Open ns-rse opened 3 months ago
Current state of failed tests is shown below (not sure if this is an improvement or not :laughing: !).
SKIPPED [1] tests/test_utils.py:674: awaiting test development
SKIPPED [2] tests/tracing/test_dnatracing_single_grain.py:157: Need to correctly prune arrays first.
SKIPPED [2] tests/tracing/test_dnatracing_single_grain.py:178: Need to correctly prune arrays first.
SKIPPED [2] tests/tracing/test_dnatracing_single_grain.py:209: Need to correctly prune arrays first.
SKIPPED [2] tests/tracing/test_dnatracing_single_grain.py:230: Need to correctly prune arrays first.
SKIPPED [2] tests/tracing/test_dnatracing_single_grain.py:306: Need to correctly prune arrays first.
SKIPPED [2] tests/tracing/test_dnatracing_single_grain.py:347: Need to correctly prune arrays first.
SKIPPED [2] tests/tracing/test_dnatracing_single_grain.py:376: Need to correctly prune arrays first.
SKIPPED [4] tests/tracing/test_dnatracing_single_grain.py:254: Need to correctly prune arrays first.
SKIPPED [2] tests/tracing/test_dnatracing_single_grain.py:278: Need to correctly prune arrays first.
SKIPPED [2] tests/tracing/test_pruning.py: two branches at the end does not have 'nibs' removed by the rm_nibs() function, instead a T-shaped junction remains. This is only removed by calling getSkeleton(method='zhang').get_skeleton() which is done under the prune_all_skeletons() method but this method is is to be removed since looping over all skeletons is outside of the scope/remit of the code and handled in process_scan().
SKIPPED [1] tests/tracing/test_pruning.py: unconditional skip
XFAIL tests/tracing/test_pruning.py::test_local_area_sum[3x3 1's; point on top edge] - Point on top edge of image.
XFAIL tests/tracing/test_pruning.py::test_local_area_sum[3x3 non-binary array; point as list] - Array is not binary.
XFAIL tests/tracing/test_pruning.py::test_local_area_sum[3x3 1's; point on left edge] - Point on left edge of image.
XFAIL tests/tracing/test_pruning.py::test_local_area_sum[3x3 1's; point on bottom edge] - Point on bottom edge of image.
XFAIL tests/tracing/test_pruning.py::test_local_area_sum[3x3 1's; point on right edge] - Point on right edge of image.
XFAIL tests/tracing/test_pruning.py::test_local_area_sum[3x3 1's; point on corner] - Point on corner of image.
ERROR tests/tracing/test_dnatracing_single_grain.py::test_gaussian_filter[linear molecule] - KeyError: 'dnatracing'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_get_disordered_trace[linear molecule, skeletonise zhang] - KeyError: 'dnatracing'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_gaussian_filter[circular molecule] - KeyError: 'dnatracing'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_get_disordered_trace[circular molecule, skeletonise zhang] - KeyError: 'dnatracing'
ERROR tests/tracing/test_nodestats.py::test_analyse_nodes - TypeError: nodeStats.__init__() missing 1 required positional argument: 'pair_odd_branches'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_get_disordered_trace[linear molecule, skeletonise topostats] - KeyError: 'dnatracing'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_get_disordered_trace[linear molecule, skeletonise lee] - KeyError: 'dnatracing'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_get_disordered_trace[circular molecule, skeletonise lee] - KeyError: 'dnatracing'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_get_disordered_trace[circular molecule, skeletonise topostats] - KeyError: 'dnatracing'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_get_disordered_trace[linear molecule, skeletonise thin] - KeyError: 'dnatracing'
ERROR tests/tracing/test_dnatracing_single_grain.py::test_get_disordered_trace[circular molecule, skeletonise thin] - KeyError: 'dnatracing'
FAILED tests/test_utils.py::test_udpate_plotting_config_adding_required_options[DPI None in main, extracted channel DPI should stay at 100] - KeyError: 'core_set'
FAILED tests/test_utils.py::test_udpate_plotting_config_adding_required_options[DPI 600 in main, extracted channel DPI should update to 600] - KeyError: 'core_set'
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[diagonal2] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[vertical] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/test_utils.py::test_create_empty_dataframe - AssertionError: assert equals failed
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[diagonal3] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[horizontal] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[circle] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[diagonal1] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_get_splined_traces[trace_image0-1.0-True-0.0-expected_spline_image0] - TypeError: dnaTrace.get_splined_traces() missing 2 required positional arguments: 'fitted_trace' and 'mol_is_circular'
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[double_L] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[blob] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_get_splined_traces[trace_image5-4.0-False-5.0-expected_spline_image5] - TypeError: dnaTrace.get_splined_traces() missing 2 required positional arguments: 'fitted_trace' and 'mol_is_circular'
