Merge pull request #117881 from ninjin/juliaclean

julia: cleanup/reorganisation

pkgs/development/compilers/julia/1.0.nix

···
   ;
 
   patches = [
-    # Julia recompiles a precompiled file if the mtime stored *in* the
-    # .ji file differs from the mtime of the .ji file.  This
-    # doesn't work in Nix because Nix changes the mtime of files in
-    # the Nix store to 1. So patch Julia to accept mtimes of 1.
-    ./allow_nix_mtime.patch
-    ./diagonal-test.patch
-    ./use-system-utf8proc-julia-1.0.patch
+    ./patches/1.0/use-system-utf8proc-julia-1.0.patch
   ];
 
   postPatch = ''
···
     sed -e '/[$](DESTDIR)[$](docdir)/d' -i Makefile
     export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
   '';
+
+  enableParallelBuilding = true;
 
   postInstall = ''
     # Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,

pkgs/development/compilers/julia/1.3.nix

···
-{ lib, stdenv, fetchurl, fetchzip, fetchFromGitHub
-# build tools
-, gfortran, m4, makeWrapper, patchelf, perl, which, python2
-, cmake
-# libjulia dependencies
-, libunwind, readline, utf8proc, zlib
-# standard library dependencies
-, curl, fftwSinglePrec, fftw, gmp, libgit2, mpfr, openlibm, openspecfun, pcre2
-# linear algebra
-, blas, lapack, arpack
-# Darwin frameworks
-, CoreServices, ApplicationServices
-}:
-
-assert (!blas.isILP64) && (!lapack.isILP64);
-
-with lib;
-
-let
-  majorVersion = "1";
-  minorVersion = "3";
-  maintenanceVersion = "1";
-  src_sha256 = "0q9a7yc3b235psrwl5ghyxgwly25lf8n818l8h6bkf2ymdbsv5p6";
-  version = "${majorVersion}.${minorVersion}.${maintenanceVersion}";
-in
-
-stdenv.mkDerivation rec {
-  pname = "julia";
-  inherit version;
-
-   src = fetchzip {
-     url = "https://github.com/JuliaLang/julia/releases/download/v${majorVersion}.${minorVersion}.${maintenanceVersion}/julia-${majorVersion}.${minorVersion}.${maintenanceVersion}-full.tar.gz";
-     sha256 = src_sha256;
-   };
-
-  prePatch = ''
-    export PATH=$PATH:${cmake}/bin
-    '';
-
-  patches = [
-    ./use-system-utf8proc-julia-1.3.patch
-
-    # Julia recompiles a precompiled file if the mtime stored *in* the
-    # .ji file differs from the mtime of the .ji file.  This
-    # doesn't work in Nix because Nix changes the mtime of files in
-    # the Nix store to 1. So patch Julia to accept mtimes of 1.
-    ./allow_nix_mtime.patch
-  ];
-
-  postPatch = ''
-    patchShebangs . contrib
-    for i in backtrace cmdlineargs; do
-      mv test/$i.jl{,.off}
-      touch test/$i.jl
-    done
-    rm stdlib/Sockets/test/runtests.jl && touch stdlib/Sockets/test/runtests.jl
-    rm stdlib/Distributed/test/runtests.jl && touch stdlib/Distributed/test/runtests.jl
-    sed -e 's/Invalid Content-Type:/invalid Content-Type:/g' -i ./stdlib/LibGit2/test/libgit2.jl
-    sed -e 's/Failed to resolve /failed to resolve /g' -i ./stdlib/LibGit2/test/libgit2.jl
-  '';
-
-  buildInputs = [
-    arpack fftw fftwSinglePrec gmp libgit2 libunwind mpfr
-    pcre2.dev blas lapack openlibm openspecfun readline utf8proc
-    zlib
-  ]
-  ++ lib.optionals stdenv.isDarwin [CoreServices ApplicationServices]
