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ModuleNotFoundError for nf-core v3.0.2 installed from bioconda #3257
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Found the culprit: We don't directly install Looking at the |
The bioconda version of nf-core tools produced errors when running commands that launched the trogon TUI. The reason was the missing package linkify, which gets pulled in as a dependency of textual in the PyPi build, but not in the conda-forge recipe. See https://github.com/Textualize/textual/blob/22770300252deb28d266fe4ed4766d6e2a2f5dd2/pyproject.toml#L44, https://github.com/conda-forge/textual-feedstock/blob/main/recipe/meta.yaml and nf-core/tools#3257.
I've added the missing dependency to the bioconda recipe here: bioconda/bioconda-recipes#51762. I'll also open a PR for adding it explicitly to the pip requirements file (even though it is technically not necessary as long as it remains specified as a mandatory extra component by |
The bioconda version of nf-core tools produced errors when running commands that launched the trogon TUI. The reason was the missing package linkify, which gets pulled in as a dependency of textual in the PyPi build, but not in the conda-forge recipe. See https://github.com/Textualize/textual/blob/22770300252deb28d266fe4ed4766d6e2a2f5dd2/pyproject.toml#L44, https://github.com/conda-forge/textual-feedstock/blob/main/recipe/meta.yaml and nf-core#3257.
The bioconda version of nf-core tools produced errors when running commands that launched the trogon TUI. The reason was the missing package linkify, which gets pulled in as a dependency of textual in the PyPi build, but not in the conda-forge recipe. See https://github.com/Textualize/textual/blob/22770300252deb28d266fe4ed4766d6e2a2f5dd2/pyproject.toml#L44, https://github.com/conda-forge/textual-feedstock/blob/main/recipe/meta.yaml and nf-core/tools#3257.
Also created a PR for the conda-forge recipe: conda-forge/textual-feedstock#150. If/when it gets added there, it would not strictly be necessary to add |
* Add missing linkify dependency The bioconda version of nf-core tools produced errors when running commands that launched the trogon TUI. The reason was the missing package linkify, which gets pulled in as a dependency of textual in the PyPi build, but not in the conda-forge recipe. See https://github.com/Textualize/textual/blob/22770300252deb28d266fe4ed4766d6e2a2f5dd2/pyproject.toml#L44, https://github.com/conda-forge/textual-feedstock/blob/main/recipe/meta.yaml and nf-core/tools#3257. * Pin linkify version Code Rabbit AI suggestion: The textual package version 0.71.0 depends on markdown-it-py[linkify]>=2.1.0, which in turn requires linkify-it-py>=2.0.0. However, checking the actual dependencies of markdown-it-py, it seems it wants linkify-it-py to be >=1,<3. * Update build number * fix typo --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
should be fixed now, thanks to the updated conda-forge recipe |
Description of the bug
The most recent version of nf-core tools gives me an error when running most commands like
nf-core pipelines create
, but only for the version installed from bioconda (mamba create -n nf-core && mamba install -c bioconda nf-core
), not forpip
/PyPi.From what I can tell, the problem lies with the different way in which
pip
andconda
resolve optional dependencies (https://stackoverflow.com/questions/42587385/install-extras-with-conda).Looking at the documentation for markdown-it-py, you can see that one of its optional components is
linkify
, whichpip
can pull in by specifyingmarkdown-it-py[linkify]
. I suspect this is not happening in the bioconda recipe.Proposed fix: add linkify to the bioconda recipe: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/nf-core/meta.yaml (and/or ping the trogon devs to do it too?).
System information
nf-core/tools version 3.0.2
Nextflow version 24.04.4 build 5917
Python 3.13.0
Operating System: Fedora Linux 40 (KDE Plasma)
Kernel: Linux 6.11.4-201.fc40.x86_64
Architecture: x86-64
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