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new fd8e1f3e65 gnu: python-pytorch-geometric: Update to commit 85cf9fc.
fd8e1f3e65 is described below
commit fd8e1f3e65696b834ba1f56180b0a9a0b03490a8
Author: David Elsing <[email protected]>
AuthorDate: Fri Jul 11 20:54:39 2025 +0200
gnu: python-pytorch-geometric: Update to commit 85cf9fc.
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 <[email protected]>
---
gnu/packages/machine-learning.scm | 172 +++++++++++++++++++-------------------
1 file changed, 88 insertions(+), 84 deletions(-)
diff --git a/gnu/packages/machine-learning.scm
b/gnu/packages/machine-learning.scm
index a058efc5c2..91c1616bc7 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -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 [email protected]
- ;; 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 [email protected]
+ ;; 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
