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julia_111{,-bin}: init at 1.11.0 (#347361)

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This commit is contained in:
Nick Cao
2024-10-17 08:38:19 -04:00
committed by GitHub
parent 2a55bdc8cf bc84d24ec9
commit 1c5fb94b3b
10 changed files with 178 additions and 246 deletions
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pkgs/development/compilers/julia/1.6-bin.nix
-72
View File
@@ -1,72 +0,0 @@
{ autoPatchelfHook, fetchurl, lib, stdenv }:
stdenv.mkDerivation rec {
pname = "julia-bin";
version = "1.6.7";
src = {
x86_64-linux = fetchurl {
url = "https://julialang-s3.julialang.org/bin/linux/x64/${lib.versions.majorMinor version}/julia-${version}-linux-x86_64.tar.gz";
sha256 = "sha256-bEUi1ZXky80AFXrEWKcviuwBdXBT0gc/mdqjnkQrKjY=";
};
}.${stdenv.hostPlatform.system} or (throw "Unsupported system: ${stdenv.hostPlatform.system}");
# Julia’s source files are in different locations for source and binary
# releases. Thus we temporarily create a symlink to allow us to share patches
# with source releases.
prePatch = ''
ln -s share/julia/test
'';
patches = [
# Source release Nix patch(es) relevant for binary releases as well.
./patches/1.6-bin/0005-nix-Enable-parallel-unit-tests-for-sandbox.patch
];
postPatch = ''
# Revert symlink hack.
rm test
# Julia fails to pick up our Certification Authority root certificates, but
# it provides its own so we can simply disable the test. Patching in the
# dynamic path to ours require us to rebuild the Julia system image.
substituteInPlace share/julia/stdlib/v${lib.versions.majorMinor version}/NetworkOptions/test/runtests.jl \
--replace '@test ca_roots_path() != bundled_ca_roots()' \
'@test_skip ca_roots_path() != bundled_ca_roots()'
'';
nativeBuildInputs = [ autoPatchelfHook ];
installPhase = ''
runHook preInstall
cp -r . $out
runHook postInstall
'';
# Breaks backtraces, etc.
dontStrip = true;
doInstallCheck = true;
preInstallCheck = ''
# Some tests require read/write access to $HOME.
export HOME="$TMPDIR"
'';
installCheckPhase = ''
runHook preInstallCheck
# Command lifted from `test/Makefile`.
$out/bin/julia \
--check-bounds=yes \
--startup-file=no \
--depwarn=error \
$out/share/julia/test/runtests.jl
runHook postInstallCheck
'';
meta = {
description = "High-level, high-performance, dynamic language for technical computing";
homepage = "https://julialang.org";
# Bundled and linked with various GPL code, although Julia itself is MIT.
license = lib.licenses.gpl2Plus;
maintainers = with lib.maintainers; [ raskin thomasjm ];
platforms = [ "x86_64-linux" ];
mainProgram = "julia";
};
}
pkgs/development/compilers/julia/default.nix
+20 -1
View File
@@ -12,7 +12,6 @@ let
in
{
julia_16-bin = wrapJulia (callPackage ./1.6-bin.nix { });
julia_19-bin = wrapJulia (callPackage
(import ./generic-bin.nix {
version = "1.9.4";
@@ -39,6 +38,17 @@ in
};
})
{ });
julia_111-bin = wrapJulia (callPackage
(import ./generic-bin.nix {
version = "1.11.1";
sha256 = {
x86_64-linux = "cca8d13dc4507e4f62a129322293313ee574f300d4df9e7db30b7b41c5f8a8f3";
