Subject: [bug#38546] [PATCH v4] Update Julia 1.3.1: almost done

From: Nicolò Balzarotti <[email-masked]>
Date: Mon, 24 Feb 2020 21:59:46 +0100

zimoun <[email-masked]> writes:

> Hi,
Hi, 
> Friendly ping. :-)

Here's a friendly 1.3.1 + HTTP.jl + dependencies patch submission.
Hopefully this time it's fine.  Package precompilation should be working
now (except json, whose cache, for some reason, is not valid and gets
rebuilt).
As a reminder: determinism is still not addressed and will be fixed in
the 1.4.0 release (hopefully, upstream is still not that responsive).
However, there are dozens of julia packages that I want to package, so
if this first batch is finally fine, more will come.

>From aa02b06ade12613f81ddc0415fb0eecffb808352 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:06:28 +0100
Subject: [PATCH 01/16] gnu: Add dsfmt.

* gnu/packages/maths.scm (dsfmt): New variable.
---
 gnu/packages/maths.scm | 72 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 10071c10d5..1c55334a7d 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -33,6 +33,7 @@
 ;;; Copyright © 2019 Nicolas Goaziou <[email-masked]>
 ;;; Copyright © 2019 Steve Sprang <[email-masked]>
 ;;; Copyright © 2019 Robert Smith <[email-masked]>
+;;; Copyright © 2020 Nicolò Balzarotti <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -373,6 +374,77 @@ semiconductors.")
     (license license:gpl3+)
     (home-page "https://www.gnu.org/software/dionysus/")))
 
+(define-public dsfmt
+  (package
+    (name "dsfmt")
+    (version "2.2.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append
+         "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-"
+         version ".tar.gz"))
+       (sha256
+        (base32
+         "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))
+       ;; julia needs those (and is the only program depending on dsfmt now)
+       (patches
+        (list
+         (origin
+           (method url-fetch)
+           (uri (string-append
+                 "https://raw.githubusercontent.com/JuliaLang/julia/"
+                 "v1.3.0/deps/patches/dSFMT.c.patch"))
+           (sha256 (base32
+                    "09mhv11bms8jsmkmdqvlcgljwhzw3b6n9nncpi2b6dla9798hw2y"))
+           (file-name "dSFMT.c.patch"))
+         (origin
+           (method url-fetch)
+           (uri (string-append
+                 "https://raw.githubusercontent.com/JuliaLang/julia/"
+                 "v1.3.0/deps/patches/dSFMT.h.patch"))
+           (sha256 (base32
+                    "1py5rd0yxic335lzka23f6x2dhncrpizpyrk57gi2f28c0p98y5n"))
+           (file-name "dSFMT.h.patch"))))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)            ;no configure script
+         (replace 'build
+           ;; upstream Makefile does not build a shared library
+           (lambda _
+             (invoke
+              "gcc"
+              ;; flags copied from julia
+              ;; https://github.com/JuliaLang/julia/blob/v1.3.0/deps/dsfmt.mk
+              "-DNDEBUG" "-DDSFMT_MEXP=19937"
+              "-fPIC" "-DDSFMT_DO_NOT_USE_OLD_NAMES"
+              "-O3" "-finline-functions" "-fomit-frame-pointer"
+              "-fno-strict-aliasing" "--param" "max-inline-insns-single=1800"
+              "-Wmissing-prototypes" "-Wall" "-std=c99" "-shared" "dSFMT.c"
+              "-o" "libdSFMT.so")))
+         (replace 'install              ;no "install" target
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((lib (string-append (assoc-ref outputs "out")
+                                       "/lib"))
+                   (inc (string-append (assoc-ref outputs "out")
+                                       "/include")))
+               (install-file "libdSFMT.so" lib)
+               (install-file "dSFMT.h" inc)
+               #t))))))
+    (synopsis "Double precision SIMD-oriented Fast Mersenne Twister")
+    (description
+     "The dSMFT package speeds up Fast Mersenne Twister generation by avoiding
+the expensive conversion of integer to double (floating point).  dSFMT directly
+generates double precision floating point pseudorandom numbers which have the
+IEEE Standard for Binary Floating-Point Arithmetic (ANSI/IEEE Std 754-1985)
+format.  dSFMT is only available on the CPUs which use IEEE 754 format double
+precision floating point numbers.")
+    (home-page "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/")
+    (license license:bsd-3)))
+
 (define-public gsl
   (package
     (name "gsl")
-- 
2.25.0

>From 2a4e73c2c4700be23092197c48465a605786683d Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:07:27 +0100
Subject: [PATCH 02/16] gnu: julia: Update to 1.3.1.

* gnu/packages/julia.scm (julia): Update to 1.3.1
* gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch: New file.
* gnu/packages/patches/julia-no-project-name-cache.patch: New file.
* gnu/local.mk: Add julia patches.
---
 gnu/local.mk                                  |   2 +
 gnu/packages/julia.scm                        | 348 +++++++++---------
 .../julia-SOURCE_DATE_EPOCH-mtime.patch       |  22 ++
 3 files changed, 188 insertions(+), 184 deletions(-)
 create mode 100644 gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 1f7cad9d32..c2273d5745 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -26,6 +26,7 @@
 # Copyright © 2019 Evan Straw <[email-masked]>
 # Copyright © 2019 Brett Gilio <[email-masked]>
 # Copyright © 2019 Amin Bandali <[email-masked]>
+# Copyright © 2020 Nicolò Balzarotti <[email-masked]>
 #
 # This file is part of GNU Guix.
 #
@@ -1038,6 +1039,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/java-xerces-bootclasspath.patch	\
   %D%/packages/patches/java-xerces-build_dont_unzip.patch	\
   %D%/packages/patches/java-xerces-xjavac_taskdef.patch	\
+  %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch	\
   %D%/packages/patches/jbig2dec-ignore-testtest.patch		\
   %D%/packages/patches/jfsutils-add-sysmacros.patch		\
   %D%/packages/patches/jfsutils-include-systypes.patch		\
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 65a5e42beb..74d214930e 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <[email-masked]>
 ;;; Copyright © 2016 Efraim Flashner <[email-masked]>
+;;; Copyright © 2020 Nicolò Balzarotti <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28,6 +29,7 @@
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages llvm)
@@ -43,18 +45,18 @@
   #:use-module (gnu packages textutils)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages ssh)
   #:use-module (gnu packages wget)
   #:use-module (ice-9 match))
 
