The action 'Setup tmate session' has timed out after 5 minutes.

test_run_topostats_process_debug schema.SchemaError: There is an error in your YAML plotting configuration file configuration. Please refer to the first error message above for details

test_run_topostats_process_all schema.SchemaError: There is an error in your YAML plotting configuration file configuration. Please refer to the first error message above for details

test_run_ordered_tracing[catenane] FileNotFoundError: [Errno 2] Unable to synchronously open file (unable to open file: name = 'D:\a\TopoStats\TopoStats\tests\resources\tracing\ordered_tracing\catenane_post_nodestats.topostats', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

test_run_ordered_tracing[minicircle] KeyError: 'topostats_file_version'

test_run_nodestats[catenane] NotImplementedError: cannot instantiate 'PosixPath' on your system

test_image_set[filters, grain_crops and disordered_tracing] TypeError: 'TopoStats' object is not subscriptable

test_save_figure[None-True-None] _tkinter.TclError: Can't find a usable init.tcl in the following directories: {C:\hostedtoolcache\windows\Python\3.11.9\x64\tcl\tcl8.6} C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tcl8.6/init.tcl: couldn't read file "C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tcl8.6/init.tcl": No error couldn't read file "C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tcl8.6/init.tcl": No error while executing "source C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tcl8.6/init.tcl" ("uplevel" body line 1) invoked from within "uplevel #0 [list source $tclfile]" This probably means that Tcl wasn't installed properly.

test_run_grainstats assert 0 == 6

test_trace_extract_height_profile _tkinter.TclError: Can't find a usable tk.tcl in the following directories: C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tcl8.6/tk8.6 C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tk8.6 C:/hostedtoolcache/windows/Python/3.11.9/lib/tk8.6 C:/hostedtoolcache/windows/Python/3.11.9/lib/tk8.6 C:/hostedtoolcache/windows/Python/lib/tk8.6 C:/hostedtoolcache/windows/Python/3.11.9/library C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tk8.6/tk.tcl: couldn't read file "C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tk8.6/ttk/scale.tcl": no such file or directory couldn't read file "C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tk8.6/ttk/scale.tcl": no such file or directory while executing "source -encoding utf-8 [file join $::ttk::library scale.tcl]" (file "C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tk8.6/ttk/ttk.tcl" line 103) invoked from within "source -encoding utf-8 C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tk8.6/ttk/ttk.tcl" ("uplevel" body line 1) invoked from within "uplevel \#0 [list source -encoding utf-8 $::ttk::library/ttk.tcl]" (file "C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tk8.6/tk.tcl" line 706) invoked from within "source C:/hostedtoolcache/windows/Python/3.11.9/x64/tcl/tk8.6/tk.tcl" ("uplevel" body line 1) invoked from within "uplevel #0 [list source $file]" This probably means that tk wasn't installed properly.

test_find_files[topostats] AssertionError: assert 5 == 6 + where 5 = len([WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/file.topostats'), WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/notebook3_image.topostats'), WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/process_scan_topostats_file_regtest.topostats'), WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/test_image/minicircle_small.topostats'), WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/tracing/ordered_tracing/minicircle_post_nodestats.topostats')])

The operation was canceled.

test_process_scan_below_height_profiles TypeError: 'TopoStats' object is not subscriptable

test_disordered_trace_grain[test re-add holes, 3 holes, one right size for re-adding] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, prune small branch] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, no pruning] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test height bias: thick curve height weighting outer, weak height bias] KeyError: 'smoothed_grain'

test_image_set[filters, grain_crops and disordered_tracing] TypeError: 'TopoStats' object is not subscriptable

test_disordered_trace_grain[test height bias: thick curve height weighting outer, strong height bias] KeyError: 'smoothed_grain'

test_disordered_trace_grain[simple slightly curved line] KeyError: 'smoothed_grain'

test_process_scan_below TypeError: 'TopoStats' object is not subscriptable

test_find_files[topostats] AssertionError: assert 5 == 6 + where 5 = len([PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/notebook3_image.topostats'), PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/file.topostats'), PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/process_scan_topostats_file_regtest.topostats'), PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/test_image/minicircle_small.topostats'), PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/tracing/ordered_tracing/minicircle_post_nodestats.topostats')])

The strategy configuration was canceled because "build.windows-latest_3_11" failed

The operation was canceled.

test_disordered_trace_grain[test re-add holes, 3 holes, one right size for re-adding] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, prune small branch] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, no pruning] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test height bias: thick curve height weighting outer, weak height bias] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test height bias: thick curve height weighting outer, strong height bias] KeyError: 'smoothed_grain'

test_disordered_trace_grain[simple slightly curved line] KeyError: 'smoothed_grain'

test_process_scan_below TypeError: 'TopoStats' object is not subscriptable

test_image_set[grains, nodestats, ordered_tracing] TypeError: 'TopoStats' object is not subscriptable

test_image_set[filters, grain_crops and disordered_tracing] TypeError: 'TopoStats' object is not subscriptable

test_find_files[topostats] AssertionError: assert 5 == 6 + where 5 = len([PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/notebook3_image.topostats'), PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/file.topostats'), PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/process_scan_topostats_file_regtest.topostats'), PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/test_image/minicircle_small.topostats'), PosixPath('/home/runner/work/TopoStats/TopoStats/tests/resources/tracing/ordered_tracing/minicircle_post_nodestats.topostats')])

The strategy configuration was canceled because "build.windows-latest_3_11" failed

The operation was canceled.

