{bio}[foss/2024a] fMRIPrep v25.0.0, Nipype v1.9.2#22732
{bio}[foss/2024a] fMRIPrep v25.0.0, Nipype v1.9.2#22732smoors merged 18 commits intoeasybuilders:developfrom
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Updated software
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| ('pydot', '3.0.3'), | ||
| ('NiBabel', '5.2.1'), | ||
| ('pytest-xdist', '3.6.1'), | ||
| ('poetry', '1.8.3'), |
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poetry doesn't seem needed for Nipype?
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poetry is there to fulfil one of the extensions needed for Nipype. But frankly, I do not recall anymore for which extension that was needed; maybe six or something else.
Is that an accepted justification? Or you prefer that poetry be dropped and that specific extension be added explicitly to list of extensions for Nipype? The drawback of the latter is having duplicate (versions) of the same package in one toolchain under two different PythonBundles.
But, I am open to your suggestion.
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@smoors : any updates on my question here? It would be nice to push this PR forwards.
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i just checked and indeed poetry is needed for rdflib. there is already an easyconfig available for it: RDFlib-7.0.0-GCCcore-13.3.0.eb, i suggest to just add it as dependency and remove the rdflib and isodate extensions.
note that if poetry is required it should be a build dependency, almost never a runtime dependency.
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Also looking at this (although installing against 2023a) and tried using the RDFlib dependency but it doesn't satisfy the following prov constraint:
rdflib<7,>=4.2.1
(See trungdong/prov@6f7ae21)
I'm therefore including rdflib and isodate in the bundle but adding poetry to the build deps as @smoors suggests.
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Correct. I also get the same error with prov:
>> Extension sanity check command '/software/Python/3.12.3-GCCcore-13.3.0/bin/python -c "import nipype"': OK
>> Check on requirements for installed Python packages with 'pip check': FAIL
== ... (took 15 secs)
== FAILED: Installation ended unsuccessfully: `/software/Python/3.12.3-GCCcore-13.3.0/bin/python -m pip check` failed:
prov 2.0.1 has requirement rdflib<7,>=4.2.1, but you have rdflib 7.0.0.@smoors : So, I am keeping the rdflib/6.3.2 and isodate/0.6.1 extensions as they were, but poetry is certainly belongs to the list of builddependencies. Please see 74febee.
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@boegelbot please test @ jsc-zen3 |
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@smoors: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de PR test command '
Test results coming soon (I hope)... Details- notification for comment with ID 3952008425 processed Message to humans: this is just bookkeeping information for me, |
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Test report by @boegelbot |
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@moravveji the build of fMRIPrep failed due to missing poetry, so i added it as build dep. |
…asyconfigs into fmriprep-2024a
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looks like in the meantime other versions of NiBabel and Nilearn have been merged |
This must have been fixed in e1ef2ad. |
Hmm ... apparently, there is a confusion in the CI's test step in taking the latest modifications in the fmriprep easyconfig in this PR. In ..., I am specifying I wonder if for some reason, the modified fmpriprep easyconfig in this PR is not updated on the test hosts which run the CI tests. |
…asyconfigs into fmriprep-2024a
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@boegelbot please test @ jsc-zen3 |
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@smoors: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de PR test command '
Test results coming soon (I hope)... Details- notification for comment with ID 3977141622 processed Message to humans: this is just bookkeeping information for me, |
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Test report by @boegelbot |
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@boegelbot please test @ jsc-zen3 |
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@smoors: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de PR test command '
Test results coming soon (I hope)... Details- notification for comment with ID 3977549049 processed Message to humans: this is just bookkeeping information for me, |
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Test report by @boegelbot |
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Going in, thanks @moravveji! |
Remarks:
fMRIPrep, some of dependencies had to be built with slightly older versions than the latest released ones.