python3Packages.fenics: drop (#431840)
This commit is contained in:
Nick Cao
@@ -506,7 +506,6 @@ in
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fanout = runTest ./fanout.nix;
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fcitx5 = runTest ./fcitx5;
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fedimintd = runTest ./fedimintd.nix;
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fenics = runTest ./fenics.nix;
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ferm = runTest ./ferm.nix;
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ferretdb = import ./ferretdb.nix { inherit pkgs runTest; };
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fider = runTest ./fider.nix;
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@@ -1,51 +0,0 @@
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{ pkgs, ... }:
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let
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fenicsScript = pkgs.writeScript "poisson.py" ''
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#!/usr/bin/env python
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from dolfin import *
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mesh = UnitSquareMesh(4, 4)
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V = FunctionSpace(mesh, "Lagrange", 1)
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def boundary(x):
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return x[0] < DOLFIN_EPS or x[0] > 1.0 - DOLFIN_EPS
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u0 = Constant(0.0)
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bc = DirichletBC(V, u0, boundary)
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u = TrialFunction(V)
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v = TestFunction(V)
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f = Expression("10*exp(-(pow(x[0] - 0.5, 2) + pow(x[1] - 0.5, 2)) / 0.02)", degree=2)
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g = Expression("sin(5*x[0])", degree=2)
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a = inner(grad(u), grad(v))*dx
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L = f*v*dx + g*v*ds
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u = Function(V)
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solve(a == L, u, bc)
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print(u)
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'';
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in
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{
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name = "fenics";
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meta = {
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maintainers = with pkgs.lib.maintainers; [ ];
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};
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nodes = {
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fenicsnode =
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{ pkgs, ... }:
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{
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environment.systemPackages = with pkgs; [
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gcc
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(python3.withPackages (ps: with ps; [ fenics ]))
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];
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};
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};
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testScript =
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{ nodes, ... }:
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''
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start_all()
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fenicsnode.succeed("${fenicsScript}")
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'';
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}
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@@ -1,311 +0,0 @@
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{
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lib,
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stdenv,
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fetchurl,
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fetchpatch,
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blas,
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boost186,
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buildPythonPackage,
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cmake,
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doxygen,
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eigen,
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hdf5,
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isPy27,
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lapack,
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mpi,
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mpi4py,
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numpy,
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pkg-config,
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pkgconfig,
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ply,
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pybind11,
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pytest,
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python,
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scotch,
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setuptools,
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six,
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sphinx,
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suitesparse,
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swig,
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sympy,
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zlib,
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nixosTests,
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}:
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let
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version = "2019.1.0";
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dijitso = buildPythonPackage {
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pname = "dijitso";
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inherit version;
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format = "setuptools";
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src = fetchurl {
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url = "https://bitbucket.org/fenics-project/dijitso/downloads/dijitso-${version}.tar.gz";
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sha256 = "1ncgbr0bn5cvv16f13g722a0ipw6p9y6p4iasxjziwsp8kn5x97a";
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};
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propagatedBuildInputs = [
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numpy
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six
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];
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nativeCheckInputs = [ pytest ];
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preCheck = ''
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export HOME=$PWD
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'';
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checkPhase = ''
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runHook preCheck
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py.test test/
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runHook postCheck
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'';
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meta = {
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description = "Distributed just-in-time shared library building";
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homepage = "https://fenicsproject.org/";
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platforms = lib.platforms.all;
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license = lib.licenses.lgpl3;
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};
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};
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fiat = buildPythonPackage {
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pname = "fiat";
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inherit version;
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format = "setuptools";
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src = fetchurl {
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url = "https://bitbucket.org/fenics-project/fiat/downloads/fiat-${version}.tar.gz";
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sha256 = "1sbi0fbr7w9g9ajr565g3njxrc3qydqjy3334vmz5xg0rd3106il";
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};
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propagatedBuildInputs = [
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numpy
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six
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sympy
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];
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nativeCheckInputs = [ pytest ];
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preCheck = ''
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# Workaround pytest 4.6.3 issue.