aarch64-linux = "bd623ef3801c5a56103464d349c7901d5cc034405ad289332c67f1e8ecc05840";
x86_64-darwin = "59885de9310788c1ed12f41e7d2c2f05eabd314888cd105d299837b76a4a7240";
aarch64-darwin = "e09d13e1c6c98452e91e698220688dd784ec8e5367e9e6443099c5f9aa2add78";
};
})
{ });
julia_19 = wrapJulia (callPackage
(import ./generic.nix {
version = "1.9.4";
@@ -57,4 +67,13 @@ in
];
})
{ });
julia_111 = wrapJulia (callPackage
(import ./generic.nix {
version = "1.11.1";
hash = "sha256-pJuATeboagP+Jsc/WIUeruH/JD1yBPK1rk28XB3CdY0=";
patches = [
./patches/1.11/0002-skip-failing-and-flaky-tests.patch
];
})
{ });
}
pkgs/development/compilers/julia/generic-bin.nix
+5
View File
@@ -24,6 +24,11 @@ let
"REPL"
# Test flaky
"ccall"
] ++ lib.optionals (lib.versionAtLeast version "1.11") [
# Test flaky
# https://github.com/JuliaLang/julia/issues/54280
"loading"
"cmdlineargs"
] ++ lib.optionals stdenv.hostPlatform.isDarwin [
# Test flaky on ofborg
"FileWatching"
pkgs/development/compilers/julia/generic.nix
+8
View File
@@ -9,12 +9,14 @@
, which
, python3
, gfortran
, cacert
, cmake
, perl
, gnum4
, openssl
, libxml2
, zlib
, buildPackages
}:
stdenv.mkDerivation rec {
@@ -42,12 +44,18 @@ stdenv.mkDerivation rec {
buildInputs = [
libxml2
zlib
] ++ lib.optionals (lib.versionAtLeast version "1.11") [
cacert
];
dontUseCmakeConfigure = true;
postPatch = ''
patchShebangs .
'' + lib.optionalString (lib.versionAtLeast version "1.11") ''
substituteInPlace deps/curl.mk \
--replace-fail 'cd $(dir $<) && $(TAR) jxf $(notdir $<)' \
'cd $(dir $<) && $(TAR) jxf $(notdir $<) && sed -i "s|/usr/bin/env perl|${lib.getExe buildPackages.perl}|" curl-$(CURL_VER)/scripts/cd2nroff'
'';
makeFlags = [
pkgs/development/compilers/julia/patches/1.11/0002-skip-failing-and-flaky-tests.patch
+25
View File
@@ -0,0 +1,25 @@
From 9da2f2596db9f4f1a61825d82d9b8c3f3b2e99aa Mon Sep 17 00:00:00 2001
From: Nick Cao <nickcao@nichi.co>
Date: Wed, 10 Jan 2024 20:58:20 -0500
Subject: [PATCH 2/2] skip failing and flaky tests
---
test/Makefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/test/Makefile b/test/Makefile
index 88dbe5b2b4..a2a7a55e20 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -28,7 +28,7 @@ default:
$(TESTS):
@cd $(SRCDIR) && \
- $(call PRINT_JULIA, $(call spawn,$(JULIA_EXECUTABLE)) --check-bounds=yes --startup-file=no --depwarn=error ./runtests.jl $@)
+ $(call PRINT_JULIA, $(call spawn,$(JULIA_EXECUTABLE)) --check-bounds=yes --startup-file=no --depwarn=error ./runtests.jl --skip NetworkOptions REPL channels FileWatching ccall loading cmdlineargs $@)
$(addprefix revise-, $(TESTS)): revise-% :
@cd $(SRCDIR) && \
--
2.43.0
pkgs/development/compilers/julia/patches/1.6-bin/0005-nix-Enable-parallel-unit-tests-for-sandbox.patch
-30
View File
@@ -1,30 +0,0 @@
From 44c2c979c4f2222567ce65f506cf47fb87482348 Mon Sep 17 00:00:00 2001
From: Pontus Stenetorp <pontus@stenetorp.se>
Date: Thu, 8 Apr 2021 04:37:44 +0000
Subject: [PATCH 5/6] nix: Enable parallel unit tests for sandbox
Disabled by default due to lack of networking in the Nix sandbox. This
greatly speeds up the build process on a multi-core system.
