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* gnu/packages/maths.scm: (python-blis, python-blis-for-thinc,
python-cvxopt, python-kiwisolver, python-libensemble, python-petsc4py):
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Change-Id: Ie00bea4d51ded909e9852e8565b1e26b1412c644
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Sharlatan Hellseher 2024-10-23 20:49:58 +01:00
parent 6781127a0b
commit 68fe21b5b2
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@ -419,47 +419,6 @@ triangulations.")
(license (license:non-copyleft "file://COPYING.txt"
"See COPYING in the distribution."))))
(define-public python-cvxopt
(package
(name "python-cvxopt")
(version "1.2.7")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/cvxopt/cvxopt")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"114z34wwx1bsv4q6xj9p5q99dffgnj9s4i4arx10g191xq9q8i5y"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'find-libraries
(lambda* (#:key inputs #:allow-other-keys)
(setenv "CVXOPT_BLAS_LIB" "openblas")
(setenv "CVXOPT_LAPACK_LIB" "openblas")
(setenv "CVXOPT_BUILD_FFTW" "1")
(setenv "CVXOPT_BUILD_GLPK" "1")
(setenv "CVXOPT_BUILD_GSL" "1")
#t)))))
(inputs
(list fftw
glpk
gsl
openblas
suitesparse))
(home-page "https://www.cvxopt.org")
(synopsis "Python library for convex optimization")
(description
"CVXOPT is a package for convex optimization based on the Python
programming language. Its main purpose is to make the development of software
for convex optimization applications straightforward by building on Python’s
extensive standard library and on the strengths of Python as a high-level
programming language.")
(license license:gpl3+)))
(define-public units
(package
(name "units")
@ -881,63 +840,6 @@ LP/MIP solver is included in the package.")
(base32
"040sfaa9jclg2nqdh83w71sv9rc1sznpnfiripjdyr48cady50a2"))))))
(define-public python-libensemble
(package
(name "python-libensemble")
(version "1.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "libensemble" version))
(sha256
(base32 "0qxb0sn624jaxjxg2ayd65zaiq1p043w3kk55w8r6drkjiar70yj"))))
(build-system pyproject-build-system)
(native-inputs (list ncurses
python-mock
python-mpi4py
python-pytest
python-pytest-cov
python-pytest-timeout))
(propagated-inputs (list python-mpmath
python-numpy
python-psutil
python-pydantic-2
python-pyyaml
python-tomli))
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'relax-psutil
(lambda _
(substitute* "setup.py"
(("psutil>=5.9.4") "psutil>=5.9.2"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; These files require MPI and call subprocesses.
(delete-file
"libensemble/tests/unit_tests/test_executor.py")
(delete-file
"libensemble/tests/unit_tests/test_executor_gpus.py")
;; This file has one failing MPI test but since tests run from
;; a shell script, they can't be disabled individually.
;; Failing test: 'test_ensemble_prevent_comms_overwrite'
(delete-file "libensemble/tests/unit_tests/test_ensemble.py")
(setenv "TERM" "xterm")
;; A very bad way to skip another MPI test.
(substitute* "libensemble/tests/run-tests.sh"
(("export UNIT_TEST_MPI_SUBDIR=.*")
"export UNIT_TEST_MPI_SUBDIR=''"))
;; Run only unit tests, regression tests require MPI.
(invoke "bash" "libensemble/tests/run-tests.sh" "-u")))))))
(home-page "https://github.com/Libensemble/libensemble")
(synopsis "Toolkit for dynamic ensembles of calculations")
(description "@code{libensemble} is a complete toolkit for dynamic
ensembles of calculations. It connects @code{deciders} to experiments or
simulations.")
(license license:bsd-3)))
(define-public linasm
(package
(name "linasm")
@ -3807,67 +3709,6 @@ functions.")
required. primesieve can generate primes and prime k-tuplets up to 264.")
(license license:bsd-2)))
(define-public python-petsc4py
(package
(name "python-petsc4py")
(version "3.21.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "petsc4py" version))
(sha256
(base32
"1kffxhcwkx6283n2p83ymanz6m8j2xmz5kpa5s8qc4f9iiah59sb"))))
(build-system python-build-system)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-before 'build 'set-PETSC_DIR
(lambda* (#:key inputs #:allow-other-keys)
;; Define path to PETSc installation.
