anybody got their conda CI tests failing with late...
# toolss
Sateesh_Peri
12/04/2025, 7:35 AManybody got their conda CI tests failing with latest multiqc update ? related PR
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Phil Ewels
12/04/2025, 8:08 AMThis is new to me. Claude thinks that it's a problem with Python 3.14:
> This is a Python 3.14 compatibility issue. The key indicator is in the path:
Copy codelib/python3.14/site-packages/
Python 3.14 is currently in alpha (scheduled for release October 2025), and thepackage isn't compatible with it yet. The specific failure is in the dataclasses implementation:networkx
```File ".../lib/python3.14/dataclasses.py", line 1401, in _add_slots
init_annotate = newcls.init.annotate
AttributeError: 'wrapper_descriptor' object has no attribute '__annotate__'```
The dependency chain causing the failure is:→multiqc→spectra→colormath→ 💥networkx
Phil Ewels
12/04/2025, 8:10 AMBut I have CI tests running with Python 3.14 and they're fine: https://github.com/MultiQC/MultiQC/actions/runs/19822611230/job/56788237418
Phil Ewels
12/04/2025, 8:11 AMThe difference is likely conda resolving older package versions vs pip getting the latest.
Looking at the dependency chain again:
Copy codemultiqc → spectra → colormath → networkx
MultiQC's CI probably uses pip which pulls the latest(3.4+ has Python 3.14 fixes), while the conda environment in nf-core/methylseq is likely resolving an oldernetworkxversion that predates 3.14 compatibility.networkx
You can verify by checking what networkx version conda resolved in that environment. The fix would be ensuring the conda environment specs for the MultiQC module pinor similar.networkx>=3.4
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Sateesh_Peri
12/04/2025, 8:14 AM> The fix would be ensuring the conda environment specs for the MultiQC module pinor similar.networkx>=3.4
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Phil Ewels
12/04/2025, 8:16 AMHmm, the Wave build looks ok though. Has
networkx-3.5Phil Ewels
12/04/2025, 8:17 AMoh wait, it's only the conda CI tests that are failing - not docker
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Sateesh_Peri
12/04/2025, 8:17 AMyup
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Phil Ewels
12/04/2025, 8:20 AMBit of a roadblock. Maybe see if you can reproduce in a codespace / interactive environment? Then try to dig out the conda installation lockfile / logs?
Phil Ewels
12/04/2025, 8:21 AMIt smells like some kind of transient version incompatibility issue, but difficult to tell
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Maxime Garcia
12/04/2025, 8:56 AMohno2
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Phil Ewels
12/04/2025, 8:57 AMIf anyone is able to repro, I can try to look into it more
Phil Ewels
12/04/2025, 9:16 AMah, let's continue here.
Phil Ewels
12/05/2025, 11:23 AMShould be resolved any minute, due to https://github.com/bioconda/bioconda-recipes/pull/61143
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Sateesh_Peri
12/05/2025, 11:39 AMsanta in town
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