Error con bundling with version 5.2

Hi,

I’m trying to compile the nodes using a new conda environment and the knime-extension-bundling=5.2. However when running the compilation, I’m getting this error:

INFO:__main__:Filling template files from /home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/bin/templates/python-extension-plugin 
and storing the resulting plugin to 
/tmp/tmpvvp617xi/com.pharmacelera.virtual_screening/src/main/python.
Using bundle name 'com.pharmacelera.virtual_screening.channel.bin'.
Using plugin template from '/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/bin/templates/conda-channel-plugin'.
Rendering plugin to '/tmp/tmpvvp617xi/com.pharmacelera.virtual_screening.channel.bin'...
Using bundle name 'com.pharmacelera.virtual_screening.channel.bin'.
Using fragment template from '/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/bin/templates/conda-channel-platform-fragment'.
Rendering fragment for linux-64 to '/tmp/tmpvvp617xi/com.pharmacelera.virtual_screening.channel.bin.linux.x86_64'...
Running 'conda-lock lock --micromamba --no-mamba -f /home/fmartin/Programs/Pharmacelera/Knime/knime-python-nodes/virtual_screening/my_conda_env.yml -c knime -c conda-forge -p linux-64 --lockfile /tmp/tmpo8f3bch4/lockfile'...
Running command failed with exit code 1. Standard output: '' Standard error: '/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/pydantic/_internal/_config.py:322: UserWarning: Valid config keys have changed in V2:
* 'allow_mutation' has been removed
  warnings.warn(message, UserWarning)
Traceback (most recent call last):
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/bin/conda-lock", line 10, in <module>
    sys.exit(main())
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/conda_lock/conda_lock.py", line 1332, in lock
    lock_func(
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/conda_lock/conda_lock.py", line 1037, in run_lock
    _conda_exe = determine_conda_executable(
  File "/home/fmartin/Programs/miniconda3/envs/knime-ext-bundling/lib/python3.9/site-packages/conda_lock/invoke_conda.py", line 59, in determine_conda_executable
    if determine_micromamba_version(str(candidate)) < LooseVersion("0.17"):
TypeError: '<' not supported between instances of 'Version' and 'LooseVersion'
'

This works with my previous conda environment using the 5.1 or 4.7. Any help? I’ve tried to follow this issue but I don’t see any solution here: UnicodeDecodeError When Bundling Pure-Python Extension - #2 by nemad

Kind regards,
Fernando

1 Like

Hi @fmgarcia85,

Thank you for your report! This is a bug in conda-lock due to a recent change in ensureconda. I opened a bug ticket at conda-lock: conda-lock fails with micromamba and ensureconda 1.4.4 · Issue #596 · conda/conda-lock · GitHub.

As a workaround, you can fix the version of ensureconda to 1.4.3 for now:

conda create -n <env-name> -c knime -c conda-forge knime-extension-bundling=5.2 ensureconda=1.4.3
4 Likes