FAILED tests/tracing/test_dnatracing_methods.py::test_get_splined_traces[trace_image1-1.0-True-10.0-expected_spline_image1] - TypeError: dnaTrace.get_splined_traces() missing 2 required positional arguments: 'fitted_trace' and 'mol_is_circular'
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[diagonal_end_single_L] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[cross] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_get_splined_traces[trace_image6-5.0-False-0.0-expected_spline_image6] - TypeError: dnaTrace.get_splined_traces() missing 2 required positional arguments: 'fitted_trace' and 'mol_is_circular'
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[diagonal_end_straight] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[singl_L] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_get_splined_traces[trace_image2-10.0-True-0.0-expected_spline_image2] - TypeError: dnaTrace.get_splined_traces() missing 2 required positional arguments: 'fitted_trace' and 'mol_is_circular'
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[figure8] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_get_splined_traces[trace_image7-5.0-False-5.0-expected_spline_image7] - TypeError: dnaTrace.get_splined_traces() missing 2 required positional arguments: 'fitted_trace' and 'mol_is_circular'
FAILED tests/tracing/test_dnatracing_methods.py::test_get_splined_traces[trace_image3-10.0-True-5.0-expected_spline_image3] - TypeError: dnaTrace.get_splined_traces() missing 2 required positional arguments: 'fitted_trace' and 'mol_is_circular'
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[three_ends] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_dnatracing_methods.py::test_get_splined_traces[trace_image4-5.0-False-5.0-expected_spline_image4] - TypeError: dnaTrace.get_splined_traces() missing 2 required positional arguments: 'fitted_trace' and 'mol_is_circular'
FAILED tests/tracing/test_dnatracing_methods.py::test_linear_or_circular[six_ends] - AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
FAILED tests/tracing/test_nodestats.py::test_connect_extended_nodes_nearest[theta_grain] - TypeError: nodeStats.__init__() missing 1 required positional argument: 'pair_odd_branches'
FAILED tests/tracing/test_nodestats.py::test_connect_extended_nodes_nearest[figure_8] - TypeError: nodeStats.__init__() missing 1 required positional argument: 'pair_odd_branches'
FAILED tests/tracing/test_nodestats.py::test_add_branches_to_labelled_image[branch_under_over_order0-catenane_node_0_matched_branches_analyse_node_branches.pkl-catenane_node_0_masked_image.pkl-branch_start_coords0-catenane_node_0_ordered_branches.pkl-pairs0-True-image_shape0-catenane_node_0_branch_image.npy-catenane_node_0_avg_image.npy] - FileNotFoundError: [Errno 2] No such file or directory: '/home/neil/work/git/hub/AFM-SPM/TopoStats/tests/resources/catenane_node_0_branch_image.npy'
FAILED tests/tracing/test_nodestats.py::test_analyse_node_branches[node 0] - FileNotFoundError: [Errno 2] No such file or directory: '/home/neil/work/git/hub/AFM-SPM/TopoStats/tests/resources/catenane_node_0_reduced_node_area.npy'
FAILED tests/test_processing.py::test_process_stages[Only filtering enabled] - AssertionError: assert 'Detection of grains disabled, returning empty data frame.' in 'INFO topostats:processing.py:858 Processing : minicircle_small\nINFO topostats:processing.py:78 [minicircle_small] Image dimensions: (64, 64...
FAILED tests/test_processing.py::test_process_scan_align_grainstats_dnatracing - KeyError: 'dnatracing'
FAILED tests/test_processing.py::test_run_grainstats - AssertionError: assert 22 == 21
FAILED tests/test_processing.py::test_process_scan_below
FAILED tests/test_processing.py::test_process_scan_above
FAILED tests/test_processing.py::test_process_scan_both - AssertionError: assert equals failed
FAILED tests/test_run_topostats.py::test_run_topostats_process_debug
Whilst working on writing unit tests for
maxgamill-sheffield/800-better-tracing
which addresses #800 I found that the tests suite does not complete as there are a number of breaking changes.In total there are 61 tests fail, output with basic details are below...
Many of these are
unexpected keyword argument
which suggests one of a few things...Common keyword arguments that crop up repeatedly in errors and possible causes/problems and other types of errors are listed below.
skeletonisation_method
- which is a new argument introduced in this branch but not updated in many test files (by far the most common cause of errors/failures).countNeighbours
- looks like an old function of thegenTracingFuncs
module that has been moved/renamed/removed.AttributeError: 'dnaTrace' object has no attribute 'mol_is_circular'. Did you mean: 'mol_is_circulars'?
- looks like a renaming issue where plural is now used, should be easy to correct.KeyError : 'green_black' is not a known colormap name
- a new colormap introduced in some manner, probably needs to be defined intopostats/theme.py
although it does have a newblu_purp_green
colormap included so perhaps what is required isgreen_black
>blu_purp_green
(personally I would favor not using abbreviations tab-auto-complete saves typing and full names are easier to remember than abbreviations soblue_purple_green
).IndexError
- crops up intest_processing.py::test_process_scan_align_grainstats_dnatracing
test_plottingfuncs.py
do not match the existing images this will need investigating and resolving.