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-rw-r--r--gnu/packages/astronomy.scm6
-rw-r--r--gnu/packages/bioinformatics.scm10
-rw-r--r--gnu/packages/chemistry.scm2
-rw-r--r--gnu/packages/computer-architecture.scm2
-rw-r--r--gnu/packages/duckdb.scm2
-rw-r--r--gnu/packages/electronics.scm4
-rw-r--r--gnu/packages/engineering.scm2
-rw-r--r--gnu/packages/geo.scm2
-rw-r--r--gnu/packages/graphics.scm4
-rw-r--r--gnu/packages/image-processing.scm2
-rw-r--r--gnu/packages/machine-learning.scm26
-rw-r--r--gnu/packages/maths.scm4
-rw-r--r--gnu/packages/networking.scm2
-rw-r--r--gnu/packages/opencl.scm2
-rw-r--r--gnu/packages/package-management.scm2
-rw-r--r--gnu/packages/physics.scm4
-rw-r--r--gnu/packages/python-check.scm2
-rw-r--r--gnu/packages/python-science.scm22
-rw-r--r--gnu/packages/python-xyz.scm16
-rw-r--r--gnu/packages/radio.scm12
-rw-r--r--gnu/packages/simulation.scm4
-rw-r--r--gnu/packages/statistics.scm4
-rw-r--r--gnu/packages/syndication.scm2
23 files changed, 69 insertions, 69 deletions
diff --git a/gnu/packages/astronomy.scm b/gnu/packages/astronomy.scm
index ad18ea1f4d6..c8ccce936b5 100644
--- a/gnu/packages/astronomy.scm
+++ b/gnu/packages/astronomy.scm
@@ -257,7 +257,7 @@ reused in several astronomical applications, such as @code{wsclean},
257 boost 257 boost
258 pkg-config 258 pkg-config
259 python 259 python
260 pybind11)) 260 pybind11-2))
261 (inputs 261 (inputs
262 (list casacore 262 (list casacore
263 cfitsio 263 cfitsio
@@ -5112,7 +5112,7 @@ CFITSIO library. Among other things, it can
5112 (list eigen 5112 (list eigen
5113 fftw)) 5113 fftw))
5114 (propagated-inputs 5114 (propagated-inputs
5115 (list pybind11 ;XXX: Double check if it needs be here. 5115 (list pybind11-2 ;XXX: Double check if it needs be here.
5116 python-astropy 5116 python-astropy
5117 python-lsstdesc-coord 5117 python-lsstdesc-coord
5118 python-numpy)) 5118 python-numpy))
@@ -7557,7 +7557,7 @@ and the Generalized Lomb-Scargle periodogram
7557 (build-system pyproject-build-system) 7557 (build-system pyproject-build-system)
7558 (native-inputs 7558 (native-inputs
7559 (list cmake-minimal 7559 (list cmake-minimal
7560 pybind11 7560 pybind11-2
7561 python-pandas 7561 python-pandas
7562 python-pytest 7562 python-pytest
7563 python-scipy 7563 python-scipy
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a08d9846cdd..88a4174b28f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3252,7 +3252,7 @@ and gene expression visualization.")
3252 python-scipy 3252 python-scipy
3253 python-threadpoolctl 3253 python-threadpoolctl
3254 python-umap-learn)) 3254 python-umap-learn))
3255 (native-inputs (list pybind11 python-pytest python-setuptools)) 3255 (native-inputs (list pybind11-2 python-pytest python-setuptools))
3256 (home-page "https://github.com/tanaylab/metacells.git") 3256 (home-page "https://github.com/tanaylab/metacells.git")
3257 (synopsis "Single-cell RNA Sequencing Analysis") 3257 (synopsis "Single-cell RNA Sequencing Analysis")
3258 (description "The metacells package implements the improved metacell 3258 (description "The metacells package implements the improved metacell
@@ -23875,7 +23875,7 @@ instruments, or Pacific Biosciences RSII or Sequel sequencers.")
23875 (inputs 23875 (inputs
23876 (list curl zlib)) 23876 (list curl zlib))
23877 (propagated-inputs 23877 (propagated-inputs
23878 (list pybind11)) 23878 (list pybind11-2))
23879 (home-page "https://github.com/aidenlab/straw") 23879 (home-page "https://github.com/aidenlab/straw")
23880 (synopsis "Stream data from .hic files") 23880 (synopsis "Stream data from .hic files")
23881 (description "Straw is library which allows rapid streaming of contact 23881 (description "Straw is library which allows rapid streaming of contact
@@ -24006,7 +24006,7 @@ e.g. from GenBank or Gff files, or Biopython SeqRecords.")
24006 ;; dependencies. 24006 ;; dependencies.
24007 (delete 'sanity-check)))) 24007 (delete 'sanity-check))))
24008 (native-inputs 24008 (native-inputs
24009 (list pybind11 24009 (list pybind11-2
24010 python-pytest 24010 python-pytest
24011 python-pypairix 24011 python-pypairix
24012 python-setuptools 24012 python-setuptools
@@ -24072,7 +24072,7 @@ browser.")
