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gnu: python-pytorch-geometric: Update to commit 85cf9fc.

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Fixes guix/guix#1043.

* gnu/packages/machine-learning.scm (python-pytorch-geometric): Update to
commit 85cf9fc.
[arguments]: Fix the 'delete-top-level-directories phase.
[propagated-inputs]: Add python-xxhash.

Signed-off-by: Andreas Enge <andreas@enge.fr>
This commit is contained in:
David Elsing 2025-07-11 20:54:39 +02:00 • committed by Andreas Enge
parent baba8a4370
commit fd8e1f3e65
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1 changed files with 88 additions and 84 deletions
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gnu/packages/machine-learning.scm
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@ -89,6 +89,7 @@
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages dejagnu)
#:use-module (gnu packages digest)
#:use-module (gnu packages documentation)
#:use-module (gnu packages freedesktop)
#:use-module (gnu packages gcc)
@ -5461,91 +5462,94 @@ Note: currently this package does not provide GPU support.")
python-sympy)))))
(define-public python-pytorch-geometric
(package
(name "python-pytorch-geometric")
(version "2.6.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pyg-team/pytorch_geometric/")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0dbxz9d22vzm7fr9kgg66hj3sf8ag2ly8qky58cxvn1hyjl5h3v7"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
;; Hangs with AttributeError: 'NoneType' object has no attribute 'rpc_async'
'(list "--ignore=test/distributed/test_rpc.py"
;; A message passing jinja template is missing
"--ignore=test/nn/conv/test_message_passing.py"
"--ignore=test/nn/test_sequential.py"
"--ignore=test/nn/models/test_basic_gnn.py"
;; These all fail with a size mismatch error such as
;; RuntimeError: shape '[-1, 2, 1, 1]' is invalid for input of size 3
"--ignore=test/explain/algorithm/test_captum_explainer.py"
;; Requires the nonfree MKL on CPU.
"--ignore=test/nn/models/test_graph_unet.py"
"-k" (string-append
;; Permissions error
"not test_packaging"
;; Unknown multiprocessing failure
" and not test_data_share_memory"
;; This can fail due to accuracy problems
" and not test_gdc"
;; These refuse to be run on CPU and really want a GPU
" and not test_add_random_walk_pe"
" and not test_asap"
" and not test_two_hop"
;; Failed when switched to python@3.11
;; typing module internals
" and not test_type_repr"))
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'delete-top-level-directories
(lambda _
;; The presence of these directories confuses the pyproject build
;; system.
(for-each delete-file-recursively
'("conda" "docker" "graphgym")))))))
(propagated-inputs
(list onnx
python-captum
python-graphviz
python-h5py
python-jinja2
python-matplotlib
python-networkx
python-numba
python-numpy
python-opt-einsum
python-pandas
python-protobuf
python-psutil
python-pyparsing
python-pytorch-lightning
python-rdflib
python-requests
python-scikit-image
python-scikit-learn
python-scipy
python-statsmodels
python-sympy
python-tabulate
python-torchmetrics
python-tqdm))
(native-inputs
(list python-flit-core
python-pytest
python-pytest-cov))
(home-page "https://pyg.org")
(synopsis "Graph Neural Network library for PyTorch")
(description
"PyG is a library built upon PyTorch to easily write and train Graph
(let ((commit "85cf9fc12b1138c1f2adbed8a761356c3f4197e7")
(revision "0"))
(package
(name "python-pytorch-geometric")
(version (git-version "2.6.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pyg-team/pytorch_geometric/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"104v3w9yv7akyxpyd8aq85mw1mncql8mvr1p1b34ph09csqh68hq"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
;; Hangs with AttributeError: 'NoneType' object has no attribute 'rpc_async'
'(list "--ignore=test/distributed/test_rpc.py"
;; A message passing jinja template is missing
"--ignore=test/nn/conv/test_message_passing.py"
"--ignore=test/nn/test_sequential.py"
"--ignore=test/nn/models/test_basic_gnn.py"
;; These all fail with a size mismatch error such as
;; RuntimeError: shape '[-1, 2, 1, 1]' is invalid for input of size 3
"--ignore=test/explain/algorithm/test_captum_explainer.py"
;; Requires the nonfree MKL on CPU.
"--ignore=test/nn/models/test_graph_unet.py"
"-k" (string-append
;; Permissions error
"not test_packaging"
;; Unknown multiprocessing failure
" and not test_data_share_memory"
;; This can fail due to accuracy problems
" and not test_gdc"
;; These refuse to be run on CPU and really want a GPU
" and not test_add_random_walk_pe"
" and not test_asap"
" and not test_two_hop"
;; Failed when switched to python@3.11
;; typing module internals
" and not test_type_repr"))
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'delete-top-level-directories
(lambda _
;; The presence of these directories confuses the pyproject build
;; system.
(for-each delete-file-recursively
'("docker" "graphgym")))))))
(propagated-inputs
(list onnx
python-captum
python-graphviz
python-h5py
python-jinja2
python-matplotlib
python-networkx
python-numba
python-numpy
python-opt-einsum
python-pandas
python-protobuf
python-psutil
python-pyparsing
python-pytorch-lightning
python-rdflib
python-requests
python-scikit-image
python-scikit-learn
python-scipy
python-statsmodels
python-sympy
python-tabulate
python-torchmetrics
python-tqdm
python-xxhash))
(native-inputs
(list python-flit-core-next
python-pytest
python-pytest-cov))
(home-page "https://pyg.org")
(synopsis "Graph Neural Network library for PyTorch")
(description
"PyG is a library built upon PyTorch to easily write and train Graph
Neural Networks for a wide range of applications related to structured data.")
(license license:expat)))
(license license:expat))))
(define-public python-lightning-cloud
(package