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.