Final linting

Author: jeromekelleher

pyproject.toml

@@ -133,8 +133,4 @@ ignore = [
     "PT006", # Wrong type passed to first argument of `pytest.mar
     "PT007", # Wrong values type in `pytest.mark.parametrize`
     "PT009", # Use a regular `assert` instead of unittest-style
-    # FIXME - line too long in debug.py
-    "E501",
-
 ]
-

sc2ts/debug.py

@@ -112,7 +112,7 @@ def line_cell(pos, prev_pos, next_pos):
             dist_to_left = 0
         if dist_to_right > 2:
             dist_to_right = 0
-        return f'<td title="{pos}" "class="run-{int(dist_to_left)}-{int(dist_to_right)}"></td>'
+        return f'<td title="{pos}" "class="run-{int(dist_to_left)}-{int(dist_to_right)}"></td>'  # noqa E501
 
     def node_mutations(self):
         muts = {}
@@ -306,19 +306,20 @@ def label(allele, default=""):
             runlength_cols = ("white", "red", "orange")
             bg_im_src = (
                 "background-image:linear-gradient(to right, {0} 50%, {1} 50%);"
-                "background-image:-webkit-linear-gradient(left, {0} 50%, {1} 50%);"  # for imgkit/wkhtmltopdf
+                # for imgkit/wkhtmltopdf
+                "background-image:-webkit-linear-gradient(left, {0} 50%, {1} 50%);"
             )
             html += "<style>"
             if font_family is not None:
                 html += f".copying-table {{font-family: '{font_family}'}}"
             html += ".copying-table .position {text-align: center; font-size: 7px}"
-            html += ".copying-table .pattern td {border:0px solid black; text-align: center; width:1em}"
+            html += ".copying-table .pattern td {border:0px solid black; text-align: center; width:1em}"  # noqa: E501
             html += ".copying-table .mut {text-align: center; font-size: 7px}"
             html += ".copying-table .ref {text-align: center; font-size: 9px}"
             html += ".copying-table {border-spacing: 0px; border-collapse: collapse}"
             html += ".copying-table .runlengths {font-size:3px; height:3px;}"
             html += ".copying-table .child-rgt {text-align: left;}"
-            html += ".copying-table .runlengths td {border-style: solid; background: white; border-width:0px 1px; border-color: black}"
+            html += ".copying-table .runlengths td {border-style: solid; background: white; border-width:0px 1px; border-color: black}"  # noqa: E501
             for left in range(len(runlength_cols)):
                 for right in range(len(runlength_cols)):
                     html += (
@@ -935,7 +936,8 @@ def node_info(node, label):
             interval_left = interval[0][0]
             if interval_left >= interval_right:
                 logger.warning(
-                    f"RE: {u} interval_right >= interval_left; moving from {interval_left}"
+                    f"RE: {u} interval_right >= interval_left; "
+                    f"moving from {interval_left}"
                     f"to {interval_right - 1}"
                 )
                 interval_left = interval_right - 1
@@ -1984,22 +1986,26 @@ def draw_svg(
         **kwargs,
     ):
         """
-        Draw an SVG representation of the tree of samples that trace to a single origin.
+        Draw an SVG representation of the tree of samples that trace to a
+        single origin.
 
         The default style is to colour mutations such that sites with a single
-        mutation in the tree are dark red, whereas sites with multiple mutations
-        show those mutations in red or magenta (magenta when a mutation immediately
-        reverts its parent mutation). Any identical mutations (from the same inherited
-        to derived state at the same site, i.e. recurrent mutations) have the count of
-        recurrent mutations appended to the label, e.g. "C842T (1/2)".
-
-        If highlight_universal_mutations is set, then mutations in the ancestry of all
-        the samples (i.e. between the root and the MRCA of all the samples) are highlighted
+        mutation in the tree are dark red, whereas sites with multiple
+        mutations show those mutations in red or magenta (magenta when a
+        mutation immediately reverts its parent mutation). Any identical
+        mutations (from the same inherited to derived state at the same site,
+        i.e. recurrent mutations) have the count of recurrent mutations
+        appended to the label, e.g. "C842T (1/2)".
+
+        If highlight_universal_mutations is set, then mutations in the ancestry
+        of all the samples (i.e. between the root and the MRCA of all the
+        samples) are highlighted
         in bold and with thicker symbol lines
 