 (define libuv-julia
-  (let ((commit "26dbe5672c33fc885462c509fe2a9b36f35866fd")
-        (revision "6"))
-    ;; When upgrading Julia, also upgrade this.
-    ;; Get the commit from https://github.com/JuliaLang/julia/blob/v1.1.1/deps/libuv.version
+  (let ((commit "35b1504507a7a4168caae3d78db54d1121b121e1"))
+    ;; When upgrading Julia, also upgrade this.  Get the commit from
+    ;; https://github.com/JuliaLang/julia/blob/v1.3.1/deps/libuv.version
     (package
       (inherit libuv)
       (name "libuv-julia")
-      (version (string-append "1.9.0-" revision "." (string-take commit 8)))
+      (version (string-append "2.0.0" "." (string-take commit 8)))
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
@@ -63,7 +65,7 @@
                 (file-name (string-append name "-" version "-checkout"))
                 (sha256
                  (base32
-                  "17pn2xmqaramilx897s9grs966i5246gi6sric5alch4g9j4685n"))))
+                  "0dn3v6fdp1z382pqg3nhjzk60l61ky9b65mfgaj29fv2da95rwjs"))))
       (build-system gnu-build-system)
       (arguments
        (substitute-keyword-arguments (package-arguments libuv)
@@ -72,14 +74,37 @@
              (delete 'autogen)))))
       (home-page "https://github.com/JuliaLang/libuv"))))
 
-(define (llvm-patch-url version name)
+(define libunwind-julia
+  ;; The Julia projects requires their patched version.
+  ;; Get from https://github.com/JuliaLang/julia/tree/master/deps/patches
+  (package
+    (inherit libunwind)
+    (name "libunwind-julia")
+    (version "1.3.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://savannah/libunwind/libunwind-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1y0l08k6ak1mqbfj6accf9s5686kljwgsl4vcqpxzk5n74wpm6a3"))
+       (patches
+        (list
+         (julia-patch "libunwind-prefer-extbl"
+                      "0lr4dafw8qyfh8sw8hhbwkql1dlhqv8px7k81y2l20hhxfgnh2m1")
+         (julia-patch "libunwind-static-arm"
+                      "1jk3bmiw61ypcchqkk1fyg5wh8wpggk574wxyfyaic870zh3lhgq")))))
+    (home-page "https://github.com/JuliaLang/tree/master/deps/")))
+
+(define (julia-patch-url version name)
   (string-append "https://raw.githubusercontent.com/JuliaLang/julia/v" version
-		 "/deps/patches/" name))
+                 "/deps/patches/" name ".patch"))
 
-(define (llvm-patch name sha)
-  (let ((version "1.1.1"))
+(define (julia-patch name sha)
+  (let ((version "1.3.1"))
     (origin (method url-fetch)
-	    (uri (llvm-patch-url version name))
+	    (uri (julia-patch-url version name))
 	    (sha256 (base32 sha))
 	    (file-name name))))
 