24072 "-DCMAKE_CXX_FLAGS=\"-I ../vendor/cereal/include/\" -fPIC" 24072 "-DCMAKE_CXX_FLAGS=\"-I ../vendor/cereal/include/\" -fPIC"
24073 "..") 24073 "..")
24074 (invoke "make"))))))) 24074 (invoke "make")))))))
24075 (propagated-inputs (list pybind11)) 24075 (propagated-inputs (list pybind11-2))
24076 (native-inputs (list cmake-minimal python-setuptools)) 24076 (native-inputs (list cmake-minimal python-setuptools))
24077 (home-page "https://github.com/nanoporetech/pyspoa") 24077 (home-page "https://github.com/nanoporetech/pyspoa")
24078 (synopsis "Python bindings for the SIMD partial order alignment library") 24078 (synopsis "Python bindings for the SIMD partial order alignment library")
@@ -24159,7 +24159,7 @@ aligner.")
24159 python-scipy 24159 python-scipy
24160 python-umap-learn 24160 python-umap-learn
24161 ;; [optional] 24161 ;; [optional]
24162 pybind11 24162 pybind11-2
24163 python-hnswlib 24163 python-hnswlib
24164 python-igraph 24164 python-igraph
24165 python-louvain)) 24165 python-louvain))
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index b487f9e1a4a..e9e6a97f9ad 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -100,7 +100,7 @@
100 mmtf-cpp 100 mmtf-cpp
101 googletest 101 googletest
102 pkg-config 102 pkg-config
103 pybind11)) 103 pybind11-2))
104 (inputs 104 (inputs
105 `(("glew" ,glew) 105 `(("glew" ,glew)
106 ("libarchive" ,libarchive) 106 ("libarchive" ,libarchive)
diff --git a/gnu/packages/computer-architecture.scm b/gnu/packages/computer-architecture.scm
index d4f4a4e2b1a..277a92e1d47 100644
--- a/gnu/packages/computer-architecture.scm
+++ b/gnu/packages/computer-architecture.scm
@@ -136,7 +136,7 @@
136 hdf5 136 hdf5
137 libpng 137 libpng
138 protobuf 138 protobuf
139 pybind11 139 pybind11-2
140 python 140 python
141 python-ply 141 python-ply
142 python-pydot 142 python-pydot
diff --git a/gnu/packages/duckdb.scm b/gnu/packages/duckdb.scm
index 5d65e27c4c1..e965f302a97 100644
--- a/gnu/packages/duckdb.scm
+++ b/gnu/packages/duckdb.scm
@@ -129,7 +129,7 @@ single-file databases with support for secondary indexes.")
129 (propagated-inputs 129 (propagated-inputs
130 (list python-adbc-driver-manager)) 130 (list python-adbc-driver-manager))
131 (native-inputs 131 (native-inputs
132 (list pybind11 132 (list pybind11-2
133 python-fsspec 133 python-fsspec
134 ;; python-google-cloud-storage ;python-grpcio fails (see: guix/guix#1436) 134 ;; python-google-cloud-storage ;python-grpcio fails (see: guix/guix#1436)
135 python-numpy 135 python-numpy
diff --git a/gnu/packages/electronics.scm b/gnu/packages/electronics.scm
index 775a3cf5b43..356348eadc1 100644
--- a/gnu/packages/electronics.scm
+++ b/gnu/packages/electronics.scm
@@ -1740,7 +1740,7 @@ layout of a circuit corresponds to the desired netlists.")
1740 (inputs 1740 (inputs
1741 (list boost 1741 (list boost
1742 eigen 1742 eigen
1743 pybind11 1743 pybind11-2
1744 qtimgui)) 1744 qtimgui))
1745 (synopsis 1745 (synopsis
1746 "Place-and-Route tool for @acronym{FPGA, Field Programmable Gate Array}") 1746 "Place-and-Route tool for @acronym{FPGA, Field Programmable Gate Array}")
@@ -2084,7 +2084,7 @@ architecture from Cologne Chip. It also provides data needed to produce a
2084 (lambda _ 2084 (lambda _
2085 (chdir "libtrellis")))))) 2085 (chdir "libtrellis"))))))
2086 (native-inputs (list python-minimal-wrapper)) 2086 (native-inputs (list python-minimal-wrapper))
2087 (inputs (list openocd boost-1.88 pybind11)) 2087 (inputs (list openocd boost-1.88 pybind11-2))
2088 (synopsis "Placement and routing for ECP5 FPGAs") 2088 (synopsis "Placement and routing for ECP5 FPGAs")
2089 (description 2089 (description
2090 "Project Trellis is a Nextpnr backend compatible with ECP5 FPGAs. 2090 "Project Trellis is a Nextpnr backend compatible with ECP5 FPGAs.
diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm
index e95d8c88cda..599eb0c248a 100644
--- a/gnu/packages/engineering.scm
+++ b/gnu/packages/engineering.scm
@@ -5298,7 +5298,7 @@ forward kinematics solvers.")