(setenv "PETSC_DIR"
(assoc-ref inputs "petsc-openmpi"))))
(add-before 'check 'mpi-setup
#$%openmpi-setup)
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "test/runtests.py")))))))
(native-inputs (list python-cython-3))
(inputs (list petsc-openmpi python-numpy))
(home-page "https://bitbucket.org/petsc/petsc4py/")
(synopsis "Python bindings for PETSc")
(description "PETSc, the Portable, Extensible Toolkit for
Scientific Computation, is a suite of data structures and routines for
the scalable (parallel) solution of scientific applications modeled by
partial differential equations. It employs the MPI standard for all
message-passing communication. @code{petsc4py} provides Python
bindings to almost all functions of PETSc.")
(license license:bsd-3)))
(define-public python-kiwisolver
(package
(name "python-kiwisolver")
(version "1.4.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "kiwisolver" version))
(sha256
(base32
"1v6nc0z9dg4am0bibji9pijci9f15z68mwrlv91a28pvawx5czp5"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-typing-extensions))
(native-inputs (list python-cppy python-pytest python-setuptools-scm))
(home-page "https://github.com/nucleic/kiwi")
(synopsis "Fast implementation of the Cassowary constraint solver")
(description
"Kiwi is an efficient C++ implementation of the Cassowary constraint
solving algorithm. Kiwi has been designed from the ground up to be
lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
Cassowary solver with typical use cases gaining a 40x improvement. Memory
savings are consistently > 5x.")
(license license:bsd-3)))
(define-public python-accupy
(package
(name "python-accupy")
@ -3909,6 +3750,168 @@ and (dot) products. It implements Kahan summation, Shewchuck's
algorithm and summation in K-fold precision.")
(license license:gpl3+)))
;; It is unfortunate that we cannot just link with the existing blis package.
(define-public python-blis
(package
(name "python-blis")
(version "0.9.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "blis" version))
(sha256
(base32
"0vrnzk9jx7fcl56q6zpa4w4mxkr4iknxs42fngn9g78zh1kc9skw"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'build 'build-ext
(lambda _
(invoke "python" "setup.py" "build_ext" "--inplace"
"-j" (number->string (parallel-job-count))))))))
(propagated-inputs (list python-numpy))
(native-inputs (list python-cython python-pytest))
(home-page "https://github.com/explosion/cython-blis")
(synopsis "Blis as a self-contained C-extension for Python")
(description
"This package provides the Blis BLAS-like linear algebra library, as a
self-contained C-extension for Python.")
(license license:bsd-3)))
(define-public python-blis-for-thinc
(package
(inherit python-blis)
(name "python-blis")
(version "0.7.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "blis" version))
(sha256
(base32
"0mvcif9g69424bk8xiflacxzpvz802ns791v2r8a6fij0sxl3mgp"))))))
(define-public python-cvxopt
(package
(name "python-cvxopt")
(version "1.2.7")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/cvxopt/cvxopt")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"114z34wwx1bsv4q6xj9p5q99dffgnj9s4i4arx10g191xq9q8i5y"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'find-libraries
(lambda* (#:key inputs #:allow-other-keys)
(setenv "CVXOPT_BLAS_LIB" "openblas")
(setenv "CVXOPT_LAPACK_LIB" "openblas")
(setenv "CVXOPT_BUILD_FFTW" "1")
(setenv "CVXOPT_BUILD_GLPK" "1")
(setenv "CVXOPT_BUILD_GSL" "1")
#t)))))
(inputs
(list fftw
glpk
gsl
openblas
suitesparse))
(home-page "https://www.cvxopt.org")
(synopsis "Python library for convex optimization")
(description
"CVXOPT is a package for convex optimization based on the Python
programming language. Its main purpose is to make the development of software
for convex optimization applications straightforward by building on Python’s
extensive standard library and on the strengths of Python as a high-level
programming language.")
(license license:gpl3+)))
(define-public python-kiwisolver
(package
(name "python-kiwisolver")
(version "1.4.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "kiwisolver" version))
(sha256
(base32
"1v6nc0z9dg4am0bibji9pijci9f15z68mwrlv91a28pvawx5czp5"))))
(build-system pyproject-build-system)
(propagated-inputs (list python-typing-extensions))
(native-inputs (list python-cppy python-pytest python-setuptools-scm))
(home-page "https://github.com/nucleic/kiwi")
(synopsis "Fast implementation of the Cassowary constraint solver")
(description
"Kiwi is an efficient C++ implementation of the Cassowary constraint
solving algorithm. Kiwi has been designed from the ground up to be
lightweight and fast. Kiwi ranges from 10x to 500x faster than the original
Cassowary solver with typical use cases gaining a 40x improvement. Memory
savings are consistently > 5x.")
