Linting failures during CI checks

[leehart]

Started happening to all PRs recently. Linting errors unrelated to code changes within the PRs themselves. It does not appear to be related to any recent changes to the code in this package, including GitHub workflows, as far as I can yet determine.

E.g.

• https://github.com/malariagen/malariagen-data-python/actions/runs/13833829346/job/38717985960?pr=731
• https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733

Run mypy malariagen_data tests --ignore-missing-imports
  mypy malariagen_data tests --ignore-missing-imports
  shell: /usr/bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/3.1[2](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:2).9/x64
    PKG_CONFIG_PATH: /opt/hostedtoolcache/Python/[3](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:3).12.9/x64/lib/pkgconfig
    Python_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.9/x6[4](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:4)
    Python2_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.9/x64
    Python3_ROOT_DIR: /opt/hostedtoolcache/Python/3.12.9/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.12.9/x64/lib
malariagen_data/anoph/genome_features.py:207: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:[5](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:5)3: note: "Range1d" defined here
malariagen_data/anoph/genome_features.py:221: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/genome_features.py:221: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/genome_features.py:221: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/genome_features.py:221: error: Unexpected keyword argument "tooltips" for "figure"  [call-arg]
malariagen_data/anoph/genome_features.py:222: error: Argument "title" to "figure" has incompatible type "str | Literal[False]"; expected "Title | str | None"  [arg-type]
malariagen_data/anoph/genome_features.py:310: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/genome_features.py:35[6](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:6): error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/genome_features.py:3[7](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:7)5: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/genome_features.py:375: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/genome_features.py:375: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/genome_features.py:375: error: Unexpected keyword argument "tooltips" for "figure"  [call-arg]
malariagen_data/anoph/genome_features.py:376: error: Argument "title" to "figure" has incompatible type "str | bool | None"; expected "Title | str | None"  [arg-type]
malariagen_data/anoph/genome_features.py:401: error: "Sequence[Model]" has no attribute "callback"  [attr-defined]
malariagen_data/anoph/genome_features.py:510: error: "list[Grid]" has no attribute "visible"  [attr-defined]
malariagen_data/anoph/genome_features.py:513: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/genome_features.py:514: error: "list[Axis]" has no attribute "major_label_overrides"  [attr-defined]
malariagen_data/anoph/genome_features.py:515: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/snp_data.py:1503: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/snp_data.py:151[8](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:8): error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/snp_data.py:1518: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/snp_data.py:1518: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/snp_data.py:1518: error: Unexpected keyword argument "tooltips" for "figure"  [call-arg]
malariagen_data/anoph/snp_data.py:1528: error: Argument "y_range" to "figure" has incompatible type "tuple[float, float]"; expected "Range"  [arg-type]
malariagen_data/anoph/snp_data.py:1533: error: "Sequence[Model]" has no attribute "name"  [attr-defined]
malariagen_data/anoph/snp_data.py:1571: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/snp_data.py:1574: error: "list[Axis]" has no attribute "major_label_overrides"  [attr-defined]
malariagen_data/anoph/snp_data.py:1578: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/snp_data.py:157[9](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:9): error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/snp_data.py:1580: error: "list[Axis]" has no attribute "minor_tick_line_color"  [attr-defined]
malariagen_data/anoph/cnv_data.py:711: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/cnv_data.py:715: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/cnv_data.py:715: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/cnv_data.py:715: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/cnv_data.py:725: error: Argument "y_range" to "figure" has incompatible type "tuple[int, Any]"; expected "Range"  [arg-type]