5298 (source 5298 (source
5299 (origin 5299 (origin
5300 (inherit (package-source orocos-kinematics-dynamics)))) 5300 (inherit (package-source orocos-kinematics-dynamics))))
5301 (native-inputs (list python pybind11 python-psutil)) 5301 (native-inputs (list python pybind11-2 python-psutil))
5302 (inputs (list orocos-kinematics-dynamics)) 5302 (inputs (list orocos-kinematics-dynamics))
5303 (arguments 5303 (arguments
5304 (list 5304 (list
diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index cdd5a91e492..f03e847d2c6 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -941,7 +941,7 @@ OpenGeoSys")
941 (native-inputs 941 (native-inputs
942 (list git 942 (list git
943 ninja 943 ninja
944 pybind11)) 944 pybind11-2))
945 (inputs 945 (inputs
946 (list boost 946 (list boost
947 eigen 947 eigen
diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm
index 47b1aadf363..452a0f2cfaf 100644
--- a/gnu/packages/graphics.scm
+++ b/gnu/packages/graphics.scm
@@ -916,7 +916,7 @@ baking tools to produce normal maps.")
916 clang 916 clang
917 flex 917 flex
918 llvm 918 llvm
919 pybind11 919 pybind11-2
920 python-wrapper)) 920 python-wrapper))
921 (inputs 921 (inputs
922 (list boost-1.83 922 (list boost-1.83
@@ -1736,7 +1736,7 @@ with strong support for multi-part, multi-channel use cases.")
1736 openjpeg 1736 openjpeg
1737 ;; openvdb ; OpenVDB needs OIIO to be built with C++17 or higher 1737 ;; openvdb ; OpenVDB needs OIIO to be built with C++17 or higher
1738 pugixml 1738 pugixml
1739 pybind11 1739 pybind11-2
1740 python-wrapper 1740 python-wrapper
1741 robin-map 1741 robin-map
1742 zlib)) 1742 zlib))
diff --git a/gnu/packages/image-processing.scm b/gnu/packages/image-processing.scm
index f9a307118f0..86962a69781 100644
--- a/gnu/packages/image-processing.scm
+++ b/gnu/packages/image-processing.scm
@@ -324,7 +324,7 @@ licences similar to the Modified BSD licence."))))
324 (native-inputs 324 (native-inputs
325 ;; XXX: OCIO has unit tests for OpenShadingLanguage, but they fail. 325 ;; XXX: OCIO has unit tests for OpenShadingLanguage, but they fail.
326 ;; They also require OIIO, but OCIO is an optional dependency to it. 326 ;; They also require OIIO, but OCIO is an optional dependency to it.
327 (list pybind11 python-wrapper)) 327 (list pybind11-2 python-wrapper))
328 (inputs 328 (inputs
329 (list expat 329 (list expat
330 freeglut 330 freeglut
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 5fbdc453a18..3c5943961e7 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -439,7 +439,7 @@ CTranslate2, which is a inference engine for transformer models.")
439 (build-system pyproject-build-system) 439 (build-system pyproject-build-system)
440 (propagated-inputs (list python-numpy python-scipy)) 440 (propagated-inputs (list python-numpy python-scipy))
441 (inputs (list fasttext)) 441 (inputs (list fasttext))
442 (native-inputs (list pybind11 python-setuptools python-wheel)))) 442 (native-inputs (list pybind11-2 python-setuptools python-wheel))))
443 443
444(define-public python-funsor 444(define-public python-funsor
445 (package 445 (package
@@ -805,7 +805,7 @@ Learning usecases.")
805 (find-files (site-packages inputs outputs) "\\.so$"))))))) 805 (find-files (site-packages inputs outputs) "\\.so$")))))))
806 (inputs (list eigen-for-python-ml-dtypes)) 806 (inputs (list eigen-for-python-ml-dtypes))
807 (propagated-inputs (list python-numpy)) 807 (propagated-inputs (list python-numpy))
808 (native-inputs (list pybind11 808 (native-inputs (list pybind11-2
809 python-absl-py 809 python-absl-py
810 python-pytest 810 python-pytest
811 python-setuptools)) 811 python-setuptools))
@@ -2047,7 +2047,7 @@ parts of speech and entities, do syntactic analysis, and more.")
2047 (append 2047 (append
2048 (list cmake-minimal 2048 (list cmake-minimal
2049 googletest 2049 googletest
2050 pybind11 2050 pybind11-2
2051 python-fb-re2 2051 python-fb-re2
2052 python-parameterized 2052 python-parameterized
2053 python-pytest 2053 python-pytest
@@ -2135,7 +2135,7 @@ operators and standard data types.")
2135 (package-transitive-supported-systems pkg))) 2135 (package-transitive-supported-systems pkg)))
2136 (list python-nbval)))) 2136 (list python-nbval))))
2137 (inputs 2137 (inputs
2138 (list onnx protobuf pybind11)) 2138 (list onnx protobuf pybind11-2))
2139 (propagated-inputs 2139 (propagated-inputs
2140 (list python-numpy)) 2140 (list python-numpy))
2141 (synopsis "Library to optimize ONNX models") 2141 (synopsis "Library to optimize ONNX models")
@@ -2257,7 +2257,7 @@ with a single function call.")
2257 nlohmann-json 2257 nlohmann-json
2258 onnx 2258 onnx
2259 protobuf 2259 protobuf
2260 pybind11 2260 pybind11-2
2261 re2-next 2261 re2-next
2262 safeint 2262 safeint
2263 zlib)) 2263 zlib))
@@ -2426,7 +2426,7 @@ than 8 bits, and at the end only some significant 8 bits are kept.")