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# See: https://bitbucket.org/fenics-project/fiat/pull-requests/59
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rm test/unit/test_quadrature.py
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rm test/unit/test_reference_element.py
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rm test/unit/test_fiat.py
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# Fix `np.float` deprecation in Numpy 1.20
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grep -lr 'np.float(' test/ | while read -r fn; do
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substituteInPlace "$fn" \
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--replace "np.float(" "np.float64("
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done
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'';
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checkPhase = ''
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runHook preCheck
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py.test test/unit/
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runHook postCheck
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'';
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meta = {
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description = "Automatic generation of finite element basis functions";
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homepage = "https://fenicsproject.org/";
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platforms = lib.platforms.all;
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license = lib.licenses.lgpl3;
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};
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};
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ufl = buildPythonPackage {
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pname = "ufl";
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inherit version;
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format = "setuptools";
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src = fetchurl {
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url = "https://bitbucket.org/fenics-project/ufl/downloads/ufl-${version}.tar.gz";
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sha256 = "04daxwg4y9c51sdgvwgmlc82nn0fjw7i2vzs15ckdc7dlazmcfi1";
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};
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propagatedBuildInputs = [
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numpy
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six
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];
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nativeCheckInputs = [ pytest ];
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checkPhase = ''
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runHook preCheck
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py.test test/
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runHook postCheck
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'';
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meta = {
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description = "Domain-specific language for finite element variational forms";
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homepage = "https://fenicsproject.org/";
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platforms = lib.platforms.all;
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license = lib.licenses.lgpl3;
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};
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};
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ffc = buildPythonPackage {
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pname = "ffc";
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inherit version;
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format = "setuptools";
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src = fetchurl {
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url = "https://bitbucket.org/fenics-project/ffc/downloads/ffc-${version}.tar.gz";
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sha256 = "1zdg6pziss4va74pd7jjl8sc3ya2gmhpypccmyd8p7c66ji23y2g";
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};
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patches = [
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(fetchpatch {
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name = "fenics-ffc-numpy2-compat.patch";
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url = "https://bitbucket.org/fenics-project/ffc/commits/245d15115b35b5ac091251fe6c84cc6474704b3c/raw";
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hash = "sha256-TcLQZ44C+uR2ryxtCBjR/5Tjn7B0S4MqoYi0nlP8JwI=";
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})
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];
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nativeBuildInputs = [ pybind11 ];
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propagatedBuildInputs = [
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dijitso
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fiat
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numpy
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six
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sympy
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ufl
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setuptools
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];
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nativeCheckInputs = [ pytest ];
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preCheck = ''
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export HOME=$PWD
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rm test/unit/ufc/finite_element/test_evaluate.py
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'';
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checkPhase = ''
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runHook preCheck
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py.test test/unit/
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runHook postCheck
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'';
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meta = {
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description = "Compiler for finite element variational forms";
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homepage = "https://fenicsproject.org/";
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platforms = lib.platforms.all;
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license = lib.licenses.lgpl3;
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};
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};
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dolfin = stdenv.mkDerivation {
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pname = "dolfin";
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inherit version;
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src = fetchurl {
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url = "https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-${version}.tar.gz";
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sha256 = "0kbyi4x5f6j4zpasch0swh0ch81w2h92rqm1nfp3ydi4a93vky33";
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};
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patches = [
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(fetchpatch {
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name = "fix-double-prefix.patch";
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url = "https://bitbucket.org/josef_kemetmueller/dolfin/commits/328e94acd426ebaf2243c072b806be3379fd4340/raw";
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sha256 = "1zj7k3y7vsx0hz3gwwlxhq6gdqamqpcw90d4ishwx5ps5ckcsb9r";
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})
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(fetchpatch {
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url = "https://bitbucket.org/fenics-project/dolfin/issues/attachments/1116/fenics-project/dolfin/1602778118.04/1116/0001-Use-__BYTE_ORDER__-instead-of-removed-Boost-endian.h.patch";
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hash = "sha256-wPaDmPU+jaD3ce3nNEbvM5p8e3zBdLozamLTJ/0ai2c=";
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})
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(fetchpatch {
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name = "fenics-boost-filesystem-1.85-compat.patch.";
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url = "https://bitbucket.org/sblauth/dolfin/commits/16fa03887b3e9ec417c484ddf92db104cb9a93f9/raw";
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hash = "sha256-ZMKfzeWlPre88cKzrj04Tj+nQWS4ixat0bBvyt3TJmk=";
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})
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];
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# https://aur.archlinux.org/cgit/aur.git/plain/PKGBUILD?h=dolfin&id=a965ad934f7b3d49a5e77fa6fb5e3c710ec2163e
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postPatch = ''
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sed -i '20 a #include <algorithm>' dolfin/geometry/IntersectionConstruction.cpp
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sed -i '26 a #include <algorithm>' dolfin/mesh/MeshFunction.h
