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khanlab / SPIMprep

A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
MIT License
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python3.12 and invalid escape sequences #23

Open akhanf opened 5 months ago

akhanf commented 5 months ago

python3.12 builds are failing -- will disable this version for now, but for future reference:

Run poetry run snakemake -np
/home/runner/.cache/pypoetry/virtualenvs/spimprep-8bLgKwXL-py3.12/lib/python3.12/site-packages/pulp/apis/xpress_api.py:322: SyntaxWarning: invalid escape sequence '\ '
  """
/home/runner/work/SPIMprep/SPIMprep/workflow/rules/common.smk:126: SyntaxWarning: invalid escape sequence '\+'
  f"sed 's/-Xmx[0-9a-z]\+/-Xmx{resources.mem_mb}m -Xms{resources.mem_mb}m/'"
NameError in file /home/runner/work/SPIMprep/SPIMprep/workflow/rules/ome_zarr.smk, line 59:
name 'prefix' is not defined
  File "/home/runner/work/SPIMprep/SPIMprep/workflow/Snakefile", line 50, in <module>
  File "/home/runner/work/SPIMprep/SPIMprep/workflow/rules/ome_zarr.smk", line 59, in <module>
Error: Process completed with exit code 1.