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petsc: 3.24.6 -> 3.25.2; bulk upgrade of petsc related packages (#519873)

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This commit is contained in:
Nick Cao
2026-06-24 01:08:39 +00:00
committed by GitHub
parent dd4c7b49b6 863a37b6d4
commit 1bf4e8513d
14 changed files with 68 additions and 89 deletions
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pkgs/by-name/do/dolfinx/package.nix
+2 -19
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@@ -2,7 +2,6 @@
lib,
stdenv,
fetchFromGitHub,
fetchpatch,
cmake,
pkg-config,
spdlog,
@@ -26,32 +25,16 @@ let
);
in
stdenv.mkDerivation (finalAttrs: {
version = "0.10.0.post5";
version = "0.11.0.post0";
pname = "dolfinx";
src = fetchFromGitHub {
owner = "fenics";
repo = "dolfinx";
tag = "v${finalAttrs.version}";
hash = "sha256-CK7YEtJtrx/Mto72RHT4Qjg5StO28Et+FeCYxk5T+8s=";
hash = "sha256-brmU6AA7lN4TyHjHcg4mHUIj/OvJ16pfspEN95M4oOE=";
};
patches = [
# Fix wrong span extent in _lift_bc_interior_facets
# https://github.com/FEniCS/dolfinx/pull/4102
(fetchpatch {
url = "https://github.com/FEniCS/dolfinx/commit/6daca34a075a6dcdfdf77feb13d55d5dbd20e4dd.patch";
hash = "sha256-b/C1MqslS2OBCt+kK/+vJjW8pmsJx2FQ36qDtFA1ewI=";
includes = [ "cpp/dolfinx/fem/assemble_vector_impl.h" ];
})
# Fix hdf5 interface for rank 1
# https://github.com/FEniCS/dolfinx/pull/4043
(fetchpatch {
url = "https://github.com/FEniCS/dolfinx/commit/fce7c44f220d4cb94c5149ad28cd1ab00909c319.patch";
hash = "sha256-EVm4Rx5UO/3pKIVvjgYAkN+i5QR+u0Nxwxotlf41t+Q=";
})
];
nativeBuildInputs = [
cmake
pkg-config
pkgs/by-name/li/libsupermesh/package.nix
+4 -4
View File
@@ -14,13 +14,13 @@
stdenv.mkDerivation (finalAttrs: {
pname = "libsupermesh";
version = "2025.4";
version = "2026.0";
src = fetchFromGitHub {
owner = "firedrakeproject";
repo = "libsupermesh";
tag = "v${finalAttrs.version}";
hash = "sha256-VIGfuSVneCBapZyU0GXyi6isUSdhD2Ylm4mCymSvzbo=";
tag = finalAttrs.version;
hash = "sha256-f/5y3XherRbN/Eq3tfivrOHByF8LAXtYN3v9Vx82m8Q=";
};
strictDeps = true;
@@ -68,7 +68,7 @@ stdenv.mkDerivation (finalAttrs: {
meta = {
homepage = "https://github.com/firedrakeproject/libsupermesh";
description = "Parallel supermeshing library";
changelog = "https://github.com/firedrakeproject/libsupermesh/releases/tag/v${finalAttrs.version}";
changelog = "https://github.com/firedrakeproject/libsupermesh/releases/tag/${finalAttrs.version}";
license = lib.licenses.lgpl2Plus;
platforms = lib.platforms.unix;
maintainers = with lib.maintainers; [ qbisi ];
pkgs/by-name/pe/petsc/fix-petsc4py-install-prefix.patch
-22
View File
@@ -1,22 +0,0 @@
diff --git a/config/BuildSystem/config/packages/petsc4py.py b/config/BuildSystem/config/packages/petsc4py.py
