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-rw-r--r--gnu/packages/simulation.scm171
1 files changed, 84 insertions, 87 deletions
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 3f2d8e136d..9e92fbcc5b 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1,6 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
-;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2021, 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
;;;
;;; This file is part of GNU Guix.
@@ -52,6 +52,7 @@
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (guix download)
+ #:use-module (guix gexp)
#:use-module (guix git-download)
#:use-module (guix svn-download)
#:use-module (guix build-system cmake)
@@ -448,8 +449,7 @@ FFC is part of the FEniCS Project.")
;; Specify directory to find the header file.
(("(^set\\(CATCH_INCLUDE_DIR ).*(/catch\\))" _ front back)
(string-append front
- "$ENV{CATCH_DIR}/include" back "\n")))
- #t))))
+ "$ENV{CATCH_DIR}/include" back "\n")))))))
(build-system cmake-build-system)
(inputs
`(("blas" ,openblas)
@@ -494,8 +494,7 @@ FFC is part of the FEniCS Project.")
(setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
(setenv "SCOTCH_DIR" (assoc-ref %build-inputs "scotch"))
(setenv "SUNDIALS_DIR" (assoc-ref %build-inputs "sundials"))
- (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))
- #t))
+ (setenv "UMFPACK_DIR" (assoc-ref %build-inputs "suitesparse"))))
(add-before 'check 'pre-check
(lambda _
;; The Dolfin repository uses git-lfs, whereby web links are
@@ -546,15 +545,15 @@ FFC is part of the FEniCS Project.")
"demo_mesh-quality_serial "
"demo_mesh-quality_mpi "
"demo_multimesh-stokes_serial "
- ")\n") port)))
- #t))
+ ")\n") port)))))
(replace 'check
- (lambda _
- (and (invoke "make" "unittests")
- (invoke "make" "demos")
- (invoke "ctest" "-R" "unittests")
- (invoke "ctest" "-R" "demo" "-R" "serial")
- (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "make" "unittests")
+ (invoke "make" "demos")
+ (invoke "ctest" "-R" "unittests")
+ (invoke "ctest" "-R" "demo" "-R" "serial")
+ (invoke "ctest" "-R" "demo" "-R" "mpi")))))))
(home-page "https://bitbucket.org/fenics-project/dolfin/")
(synopsis "Problem solving environment for differential equations")
(description
@@ -609,6 +608,10 @@ user interface to the FEniCS core components and external libraries.")
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'relax-requirements
+ (lambda _
+ (substitute* "python/setup.py"
+ (("pybind11==") "pybind11>="))))
(add-after 'patch-source-shebangs 'set-paths
(lambda _
;; Define paths to store locations.
@@ -659,17 +662,18 @@ user interface to the FEniCS core components and external libraries.")
;; Restrict OpenBLAS to MPI-only in preference to MPI+OpenMP.
(setenv "OPENBLAS_NUM_THREADS" "1")))
(replace 'check
- (lambda _
- (with-directory-excursion "test"
- ;; Note: The test test_snes_set_from_options() in the file
- ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
- ;; Limit the number of jobs to 3 as 500 MiB of memory is used
- ;; per process.
- (invoke "mpirun" "-np" (number->string
- (min 3 (parallel-job-count)))
- "python" "-B" "-m"
- "pytest" "unit" "--ignore"
- "unit/nls/test_PETScSNES_solver.py"))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "test"
+ ;; Note: The test test_snes_set_from_options() in the file
+ ;; unit/nls/test_PETScSNES_solver.py fails and is ignored.
+ ;; Limit the number of jobs to 3 as 500 MiB of memory is used
+ ;; per process.
+ (invoke "mpirun" "-np" (number->string
+ (min 3 (parallel-job-count)))
+ "python" "-B" "-m"
+ "pytest" "unit" "--ignore"
+ "unit/nls/test_PETScSNES_solver.py")))))
(add-after 'install 'install-demo-files
(lambda* (#:key outputs #:allow-other-keys)
(let* ((demos (string-append
@@ -773,37 +777,35 @@ river flooding.")