@@ -98,41 +123,44 @@
               ;; but they are required to build Julia.
               ;; Discussion: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919628
               (patches
-               (list
-	        (llvm-patch "llvm-6.0-D44650.patch"
-			    "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
-	        (llvm-patch "llvm-6.0-DISABLE_ABI_CHECKS.patch"
-			    "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
-	        (llvm-patch "llvm-6.0-NVPTX-addrspaces.patch"
-			    "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
-	        (llvm-patch "llvm-6.0.0_D27296-libssp.patch"
-			    "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
-	        (llvm-patch "llvm-D27629-AArch64-large_model_6.0.1.patch"
-			    "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
-	        (llvm-patch "llvm-D34078-vectorize-fdiv.patch"
-			    "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
-	        (llvm-patch "llvm-D42262-jumpthreading-not-i1.patch"
-			    "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
-	        (llvm-patch "llvm-D44892-Perf-integration.patch"
-			    "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
-	        (llvm-patch "llvm-D46460.patch"
-			    "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
-	        (llvm-patch "llvm-D49832-SCEVPred.patch"
-			    "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
-	        (llvm-patch "llvm-D50010-VNCoercion-ni.patch"
-			    "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
-	        (llvm-patch "llvm-D50167-scev-umin.patch"
-			    "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
-	        (llvm-patch "llvm-OProfile-line-num.patch"
-			    "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
-	        (llvm-patch "llvm-PPC-addrspaces.patch"
-			    "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
-	        (llvm-patch "llvm-rL323946-LSRTy.patch"
-			    "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
-	        (llvm-patch "llvm-rL326967-aligned-load.patch"
-			    "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
-	        (llvm-patch "llvm-rL327898.patch"
-			    "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq")))))
+               (map (match-lambda
+                      ((name hash)
+                       (julia-patch name hash)))
+                    (list
+                     '("llvm-6.0-D44650"
+                       "1336q4vqayr94wdcnlmcxh90mjdh34dzw9x2cbiqjnx9b1j8fxyb")
+                     '("llvm-6.0-DISABLE_ABI_CHECKS"
+                       "014fawd1ba7yckalypfld22zgic87x9nx3cim42zrwygywd36pyg")
+                     '("llvm-6.0-NVPTX-addrspaces"
+                       "1qdi2zmrjsrj0h84zv2vyly2hjcn4f67mfy0s1q353g4v4jkscqc")
+                     '("llvm-6.0.0_D27296-libssp"
+                       "0s5hi2r1j63i8m6ig1346crx2aiv9f7rgb3mg80kw1wx5y7pdpfh")
+                     '("llvm-D27629-AArch64-large_model_6.0.1"
+                       "1qrshmlqvnasdyc158vfn3hnbigqph3lsq7acb9w8lwkpnnm2j4z")
+                     '("llvm-D34078-vectorize-fdiv"
+                       "1696hg84a0jxcnggvqsc2cdp271hf9a44p4qsd078qm1mfawkaay")
+                     '("llvm-D42262-jumpthreading-not-i1"
+                       "1c8w210gwidbnkkw8anp17dk5pnxws2fl3mb2qxh7y9wzfpixgaq")
+                     '("llvm-D44892-Perf-integration"
+                       "0r37jd0ssh2k1pndkfd5blgpg9z90im4vlzprhb0n0wwz45g4b05")
+                     '("llvm-D46460"
+                       "1miqgswdc0qvbaf4571c2xkxyp9ais06b1bcpa83sq22vr4hbsfb")
+                     '("llvm-D49832-SCEVPred"
+                       "0v5c88hgqj6dymv3j86ca5mhpqab5fbnrvjiw1nvnrnya9l4dlbn")
+                     '("llvm-D50010-VNCoercion-ni"
+                       "0iblb3q1xixwrb12jpb89h3ywmqmzdp6aqp416j4ncwakyjhhfkp")
+                     '("llvm-D50167-scev-umin"
+                       "1f2rakcnnyhr7w10k7gqg0k0491pyvx5ijplivw557f714ys3q6v")
+                     '("llvm-OProfile-line-num"
+                       "1jvbbmwyags0xfwamb13qrf3rgcz9i1r03m9lava7swag8xb78c7")
+                     '("llvm-PPC-addrspaces"
+                       "1f23nhsxh2s3jskbgs7da9nwg3s1hrkbk5aahl08x41wi3mny01p")
+                     '("llvm-rL323946-LSRTy"
+                       "10cz3vy1yw0w643z7xx021wa4kymx9fcm3bjg61s6vzdqd6d9fns")
+                     '("llvm-rL326967-aligned-load"
+                       "04jxnv32yj5x17hqhi8g2p8rhgp38gmjzr871w7z8s44pq10v9v4")
+                     '("llvm-rL327898"
+                       "15ah49gbsll23z28kpyahi5vl0fh3fkxcgd1zmxxdcl96s3x8bnq"))))))
     (arguments
      (substitute-keyword-arguments (package-arguments llvm-6)
        ((#:configure-flags flags)
@@ -158,7 +186,7 @@
 (define-public julia
   (package
     (name "julia")
-    (version "1.1.1")
+    (version "1.3.1")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -166,7 +194,9 @@
                     version "/julia-" version ".tar.gz"))
               (sha256
                (base32
-                "0hk983mywimclgnjc41zmlppm5kfdz2aj85ky07p49ilcqxi998f"))))
+                "1nwkmr9j55g1zkxdchnid1h022s0is52vx23niksshgvh793g41x"))
+              (patches
+               (search-patches "julia-SOURCE_DATE_EPOCH-mtime.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:test-target "test"
@@ -188,30 +218,25 @@
          (add-after 'unpack 'prepare-deps
            (lambda* (#:key inputs #:allow-other-keys)
              (mkdir "deps/srccache")
-             (copy-file (assoc-ref inputs "dsfmt")
-                        "deps/srccache/dsfmt-2.2.3.tar.gz")
+             ;; no USE_SYSTEM_{OBJCONV/LIBWHICH}
              (copy-file (assoc-ref inputs "objconv")
                         "deps/srccache/objconv.zip")
-             (copy-file (assoc-ref inputs "suitesparse")
-                        "deps/srccache/SuiteSparse-4.4.5.tar.gz")
-             (copy-file (string-append (assoc-ref inputs "virtualenv")
-                                       "/bin/virtualenv")
-                        "julia-env")
              (copy-file (assoc-ref inputs "libwhich")
                         (string-append "deps/srccache/libwhich-"
                                        "81e9723c0273d78493dc8c8ed570f68d9ce7e89e"
                                        ".tar.gz"))
-             (copy-file (assoc-ref inputs "rmath")
-                        "deps/srccache/Rmath-julia-0.1.tar.gz")
 