index 4a58243..831aa04 100644
--- a/config/BuildSystem/config/packages/petsc4py.py
+++ b/config/BuildSystem/config/packages/petsc4py.py
@@ -37,7 +37,7 @@ class Configure(config.package.Package):
def Install(self):
import os
- installLibPath = os.path.join(self.installDir, 'lib')
+ installLibPath = os.path.join(self.installDir, '@PYTHON_SITEPACKAGES@')
if self.setCompilers.isDarwin(self.log):
apple = 'You may need to\n (csh/tcsh) setenv MACOSX_DEPLOYMENT_TARGET 10.X\n (sh/bash) MACOSX_DEPLOYMENT_TARGET=10.X; export MACOSX_DEPLOYMENT_TARGET\nbefore running make on PETSc'
else:
@@ -70,7 +70,7 @@ class Configure(config.package.Package):
newdir += 'NUMPY_INCLUDE="'+numpy_include+'" '
self.addDefine('HAVE_PETSC4PY',1)
- self.addDefine('PETSC4PY_INSTALL_PATH','"'+os.path.join(self.installdir.dir,'lib')+'"')
+ self.addDefine('PETSC4PY_INSTALL_PATH','"'+installLibPath+'"')
self.addMakeMacro('PETSC4PY','yes')
self.addMakeRule('petsc4pybuild','', \
['@echo "*** Building petsc4py ***"',\
pkgs/by-name/pe/petsc/package.nix
+18 -14
View File
@@ -3,7 +3,6 @@
newScope,
stdenv,
fetchzip,
replaceVars,
bash,
pkg-config,
gfortran,
@@ -110,24 +109,24 @@ let
in
stdenv.mkDerivation (finalAttrs: {
pname = "petsc";
version = "3.24.6";
version = "3.25.2";
src = fetchzip {
url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${finalAttrs.version}.tar.gz";
hash = "sha256-PIW+dnIgnzQjpHqNBi4k730Bg7goO3G9zYVYoehvn7k=";
hash = "sha256-Q+QrOdSZO9wqdQKKVfhJzKaB3U80WdlegYtdZW7ScCg=";
};
patches = [
(replaceVars ./fix-petsc4py-install-prefix.patch {
PYTHON_SITEPACKAGES = python3Packages.python.sitePackages;
})
];
postPatch = ''
patchShebangs ./lib/petsc/bin
substituteInPlace config/example_template.py \
--replace-fail "/usr/bin/env bash" "${bash}/bin/bash"
substituteInPlace config/BuildSystem/config/packages/petsc4py.py \
--replace-fail "installLibPath = os.path.join(self.installDir, 'lib')" \
"installLibPath = os.path.join(self.installDir, '${python3Packages.python.sitePackages}')" \
--replace-fail "self.addDefine('PETSC4PY_INSTALL_PATH','\"'+os.path.join(self.installdir.dir,'lib')+'\"')" \
"self.addDefine('PETSC4PY_INSTALL_PATH','\"'+installLibPath+'\"')"
'';
strictDeps = true;
@@ -232,11 +231,16 @@ stdenv.mkDerivation (finalAttrs: {
# the library is installed and available.
doInstallCheck = true;
installCheckTarget = "check_install";
# The PETSC4PY=no flag disables the ex100 test,
# which compiles C code to load Python modules for solving a math problem.
# This test fails on the Darwin platform but is rarely a common use case for petsc4py.
installCheckFlags = lib.optional stdenv.hostPlatform.isDarwin "PETSC4PY=no";