-  ;
-
-  nativeBuildInputs = [ curl gfortran m4 makeWrapper patchelf perl python2 which ];
-
-  makeFlags =
-    let
-      arch = head (splitString "-" stdenv.system);
-      march = {
-        x86_64 = stdenv.hostPlatform.gcc.arch or "x86-64";
-        i686 = "pentium4";
-        aarch64 = "armv8-a";
-      }.${arch}
-              or (throw "unsupported architecture: ${arch}");
-      # Julia requires Pentium 4 (SSE2) or better
-      cpuTarget = { x86_64 = "x86-64"; i686 = "pentium4"; aarch64 = "generic"; }.${arch}
-                  or (throw "unsupported architecture: ${arch}");
-    in [
-      "ARCH=${arch}"
-      "MARCH=${march}"
-      "JULIA_CPU_TARGET=${cpuTarget}"
-      "PREFIX=$(out)"
-      "prefix=$(out)"
-      "SHELL=${stdenv.shell}"
-
-      (lib.optionalString (!stdenv.isDarwin) "USE_SYSTEM_BLAS=1")
-      "USE_BLAS64=${if blas.isILP64 then "1" else "0"}"
-
-      "USE_SYSTEM_LAPACK=1"
-
-      "USE_SYSTEM_ARPACK=1"
-      "USE_SYSTEM_FFTW=1"
-      "USE_SYSTEM_GMP=1"
-      "USE_SYSTEM_LIBGIT2=1"
-      "USE_SYSTEM_LIBUNWIND=1"
-
-      "USE_SYSTEM_MPFR=1"
-      "USE_SYSTEM_OPENLIBM=1"
-      "USE_SYSTEM_OPENSPECFUN=1"
-      "USE_SYSTEM_PATCHELF=1"
-      "USE_SYSTEM_PCRE=1"
-      "PCRE_CONFIG=${pcre2.dev}/bin/pcre2-config"
-      "PCRE_INCL_PATH=${pcre2.dev}/include/pcre2.h"
-      "USE_SYSTEM_READLINE=1"
-      "USE_SYSTEM_UTF8PROC=1"
-      "USE_SYSTEM_ZLIB=1"
-
-      "USE_BINARYBUILDER=0"
-    ];
-
-  LD_LIBRARY_PATH = makeLibraryPath [
-    arpack fftw fftwSinglePrec gmp libgit2 mpfr blas openlibm
-    openspecfun pcre2 lapack
-  ];
-
-  # Other versions of Julia pass the tests, but we are not sure why these fail.
-  doCheck = false;
-  checkTarget = "testall";
-  # Julia's tests require read/write access to $HOME
-  preCheck = ''
-    export HOME="$NIX_BUILD_TOP"
-  '';
-
-  preBuild = ''
-    sed -e '/^install:/s@[^ ]*/doc/[^ ]*@@' -i Makefile
-    sed -e '/[$](DESTDIR)[$](docdir)/d' -i Makefile
-    export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
-  '';
-
-  postInstall = ''
-    # Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,
-    # as using a wrapper with LD_LIBRARY_PATH causes segmentation
-    # faults when program returns an error:
-    #   $ julia -e 'throw(Error())'
-    find $(echo $LD_LIBRARY_PATH | sed 's|:| |g') -maxdepth 1 -name '*.${if stdenv.isDarwin then "dylib" else "so"}*' | while read lib; do
-      if [[ ! -e $out/lib/julia/$(basename $lib) ]]; then
-        ln -sv $lib $out/lib/julia/$(basename $lib)
-      fi
-    done
-  '';
-
-  passthru = {
-    inherit majorVersion minorVersion maintenanceVersion;
-    site = "share/julia/site/v${majorVersion}.${minorVersion}";
-  };
-
-  meta = {
-    description = "High-level performance-oriented dynamical language for technical computing";
-    homepage = "https://julialang.org/";
-    license = lib.licenses.mit;
-    maintainers = with lib.maintainers; [ raskin rob garrison ];
-    platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
-    broken = stdenv.isi686;
-  };
-}

pkgs/development/compilers/julia/1.5.nix

···
   };
 