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sed -i '25 a #include <cstdint>' dolfin/mesh/MeshConnectivity.h
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'';
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propagatedBuildInputs = [
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dijitso
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fiat
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numpy
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six
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ufl
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];
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nativeBuildInputs = [
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cmake
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doxygen
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pkg-config
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];
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buildInputs = [
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boost186
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dijitso
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eigen
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ffc
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fiat
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hdf5
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mpi
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numpy
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blas
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lapack
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ply
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python
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scotch
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six
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sphinx
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suitesparse
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swig
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sympy
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ufl
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zlib
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];
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cmakeFlags = [
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"-DDOLFIN_CXX_FLAGS=-std=c++11"
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"-DDOLFIN_AUTO_DETECT_MPI=ON"
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"-DDOLFIN_ENABLE_CHOLMOD=ON"
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"-DDOLFIN_ENABLE_DOCS=ON"
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"-DDOLFIN_ENABLE_HDF5=ON"
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"-DDOLFIN_ENABLE_MPI=ON"
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"-DDOLFIN_ENABLE_SCOTCH=ON"
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"-DDOLFIN_ENABLE_UMFPACK=ON"
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"-DDOLFIN_ENABLE_ZLIB=ON"
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"-DDOLFIN_SKIP_BUILD_TESTS=ON" # Otherwise SCOTCH is not found
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# TODO: Enable the following features
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"-DDOLFIN_ENABLE_PARMETIS=OFF"
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"-DDOLFIN_ENABLE_PETSC=OFF"
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"-DDOLFIN_ENABLE_SLEPC=OFF"
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"-DDOLFIN_ENABLE_TRILINOS=OFF"
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];
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installCheckPhase = ''
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source $out/share/dolfin/dolfin.conf
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make runtests
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'';
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meta = {
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description = "FEniCS Problem Solving Environment in Python and C++";
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homepage = "https://fenicsproject.org/";
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license = lib.licenses.lgpl3;
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};
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};
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python-dolfin = buildPythonPackage rec {
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pname = "dolfin";
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inherit version;
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format = "setuptools";
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disabled = isPy27;
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src = dolfin.src;
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sourceRoot = "${pname}-${version}/python";
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nativeBuildInputs = [
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pybind11
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cmake
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];
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dontUseCmakeConfigure = true;
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preConfigure = ''
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export CMAKE_PREFIX_PATH=${pybind11}/share/cmake/pybind11:$CMAKE_PREFIX_PATH
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substituteInPlace setup.py --replace "pybind11==2.2.4" "pybind11"
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substituteInPlace dolfin/jit/jit.py \
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--replace 'pkgconfig.exists("dolfin")' 'pkgconfig.exists("${dolfin}/lib/pkgconfig/dolfin.pc")' \
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--replace 'pkgconfig.parse("dolfin")' 'pkgconfig.parse("${dolfin}/lib/pkgconfig/dolfin.pc")'
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'';
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buildInputs = [
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dolfin
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boost186
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];
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propagatedBuildInputs = [
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dijitso
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ffc
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mpi4py
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numpy
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ufl
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pkgconfig
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pybind11
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];
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doCheck = false; # Tries to orte_ess_init and call ssh to localhost
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passthru.tests = {
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inherit (nixosTests) fenics;
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};
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meta = {
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description = "Python bindings for the DOLFIN FEM compiler";
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homepage = "https://fenicsproject.org/";
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platforms = lib.platforms.all;
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license = lib.licenses.lgpl3;
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};
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};
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in
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python-dolfin
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@@ -253,6 +253,7 @@ mapAliases ({
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fastpair = throw "fastpair is unmaintained upstream and has therefore been removed"; # added 2024-05-01
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faulthandler = throw "faulthandler is built into ${python.executable}"; # added 2021-07-12
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inherit (super.pkgs) fetchPypi; # added 2023-05-25
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fenics = throw "fenics has been removed, use fenics-dolfinx instead"; # added 2025-08-07
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filebrowser_safe = filebrowser-safe; # added 2024-01-03
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filemagic = throw "inactive since 2014, so use python-magic instead"; # added 2022-11-19
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flaskbabel = flask-babel; # added 2023-01-19
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@@ -5055,8 +5055,6 @@ self: super: with self; {
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feedparser = callPackage ../development/python-modules/feedparser { };
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fenics = callPackage ../development/python-modules/fenics { hdf5 = pkgs.hdf5_1_10; };
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fenics-basix = callPackage ../development/python-modules/fenics-basix { };
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fenics-dolfinx = callPackage ../development/python-modules/fenics-dolfinx { };
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Reference in New Issue
Block a user