# check_install is defined in PETSc's top-level makefile. Select it directly
# instead of the default GNUmakefile wrapper, then check the installed prefix
# by pointing PETSC_DIR at $out. PETSC_ARCH must be empty for prefix installs,
# where lib/petsc/conf is not nested below an architecture-specific build dir.
installCheckFlags = [
"-f"
"makefile"
"PETSC_DIR=${placeholder "out"}"
"PETSC_ARCH="
];
nativeInstallCheckInputs = [
mpiCheckPhaseHook
pkgs/by-name/sl/slepc/package.nix
+2 -2
View File
@@ -21,13 +21,13 @@ let
in
stdenv.mkDerivation (finalAttrs: {
pname = "slepc";
version = "3.24.3";
version = "3.25.1";
src = fetchFromGitLab {
owner = "slepc";
repo = "slepc";
tag = "v${finalAttrs.version}";
hash = "sha256-eCCdADdhatarzordwPKpJPIQbFWYngMlJvMBoVcTOWk=";
hash = "sha256-CLZ3l9H41MrXa4IEkiiGS7VSs3ASNk5/DnLMmJ7NY5U=";
};
postPatch = ''
pkgs/development/python-modules/fenics-basix/default.nix
+2 -2
View File
@@ -20,14 +20,14 @@
buildPythonPackage (finalAttrs: {
pname = "fenics-basix";
version = "0.10.0.post0";
version = "0.11.0";
pyproject = true;
src = fetchFromGitHub {
owner = "fenics";
repo = "basix";
tag = "v${finalAttrs.version}";
hash = "sha256-iKG6Cs28D0scPEIRKoGk/CgquKzGZvIjf4UIj4MQXHA=";
hash = "sha256-MBrK7O3iQ0XFONebbAFXBom9i985EyTAXrOlSMiIpk8=";
};
dontUseCmakeConfigure = true;
pkgs/development/python-modules/fenics-ffcx/default.nix
+2 -2
View File
@@ -15,14 +15,14 @@
buildPythonPackage (finalAttrs: {
pname = "fenics-ffcx";
version = "0.10.1.post0";
version = "0.11.0";
pyproject = true;
src = fetchFromGitHub {
owner = "fenics";
repo = "ffcx";
tag = "v${finalAttrs.version}";
hash = "sha256-uV3sfK6tpdoVf+O/EYZw3yR1PdqkoXt4q66zwQ8h/Ks=";
hash = "sha256-pAnoCLf1ObJ2jDOdQ0cr3qu3z+rNeAVFPnvegp/KqeM=";
};
pythonRelaxDeps = [
pkgs/development/python-modules/fenics-ufl/default.nix
+2 -2
View File
@@ -9,14 +9,14 @@
buildPythonPackage (finalAttrs: {
pname = "fenics-ufl";
version = "2025.2.1";
version = "2026.1.0";
pyproject = true;
src = fetchFromGitHub {
owner = "fenics";
repo = "ufl";
tag = finalAttrs.version;
hash = "sha256-7hibe/oVueK5YORhA81641b5UcE4MVyQvgVD0Fngje4=";
hash = "sha256-FwU9QmkyYuUfxt4v8sHFv+YNHldx1g0e/TDezijTUb4=";
};
build-system = [
pkgs/development/python-modules/firedrake-fiat/default.nix
+8 -9
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@@ -2,37 +2,36 @@
lib,
buildPythonPackage,
fetchFromGitHub,
fetchFromBitbucket,
setuptools,
numpy,
scipy,
sympy,
recursivenodes,
symengine,
fenics-ufl,
firedrake-ufl,
pytestCheckHook,
nix-update-script,
}:
buildPythonPackage (finalAttrs: {
pname = "firedrake-fiat";
version = "2025.10.1";
version = "2026.4.0";
pyproject = true;
src = fetchFromGitHub {
owner = "firedrakeproject";
repo = "fiat";
tag = finalAttrs.version;
hash = "sha256-x1/gf/QVez6GxPUafxdhxqyT0MkL6w2Qz6VAxRNufdc=";
hash = "sha256-aO4iFDwt9l5+s+96kjxja92OWnJb64OBpYXu6oxk51c=";
};
postPatch =
let
fiat-reference-data = fetchFromBitbucket {
owner = "fenics-project";
fiat-reference-data = fetchFromGitHub {
owner = "firedrakeproject";
repo = "fiat-reference-data";
rev = "0c8c97f7e4919402129e5ff3b54e3f0b9e902b7c";
hash = "sha256-vdCkmCkKvLSYACF6MnZ/WuKuCNAoC3uu1A/9m9KwBK8=";
rev = "508bd755e024010f6fc691a36e51a8f4d7de7efe";
hash = "sha256-Ylq5u3d54SnCiB3nLRkkQu7IkRVuMcUWPgIjn7SIQ0M=";
};
in
''