2426 libwebp 2426 libwebp
2427 libx11 2427 libx11
2428 openblas 2428 openblas
2429 pybind11 2429 pybind11-2
2430 zlib)) 2430 zlib))
2431 (synopsis 2431 (synopsis
2432 "Toolkit for making machine learning and data analysis applications in 2432 "Toolkit for making machine learning and data analysis applications in
@@ -3791,7 +3791,7 @@ find_library(ML_DTYPES_LIBRARIES
3791 (native-inputs 3791 (native-inputs
3792 (list pkg-config 3792 (list pkg-config
3793 googletest 3793 googletest
3794 pybind11 3794 pybind11-2
3795 python-setuptools 3795 python-setuptools
3796 python-wrapper ;for its /bin 3796 python-wrapper ;for its /bin
3797 swig-4.0 3797 swig-4.0
@@ -4543,7 +4543,7 @@ multiplications and convolution library for server-side inference.")
4543 ;; There are no tests 4543 ;; There are no tests
4544 #:tests? #f)) 4544 #:tests? #f))
4545 (inputs (list libuv)) 4545 (inputs (list libuv))
4546 (native-inputs (list googletest pkg-config pybind11 libnop)) 4546 (native-inputs (list googletest pkg-config pybind11-2 libnop))
4547 (home-page "https://github.com/pytorch/tensorpipe") 4547 (home-page "https://github.com/pytorch/tensorpipe")
4548 (synopsis "Tensor-aware point-to-point communication primitive for 4548 (synopsis "Tensor-aware point-to-point communication primitive for
4549machine learning") 4549machine learning")
@@ -5190,7 +5190,7 @@ PyTorch.")
5190 openssl ; for cpp-httplib 5190 openssl ; for cpp-httplib
5191 pthreadpool 5191 pthreadpool
5192 protobuf 5192 protobuf
5193 pybind11 5193 pybind11-2
5194 ;; qnnpack 5194 ;; qnnpack
5195 qnnpack-pytorch 5195 qnnpack-pytorch
5196 rdma-core 5196 rdma-core
@@ -5906,7 +5906,7 @@ implementations and an easy-to-use API to create custom metrics. It offers:
5906 python-pillow 5906 python-pillow
5907 python-pytorch)) 5907 python-pytorch))
5908 (native-inputs 5908 (native-inputs
5909 (list pybind11 5909 (list pybind11-2
5910 python-pytest 5910 python-pytest
5911 python-setuptools 5911 python-setuptools
5912 python-wheel 5912 python-wheel
@@ -6186,7 +6186,7 @@ models on CPU and GPU.")
6186 (native-inputs (list ctranslate2 6186 (native-inputs (list ctranslate2
6187 python-setuptools 6187 python-setuptools
6188 python-wheel 6188 python-wheel
6189 pybind11 6189 pybind11-2
6190 python-pyyaml 6190 python-pyyaml
6191 python-numpy)))) 6191 python-numpy))))
6192 6192
@@ -6324,7 +6324,7 @@ a Qt interface for Argos Translate.")
6324 (propagated-inputs 6324 (propagated-inputs
6325 (list python-numpy python-scikit-learn python-scipy)) 6325 (list python-numpy python-scikit-learn python-scipy))
6326 (native-inputs 6326 (native-inputs
6327 (list pybind11 6327 (list pybind11-2
6328 python-pytest 6328 python-pytest
6329 python-setuptools 6329 python-setuptools
6330 python-setuptools-scm 6330 python-setuptools-scm
@@ -7120,7 +7120,7 @@ add_subdirectory[(][.][.]/[.][.]/dlib/external/pybind11 pybind11_build[)]")
7120 (list cmake-minimal 7120 (list cmake-minimal
7121 perl 7121 perl
7122 pkg-config 7122 pkg-config
7123 pybind11 7123 pybind11-2
7124 python-pytest 7124 python-pytest
7125 python-setuptools)))) 7125 python-setuptools))))
7126 7126
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 0cb46da240b..8316a2a5504 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -4367,7 +4367,7 @@ primes and prime k-tuplets up to 264.")
4367 "/include/eigen3/") 4367 "/include/eigen3/")
4368 "\"],")))))))) 4368 "\"],"))))))))
4369 (native-inputs 4369 (native-inputs
4370 (list pybind11 4370 (list pybind11-2
4371 python-matplotx 4371 python-matplotx
4372 python-perfplot 4372 python-perfplot
4373 python-pytest 4373 python-pytest
@@ -4483,7 +4483,7 @@ programming language.")
4483 (setenv "DUCC0_OPTIMIZATION" "portable-strip")))))) 4483 (setenv "DUCC0_OPTIMIZATION" "portable-strip"))))))
4484 (native-inputs 4484 (native-inputs
4485 (list cmake-minimal 4485 (list cmake-minimal
4486 pybind11 4486 pybind11-2
4487 python-nanobind 4487 python-nanobind
4488 python-pytest 4488 python-pytest
4489 python-pytest-xdist 4489 python-pytest-xdist
diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm
index d2bf99b2588..8ee6a317242 100644
--- a/gnu/packages/networking.scm
+++ b/gnu/packages/networking.scm
@@ -559,7 +559,7 @@ components.")