 	     ;; needed by libwhich
 	     (setenv "LD_LIBRARY_PATH"
 		     (string-join (map (lambda (pkg)
                                          (string-append (assoc-ref inputs pkg)
                                                         "/lib"))
-                                       '("arpack-ng" "fftw" "gmp" "lapack"
-			                 "libgit2" "mpfr" "openblas" "openlibm"
-			                 "openspecfun" "pcre2"))
+                                       '("arpack-ng" "curl" "dsfmt"
+                                         "gmp" "lapack"
+                                         "libssh2" "libgit2"
+                                         "mbedtls" "mpfr"
+                                         "openblas" "openlibm" "pcre2"
+                                         "suitesparse"))
                                   ":"))
 	     #t))
          ;; FIXME: Building the documentation requires Julia packages that
@@ -233,44 +258,12 @@
           ;; using the output of "/sbin/ldconfig -p".  Since ldconfig is not
           ;; used in Guix, we patch runtime_ccall.cpp to contain a static map.
           (lambda* (#:key inputs #:allow-other-keys)
-            (use-modules (ice-9 match))
-            (substitute* "src/runtime_ccall.cpp"
-              ;; Patch out invocations of '/sbin/ldconfig' to avoid getting
-              ;; error messages about missing '/sbin/ldconfig' on Guix System.
-              (("popen\\(.*ldconfig.*\\);")
-               "NULL;\n")
-
-              ;; Populate 'sonameMap'.
-              (("jl_read_sonames.*;")
-               (string-join
-                (map (match-lambda
-                       ((input libname soname)
-                        (string-append
-                         "sonameMap[\"" libname "\"] = "
-                         "\"" (assoc-ref inputs input) "/lib/" soname "\";")))
-                     '(("libc"        "libc"           "libc.so.6")
-                       ("pcre2"       "libpcre2-8"     "libpcre2-8.so")
-                       ("mpfr"        "libmpfr"        "libmpfr.so")
-                       ("openblas"    "libblas"        "libopenblas.so")
-                       ("arpack-ng"   "libarpack"      "libarpack.so")
-                       ("lapack"      "liblapack"      "liblapack.so")
-                       ("libgit2"     "libgit2"        "libgit2.so")
-                       ("gmp"         "libgmp"         "libgmp.so")
-                       ("openspecfun" "libopenspecfun" "libopenspecfun.so")
-                       ("fftw"        "libfftw3"       "libfftw3_threads.so")
-                       ("fftwf"       "libfftw3f"      "libfftw3f_threads.so"))))))
-            (substitute* "base/math.jl"
-              (("const libm = Base.libm_name")
-               (string-append "const libm = \""
-                              (assoc-ref inputs "openlibm")
-                              "/lib/libopenlibm.so"
-                              "\""))
-              (("const openspecfun = \"libopenspecfun\"")
-               (string-append "const openspecfun = \""
-                              (assoc-ref inputs "openspecfun")
-                              "/lib/libopenspecfun.so"
-                              "\"")))
-            #t))
+             (substitute* "base/math.jl"
+               (("const libm = Base.libm_name")
+                (string-append "const libm = \""
+                               (assoc-ref inputs "openlibm")
+                               "/lib/libopenlibm.so"
+                               "\"")))))
          (add-before 'build 'fix-include-and-link-paths
           (lambda* (#:key inputs #:allow-other-keys)
             ;; LIBUTF8PROC is a linker flag, not a build target.  It is
@@ -278,10 +271,10 @@
             ;; collection of build targets and a list of libraries to link
             ;; against.
             (substitute* "src/flisp/Makefile"
-              (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
-               "$(BUILDDIR)/$(EXENAME): $(OBJS) $(LLT_release)")
-              (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug: \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
-               "$(BUILDDIR)/$(EXENAME)-debug: $(DOBJS) $(LLT_debug)"))
+               (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)\\$\\(EXE\\): \\$\\(OBJS\\) \\$\\(LIBFILES_release\\)")
+                "$(BUILDDIR)/$(EXENAME)$(EXE): $(OBJS) $(LLT_release)")
+               (("\\$\\(BUILDDIR\\)/\\$\\(EXENAME\\)-debug$(EXE): \\$\\(DOBJS\\) \\$\\(LIBFILES_debug\\)")
+                "$(BUILDDIR)/$(EXENAME)-debug\\$\\(EXE\\): $(DOBJS) $(LLT_debug)"))
 
             ;; The REPL must be linked with libuv.
             (substitute* "ui/Makefile"
@@ -296,39 +289,50 @@
                               "/include/uv/errno.h")))
             #t))
          (add-before 'build 'replace-default-shell
-          (lambda _
-            (substitute* "base/client.jl"
-              (("/bin/sh") (which "sh")))
-            #t))
-         (add-after 'unpack 'hardcode-paths
            (lambda _
-             (substitute* "stdlib/InteractiveUtils/src/InteractiveUtils.jl"
-               (("`which") (string-append "`" (which "which")))
-               (("`wget")  (string-append "`" (which "wget"))))
+             (substitute* "base/client.jl"
+               (("/bin/sh") (which "sh")))
+             #t))
+         (add-before 'build 'fix-precompile
+           (lambda _
+             (substitute* "base/loading.jl"
+               (("something(Base.active_project(), \"\")") "\"\""))
              #t))
          (add-before 'check 'disable-broken-tests
            (lambda _
-             (define (touch file-name)
-               (call-with-output-file file-name (const #t)))
-	     ;; FIXME: All git tests works except this one. But *THIS* "fix"
-             ;; is not working, so right now I'm disabling all libgit2.jl tests
-	     ;; (substitute* "stdlib/LibGit2/test/libgit2.jl"
-	     ;; (("!LibGit2.use_http_path(cfg, github_cred)") "true")
-	     ;; (("LibGit2.use_http_path(cfg, mygit_cred)") "true"))
-             (map (lambda (test)
-                    (delete-file test)
-                    (touch test))
-	          '("stdlib/Sockets/test/runtests.jl"
-		    "stdlib/Distributed/test/runtests.jl"
-                    ;; FIXME: see above
-		    "stdlib/LibGit2/test/libgit2.jl"))
-	     (substitute* "test/choosetests.jl"
-	       ;; These tests fail, probably because some of the input
-	       ;; binaries have been stripped and thus backtraces don't look
-	       ;; as expected.
-	       (("\"backtrace\",") "")
-	       (("\"cmdlineargs\",") ""))
-	     #t)))
+             (substitute* "test/choosetests.jl"
+               (("tests = testnames")
+                ;; Those failings are not deterministic.  They depends on the
+                ;; running order.  I think it depends on the number of
+                ;; runners, disabling it for now
+                ;; https://github.com/JuliaLang/julia/issues/34330
+                "tests = filter(e->!in(e,[\"backtrace\",\"exceptions\",
+                                          \"stress\",\"precompile\",
+                                          \"client\",\"stacktraces\"]),
+                                       testnames)"))
+             ;; When HOME is not set, julia calls uv_os_homedir, which in
+             ;; turns call getpwuid_r. Add the HOME env variable to the
+             ;; external julia call to fix this
+             (substitute* "test/cmdlineargs.jl"
+               (("\"JULIA_PROJECT\"") "\"HOME\"=>\"/tmp\", \"JULIA_PROJECT\""))
+             ;; Marking the test as broken as it's a known bug:
+             ;; https://github.com/JuliaLang/julia/issues/32377
+             (substitute* "stdlib/REPL/test/replcompletions.jl"
+               (("@test count") "@test_broken count"))
+             #t))
+	 (add-after 'install 'make-wrapper
+	   (lambda* (#:key inputs outputs #:allow-other-keys)
+	     (let* ((out (assoc-ref outputs "out"))
+		    (bin (string-append out "/bin"))
+		    (program "julia"))
+	       (with-directory-excursion bin
+		 (wrap-program program
+		   `("JULIA_LOAD_PATH" ":" prefix
+		     ("" "$JULIA_LOAD_PATH")))
+		 (wrap-program program
+		   `("JULIA_DEPOT_PATH" ":" prefix
+		     ("" "$JULIA_DEPOT_PATH"))))
+	       #t))))
        #:make-flags
        (list
         (string-append "prefix=" (assoc-ref %outputs "out"))
@@ -346,25 +350,20 @@
            (_ "MARCH=UNSUPPORTED"))
 