malariagen_data/anoph/cnv_data.py:759: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/cnv_data.py:760: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/cnv_data.py:926: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/cnv_data.py:917: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/cnv_data.py:917: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/cnv_data.py:917: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/cnv_data.py:917: error: Unexpected keyword argument "tooltips" for "figure"  [call-arg]
malariagen_data/anoph/cnv_data.py:927: error: Argument "y_range" to "figure" has incompatible type "tuple[float, Any]"; expected "Range"  [arg-type]
malariagen_data/anoph/cnv_data.py:933: error: Argument "palette" to "LinearColorMapper" has incompatible type "Sequence[str] | None"; expected "Sequence[str | tuple[int, int, int] | tuple[int, int, int, float]] | str"  [arg-type]
malariagen_data/anoph/cnv_data.py:947: error: Unexpected keyword argument "color_mapper" for "image" of "GlyphAPI"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/plotting/glyph_api.pyi:6[10](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:10): note: "image" of "GlyphAPI" defined here
malariagen_data/anoph/cnv_data.py:948: error: Argument "source" to "image" of "GlyphAPI" has incompatible type "dict[str, list[Any]]"; expected "ColumnarDataSource | dict[str, Sequence[Any] | ndarray[Any, dtype[Any]] | Series[Any] | Index[Any]] | DataFrame | GroupBy[Any]"  [arg-type]
malariagen_data/anoph/cnv_data.py:958: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/cnv_data.py:960: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/cnv_data.py:961: error: Argument "ticks" to "FixedTicker" has incompatible type "ndarray[Any, dtype[signedinteger[Any]]]"; expected "Sequence[float]"  [arg-type]
malariagen_data/anoph/cnv_data.py:963: error: "list[Axis]" has no attribute "major_label_overrides"  [attr-defined]
malariagen_data/anoph/cnv_data.py:964: error: "list[Axis]" has no attribute "major_label_text_font_size"  [attr-defined]
malariagen_data/anoph/h1x.py:221: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/h1x.py:229: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/h1x.py:229: error: Unexpected keyword argument "active_inspect" for "figure"  [call-arg]
malariagen_data/anoph/h1x.py:229: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/h1x.py:229: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/h1x.py:230: error: Argument "title" to "figure" has incompatible type "str | bool"; expected "Title | str | None"  [arg-type]
malariagen_data/anoph/h1x.py:248: error: Argument "y_range" to "figure" has incompatible type "tuple[int, int]"; expected "Range"  [arg-type]
malariagen_data/anoph/h1x.py:263: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/h1x.py:264: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/h12.py:187: error: Unexpected keyword argument "x_axis_type" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:221: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/h12.py:393: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/h12.py:401: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:401: error: Unexpected keyword argument "active_inspect" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:401: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:401: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:402: error: Argument "title" to "figure" has incompatible type "str | bool | None"; expected "Title | str | None"  [arg-type]
malariagen_data/anoph/h12.py:420: error: Argument "y_range" to "figure" has incompatible type "tuple[int, int]"; expected "Range"  [arg-type]
malariagen_data/anoph/h12.py:435: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/h12.py:436: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/h12.py:597: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/h12.py:604: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:604: error: Unexpected keyword argument "active_inspect" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:604: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:604: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/h12.py:605: error: Argument "title" to "figure" has incompatible type "str | bool | None"; expected "Title | str | None"  [arg-type]
malariagen_data/anoph/h12.py:623: error: Argument "y_range" to "figure" has incompatible type "tuple[int, int]"; expected "Range"  [arg-type]
malariagen_data/anoph/h12.py:641: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/h12.py:642: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/h12.py:804: error: "Model" has no attribute "x_range"  [attr-defined]
malariagen_data/anoph/h12.py:816: error: "Model" has no attribute "x_range"  [attr-defined]
malariagen_data/anoph/g123.py:359: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/g123.py:367: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/g123.py:367: error: Unexpected keyword argument "active_inspect" for "figure"  [call-arg]
malariagen_data/anoph/g123.py:367: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/g123.py:367: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/g123.py:368: error: Argument "title" to "figure" has incompatible type "str | bool | None"; expected "Title | str | None"  [arg-type]