   patches = [
-    ./use-system-utf8proc-julia-1.3.patch
-
-    # Julia recompiles a precompiled file if the mtime stored *in* the
-    # .ji file differs from the mtime of the .ji file.  This
-    # doesn't work in Nix because Nix changes the mtime of files in
-    # the Nix store to 1. So patch Julia to accept mtimes of 1.
-    ./allow_nix_mtime.patch
+    ./patches/1.5/use-system-utf8proc-julia-1.3.patch
   ];
 
   postPatch = ''
···
     sed -e '/[$](DESTDIR)[$](docdir)/d' -i Makefile
     export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
   '';
+
+  enableParallelBuilding = true;
 
   postInstall = ''
     # Symlink shared libraries from LD_LIBRARY_PATH into lib/julia,

pkgs/development/compilers/julia/README.md

···
+Julia
+=====
+
+[Julia][julia], as a full-fledged programming language with an extensive
+standard library that covers numerical computing, can be somewhat challenging to
+package. This file aims to provide pointers which could not easily be included
+as comments in the expressions themselves.
+
+[julia]: https://julialang.org
+
+For Nixpkgs, the manual is as always your primary reference, and for the Julia
+side of things you probably want to familiarise yourself with the [README
+][readme], [build instructions][build], and [release process][release_process].
+Remember that these can change between Julia releases, especially if the LTS and
+release branches have deviated greatly. A lot of the build process is
+underdocumented and thus there is no substitute for digging into the code that
+controls the build process. You are very likely to need to use the test suite to
+locate and address issues and in the end passing it, while only disabling a
+minimal set of broken or incompatible tests you think you have a good reason to
+disable, is your best bet at arriving at a solid derivation.
+
+[readme]: https://github.com/JuliaLang/julia/blob/master/README.md
+[build]: https://github.com/JuliaLang/julia/blob/master/doc/build/build.md
+[release_process]: https://julialang.org/blog/2019/08/release-process

pkgs/development/compilers/julia/allow_nix_mtime.patch

···
-From f79775378a9eeec5b99f18cc95735b12d172aba3 Mon Sep 17 00:00:00 2001
-From: Tom McLaughlin <[e-mail]>
-Date: Wed, 12 Dec 2018 13:01:32 -0800
-Subject: [PATCH] Patch to make work better with nix
-
----
- base/loading.jl | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/base/loading.jl b/base/loading.jl
-index 51201b98b6..b40c0690f6 100644
---- a/base/loading.jl
-+++ b/base/loading.jl
-@@ -1384,7 +1384,7 @@ function stale_cachefile(modpath::String, cachefile::String)
-                 # Issue #13606: compensate for Docker images rounding mtimes
-                 # Issue #20837: compensate for GlusterFS truncating mtimes to microseconds
-                 ftime = mtime(f)
--                if ftime != ftime_req && ftime != floor(ftime_req) && ftime != trunc(ftime_req, digits=6)
-+                if ftime != ftime_req && ftime != floor(ftime_req) && ftime != trunc(ftime_req, digits=6) && ftime != 1.0
-                     @debug "Rejecting stale cache file $cachefile (mtime $ftime_req) because file $f (mtime $ftime) has changed"
-                     return true
-                 end
--- 
-2.17.1
-

pkgs/development/compilers/julia/diagonal-test.patch

···
-From 9eb180c523b877a53b9e1cf53a4d5e6dad3d7bfe Mon Sep 17 00:00:00 2001
-From: Lars Jellema <[e-mail]>
-Date: Sat, 19 Sep 2020 13:52:20 +0200
-Subject: [PATCH] Use approximate comparisons for diagonal tests
-
----
- stdlib/LinearAlgebra/test/diagonal.jl | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/stdlib/LinearAlgebra/test/diagonal.jl b/stdlib/LinearAlgebra/test/diagonal.jl
-index e420d5bc6d..7f1b5d0aec 100644
---- a/stdlib/LinearAlgebra/test/diagonal.jl
-+++ b/stdlib/LinearAlgebra/test/diagonal.jl
-@@ -450,8 +450,8 @@ end
-         M = randn(T, 5, 5)
-         MM = [randn(T, 2, 2) for _ in 1:2, _ in 1:2]
-         for transform in (identity, adjoint, transpose, Adjoint, Transpose)
--            @test lmul!(transform(D), copy(M)) == *(transform(Matrix(D)), M)
--            @test rmul!(copy(M), transform(D)) == *(M, transform(Matrix(D)))
-+            @test lmul!(transform(D), copy(M)) ≈ *(transform(Matrix(D)), M)
-+            @test rmul!(copy(M), transform(D)) ≈ *(M, transform(Matrix(D)))
-             @test lmul!(transform(DD), copy(MM)) == *(transform(fullDD), MM)
-             @test rmul!(copy(MM), transform(DD)) == *(MM, transform(fullDD))
-         end
--- 
-2.28.0
-