@@ -46,7 +45,7 @@ buildPythonPackage (finalAttrs: {
scipy
sympy
recursivenodes
fenics-ufl
firedrake-ufl
symengine
];
pkgs/development/python-modules/firedrake-ufl/default.nix
+12
View File
@@ -0,0 +1,12 @@
{
fenics-ufl,
}:
fenics-ufl.overrideAttrs (oldAttrs: rec {
version = "2025.3.0";
src = oldAttrs.src.override {
tag = version;
hash = "sha256-BFeVwurTsFNirpjZlgaABzw/cLzWxXwbCHJQBHrLuOY=";
};
})
pkgs/development/python-modules/firedrake/default.nix
+5 -9
View File
@@ -15,7 +15,7 @@
decorator,
cachetools,
mpi4py,
fenics-ufl,
firedrake-ufl,
firedrake-fiat,
h5py,
libsupermesh,
@@ -34,7 +34,6 @@
scipy,
sympy,
islpy,
vtk,
matplotlib,
immutabledict,
@@ -59,20 +58,20 @@ let
in
buildPythonPackage (finalAttrs: {
pname = "firedrake";
version = "2025.10.3";
version = "2026.4.1";
pyproject = true;
src = fetchFromGitHub {
owner = "firedrakeproject";
repo = "firedrake";
tag = finalAttrs.version;
hash = "sha256-9AkyVM0dpjdQqpuOBN60lCKIZJR0HXpp0g1Am/xUwbI=";
hash = "sha256-scsxxs9k280R9+mM5CC7aIkKJ8rR1faexnUuMrDO9+k=";
};
# relax build-dependency petsc4py
postPatch = ''
substituteInPlace pyproject.toml --replace-fail \
"petsc4py==3.24.5" "petsc4py"
"petsc4py==3.25.0" "petsc4py"
'';
pythonRelaxDeps = [
@@ -99,7 +98,7 @@ buildPythonPackage (finalAttrs: {
decorator
cachetools
firedrakePackages.mpi4py
fenics-ufl
firedrake-ufl
firedrake-fiat
firedrakePackages.h5py
immutabledict
@@ -118,9 +117,6 @@ buildPythonPackage (finalAttrs: {
rtree
scipy
sympy
# vtk optional required by IO module, we can make it a hard dependency in nixpkgs,
# see https://github.com/firedrakeproject/firedrake/pull/4713
vtk
# required by script spydump
matplotlib
]
pkgs/development/python-modules/petsctools/default.nix
+7 -2
View File
@@ -11,14 +11,14 @@
buildPythonPackage (finalAttrs: {
pname = "petsctools";
version = "2025.3";
version = "2026.0";
pyproject = true;
src = fetchFromGitHub {
owner = "firedrakeproject";
repo = "petsctools";
tag = finalAttrs.version;
hash = "sha256-5SV34KhympX58lWfFaQo5lVOeafcc/Y8HvYtZtY+4Eo=";
hash = "sha256-IMDPjhyehOkyifSJ7nOJQbZu21w6Xyyz9fv/WLDpEgQ=";
};
build-system = [
@@ -43,6 +43,11 @@ buildPythonPackage (finalAttrs: {
]
++ finalAttrs.passthru.optional-dependencies.petsc4py;
disabledTests = [
# Expects a double slash when PETSC_ARCH is empty.
"test_get_petsc_dirs"
];
meta = {
homepage = "https://github.com/firedrakeproject/petsctools";
description = "Pythonic extensions for petsc4py and slepc4py";
pkgs/development/python-modules/pyadjoint-ad/default.nix
+2 -2
View File
@@ -11,14 +11,14 @@
buildPythonPackage (finalAttrs: {
pname = "pyadjoint-ad";
version = "2025.10.1";
version = "2026.4.1";
pyproject = true;
src = fetchFromGitHub {
owner = "dolfin-adjoint";
repo = "pyadjoint";
tag = finalAttrs.version;
hash = "sha256-UI1eRB9hy4lb/s18NjaAyjH3HvDwRbRzk0ZuWxf1Uuc=";
hash = "sha256-ChtZQ5MJeQt1CqAsFHTCwbIJrcwBKlNxSF5zi6pHLsA=";
};
build-system = [
pkgs/top-level/python-packages.nix
+2
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@@ -5662,6 +5662,8 @@ self: super: with self; {
firedrake-fiat = callPackage ../development/python-modules/firedrake-fiat { };
firedrake-ufl = callPackage ../development/python-modules/firedrake-ufl { };
fireflyalgorithm = callPackage ../development/python-modules/fireflyalgorithm { };
firetv = callPackage ../development/python-modules/firetv { };