malariagen_data/anoph/g123.py:386: error: Argument "y_range" to "figure" has incompatible type "tuple[int, int]"; expected "Range"  [arg-type]
malariagen_data/anoph/g123.py:402: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/g123.py:403: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/g123.py:556: error: Unexpected keyword argument "x_axis_type" for "figure"  [call-arg]
malariagen_data/anoph/g123.py:557: error: Argument "title" to "figure" has incompatible type "str | bool | None"; expected "Title | str | None"  [arg-type]
malariagen_data/anoph/g123.py:590: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anoph/fst.py:2[11](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:12): error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.[12](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:13)/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anoph/fst.py:219: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anoph/fst.py:219: error: Unexpected keyword argument "active_inspect" for "figure"  [call-arg]
malariagen_data/anoph/fst.py:219: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anoph/fst.py:219: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anoph/fst.py:220: error: Argument "title" to "figure" has incompatible type "str | bool"; expected "Title | str | None"  [arg-type]
malariagen_data/anoph/fst.py:238: error: Argument "y_range" to "figure" has incompatible type "tuple[int, int]"; expected "Range"  [arg-type]
malariagen_data/anoph/fst.py:254: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anoph/fst.py:255: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anopheles.py:294: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anopheles.py:300: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anopheles.py:300: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anopheles.py:300: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anopheles.py:310: error: Argument "y_range" to "figure" has incompatible type "tuple[int, Any]"; expected "Range"  [arg-type]
malariagen_data/anopheles.py:328: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anopheles.py:633: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anopheles.py:646: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anopheles.py:646: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anopheles.py:646: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anopheles.py:647: error: Argument "title" to "figure" has incompatible type "str | bool | None"; expected "Title | str | None"  [arg-type]
malariagen_data/anopheles.py:680: error: "list[Grid]" has no attribute "visible"  [attr-defined]
malariagen_data/anopheles.py:681: error: "list[Axis]" has no attribute "ticker"  [attr-defined]
malariagen_data/anopheles.py:682: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anopheles.py:1517: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anopheles.py:1525: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anopheles.py:1525: error: Unexpected keyword argument "active_inspect" for "figure"  [call-arg]
malariagen_data/anopheles.py:1525: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anopheles.py:1525: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anopheles.py:1526: error: Argument "title" to "figure" has incompatible type "str | bool | None"; expected "Title | str | None"  [arg-type]
malariagen_data/anopheles.py:1571: error: Unexpected keyword argument "size" for "circle" of "GlyphAPI"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/plotting/glyph_api.pyi:547: note: "circle" of "GlyphAPI" defined here
malariagen_data/anopheles.py:1581: error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
malariagen_data/anopheles.py:2047: error: Unexpected keyword argument "bounds" for "Range1d"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/models/ranges.pyi:53: note: "Range1d" defined here
malariagen_data/anopheles.py:2058: error: Unexpected keyword argument "tools" for "figure"  [call-arg]
malariagen_data/anopheles.py:2058: error: Unexpected keyword argument "active_inspect" for "figure"  [call-arg]
malariagen_data/anopheles.py:2058: error: Unexpected keyword argument "active_scroll" for "figure"  [call-arg]
malariagen_data/anopheles.py:2058: error: Unexpected keyword argument "active_drag" for "figure"  [call-arg]
malariagen_data/anopheles.py:2059: error: Argument "title" to "figure" has incompatible type "str | bool"; expected "Title | str | None"  [arg-type]
malariagen_data/anopheles.py:2103: error: Unexpected keyword argument "size" for "circle" of "GlyphAPI"  [call-arg]
/opt/hostedtoolcache/Python/3.12.9/x64/lib/python3.12/site-packages/bokeh/plotting/glyph_api.pyi:547: note: "circle" of "GlyphAPI" defined here
malariagen_data/anopheles.py:21[13](https://github.com/malariagen/malariagen-data-python/actions/runs/13854247698/job/38767444733?pr=733#step:6:14): error: "list[Axis]" has no attribute "axis_label"  [attr-defined]
Found 133 errors in 8 files (checked 96 source files)
Error: Process completed with exit code 1.