(define-public python-meshio
(package
(name "python-meshio")
- (version "4.4.6")
+ (version "5.3.4")
(source
- (origin
- (method url-fetch)
- (uri (pypi-uri "meshio" version))
- (sha256
- (base32
- "0kv832s2vyff30zz8yqypw5jifwdanvh5x56d2bzkvy94h4jlddy"))
- (snippet
- '(begin
- (let ((file (open-file "setup.py" "a")))
- (display "from setuptools import setup\nsetup()" file)
- (close-port file))
- #t))))
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "meshio" version))
+ (sha256
+ (base32
+ "1w39qcg0rw5kb04j7sa45fnqd6k20fsdgrf62cmw2ygjgwnnjh72"))
+ (snippet
+ '(let ((file (open-file "setup.py" "a")))
+ (display "from setuptools import setup\nsetup()" file)
+ (close-port file)))))
(build-system python-build-system)
(inputs
- `(("h5py" ,python-h5py)
- ("netcdf4" ,python-netcdf4)))
+ (list python-h5py
+ python-netcdf4))
(native-inputs
- `(("pytest" ,python-pytest)))
+ (list python-pytest))
(propagated-inputs
- `(("importlib-metadata" ,python-importlib-metadata)
- ("numpy" ,python-numpy)))
+ (list python-importlib-metadata
+ python-numpy
+ python-rich))
(arguments
- `(#:phases
+ '(#:phases
(modify-phases %standard-phases
(replace 'check
- (lambda* (#:key outputs inputs #:allow-other-keys)
- (add-installed-pythonpath inputs outputs)
- (invoke "python" "-m" "pytest" "-v" "tests")
- #t)))))
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "-m" "pytest" "-v" "tests")))))))
(home-page "https://github.com/nschloe/meshio")
(synopsis "I/O for mesh files")
(description "There are various file formats available for
@@ -817,48 +819,43 @@ tools and a collection of Python modules for programmatic use.")
(define-public python-pygmsh
(package
(name "python-pygmsh")
- (version "7.1.11")
+ (version "7.1.17")
(source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/nschloe/pygmsh")
- (commit version)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0g4yllmxks7yb50vild5xi1cma0yl16vsq6rfvdwmqaj4hwxcabk"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- (let ((file (open-file "setup.py" "a")))
- (display "from setuptools import setup\nsetup()" file)
- (close-port file))
- ;; A reference to setuptools in the configuration file
- ;; triggers an attempt to download the package from pypi.
- ;; The reference is not needed since the package is
- ;; provided by the build system.
- (substitute* "setup.cfg"
- (("^[[:blank:]]+setuptools>=42\n") ""))
- #t))))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/nschloe/pygmsh")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "11flp2c4ynk1fhanf4mqyzrpd0gjbnv6afrwwc7xi3mb6ms69lr0"))))
(build-system python-build-system)
- (native-inputs
- `(("pytest" ,python-pytest)
- ("wheel" ,python-wheel)))
- (propagated-inputs
- `(("importlib-metadata" ,python-importlib-metadata)
- ("gmsh" ,gmsh)
- ("meshio" ,python-meshio)
- ("numpy" ,python-numpy)))
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key inputs outputs tests? #:allow-other-keys)
- (when tests?
- (add-installed-pythonpath inputs outputs)
- (invoke "python" "-m" "pytest" "-v" "tests"))
- #t)))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'workaround-gmsh-detection-failure
+ (lambda _
+ ;; Due to lack of metadata, the gmsh Python package is not
+ ;; detected although importable.
+ (substitute* "pyproject.toml"
+ (("\"gmsh\",") ""))))
+ ;; XXX: PEP 517 manual build copied from python-isort.
+ (replace 'build
+ (lambda _
+ (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-v" "tests"))))
+ (replace 'install
+ (lambda _
+ (let ((whl (car (find-files "dist" "\\.whl$"))))
+ (invoke "pip" "--no-cache-dir" "--no-input"
+ "install" "--no-deps" "--prefix" #$output whl)))))))
+ (native-inputs (list python-pypa-build python-flit-core python-pytest))
+ (propagated-inputs (list gmsh python-meshio python-numpy))
(home-page "https://github.com/nschloe/pygmsh")
(synopsis "Python frontend for Gmsh")
(description "The goal of @code{pygmsh} is to combine the power of
@@ -867,7 +864,7 @@ the methods and functions that comprise the Gmsh Python API. In this
way the meshing of complex geometries using high-level abstractions is
made possible. The package provides a Python library together with a
command-line utility for mesh optimisation.")
- (license license:lgpl3)))
+ (license license:gpl3+)))
(define-public python-dolfin-adjoint
(package
generated by cgit v1.2.3 (git 2.47.1) at 2025-01-22 04:42:21 +0000