---
test/runtests.jl | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/test/runtests.jl b/test/runtests.jl
index 2f9cd058bb..2f8c19fa32 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -83,8 +83,9 @@ prepend!(tests, linalg_tests)
import LinearAlgebra
cd(@__DIR__) do
n = 1
- if net_on
- n = min(Sys.CPU_THREADS, length(tests))
+ if net_on || haskey(ENV, "NIX_BUILD_CORES")
+ x = haskey(ENV, "NIX_BUILD_CORES") ? parse(Int, ENV["NIX_BUILD_CORES"]) : Sys.CPU_THREADS
+ n = min(x, Sys.CPU_THREADS, length(tests))
n > 1 && addprocs_with_testenv(n)
LinearAlgebra.BLAS.set_num_threads(1)
end
--
2.29.3
pkgs/development/julia-modules/package-closure.nix
+13 -137
View File
@@ -10,131 +10,6 @@
}:
let
# The specific package resolution code depends on the Julia version
# These are pretty similar and could be combined to reduce duplication
resolveCode = if lib.versionOlder julia.version "1.7" then resolveCode1_6 else resolveCode1_8;
resolveCode1_6 = ''
import Pkg.API: check_package_name
import Pkg.Types: Context!, PRESERVE_NONE, manifest_info, project_deps_resolve!, registry_resolve!, stdlib_resolve!, ensure_resolved
import Pkg.Operations: _resolve, assert_can_add, is_dep, update_package_add
foreach(pkg -> check_package_name(pkg.name, :add), pkgs)
pkgs = deepcopy(pkgs) # deepcopy for avoid mutating PackageSpec members
Context!(ctx)
project_deps_resolve!(ctx, pkgs)
registry_resolve!(ctx, pkgs)
stdlib_resolve!(pkgs)
ensure_resolved(ctx, pkgs, registry=true)
assert_can_add(ctx, pkgs)
for (i, pkg) in pairs(pkgs)
entry = manifest_info(ctx, pkg.uuid)
pkgs[i] = update_package_add(ctx, pkg, entry, is_dep(ctx, pkg))
end
foreach(pkg -> ctx.env.project.deps[pkg.name] = pkg.uuid, pkgs)
pkgs, deps_map = _resolve(ctx, pkgs, PRESERVE_NONE)
'';
resolveCode1_8 = ''
import Pkg.API: handle_package_input!
import Pkg.Types: PRESERVE_NONE, UUID, VersionSpec, project_deps_resolve!, registry_resolve!, stdlib_resolve!, ensure_resolved
import Pkg.Operations: _resolve, assert_can_add, update_package_add
import TOML
foreach(handle_package_input!, pkgs)
# The handle_package_input! call above clears pkg.path, so we have to apply package overrides after
overrides = Dict{String, String}(${builtins.concatStringsSep ", " (lib.mapAttrsToList (name: path: ''"${name}" => "${path}"'') packageOverrides)})
println("Package overrides: ")
println(overrides)
for pkg in pkgs
if pkg.name in keys(overrides)
pkg.path = overrides[pkg.name]
# Try to read the UUID from $(pkg.path)/Project.toml. If successful, put the package into ctx.env.project.deps.
# This is necessary for the ensure_resolved call below to succeed, and will allow us to use an override even
# if it does not appear in the registry.
# See https://github.com/NixOS/nixpkgs/issues/279853
project_toml = joinpath(pkg.path, "Project.toml")
if isfile(project_toml)
toml_data = TOML.parsefile(project_toml)
if haskey(toml_data, "uuid")
ctx.env.project.deps[pkg.name] = UUID(toml_data["uuid"])
end
end
end
end
project_deps_resolve!(ctx.env, pkgs)
registry_resolve!(ctx.registries, pkgs)
stdlib_resolve!(pkgs)
ensure_resolved(ctx, ctx.env.manifest, pkgs, registry=true)
assert_can_add(ctx, pkgs)
for (i, pkg) in pairs(pkgs)
entry = Pkg.Types.manifest_info(ctx.env.manifest, pkg.uuid)
is_dep = any(uuid -> uuid == pkg.uuid, [uuid for (name, uuid) in ctx.env.project.deps])
pkgs[i] = update_package_add(ctx, pkg, entry, is_dep)
end
foreach(pkg -> ctx.env.project.deps[pkg.name] = pkg.uuid, pkgs)
# Save the original pkgs for later. We might need to augment it with the weak dependencies
orig_pkgs = pkgs
pkgs, deps_map = _resolve(ctx.io, ctx.env, ctx.registries, pkgs, PRESERVE_NONE, ctx.julia_version)
if VERSION >= VersionNumber("1.9")