         "CONFIG_SHELL=bash"     ;needed to build bundled libraries
-        "USE_SYSTEM_DSFMT=0"    ;not packaged for Guix and upstream has no
-                                ;build system for a shared library.
+        ;; list of "USE_SYSTEM_*" is here:
+        ;; https://github.com/JuliaLang/julia/blob/v1.3.1/Make.inc
+        "USE_SYSTEM_DSFMT=1"
+        "USE_SYSTEM_P7ZIP=1"
         "USE_SYSTEM_LAPACK=1"
         "USE_SYSTEM_BLAS=1"
         "USE_BLAS64=0"          ;needed when USE_SYSTEM_BLAS=1
         "LIBBLAS=-lopenblas"
         "LIBBLASNAME=libopenblas"
 
-        "USE_SYSTEM_FFTW=1"
-        "LIBFFTWNAME=libfftw3"
-        "LIBFFTWFNAME=libfftw3f"
-
-        ;; TODO: Suitesparse does not install shared libraries, so we cannot
-        ;; use the suitesparse package.
-        ;; "USE_SYSTEM_SUITESPARSE=1"
-        ;; (string-append "SUITESPARSE_INC=-I "
-        ;;                (assoc-ref %build-inputs "suitesparse")
-        ;;                "/include")
-
+        "USE_SYSTEM_SUITESPARSE=1"
+        (string-append "SUITESPARSE_INC=-I "
+                       (assoc-ref %build-inputs "suitesparse")
+                       "/include")
         "USE_GPL_LIBS=1"        ;proudly
         "USE_SYSTEM_UTF8PROC=1"
         (string-append "UTF8PROC_INC="
@@ -390,11 +389,16 @@
 	"USE_SYSTEM_MPFR=1"
 	"USE_SYSTEM_ARPACK=1"
 	"USE_SYSTEM_LIBGIT2=1"
-	"USE_SYSTEM_ZLIB=1"
-	"USE_SYSTEM_OPENSPECFUN=1")))
+        (string-append "LIBUV="
+                       (assoc-ref %build-inputs "libuv")
+                       "/lib/libuv.so")
+        (string-append "LIBUV_INC="
+                       (assoc-ref %build-inputs "libuv")
+                       "/include")
+        "USE_SYSTEM_ZLIB=1")))
     (inputs
      `(("llvm" ,llvm-julia)
-
+       ("p7zip" ,p7zip)
        ;; The bundled version is 3.3.0 so stick to that version.  With other
        ;; versions, we get test failures in 'linalg/arnoldi' as described in
        ;; <https://bugs.gnu.org/30282>.
@@ -403,12 +407,12 @@
        ("coreutils" ,coreutils) ;for bindings to "mkdir" and the like
        ("lapack" ,lapack)
        ("openblas" ,openblas) ;Julia does not build with Atlas
-       ("libunwind" ,libunwind)
+       ("libunwind" ,libunwind-julia)
        ("openlibm" ,openlibm)
-       ("openspecfun" ,openspecfun)
+       ("mbedtls" ,mbedtls-apache)
+       ("curl" ,curl)
        ("libgit2" ,libgit2)
-       ("fftw" ,fftw)
-       ("fftwf" ,fftwf)
+       ("libssh2" ,libssh2)
        ("fortran" ,gfortran)
        ("libuv" ,libuv-julia)
        ("pcre2" ,pcre2)
@@ -418,31 +422,12 @@
        ("which" ,which)
        ("zlib" ,zlib)
        ("gmp" ,gmp)
-       ("virtualenv" ,python2-virtualenv)
+       ("suitesparse" ,suitesparse)
        ;; FIXME: The following inputs are downloaded from upstream to allow us
        ;; to use the lightweight Julia release tarball.  Ideally, these inputs
        ;; would eventually be replaced with proper Guix packages.
-
-       ;; TODO: run "make -f contrib/repackage_system_suitesparse4.make" to copy static lib
-       ;; Find dependency versions here:
-       ;; https://raw.githubusercontent.com/JuliaLang/julia/77a2c1e245c85812dc1c7687540beedecc52758f/deps/Versions.make
-       ("rmath"
-	,(origin
-	   (method git-fetch)
-	   (uri (git-reference
-                 (url "https://github.com/JuliaLang/Rmath-julia")
-                 (commit "v0.1")))
-           (file-name "rmath-julia-0.1-checkout")
-	   (sha256
-	    (base32
-	     "1zkpy0cg5zivq40zbhbdgj9128fqzs2j94wkwih8nc6xaj3gp9p6"))))
-       ("suitesparse"
-        ,(origin
-           (method url-fetch)
-           (uri "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.5.tar.gz")
-           (sha256
-            (base32
-             "1jcbxb8jx5wlcixzf6n5dca2rcfx6mlcms1k2rl5gp67ay3bix43"))))
+       ;; Find dependencies versions here:
+       ;; https://raw.githubusercontent.com/JuliaLang/julia/v1.3.0/deps/Versions.make
        ("objconv"
         ,(origin
            (method url-fetch)
@@ -466,16 +451,8 @@
                                        ".tar.gz"))
 	     (sha256
 	      (base32
-	       "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
-       ("dsfmt"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append
-                 "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/"
-                 "SFMT/dSFMT-src-2.2.3.tar.gz"))
-           (sha256
-            (base32
-             "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42"))))))
+               "1p7zg31kpmpbmh1znrk1xrbd074agx13b9q4dcw8n2zrwwdlbz3b")))))
+       ("dsfmt" ,dsfmt)))
     (native-inputs
      `(("openssl" ,openssl)
        ("perl" ,perl)
@@ -485,7 +462,10 @@
     (native-search-paths
      (list (search-path-specification
             (variable "JULIA_LOAD_PATH")
-            (files (list "share/julia/packages/")))))
+            (files (list "share/julia/packages/")))
+           (search-path-specification
+            (variable "JULIA_DEPOT_PATH")
+            (files (list "share/julia/")))))
     ;; Julia is not officially released for ARM and MIPS.
     ;; See https://github.com/JuliaLang/julia/issues/10639
     (supported-systems '("i686-linux" "x86_64-linux" "aarch64-linux"))
diff --git a/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
new file mode 100644
index 0000000000..b60f284923
--- /dev/null
+++ b/gnu/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch
@@ -0,0 +1,22 @@
+Fix one of upstream non-determinism, tracked here:
+
+https://github.com/JuliaLang/julia/issues/34115
+https://github.com/JuliaLang/julia/issues/25900
+
+
+Patch by Nicoló Balzarotti <[email-masked]>.
+
+--- a/base/loading.jl
++++ b/base/loading.jl
+@@ -807,7 +807,10 @@
+         path = normpath(joinpath(dirname(prev), _path))
+     end
+     if _track_dependencies[]
+-        push!(_require_dependencies, (mod, path, mtime(path)))
++          push!(_require_dependencies,
++                (mod, path,
++                 haskey(ENV, "SOURCE_DATE_EPOCH") ?
++                 parse(Float64, ENV["SOURCE_DATE_EPOCH"]) : mtime(path)))
+     end
+     return path, prev
+ end
-- 
2.25.0