test_disordered_trace_grain[test re-add holes, 3 holes, one right size for re-adding] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, prune small branch] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, no pruning] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test height bias: thick curve height weighting outer, weak height bias] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test height bias: thick curve height weighting outer, strong height bias] KeyError: 'smoothed_grain'

test_disordered_trace_grain[simple slightly curved line] KeyError: 'smoothed_grain'

test_save_figure[None-True-None] _tkinter.TclError: Can't find a usable tk.tcl in the following directories: C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tcl8.6/tk8.6 C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tk8.6 C:/hostedtoolcache/windows/Python/3.10.11/lib/tk8.6 C:/hostedtoolcache/windows/Python/3.10.11/lib/tk8.6 C:/hostedtoolcache/windows/Python/lib/tk8.6 C:/hostedtoolcache/windows/Python/3.10.11/library C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tk8.6/tk.tcl: couldn't read file "C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tk8.6/ttk/spinbox.tcl": no such file or directory couldn't read file "C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tk8.6/ttk/spinbox.tcl": no such file or directory while executing "source -encoding utf-8 [file join $::ttk::library spinbox.tcl] " (file "C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tk8.6/ttk/ttk.tcl" line 109) invoked from within "source -encoding utf-8 C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tk8.6/ttk/ttk.tcl" ("uplevel" body line 1) invoked from within "uplevel \#0 [list source -encoding utf-8 $::ttk::library/ttk.tcl]" (file "C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tk8.6/tk.tcl" line 706) invoked from within "source C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tk8.6/tk.tcl" ("uplevel" body line 1) invoked from within "uplevel #0 [list source $file]" This probably means that tk wasn't installed properly.

test_run_grainstats assert 0 == 6

test_find_files[topostats] AssertionError: assert 5 == 6 + where 5 = len([WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/file.topostats'), WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/notebook3_image.topostats'), WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/process_scan_topostats_file_regtest.topostats'), WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/test_image/minicircle_small.topostats'), WindowsPath('D:/a/TopoStats/TopoStats/tests/resources/tracing/ordered_tracing/minicircle_post_nodestats.topostats')])

test_trace_extract_height_profile _tkinter.TclError: Can't find a usable init.tcl in the following directories: {C:\hostedtoolcache\windows\Python\3.10.11\x64\tcl\tcl8.6} C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tcl8.6/init.tcl: couldn't read file "C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tcl8.6/init.tcl": No error couldn't read file "C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tcl8.6/init.tcl": No error while executing "source C:/hostedtoolcache/windows/Python/3.10.11/x64/tcl/tcl8.6/init.tcl" ("uplevel" body line 1) invoked from within "uplevel #0 [list source $tclfile]" This probably means that Tcl wasn't installed properly.

The strategy configuration was canceled because "build.windows-latest_3_11" failed

The operation was canceled.

test_process_scan_below_height_profiles TypeError: 'TopoStats' object is not subscriptable

test_image_set[all] TypeError: 'TopoStats' object is not subscriptable

test_disordered_trace_grain[test re-add holes, 3 holes, one right size for re-adding] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, prune small branch] KeyError: 'smoothed_grain'

test_process_scan_below TypeError: 'TopoStats' object is not subscriptable

test_disordered_trace_grain[test pruning: thick curve with tail, no pruning] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test height bias: thick curve height weighting outer, weak height bias] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test height bias: thick curve height weighting outer, strong height bias] KeyError: 'smoothed_grain'

test_disordered_trace_grain[simple slightly curved line] KeyError: 'smoothed_grain'

test_find_files[topostats] AssertionError: assert 5 == 6 + where 5 = len([PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/process_scan_topostats_file_regtest.topostats'), PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/notebook3_image.topostats'), PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/file.topostats'), PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/tracing/ordered_tracing/minicircle_post_nodestats.topostats'), PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/test_image/minicircle_small.topostats')])

The strategy configuration was canceled because "build.windows-latest_3_11" failed

The operation was canceled.

test_process_scan_below_height_profiles TypeError: 'TopoStats' object is not subscriptable

test_image_set[all] TypeError: 'TopoStats' object is not subscriptable

test_disordered_trace_grain[test re-add holes, 3 holes, one right size for re-adding] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, prune small branch] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test pruning: thick curve with tail, no pruning] KeyError: 'smoothed_grain'

test_disordered_trace_grain[test height bias: thick curve height weighting outer, weak height bias] KeyError: 'smoothed_grain'

test_process_scan_below TypeError: 'TopoStats' object is not subscriptable

test_disordered_trace_grain[test height bias: thick curve height weighting outer, strong height bias] KeyError: 'smoothed_grain'

test_disordered_trace_grain[simple slightly curved line] KeyError: 'smoothed_grain'

test_find_files[topostats] AssertionError: assert 5 == 6 + where 5 = len([PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/process_scan_topostats_file_regtest.topostats'), PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/notebook3_image.topostats'), PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/file.topostats'), PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/tracing/ordered_tracing/minicircle_post_nodestats.topostats'), PosixPath('/Users/runner/work/TopoStats/TopoStats/tests/resources/test_image/minicircle_small.topostats')])

The strategy configuration was canceled because "build.windows-latest_3_11" failed

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in arccos

invalid value encountered in arccos

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in arccos

invalid value encountered in arccos

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in arccos

invalid value encountered in arccos

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in arccos

invalid value encountered in arccos

invalid value encountered in scalar divide

invalid value encountered in scalar divide

invalid value encountered in scalar divide