while true
# Check for weak dependencies, which appear on the RHS of the deps_map but not in pkgs.
# Build up weak_name_to_uuid
uuid_to_name = Dict()
for pkg in pkgs
uuid_to_name[pkg.uuid] = pkg.name
end
weak_name_to_uuid = Dict()
for (uuid, deps) in pairs(deps_map)
for (dep_name, dep_uuid) in pairs(deps)
if !haskey(uuid_to_name, dep_uuid)
weak_name_to_uuid[dep_name] = dep_uuid
end
end
end
if isempty(weak_name_to_uuid)
break
end
# We have nontrivial weak dependencies, so add each one to the initial pkgs and then re-run _resolve
println("Found weak dependencies: $(keys(weak_name_to_uuid))")
orig_uuids = Set([pkg.uuid for pkg in orig_pkgs])
for (name, uuid) in pairs(weak_name_to_uuid)
if uuid in orig_uuids
continue
end
pkg = PackageSpec(name, uuid)
push!(orig_uuids, uuid)
push!(orig_pkgs, pkg)
ctx.env.project.deps[name] = uuid
entry = Pkg.Types.manifest_info(ctx.env.manifest, uuid)
orig_pkgs[length(orig_pkgs)] = update_package_add(ctx, pkg, entry, false)
end
global pkgs, deps_map = _resolve(ctx.io, ctx.env, ctx.registries, orig_pkgs, PRESERVE_NONE, ctx.julia_version)
end
end
'';
juliaExpression = packageNames: ''
import Pkg
Pkg.Registry.add(Pkg.RegistrySpec(path="${augmentedRegistry}"))
@@ -144,7 +19,7 @@ let
input = ${lib.generators.toJSON {} packageNames}
if isfile("extra_package_names.txt")
append!(input, readlines("extra_package_names.txt"))
append!(input, readlines("extra_package_names.txt"))
end
input = unique(input)
@@ -155,20 +30,21 @@ let
ctx = Context()
${resolveCode}
overrides = Dict{String, String}(${builtins.concatStringsSep ", " (lib.mapAttrsToList (name: path: ''"${name}" => "${path}"'') packageOverrides)})
${builtins.readFile ./resolve_packages.jl}
open(ENV["out"], "w") do io
for spec in pkgs
println(io, "- name: " * spec.name)
println(io, " uuid: " * string(spec.uuid))
println(io, " version: " * string(spec.version))
if endswith(spec.name, "_jll") && haskey(deps_map, spec.uuid)
println(io, " depends_on: ")
for (dep_name, dep_uuid) in pairs(deps_map[spec.uuid])
println(io, " \"$(dep_name)\": \"$(dep_uuid)\"")
end
for spec in pkgs
println(io, "- name: " * spec.name)
println(io, " uuid: " * string(spec.uuid))
println(io, " version: " * string(spec.version))
if endswith(spec.name, "_jll") && haskey(deps_map, spec.uuid)
println(io, " depends_on: ")
for (dep_name, dep_uuid) in pairs(deps_map[spec.uuid])
println(io, " \"$(dep_name)\": \"$(dep_uuid)\"")
end
end
end
end
end
'';
in
pkgs/development/julia-modules/resolve_packages.jl
+99
View File
@@ -0,0 +1,99 @@
import Pkg.API: handle_package_input!
import Pkg.Types: PRESERVE_NONE, UUID, VersionSpec, project_deps_resolve!, registry_resolve!, stdlib_resolve!, ensure_resolved
import Pkg.Operations: _resolve, assert_can_add, update_package_add
import TOML
foreach(handle_package_input!, pkgs)
# The handle_package_input! call above clears pkg.path, so we have to apply package overrides after
println("Package overrides: ")
println(overrides)
for pkg in pkgs
if pkg.name in keys(overrides)
pkg.path = overrides[pkg.name]
