}</{}>'
+    ).format(tag, tag)
 
     @classmethod
     def as_references(cls, refs, keys=[]):
@@ -171,7 +171,9 @@ def find_reference_keys(self, refs, keys=[]):
 
         Track the order of the keys for a final bibliography cell.
         """
-        matches = [x for x in re.split(refs.regex, self.source) if x is not None]
+        matches = [
+            x for x in re.split(refs.regex, self.source) if x is not None
+        ]
         new_source = ""
 
         while len(matches) > 1:
@@ -191,7 +193,9 @@ def find_reference_keys(self, refs, keys=[]):
             elif prev_char in ('"', "'"):
                 new_source += before.rsplit("<", maxsplit=1)[0]
                 if len(matches) > 2:
-                    matches[2] = matches[2].split(self.close_tag, maxsplit=1)[-1]
+                    matches[2] = matches[2].split(self.close_tag, maxsplit=1)[
+                        -1
+                    ]
             tag = self.tagline.format(key=key, authors=authors, url=url)
             new_source += tag
             matches.pop(0)
@@ -322,7 +326,9 @@ def clean_all_notebooks(notebooks):
     if len(errs):
         errmsgs = ["{}: {}".format(nb, err) for nb, err in errs]
         delim = "\n" + "===" * 10 + "\n"
-        raise ValueError("Notebooks have errors: {}".format(delim.join(errmsgs)))
+        raise ValueError(
+            "Notebooks have errors: {}".format(delim.join(errmsgs))
+        )
 
 
 if __name__ == "__main__":

doc/source/scripts/core.py

@@ -75,17 +75,27 @@
     for c in _TOPOLOGY_ATTRS.values()
 }
 
-base_attrnames = set(["atomattrs", "residueattrs", "segmentattrs", "topologyattrs"])
+base_attrnames = set(
+    ["atomattrs", "residueattrs", "segmentattrs", "topologyattrs"]
+)
 
 core_attrnames = set(["indices", "resindices", "segindices"])
 
 BASE_ATTRS = {k: v for k, v in ATTRS.items() if k in base_attrnames}
 
 NON_BASE_ATTRS = {k: v for k, v in ATTRS.items() if k not in base_attrnames}
 
-NON_CORE_ATTRS = {k: v for k, v in NON_BASE_ATTRS.items() if k not in core_attrnames}
+NON_CORE_ATTRS = {
+    k: v for k, v in NON_BASE_ATTRS.items() if k not in core_attrnames
+}
 
 TOPOLOGY_CLS = sorted(
-    set([x for x in _TOPOLOGY_ATTRS.values() if x.attrname in NON_CORE_ATTRS.keys()]),
+    set(
+        [
+            x
+            for x in _TOPOLOGY_ATTRS.values()
+            if x.attrname in NON_CORE_ATTRS.keys()
+        ]
+    ),
     key=lambda x: x.attrname,
 )

doc/source/scripts/gen_format_overview_classes.py

@@ -35,7 +35,14 @@ class FormatOverview(TableWriter):
     filename = "formats/format_overview.txt"
     include_table = "Table of all supported formats in MDAnalysis"
     preprocess = ["keys"]
-    headings = ["File type", "Description", "Topology", "Coordinates", "Read", "Write"]
+    headings = [
+        "File type",
+        "Description",
+        "Topology",
+        "Coordinates",
+        "Read",
+        "Write",
+    ]
 
     def _set_up_input(self):
         return sorted_types
@@ -80,7 +87,9 @@ def _write(self, fmt, handlers):
 
 class CoordinateReaders(FormatOverview):
     filename = "formats/coordinate_readers.txt"
-    include_table = "Table of supported coordinate readers and the information read"
+    include_table = (
+        "Table of supported coordinate readers and the information read"
+    )
     headings = ["File type", "Description", "Velocities", "Forces"]
 
     def _set_up_input(self):

doc/source/scripts/gen_standard_selections.py

@@ -36,8 +36,14 @@ def get_lines(self, klass, attr, sort=False, n=8):
 