pkgs/development/compilers/julia/update-1.5.py

···
-#!/usr/bin/env nix-shell
-#!nix-shell -i python3 -p python3 python3Packages.requests
-
-import os
-import re
-import requests
-import subprocess
-
-latest = requests.get("https://api.github.com/repos/JuliaLang/julia/releases/latest").json()["tag_name"]
-assert latest[0] == "v"
-major, minor, patch = latest[1:].split(".")
-assert major == "1"
-# When a new minor version comes out we'll have to refactor/copy this update script.
-assert minor == "5"
-
-sha256 = subprocess.check_output(["nix-prefetch-url", "--unpack", f"https://github.com/JuliaLang/julia/releases/download/v{major}.{minor}.{patch}/julia-{major}.{minor}.{patch}-full.tar.gz"], text=True).strip()
-
-nix_path = os.path.join(os.path.dirname(__file__), "1.5.nix")
-nix0 = open(nix_path, "r").read()
-nix1 = re.sub("maintenanceVersion = \".*\";", f"maintenanceVersion = \"{patch}\";", nix0)
-nix2 = re.sub("src_sha256 = \".*\";", f"src_sha256 = \"{sha256}\";", nix1)
-open(nix_path, "w").write(nix2)

pkgs/top-level/aliases.nix

···
   kodiPlain = kodi;
   kodiPlainWayland = kodi-wayland;
   jellyfin_10_5 = throw "Jellyfin 10.5 is no longer supported and contains a security vulnerability. Please upgrade to a newer version."; # added 2021-04-26
-  julia_07 = throw "julia_07 is deprecated in favor of julia_10 LTS"; # added 2020-09-15
-  julia_11 = throw "julia_11 is deprecated in favor of latest Julia version"; # added 2020-09-15
+  julia_07 = throw "julia_07 has been deprecated in favor of the latest LTS version"; # added 2020-09-15
+  julia_1 = throw "julia_1 has been deprecated in favor of julia_10 as it was ambiguous"; # added 2021-03-13
+  julia_11 = throw "julia_11 has been deprecated in favor of the latest stable version"; # added 2020-09-15
+  julia_13 = throw "julia_13 has been deprecated in favor of the latest stable version"; # added 2021-03-13
   kdeconnect = plasma5Packages.kdeconnect-kde; # added 2020-10-28
   kdiff3-qt5 = kdiff3; # added 2017-02-18
   keepass-keefox = keepass-keepassrpc; # backwards compatibility alias, added 2018-02

pkgs/top-level/all-packages.nix

···
 
   julia_10 = callPackage ../development/compilers/julia/1.0.nix {
     gmp = gmp6;
-    inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
+    inherit (darwin.apple_sdk.frameworks) ApplicationServices CoreServices;
     libgit2 = libgit2_0_27;
-  };
-
-  julia_13 = callPackage ../development/compilers/julia/1.3.nix {
-    gmp = gmp6;
-    inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
   };
 
   julia_15 = callPackage ../development/compilers/julia/1.5.nix {
-    inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
+    inherit (darwin.apple_sdk.frameworks) ApplicationServices CoreServices;
   };
 
-  julia_1 = julia_10;
-  julia = julia_15;
+  julia-lts = julia_10;
+  julia-stable = julia_15;
+  julia = julia-lts;
 
   jwasm =  callPackage ../development/compilers/jwasm { };