559 libtiff 559 libtiff
560 libyaml 560 libyaml
561 libyuv 561 libyuv
562 pybind11 562 pybind11-2
563 python-jinja2 563 python-jinja2
564 python-ply 564 python-ply
565 qtbase) 565 qtbase)
diff --git a/gnu/packages/opencl.scm b/gnu/packages/opencl.scm
index 39ce8cd29dd..5ac1c6733b9 100644
--- a/gnu/packages/opencl.scm
+++ b/gnu/packages/opencl.scm
@@ -355,7 +355,7 @@ A lexer, @code{pytools.lex}.
355 (native-inputs 355 (native-inputs
356 (list cmake-minimal 356 (list cmake-minimal
357 pocl 357 pocl
358 pybind11 358 pybind11-2
359 python-mako 359 python-mako
360 python-nanobind 360 python-nanobind
361 python-pytest 361 python-pytest
diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index 73f57738fef..8454f722c43 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1839,7 +1839,7 @@ foundation for the Mamba package manager.")
1839 (list cmake-minimal 1839 (list cmake-minimal
1840 ninja 1840 ninja
1841 pkg-config 1841 pkg-config
1842 pybind11 1842 pybind11-2
1843 python-scikit-build 1843 python-scikit-build
1844 python-pytest 1844 python-pytest
1845 python-setuptools)) 1845 python-setuptools))
diff --git a/gnu/packages/physics.scm b/gnu/packages/physics.scm
index f6d63e10163..851977abbfc 100644
--- a/gnu/packages/physics.scm
+++ b/gnu/packages/physics.scm
@@ -225,7 +225,7 @@ Version: ~a
225 (list catch2-3 225 (list catch2-3
226 cmake-minimal 226 cmake-minimal
227 highfive 227 highfive
228 pybind11 228 pybind11-2
229 python-wrapper 229 python-wrapper
230 python-setuptools 230 python-setuptools
231 python-setuptools-scm)) 231 python-setuptools-scm))
@@ -275,7 +275,7 @@ scattering simulations.")
275 (for-each (lambda (test) 275 (for-each (lambda (test)
276 (invoke "python" test)) 276 (invoke "python" test))
277 (find-files "tests" "^test_.*\\.py$")))))))) 277 (find-files "tests" "^test_.*\\.py$"))))))))
278 (native-inputs (list pybind11 python-setuptools cmake python-pytest 278 (native-inputs (list pybind11-2 python-setuptools cmake python-pytest
279 python-numpy)) 279 python-numpy))
280 (inputs (list eigen)) 280 (inputs (list eigen))
281 (home-page "https://github.com/ralna/gofit") 281 (home-page "https://github.com/ralna/gofit")
diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index e92ed6b6cf4..b544de336fa 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -5151,7 +5151,7 @@ unused.")
5151 (native-inputs 5151 (native-inputs
5152 (list cmake-minimal 5152 (list cmake-minimal
5153 ninja 5153 ninja
5154 pybind11 5154 pybind11-2
5155 python-pytest-bootstrap 5155 python-pytest-bootstrap
5156 python-scikit-build 5156 python-scikit-build
5157 python-setuptools)) 5157 python-setuptools))
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 1175752e07c..b48896ef490 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -190,7 +190,7 @@
190 (number->string (parallel-job-count)) 190 (number->string (parallel-job-count))
191 "1") 191 "1")
192 "-E" (string-join ignored-tests "|"))))))))) 192 "-E" (string-join ignored-tests "|")))))))))
193 (native-inputs (list openssh-sans-x python python-numpy pybind11 zip)) 193 (native-inputs (list openssh-sans-x python python-numpy pybind11-2 zip))
194 (inputs (list gsl hdf5 openmpi postgresql)) 194 (inputs (list gsl hdf5 openmpi postgresql))
195 (propagated-inputs (list python-pyyaml)) ;for the Python bindings 195 (propagated-inputs (list python-pyyaml)) ;for the Python bindings
196 (home-page "http://pyre.orthologue.com/") 196 (home-page "http://pyre.orthologue.com/")
@@ -574,7 +574,7 @@ higher scores.")
574 ;; a way to use a system library. 574 ;; a way to use a system library.
575 (propagated-inputs (list python-numpy)) 575 (propagated-inputs (list python-numpy))
576 (native-inputs (list cmake-minimal 576 (native-inputs (list cmake-minimal
577 pybind11 577 pybind11-2
578 python-pytest 578 python-pytest
579 python-pytest-benchmark 579 python-pytest-benchmark
580 python-scikit-build-core 580 python-scikit-build-core
@@ -812,7 +812,7 @@ it can be used for displaying many qualitatively different samples.")
812 ;; verbose=True for more information. 812 ;; verbose=True for more information.
