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shelley-bio-batch crashes with AttributeError: 'str' object has no attribute 'substitute' #5

@Mitchob

Description

@Mitchob

Description

Running shelley-bio-batch with multiple tools causes a crash during table rendering via rich.
The tool starts correctly and displays the header UI, but fails when attempting to render the tools table. I have no current workaround.

Command tested:

shelley-bio-batch samtools fastqc bowtie2

Expected Behavior

  • Display the tools table
  • Proceed with building modules for the listed tools

but It crashes with the following traceback:

Traceback (most recent call last):
  File "/usr/local/bin/shelley-bio-batch", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/opt/shelley-bio/bin/shelley-bio-batch", line 16, in <module>
    main()
  File "/opt/shelley-bio/shelley_bio/scripts/batch_builder.py", line 160, in main
    sys.exit(batch_build_modules(tools))
  File "/opt/shelley-bio/shelley_bio/scripts/batch_builder.py", line 94, in batch_build_modules
    console.print(tools_table)
  File "/usr/local/lib/python3.10/dist-packages/rich/console.py", line 1724, in print
    extend(render(renderable, render_options))
  File "/usr/local/lib/python3.10/dist-packages/rich/console.py", line 1345, in render
    for render_output in iter_render:
  File "/usr/local/lib/python3.10/dist-packages/rich/table.py", line 515, in __rich_console__
    yield from self._render(console, render_options, widths)
  File "/usr/local/lib/python3.10/dist-packages/rich/table.py", line 768, in _render
    self.box.substitute(
AttributeError: 'str' object has no attribute 'substitute'

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