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ReproNim / neurodocker

Generate custom Docker and Singularity images, and minimize existing containers
https://www.repronim.org/neurodocker/
Apache License 2.0
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using copy command in Neurodocker leads to failed to process "'": unexpected end of statement while looking for matching single-quote error #504

Closed stebo85 closed 1 year ago

stebo85 commented 1 year ago

I am using the neurodocker command "copy" to add a readme file to the containers being build:

--copy README.md /README.md \

Since the latest changes in neurodocker this step now fails with

Step 23/26 : COPY ["(", "'", "R", "E", "A", "D", "M", "E", ".", "m", "d", "'", ",", " ", "'", "/", "R", "E", "A", "D", "M", "E", ".", "m", "d", "'", ")"] failed to process "'": unexpected end of statement while looking for matching single-quote

Does anyone by any chance have an idea what that could be?

It might also be totally unrelated to neurodocker and caused by any other recent changes - just wondering if anyone has an idea before I spend more time on this rabbit hole :p

Remi-Gau commented 1 year ago

Should have been patched today already in version 0.9.4.

satra commented 1 year ago

@stebo85 - before you update can you quickly check that your previous command now raises an exception about a bad version?

stebo85 commented 1 year ago

ahh, wonderful!

Both things are working:

0.9.3 gives a warning:

WARNING: The candidate selected for download or install is a yanked version: 'neurodocker' candidate (version 0.9.3 at https://files.pythonhosted.org/packages/82/ac/47382cd88ba5dafb8c4f052ef423052d822c4bb24a2bcb67e44bace4b299/neurodocker-0.9.3-py3-none-any.whl#sha256=e7cf18baa41a387437d08cfd634ec9de628844c4ba5ecf8fb16de0c7134c60a8 (from https://pypi.org/simple/neurodocker/) (requires-python:>=3.8)) Reason for being yanked: Bug in --copy and --entrypoint options

and 0.9.4 fixed the problem :)

Sorry - I should have tried updating first

Thank you Steffen