TypeError: gridplot() got an unexpected keyword argument 'plot_width'

[BartoszDombrow]

Hello,

I have an error:

Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.12/bin/nanoQC", line 8, in sys.exit(main()) ^^^^^^ File "/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/nanoQC/nanoQC.py", line 43, in main save(gridplot(children=[[hist], seq_plots, qual_plots], ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: gridplot() got an unexpected keyword argument 'plot_width'

Could you please help me with that issue?

Python 3.12.1 nanoQC 0.9.4

[weronikajaskowiak]

Hello, I have also encountered this problem, Python 2.7.18 and NanoQC 0.9.4 I would appreciate your help.

[pelutz]

Same error here:

Traceback (most recent call last): File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/bin/nanoQC", line 8, in sys.exit(main()) ^^^^^^ File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/nanoQC/nanoQC.py", line 43, in main save(gridplot(children=[[hist], seq_plots, qual_plots], ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: gridplot() got an unexpected keyword argument 'plot_width'

The NanoQC.log indicated: 2024-09-08 21:27:10,217 NanoQC started. 2024-09-08 22:06:44,937 Extracting nucleotides and quality scores. 2024-09-08 22:54:07,539 Using 4280008 reads with a minimum length of 200bp for plotting 2024-09-08 22:54:07,540 Creating plots... 2024-09-08 22:59:29,158 Per base sequence content and quality completed.

I had installed nanoqc 0.9.4 in a Conda environment using pip (installation did not work via bioconda), along with python 3.12.5 and bokeh 3.0.0, on a Red Hat linux server. Since apparently plot_width has been replaced by width as of bokeh 3.0.0, I tried to downgrade bokeh to v2.4.3, but got another (much earlier) error:

Traceback (most recent call last): File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/bin/nanoQC", line 5, in from nanoQC.nanoQC import main File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/nanoQC/nanoQC.py", line 10, in from bokeh.plotting import figure, save, output_file File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/bokeh/plotting/init.py", line 22, in from . import figure as _figure ; _figure ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/bokeh/plotting/figure.py", line 25, in from ..core.properties import ( File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/bokeh/core/properties.py", line 273, in from .property.auto import Auto; Auto ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/bokeh/core/property/auto.py", line 24, in from .enum import Enum File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/bokeh/core/property/enum.py", line 27, in from .primitive import String File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/bokeh/core/property/primitive.py", line 37, in bokeh_bool_types += (np.bool8,) ^^^^^^^^ File "/home2020/home/inci/plutz/miniforge3/envs/nanoqc/lib/python3.12/site-packages/numpy/init.py", line 414, in getattr raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'bool8'. Did you mean: 'bool'?

Thanks in advance for your help, Best, PE

[jtamames]

Same here. Anybody there caring about issues?

[wdecoster]

Thank you for your patience. This should be solved in v0.10.0!