813 "TestOpRelConeQuad::test_oprelcone_2"))))) 813 "TestOpRelConeQuad::test_oprelcone_2")))))
814 (native-inputs 814 (native-inputs
815 (list pybind11 815 (list pybind11-2
816 python-pytest 816 python-pytest
817 python-setuptools)) 817 python-setuptools))
818 (propagated-inputs 818 (propagated-inputs
@@ -1468,7 +1468,7 @@ Features:
1468 (list #:test-flags #~(list "-k" "not test_interactive_pyside6"))) 1468 (list #:test-flags #~(list "-k" "not test_interactive_pyside6")))
1469 (native-inputs 1469 (native-inputs
1470 (list cmake-minimal 1470 (list cmake-minimal
1471 pybind11 1471 pybind11-2
1472 python-annotated-types 1472 python-annotated-types
1473 python-boost-histogram 1473 python-boost-histogram
1474 python-ipykernel 1474 python-ipykernel
@@ -2363,7 +2363,7 @@ web, by sharing data and other research outputs.")
2363 (native-inputs 2363 (native-inputs
2364 (list cmake-minimal 2364 (list cmake-minimal
2365 osqp 2365 osqp
2366 pybind11 2366 pybind11-2
2367 python-pytest 2367 python-pytest
2368 python-pytorch 2368 python-pytorch
2369 python-scikit-build-core 2369 python-scikit-build-core
@@ -2501,7 +2501,7 @@ different units.")
2501 (delete-file-recursively "pyamg")))))) 2501 (delete-file-recursively "pyamg"))))))
2502 (build-system pyproject-build-system) 2502 (build-system pyproject-build-system)
2503 (native-inputs 2503 (native-inputs
2504 (list pybind11 2504 (list pybind11-2
2505 python-cppheaderparser 2505 python-cppheaderparser
2506 python-pytest 2506 python-pytest
2507 python-pyyaml 2507 python-pyyaml
@@ -2690,7 +2690,7 @@ or as a TikZ file for use in LaTeX documents;
2690 (build-system pyproject-build-system) 2690 (build-system pyproject-build-system)
2691 (native-inputs 2691 (native-inputs
2692 (list cmake-minimal 2692 (list cmake-minimal
2693 pybind11 2693 pybind11-2
2694 python-pytest 2694 python-pytest
2695 python-setuptools)) 2695 python-setuptools))
2696 (propagated-inputs (list python-numpy python-scipy)) 2696 (propagated-inputs (list python-numpy python-scipy))
@@ -2929,7 +2929,7 @@ genetic variation data.")
2929 python-pathspec 2929 python-pathspec
2930 python-tomli 2930 python-tomli
2931 python-typing-extensions)) 2931 python-typing-extensions))
2932 (native-inputs (list pybind11 2932 (native-inputs (list pybind11-2
2933 python-cattrs 2933 python-cattrs
2934 python-fastjsonschema 2934 python-fastjsonschema
2935 python-hatch-fancy-pypi-readme 2935 python-hatch-fancy-pypi-readme
@@ -3419,7 +3419,7 @@ cross-validation.")
3419 (inputs 3419 (inputs
3420 (list boost-1.88 3420 (list boost-1.88
3421 openblas 3421 openblas
3422 pybind11 3422 pybind11-2
3423 qhull 3423 qhull
3424 xsimd)) 3424 xsimd))
3425 (propagated-inputs 3425 (propagated-inputs
@@ -4740,7 +4740,7 @@ readable.")
4740 (("#include <nonstd/string_view.hpp>") 4740 (("#include <nonstd/string_view.hpp>")
4741 "#include <cstdint>\n#include <nonstd/string_view.hpp>"))))))) 4741 "#include <cstdint>\n#include <nonstd/string_view.hpp>")))))))
4742 (native-inputs 4742 (native-inputs
4743 (list pybind11 4743 (list pybind11-2
4744 python-cython 4744 python-cython
4745 python-setuptools)) 4745 python-setuptools))
4746 (inputs 4746 (inputs
@@ -5869,7 +5869,7 @@ science including tools for accessing data sets in Python.")
5869 "12i68jj9n1qj9phjnj6f0kmfhlsd3fqjlk9p6d4gs008azw5m8yn")))) 5869 "12i68jj9n1qj9phjnj6f0kmfhlsd3fqjlk9p6d4gs008azw5m8yn"))))
5870 (build-system pyproject-build-system) 5870 (build-system pyproject-build-system)
5871 (propagated-inputs (list python-numpy-1)) 5871 (propagated-inputs (list python-numpy-1))
5872 (native-inputs (list pybind11 python-pytest python-setuptools)) 5872 (native-inputs (list pybind11-2 python-pytest python-setuptools))
5873 (home-page "https://github.com/nschloe/pyfma") 5873 (home-page "https://github.com/nschloe/pyfma")
5874 (synopsis "Fused multiply-add for Python") 5874 (synopsis "Fused multiply-add for Python")
5875 (description "@code{pyfma} provides an implementation of fused 5875 (description "@code{pyfma} provides an implementation of fused
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0ec525b8f9b..59921e00f9b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -542,7 +542,7 @@ compare against a vast section of other version formats.")
542 ;; tests: 22304 passed, 524 skipped 542 ;; tests: 22304 passed, 524 skipped
543 (native-inputs 543 (native-inputs
544 (list cmake-minimal 544 (list cmake-minimal
545 pybind11 545 pybind11-2
546 python-pytest 546 python-pytest
547 python-scikit-build-core)) 547 python-scikit-build-core))
548 (propagated-inputs 548 (propagated-inputs
@@ -3374,7 +3374,7 @@ into dataclasses.")