>From 69bfdff9a8772bbe9254c9cd3a97966e059060af Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:28:45 +0100
Subject: [PATCH 03/16] gnu: julia-build-system: Enable tests, fix
 precompilation.

---
 guix/build-system/julia.scm       |  2 +-
 guix/build/julia-build-system.scm | 71 +++++++++++++++----------------
 2 files changed, 36 insertions(+), 37 deletions(-)

diff --git a/guix/build-system/julia.scm b/guix/build-system/julia.scm
index 488fe9bb1d..d3cb41c054 100644
--- a/guix/build-system/julia.scm
+++ b/guix/build-system/julia.scm
@@ -75,7 +75,7 @@
 
 (define* (julia-build store name inputs
                       #:key source
-                      (tests? #f)
+                      (tests? #t)
                       (phases '(@ (guix build julia-build-system)
                                   %standard-phases))
                       (outputs '("out"))
diff --git a/guix/build/julia-build-system.scm b/guix/build/julia-build-system.scm
index ff6fcf5fe3..2916775c9d 100644
--- a/guix/build/julia-build-system.scm
+++ b/guix/build/julia-build-system.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2019 Nicolò Balzarotti <[email-masked]>
+;;; Copyright © 2019, 2020 Nicolò Balzarotti <[email-masked]>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -37,54 +37,53 @@
 ;; subpath where we store the package content
 (define %package-path "/share/julia/packages/")
 
-(define (generate-load-path inputs outputs)
-  (string-append
-   (string-join (map (match-lambda
-                       ((_ . path)
-                        (string-append path %package-path)))
-                     ;; Restrict to inputs beginning with "julia-".
-                     (filter (match-lambda
-                               ((name . _)
-                                (string-prefix? "julia-" name)))
-                             inputs))
-                ":")
-   (string-append ":" (assoc-ref outputs "out") %package-path)
-   ;; stdlib is always required to find Julia's standard libraries.
-   ;; usually there are other two paths in this variable:
-   ;; "@" and "@v#.#"
-   ":@stdlib"))
-
 (define* (install #:key source inputs outputs #:allow-other-keys)
   (let* ((out (assoc-ref outputs "out"))
          (package-dir (string-append out %package-path
-                                     (string-append
-                                      (strip-store-file-name source)))))
-    (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
+                                     (strip-store-file-name source))))
     (mkdir-p package-dir)
-    (copy-recursively source package-dir))
+    (copy-recursively (getcwd) package-dir))
   #t)
 
-;; TODO: Precompilation is working, but I don't know how to tell
-;; julia to use use it. If (on rantime) we set HOME to
-;; store path, julia tries to write files there (failing)
 (define* (precompile #:key source inputs outputs #:allow-other-keys)
   (let* ((out (assoc-ref outputs "out"))
          (builddir (string-append out "/share/julia/"))
          (package (strip-store-file-name source)))
     (mkdir-p builddir)
     (setenv "JULIA_DEPOT_PATH" builddir)
-    (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
-    ;; Actual precompilation
-    (invoke-julia (string-append "using " package)))
+    ;; add new package dir to the load path
+    (setenv "JULIA_LOAD_PATH"
+            (string-append builddir "packages/"
+                           (if (getenv "JULIA_LOAD_PATH")
+                               (string-append ":" (getenv "JULIA_LOAD_PATH"))
+                               "")))
+    ;; Actual precompilation.
+    (invoke-julia
+     ;; when using julia as a user, julia writes precompile cache to the first
+     ;; entry of the DEPOT_PATH list (by default, the home dir).  We want to
+     ;; write it to the store, so let's push the store path as the first
+     ;; element of DEPOT_PATH.  Once the cache file exists, this hack is not
+     ;; needed anymore (like in the check phase).  If the user install new
+     ;; pacakges, those will be installed and precompiled in the home dir
+     (string-append "pushfirst!(DEPOT_PATH, pop!(DEPOT_PATH)); using " package)))
   #t)
 