 if __name__ == "__main__":
     StandardSelectionTable("protein", sel.ProteinSelection, "prot_res", True)
-    StandardSelectionTable("protein_backbone", sel.BackboneSelection, "bb_atoms")
+    StandardSelectionTable(
+        "protein_backbone", sel.BackboneSelection, "bb_atoms"
+    )
     StandardSelectionTable("nucleic", sel.NucleicSelection, "nucl_res")
-    StandardSelectionTable("nucleic_backbone", sel.NucleicBackboneSelection, "bb_atoms")
+    StandardSelectionTable(
+        "nucleic_backbone", sel.NucleicBackboneSelection, "bb_atoms"
+    )
     StandardSelectionTable("base", sel.BaseSelection, "base_atoms")
-    StandardSelectionTable("nucleic_sugar", sel.NucleicSugarSelection, "sug_atoms")
+    StandardSelectionTable(
+        "nucleic_sugar", sel.NucleicSugarSelection, "sug_atoms"
+    )

doc/source/scripts/gen_topologyparser_attrs.py

@@ -79,10 +79,17 @@
 
 
 class TopologyParsers(TableWriter):
-    headings = ["Format", "Description", "Attributes read", "Attributes guessed"]
+    headings = [
+        "Format",
+        "Description",
+        "Attributes read",
+        "Attributes guessed",
+    ]
     preprocess = ["keys"]
     filename = "formats/topology_parsers.txt"
-    include_table = "Table of supported topology parsers and the attributes read"
+    include_table = (
+        "Table of supported topology parsers and the attributes read"
+    )
     sort = True
 
     def __init__(self):
@@ -133,7 +140,9 @@ def __init__(self, attrs):
 
     def _set_up_input(self):
         return sorted(
-            [x, *y] for x, y in NON_CORE_ATTRS.items() if x not in MANDATORY_ATTRS
+            [x, *y]
+            for x, y in NON_CORE_ATTRS.items()
+            if x not in MANDATORY_ATTRS
         )
 
     def _atom(self, name, singular, *args):

doc/source/scripts/gen_unit_tables.py

@@ -32,7 +32,8 @@ def write_unit_table(filename):
             f.write("\n\n")
             f.write(
                 textwrap.indent(
-                    tabulate.tabulate(lines, headers=headings, tablefmt="rst"), "    "
+                    tabulate.tabulate(lines, headers=headings, tablefmt="rst"),
+                    "    ",
                 )
             )
             f.write("\n")

doc/source/scripts/tests/snapshot/test_gen_standard_selections.py

@@ -6,7 +6,9 @@
 
 def test_StandardSelectionTable_protein(snapshot):
     with patch("builtins.open"):
-        ss = StandardSelectionTable("protein", sel.ProteinSelection, "prot_res", True)
+        ss = StandardSelectionTable(
+            "protein", sel.ProteinSelection, "prot_res", True
+        )
     assert ss.lines == snapshot
 
 
@@ -20,7 +22,9 @@ def test_StandardSelectionTable_protein_backbone(snapshot):
 
 def test_StandardSelectionTable_nucleic(snapshot):
     with patch("builtins.open"):
-        ss = StandardSelectionTable("nucleic", sel.NucleicSelection, "nucl_res", True)
+        ss = StandardSelectionTable(
+            "nucleic", sel.NucleicSelection, "nucl_res", True
+        )
     assert ss.lines == snapshot
 
 
@@ -34,7 +38,9 @@ def test_StandardSelectionTable_nucleic_backbone(snapshot):
 
 def test_StandardSelectionTable_base(snapshot):
     with patch("builtins.open"):
-        ss = StandardSelectionTable("base", sel.BaseSelection, "base_atoms", True)
+        ss = StandardSelectionTable(
+            "base", sel.BaseSelection, "base_atoms", True
+        )
     assert ss.lines == snapshot
 
 

doc/source/scripts/tests/snapshot/test_gen_topologyparser_attrs.py

@@ -1,6 +1,10 @@
 from unittest.mock import patch
 
-from gen_topologyparser_attrs import ConnectivityAttrs, TopologyAttrs, TopologyParsers
+from gen_topologyparser_attrs import (
+    ConnectivityAttrs,
+    TopologyAttrs,
+    TopologyParsers,
+)
 from MDAnalysis.core import selection as sel
 
 

doc/source/scripts/tests/snapshot/test_gen_unit_tables.py

@@ -8,6 +8,8 @@ def test_write_unit_table(snapshot):
     with patch.object(Path, "open", mock_open()) as mock_open_file:
         write_unit_table(filename=Path())
 
-    lines = [args[0] for args in mock_open_file.return_value.write.call_args_list]
+    lines = [
+        args[0] for args in mock_open_file.return_value.write.call_args_list
+    ]
     # Exclude the first line, because it contains "Generated by /home/username/..."
     assert lines[1:] == snapshot