3374 ;; Tests that pass but avoided for load reasons. 3374 ;; Tests that pass but avoided for load reasons.
3375 "-k" "not test_filled_random_big and not test_lines_random_big"))) 3375 "-k" "not test_filled_random_big and not test_lines_random_big")))
3376 (native-inputs 3376 (native-inputs
3377 (list pybind11 3377 (list pybind11-2
3378 python-meson 3378 python-meson
3379 python-pytest 3379 python-pytest
3380 python-wurlitzer)) 3380 python-wurlitzer))
@@ -5483,7 +5483,7 @@ interface utility to parse @url{https://hjson.github.io/, HJSON}) documents.")
5483 ((", '-march=native'") 5483 ((", '-march=native'")
5484 ""))))))) 5484 "")))))))
5485 (native-inputs 5485 (native-inputs
5486 (list pybind11 5486 (list pybind11-2
5487 python-pytest 5487 python-pytest
5488 python-setuptools)) 5488 python-setuptools))
5489 (propagated-inputs 5489 (propagated-inputs
@@ -9242,7 +9242,7 @@ browser.")
9242 (native-inputs 9242 (native-inputs
9243 (list python-setuptools)) 9243 (list python-setuptools))
9244 (inputs 9244 (inputs
9245 (list pybind11 9245 (list pybind11-2
9246 static-abseil-cpp 9246 static-abseil-cpp
9247 python)) 9247 python))
9248 (propagated-inputs 9248 (propagated-inputs
@@ -12075,7 +12075,7 @@ comparison.
12075 (native-inputs 12075 (native-inputs
12076 (list pkg-config 12076 (list pkg-config
12077 python-meson 12077 python-meson
12078 pybind11 12078 pybind11-2
12079 python-pytest 12079 python-pytest
12080 python-pytest-timeout 12080 python-pytest-timeout
12081 python-pytest-xdist 12081 python-pytest-xdist
@@ -12812,7 +12812,7 @@ Python list with elements of type @code{PIL.Image} (from the
12812 (base32 "0hpnb63xp8yaflah3i1z5azh6mg36rz0liy27km47417w2q72v0c")))) 12812 (base32 "0hpnb63xp8yaflah3i1z5azh6mg36rz0liy27km47417w2q72v0c"))))
12813 (build-system pyproject-build-system) 12813 (build-system pyproject-build-system)
12814 (native-inputs 12814 (native-inputs
12815 (list pybind11 12815 (list pybind11-2
12816 python-attrs 12816 python-attrs
12817 python-hypothesis 12817 python-hypothesis
12818 python-setuptools-scm 12818 python-setuptools-scm
@@ -14588,7 +14588,7 @@ connect strings, then issue SQL commands within IPython or IPython Notebook.")
14588 python-setuptools 14588 python-setuptools
14589 python-wheel 14589 python-wheel
14590 cmake-minimal 14590 cmake-minimal
14591 pybind11)) 14591 pybind11-2))
14592 (home-page "https://github.com/metaopt/optree") 14592 (home-page "https://github.com/metaopt/optree")
14593 (synopsis "Optimized PyTree Utilities") 14593 (synopsis "Optimized PyTree Utilities")
14594 (description "This package contains operations on PyTrees (a tree made of 14594 (description "This package contains operations on PyTrees (a tree made of
@@ -26645,7 +26645,7 @@ commit, but it also includes some other useful statistics.")
26645binding is created using the standard @code{ctypes} library.") 26645binding is created using the standard @code{ctypes} library.")
26646 (license license:isc))) 26646 (license license:isc)))
26647 26647
26648(define-public pybind11 26648(define-public pybind11-2
26649 (package 26649 (package
26650 (name "pybind11") 26650 (name "pybind11")
26651 (version "2.13.6") 26651 (version "2.13.6")
diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm
index add35696291..d2b2026a970 100644
--- a/gnu/packages/radio.scm
+++ b/gnu/packages/radio.scm
@@ -1042,7 +1042,7 @@ used by RDS Spy, and audio files containing @dfn{multiplex} signals (MPX).")
1042 js-mathjax 1042 js-mathjax
1043 orc 1043 orc
1044 pkg-config 1044 pkg-config
1045 pybind11 1045 pybind11-2
1046 python-cheetah 1046 python-cheetah
1047 python-mako 1047 python-mako
1048 python-pyzmq 1048 python-pyzmq
@@ -1140,7 +1140,7 @@ environment.")
1140 (add-after 'install 'wrap-python 1140 (add-after 'install 'wrap-python
1141 (assoc-ref py:%standard-phases 'wrap))))) 1141 (assoc-ref py:%standard-phases 'wrap)))))
1142 (native-inputs 1142 (native-inputs
1143 (list doxygen pkg-config pybind11 python-mako python-six)) 1143 (list doxygen pkg-config pybind11-2 python-mako python-six))
1144 (inputs 1144 (inputs
1145 (list airspy 1145 (list airspy
1146 airspyhf 1146 airspyhf
@@ -1226,7 +1226,7 @@ primitives for SDR (Software Defined Radio).")