# Try to read the UUID from $(pkg.path)/Project.toml. If successful, put the package into ctx.env.project.deps.
# This is necessary for the ensure_resolved call below to succeed, and will allow us to use an override even
# if it does not appear in the registry.
# See https://github.com/NixOS/nixpkgs/issues/279853
project_toml = joinpath(pkg.path, "Project.toml")
if isfile(project_toml)
toml_data = TOML.parsefile(project_toml)
if haskey(toml_data, "uuid")
ctx.env.project.deps[pkg.name] = UUID(toml_data["uuid"])
end
end
end
end
project_deps_resolve!(ctx.env, pkgs)
registry_resolve!(ctx.registries, pkgs)
stdlib_resolve!(pkgs)
ensure_resolved(ctx, ctx.env.manifest, pkgs, registry=true)
assert_can_add(ctx, pkgs)
for (i, pkg) in pairs(pkgs)
entry = Pkg.Types.manifest_info(ctx.env.manifest, pkg.uuid)
is_dep = any(uuid -> uuid == pkg.uuid, [uuid for (name, uuid) in ctx.env.project.deps])
if VERSION >= VersionNumber("1.11")
pkgs[i] = update_package_add(ctx, pkg, entry, nothing, nothing, is_dep)
else
pkgs[i] = update_package_add(ctx, pkg, entry, is_dep)
end
end
foreach(pkg -> ctx.env.project.deps[pkg.name] = pkg.uuid, pkgs)
# Save the original pkgs for later. We might need to augment it with the weak dependencies
orig_pkgs = pkgs
pkgs, deps_map = _resolve(ctx.io, ctx.env, ctx.registries, pkgs, PRESERVE_NONE, ctx.julia_version)
if VERSION >= VersionNumber("1.9")
while true
# Check for weak dependencies, which appear on the RHS of the deps_map but not in pkgs.
# Build up weak_name_to_uuid
uuid_to_name = Dict()
for pkg in pkgs
uuid_to_name[pkg.uuid] = pkg.name
end
weak_name_to_uuid = Dict()
for (uuid, deps) in pairs(deps_map)
for (dep_name, dep_uuid) in pairs(deps)
if !haskey(uuid_to_name, dep_uuid)
weak_name_to_uuid[dep_name] = dep_uuid
end
end
end
if isempty(weak_name_to_uuid)
break
end
# We have nontrivial weak dependencies, so add each one to the initial pkgs and then re-run _resolve
println("Found weak dependencies: $(keys(weak_name_to_uuid))")
orig_uuids = Set([pkg.uuid for pkg in orig_pkgs])
for (name, uuid) in pairs(weak_name_to_uuid)
if uuid in orig_uuids
continue
end
pkg = PackageSpec(name, uuid)
push!(orig_uuids, uuid)
push!(orig_pkgs, pkg)
ctx.env.project.deps[name] = uuid
entry = Pkg.Types.manifest_info(ctx.env.manifest, uuid)
if VERSION >= VersionNumber("1.11")
orig_pkgs[length(orig_pkgs)] = update_package_add(ctx, pkg, entry, nothing, nothing, false)
else
orig_pkgs[length(orig_pkgs)] = update_package_add(ctx, pkg, entry, false)
end
end
global pkgs, deps_map = _resolve(ctx.io, ctx.env, ctx.registries, orig_pkgs, PRESERVE_NONE, ctx.julia_version)
end
end
pkgs/top-level/aliases.nix
+1
View File
@@ -779,6 +779,7 @@ mapAliases {
jsawk = throw "'jsawk' has been removed because it is unmaintained upstream"; # Added 2028-08-07
# Julia
julia_16-bin = throw "'julia_16-bin' has been removed from nixpkgs as it has reached end of life"; # Added 2024-10-08
julia_18 = throw "'julia_18' has been removed from nixpkgs as it has reached end of life"; # Added 2024-01-11
julia_18-bin = throw "'julia_18-bin' has been removed from nixpkgs as it has reached end of life"; # Added 2024-01-11
pkgs/top-level/all-packages.nix
+7 -6
View File
@@ -15142,18 +15142,19 @@ with pkgs;
juniper = callPackage ../development/compilers/juniper { };
inherit (callPackage ../development/compilers/julia { })
julia_16-bin
julia_19-bin
julia_110-bin
julia_111-bin
julia_19
julia_110;
julia_110
julia_111;
julia-lts = julia_16-bin;
julia-stable = julia_110;
julia-lts = julia_110-bin;
julia-stable = julia_111;
julia = julia-stable;
julia-lts-bin = julia_16-bin;
julia-stable-bin = julia_110-bin;
julia-lts-bin = julia_110-bin;
julia-stable-bin = julia_111-bin;
julia-bin = julia-stable-bin;
kind2 = darwin.apple_sdk_11_0.callPackage ../development/compilers/kind2 { };