(license license:bsd-3)))
(define-public python-libensemble
(package
(name "python-libensemble")
(version "1.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "libensemble" version))
(sha256
(base32 "0qxb0sn624jaxjxg2ayd65zaiq1p043w3kk55w8r6drkjiar70yj"))))
(build-system pyproject-build-system)
(native-inputs (list ncurses
python-mock
python-mpi4py
python-pytest
python-pytest-cov
python-pytest-timeout))
(propagated-inputs (list python-mpmath
python-numpy
python-psutil
python-pydantic-2
python-pyyaml
python-tomli))
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'relax-psutil
(lambda _
(substitute* "setup.py"
(("psutil>=5.9.4") "psutil>=5.9.2"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
;; These files require MPI and call subprocesses.
(delete-file
"libensemble/tests/unit_tests/test_executor.py")
(delete-file
"libensemble/tests/unit_tests/test_executor_gpus.py")
;; This file has one failing MPI test but since tests run from
;; a shell script, they can't be disabled individually.
;; Failing test: 'test_ensemble_prevent_comms_overwrite'
(delete-file "libensemble/tests/unit_tests/test_ensemble.py")
(setenv "TERM" "xterm")
;; A very bad way to skip another MPI test.
(substitute* "libensemble/tests/run-tests.sh"
(("export UNIT_TEST_MPI_SUBDIR=.*")
"export UNIT_TEST_MPI_SUBDIR=''"))
;; Run only unit tests, regression tests require MPI.
(invoke "bash" "libensemble/tests/run-tests.sh" "-u")))))))
(home-page "https://github.com/Libensemble/libensemble")
(synopsis "Toolkit for dynamic ensembles of calculations")
(description "@code{libensemble} is a complete toolkit for dynamic
ensembles of calculations. It connects @code{deciders} to experiments or
simulations.")
(license license:bsd-3)))
(define-public python-ndim
(package
(name "python-ndim")
@ -3974,6 +3977,44 @@ recurrence schemes. Furthermore, all functions are fully vectorized and
can return results in exact arithmetic.")
(license license:gpl3+)))
(define-public python-petsc4py
(package
(name "python-petsc4py")
(version "3.21.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "petsc4py" version))
(sha256
(base32
"1kffxhcwkx6283n2p83ymanz6m8j2xmz5kpa5s8qc4f9iiah59sb"))))
(build-system python-build-system)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(add-before 'build 'set-PETSC_DIR
(lambda* (#:key inputs #:allow-other-keys)
;; Define path to PETSc installation.
(setenv "PETSC_DIR"
(assoc-ref inputs "petsc-openmpi"))))
(add-before 'check 'mpi-setup
#$%openmpi-setup)
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "python" "test/runtests.py")))))))
(native-inputs (list python-cython-3))
(inputs (list petsc-openmpi python-numpy))
(home-page "https://bitbucket.org/petsc/petsc4py/")
(synopsis "Python bindings for PETSc")
(description "PETSc, the Portable, Extensible Toolkit for
Scientific Computation, is a suite of data structures and routines for
the scalable (parallel) solution of scientific applications modeled by
partial differential equations. It employs the MPI standard for all
message-passing communication. @code{petsc4py} provides Python
bindings to almost all functions of PETSc.")
(license license:bsd-3)))
(define-public python-quadpy
(package
(name "python-quadpy")
@ -5442,47 +5483,6 @@ access to BLIS implementations via traditional BLAS routine calls.")
(define ignorance blis)
;; It is unfortunate that we cannot just link with the existing blis package.
(define-public python-blis
(package
(name "python-blis")
(version "0.9.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "blis" version))
(sha256
(base32
"0vrnzk9jx7fcl56q6zpa4w4mxkr4iknxs42fngn9g78zh1kc9skw"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
'(modify-phases %standard-phases
(add-after 'build 'build-ext
(lambda _
(invoke "python" "setup.py" "build_ext" "--inplace"
"-j" (number->string (parallel-job-count))))))))
(propagated-inputs (list python-numpy))
(native-inputs (list python-cython python-pytest))
(home-page "https://github.com/explosion/cython-blis")
(synopsis "Blis as a self-contained C-extension for Python")
(description
"This package provides the Blis BLAS-like linear algebra library, as a
self-contained C-extension for Python.")
(license license:bsd-3)))
(define-public python-blis-for-thinc
(package
(inherit python-blis)
(name "python-blis")
(version "0.7.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "blis" version))
(sha256
(base32
"0mvcif9g69424bk8xiflacxzpvz802ns791v2r8a6fij0sxl3mgp"))))))
(define-public openlibm
(package
(name "openlibm")