1226 (list cppunit 1226 (list cppunit
1227 doxygen 1227 doxygen
1228 pkg-config 1228 pkg-config
1229 pybind11 1229 pybind11-2
1230 python-numpy)) 1230 python-numpy))
1231 (inputs 1231 (inputs
1232 (list boost-1.83 1232 (list boost-1.83
@@ -1278,7 +1278,7 @@ DMR, NXDN, P25, etc.")
1278 (native-inputs 1278 (native-inputs
1279 (list doxygen 1279 (list doxygen
1280 pkg-config 1280 pkg-config
1281 pybind11 1281 pybind11-2
1282 python 1282 python
1283 python-numpy 1283 python-numpy
1284 python-six)) 1284 python-six))
@@ -1332,7 +1332,7 @@ to the fix block above.
1332 (add-after 'install 'wrap-python 1332 (add-after 'install 'wrap-python
1333 (assoc-ref py:%standard-phases 'wrap))))) 1333 (assoc-ref py:%standard-phases 'wrap)))))
1334 (native-inputs 1334 (native-inputs
1335 (list pkg-config pybind11 python-six)) 1335 (list pkg-config pybind11-2 python-six))
1336 (inputs 1336 (inputs
1337 (list boost-1.83 1337 (list boost-1.83
1338 gmp 1338 gmp
@@ -2007,7 +2007,7 @@ operators.")
2007 googletest 2007 googletest
2008 libusb 2008 libusb
2009 mesa 2009 mesa
2010 pybind11 2010 pybind11-2
2011 python 2011 python
2012 python-numpy 2012 python-numpy
2013 soapysdr 2013 soapysdr
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index bcc44275595..14f1f0fc18f 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1220,7 +1220,7 @@ demos = [d for d in demos if d[0].stem not in excludeList]~%"
1220 (inputs 1220 (inputs
1221 (modify-inputs (package-inputs fenics-dolfin) 1221 (modify-inputs (package-inputs fenics-dolfin)
1222 (delete "python") 1222 (delete "python")
1223 (prepend pybind11 python-matplotlib))) 1223 (prepend pybind11-2 python-matplotlib)))
1224 (native-inputs 1224 (native-inputs
1225 (modify-inputs (package-native-inputs fenics-dolfin) 1225 (modify-inputs (package-native-inputs fenics-dolfin)
1226 (prepend cmake-minimal 1226 (prepend cmake-minimal
@@ -1508,7 +1508,7 @@ counters and tunnels).")
1508 ;; has already been loaded. 1508 ;; has already been loaded.
1509 (delete 'sanity-check)))) 1509 (delete 'sanity-check))))
1510 (inputs 1510 (inputs
1511 (list fenics openmpi pybind11)) 1511 (list fenics openmpi pybind11-2))
1512 (native-inputs 1512 (native-inputs
1513 (list pkg-config 1513 (list pkg-config
1514 python-decorator 1514 python-decorator
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index 4b3ce96f62b..b3d749d8db7 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -737,7 +737,7 @@ covariance @url{https://github.com/vnmabus/dcor#sr14,[SR14]}
737 (build-system pyproject-build-system) 737 (build-system pyproject-build-system)
738 (native-inputs 738 (native-inputs
739 (list cmake-minimal ;TODO: propagate from python-scikit-build-core 739 (list cmake-minimal ;TODO: propagate from python-scikit-build-core
740 pybind11 740 pybind11-2
741 python-pytest 741 python-pytest
742 python-scikit-build-core)) 742 python-scikit-build-core))
743 (propagated-inputs 743 (propagated-inputs
@@ -1108,7 +1108,7 @@ sampler for Markov chain Monte Carlo (MCMC).")
1108 (build-system pyproject-build-system) 1108 (build-system pyproject-build-system)
1109 (native-inputs 1109 (native-inputs
1110 (list cmake-minimal 1110 (list cmake-minimal
1111 pybind11 1111 pybind11-2
1112 python-pytest 1112 python-pytest
1113 python-scikit-build-core 1113 python-scikit-build-core
1114 python-setuptools-scm)) 1114 python-setuptools-scm))
diff --git a/gnu/packages/syndication.scm b/gnu/packages/syndication.scm
index 3c49c6780b4..f3db338bb37 100644
--- a/gnu/packages/syndication.scm
+++ b/gnu/packages/syndication.scm
@@ -478,7 +478,7 @@ to create RSS feeds for websites that don't provide any.")
478 (sha256 478 (sha256
479 (base32 "1fl362920n6nz4x9wihyzbr82d9cy60sknhmajj62whd5gs49sbw")))) 479 (base32 "1fl362920n6nz4x9wihyzbr82d9cy60sknhmajj62whd5gs49sbw"))))
480 (build-system meson-build-system) 480 (build-system meson-build-system)
481 (inputs (list fmt tidy-html pybind11 python pugixml)) 481 (inputs (list fmt tidy-html pybind11-2 python pugixml))
482 (native-inputs (list cmake-minimal pkg-config)) ; need cmake to find pybind11 482 (native-inputs (list cmake-minimal pkg-config)) ; need cmake to find pybind11
483 (home-page "https://gitlab.com/gabmus/syndication-domination") 483 (home-page "https://gitlab.com/gabmus/syndication-domination")
484 (synopsis "RSS/Atom feed parser") 484 (synopsis "RSS/Atom feed parser")