-        If genetic_regions is set, it should be a dictionary mapping (start, end) tuples
-        to region names. These will be drawn as coloured rectangles on the x-axis. If None,
-        a default selection of SARS-CoV-2 genes will be used.
+        If genetic_regions is set, it should be a dictionary mapping (start,
+        end) tuples to region names. These will be drawn as coloured rectangles
+        on the x-axis. If None, a default selection of SARS-CoV-2 genes will be
+        used.
         """
         if x_regions is None:
             x_regions = {
@@ -2034,7 +2040,7 @@ def draw_svg(
             }
         elif node_labels == "pango+country":
             node_labels = {
-                n.id: f"{n.metadata.get(pango_md, '')}:{country_abbr(n.metadata.get('Country', ''))}"
+                n.id: f"{n.metadata.get(pango_md, '')}:{country_abbr(n.metadata.get('Country', ''))}"  # noqa E501
                 for n in ts.nodes()
                 if pango_md in n.metadata or "Country" in n.metadata
             }
@@ -2082,7 +2088,10 @@ def draw_svg(
             }
         # some default styles
         styles = [
-            ".mut .lab {fill: darkred} .mut .sym {stroke: darkred} .background path {fill: white}"
+            (
+                ".mut .lab {fill: darkred} .mut .sym {stroke: darkred} "
+                ".background path {fill: white}"
+            )
         ]
         if len(multiple_mutations) > 0:
             lab_css = ", ".join(f".mut.m{m} .lab" for m in multiple_mutations)
@@ -2130,14 +2139,20 @@ def draw_svg(
 
             # Find SVG positions of the X axis
             m = re.search(
-                r'class="x-axis".*?class="ax-line" x1="([\d\.]+)" x2="([\d\.]+)" y1="([\d\.]+)"',
+                r'class="x-axis".*?class="ax-line" x1="([\d\.]+)" x2="([\d\.]+)" y1="([\d\.]+)"',  # noqa E501
                 svg,
             )
             assert m is not None
             x1, x2, y1 = float(m.group(1)), float(m.group(2)), float(m.group(3))
             xdiff = x2 - x1
-            x_box_svg = '<rect fill="yellow" stroke="black" x="{x}" width="{w}" y="{y}" height="{h}" />'
-            x_name_svg = '<text text-anchor="middle" alignment-baseline="hanging" x="{x}" y="{y}">{name}</text>'
+            x_box_svg = (
+                '<rect fill="yellow" stroke="black" x="{x}" '
+                'width="{w}" y="{y}" height="{h}" />'
+            )
+            x_name_svg = (
+                '<text text-anchor="middle" alignment-baseline="hanging" '
+                'x="{x}" y="{y}">{name}</text>'
+            )
             x_scale = xdiff / ts.sequence_length
             x_boxes = [
                 x_box_svg.format(

tests/sc2ts_fixtures.py

@@ -170,7 +170,8 @@ def fx_ts_map(tmp_path, fx_data_cache, fx_dataset, fx_match_db):
                 **extra_kwargs,
             )
             print(
-                f"INFERRED {date} nodes={last_ts.num_nodes} mutations={last_ts.num_mutations}"
+                f"INFERRED {date} nodes={last_ts.num_nodes} "
+                f"mutations={last_ts.num_mutations}"
             )
             cache_path = fx_data_cache / f"{date}.ts"
             last_ts.dump(cache_path)
@@ -289,7 +290,8 @@ def recombinant_example_2(tmp_path, fx_ts_map, fx_dataset, ds_path):
     ts_path = tmp_path / "intermediate.ts"
     ts.dump(ts_path)
 
-    # Now run again with the recombinant of these two, encoding the interval in the # name
+    # Now run again with the recombinant of these two, encoding the interval
+    # in the name
     date = "2020-03-02"
     left = start + 3 + 1
     right = end - 3 + 1
@@ -367,7 +369,8 @@ def recombinant_example_3(tmp_path, fx_ts_map, fx_dataset, ds_path):
     ts_path = tmp_path / "intermediate.ts"
     ts.dump(ts_path)
 
-    # Now run again with the recombinant of these three, encoding the intervals in the name
+    # Now run again with the recombinant of these three, encoding the intervals
+    # in the name
     date = "2020-03-02"
     left = start + 3 + 1
     right = end - 3 + 1