-(define* (check #:key source inputs outputs #:allow-other-keys)
-  (let* ((out (assoc-ref outputs "out"))
-         (package (strip-store-file-name source))
-         (builddir (string-append out "/share/julia/")))
-    (setenv "JULIA_DEPOT_PATH" builddir)
-    (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
-    (invoke-julia (string-append "using Pkg;Pkg.test(\"" package "\")")))
+(define* (check #:key tests? source outputs #:allow-other-keys)
+  (if tests?
+      (let* ((out (assoc-ref outputs "out"))
+             (package (strip-store-file-name source))
+             (builddir (string-append out "/share/julia/")))
+        (setenv "HOME" "/tmp")
+        (setenv "JULIA_DEPOT_PATH" builddir)
+        (setenv "JULIA_LOAD_PATH"
+                (string-append builddir "packages/" ":"
+                               (or (getenv "JULIA_LOAD_PATH")
+                                   "")))
+        ;; tests assume they are run from the test directory
+        (with-directory-excursion
+            (string-append builddir "packages/" package "/test/")
+          (invoke "julia" "runtests.jl")))
+      (format #t "test suite not run~%"))
   #t)
 
 (define (julia-create-package-toml outputs source
@@ -119,7 +118,7 @@ version = \"" version "\"
     (delete 'check) ; tests must be run after installation
     (replace 'install install)
     (add-after 'install 'precompile precompile)
-    ;; (add-after 'install 'check check)
+    (add-after 'precompile 'check check)
     ;; TODO: In the future we could add a "system-image-generation" phase
     ;; where we use PackageCompiler.jl to speed up package loading times
     (delete 'configure)
-- 
2.25.0

>From a185f2d8112d55fe34fe5640edc6e4f46fece226 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:30:39 +0100
Subject: [PATCH 04/16] gnu: Add julia-compat.

* gnu/packages/julia-xyz.scm (julia-compat): New variable.
* gnu/packages/julia-xyz.scm: New file.
* gnu/local.mk: Add gnu/packages/julia-xyz.scm.
---
 gnu/local.mk               |  1 +
 gnu/packages/julia-xyz.scm | 45 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 46 insertions(+)
 create mode 100644 gnu/packages/julia-xyz.scm

diff --git a/gnu/local.mk b/gnu/local.mk
index c2273d5745..1ebcc45a4c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -281,6 +281,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/jrnl.scm				\
   %D%/packages/jose.scm				\
   %D%/packages/julia.scm			\
+  %D%/packages/julia-xyz.scm			\
   %D%/packages/jupyter.scm			\
   %D%/packages/kawa.scm				\
   %D%/packages/kde.scm				\
diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
new file mode 100644
index 0000000000..abcfc4d0cf
--- /dev/null
+++ b/gnu/packages/julia-xyz.scm
@@ -0,0 +1,45 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2020 Nicolò Balzarotti <[email-masked]>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages julia-xyz)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system julia))
+
+(define-public julia-compat
+  (package
+    (name "julia-compat")
+    (version "3.6.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaLang/Compat.jl")
+             (commit (string-append "v" version))))
+       (file-name "Compat")
+       (sha256
+        (base32 "0dxy0kpwgz3a9w665lp154x9yrnic89f2b27b1nmh69jhnnb2zgr"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaLang/Compat.jl")
+    (synopsis "Compatibility across Julia versions")
+    (description "The Compat package is designed to ease interoperability
+between older and newer versions of the Julia language.  The Compat package
+provides a macro that lets you use the latest syntax in a backwards-compatible
+way.")
+    (license license:expat)))
-- 
2.25.0

>From a7a34a28d99bd9411d18e0e7f3d4efb406f2a817 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:33:08 +0100
Subject: [PATCH 05/16] gnu: Add julia-sha.

* gnu/packages/julia-xyz.scm (julia-sha): New variable.
---
 gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index abcfc4d0cf..91d497a0ce 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -43,3 +43,27 @@ between older and newer versions of the Julia language.  The Compat package
 provides a macro that lets you use the latest syntax in a backwards-compatible
 way.")
     (license license:expat)))
+
+(define-public julia-sha
+  (package
+    (name "julia-sha")
+    (version "0.5.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/staticfloat/SHA.jl")
+             ;; tests fixed in this untagged version
+             (commit "97b17a7fabf894257726c33cbd78255ac380906d")))
+       (file-name "SHA")
+       (sha256
+        (base32 "169y78cmppj117cmh8ncnyh381caf9dsklaks5l40mia9jdcqbgl"))))
+    (build-system julia-build-system)
+    (propagated-inputs `(("julia-compat" ,julia-compat)))
+    (home-page "https://github.com/staticfloat/SHA.jl")
+    (synopsis
+     "Performant, 100% native-julia SHA1, SHA2, and SHA3 implementation")
+    (description "Julia package implementing SHA algorithms.  Each exported
+function takes in either an @code{Array{UInt8}}, a @code{ByteString} or an
+@code{IO} object.")
+    (license license:expat)))
-- 
2.25.0

>From 3fae18e43bd9cd0931d153a0b47bd2ba90d7eedb Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:42:00 +0100
Subject: [PATCH 06/16] gnu: Add julia-binaryprovider.

* gnu/packages/julia-xyz.scm (julia-binaryprovider): New variable.
---
 gnu/packages/julia-xyz.scm | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 91d497a0ce..86c0a6c3e9 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -20,7 +20,33 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix git-download)
-  #:use-module (guix build-system julia))
+  #:use-module (guix build-system julia)
+  #:use-module (gnu packages curl))
+
+(define-public julia-binaryprovider
+  (package
+    (name "julia-binaryprovider")
+    (version "0.5.8")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaPackaging/BinaryProvider.jl")
+             (commit (string-append "v" version))))
+       (file-name "BinaryProvider")
+       (sha256
+        (base32 "174jmg4w8ncgfhdvfnm0p4cnlayw31j4s9sksqlwz1sipywqvww7"))))
+    (build-system julia-build-system)
+    ;; We don't really need BinaryProvider (as guix provides the binaries) but
+    ;; since it's a dependency of other packages we want to precompile it.
+    (arguments `(#:tests? #f))
+    (propagated-inputs `(("julia-sha" ,julia-sha)))
+    (inputs `(("curl" ,curl)))
+    (home-page "https://github.com/JuliaPackaging/BinaryProvider.jl")
+    (synopsis "Reliable Binary provider for Julia")
+    (description "@code{BinaryProvider.jl} simplifies the installation of
+binaries required by julia packages.")
+    (license license:expat)))
 
 (define-public julia-compat
   (package
-- 
2.25.0

>From 3f4e7fdbe183b950ef57c71b25de13ffc29eea68 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:42:59 +0100
Subject: [PATCH 07/16] gnu: Add julia-inifile.

* gnu/packages/julia-xyz.scm (julia-inifile): New variable.
---
 gnu/packages/julia-xyz.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 86c0a6c3e9..213aa0543c 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -70,6 +70,26 @@ provides a macro that lets you use the latest syntax in a backwards-compatible
 way.")
     (license license:expat)))
 
+(define-public julia-inifile
+  (package
+    (name "julia-inifile")
+    (version "0.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaIO/IniFile.jl")
+             (commit "8ba59958495fa276d6489d2c3903e765d75e0bc0")))
+       (file-name "IniFile")
+       (sha256
+        (base32 "11h6f99jpbg729lplw841m68jprka7q3n8yw390bndlmcdsjabpd"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaIO/IniFile.jl")
+    (synopsis "Reading Windows-style INI files")
+    (description "This is a julia package that defines an IniFile type that
+allows to interface with @file{.ini} files.")
+    (license license:expat)))
+
 (define-public julia-sha
   (package
     (name "julia-sha")
-- 
2.25.0

>From 44e8535f4e8b72cdb99c396dab53badcd5b02073 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:43:37 +0100
Subject: [PATCH 08/16] gnu: Add julia-mbedtls.

* gnu/packages/julia-xyz.scm (julia-mbedtls): New variable.
---
 gnu/packages/julia-xyz.scm | 55 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 54 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 213aa0543c..508b4835ca 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -21,7 +21,8 @@
   #:use-module (guix packages)
   #:use-module (guix git-download)
   #:use-module (guix build-system julia)
-  #:use-module (gnu packages curl))
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages tls))
 
 (define-public julia-binaryprovider
   (package
@@ -90,6 +91,58 @@ way.")
 allows to interface with @file{.ini} files.")
     (license license:expat)))
 
+(define-public julia-mbedtls
+  (package
+    (name "julia-mbedtls")
+    (version "0.7.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaLang/MbedTLS.jl")
+             (commit (string-append "v" version))))
+       (file-name "MbedTLS")
+       (sha256
+        (base32 "1a8snw9gi21lm6r3kh6ly7ngi99s9k5shqkfiizj3g9li20q23h2"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     `(("julia-binaryprovider" ,julia-binaryprovider)))
+    (inputs `(("mbedtls-apache" ,mbedtls-apache)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'disable-network-tests
+           (lambda _
+             (substitute* "test/runtests.jl"
+               (("testhost =") "return #"))
+             #t))
+         ;; Add binary dependency paths
+         (add-before 'precompile 'build-deps
+           (lambda* (#:key outputs source inputs #:allow-other-keys)
+             (let ((f (open-file
+                       (string-append
+                        (assoc-ref outputs "out")
+                        "/share/julia/packages/"
+                        (string-append
+                         (strip-store-file-name source) "/deps/deps.jl"))
+                       "w")))
+               (display (string-append "const libmbedcrypto = \""
+                                       (assoc-ref inputs "mbedtls-apache")
+                                       "/lib/libmbedcrypto.so\"\n") f)
+               (display (string-append "const libmbedtls = \""
+                                       (assoc-ref inputs "mbedtls-apache")
+                                       "/lib/libmbedtls.so\"\n") f)
+               (display (string-append "const libmbedx509 = \""
+                                       (assoc-ref inputs "mbedtls-apache")
+                                       "/lib/libmbedx509.so\"\n") f)
+               (close-port f))
+             #t)))))
+    (home-page "https://github.com/JuliaLang/MbedTLS.jl")
+    (synopsis "Apache's mbed TLS library wrapper")
+    (description "@code{MbedTLS.jl} provides a wrapper around the mbed TLS and
+cryptography C libary for Julia.")
+    (license license:expat)))
+
 (define-public julia-sha
   (package
     (name "julia-sha")
-- 
2.25.0

>From 2f205551cf5193a4d41541ba772b1db10f2f9248 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:46:35 +0100
Subject: [PATCH 09/16] gnu: Add julia-bufferedstreams.

* gnu/packages/julia-xyz.scm (julia-bufferedstreams): New variable.
---
 gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 508b4835ca..c26765f2a4 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -49,6 +49,31 @@
 binaries required by julia packages.")
     (license license:expat)))
 
+(define-public julia-bufferedstreams
+  (package
+    (name "julia-bufferedstreams")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/BioJulia/BufferedStreams.jl")
+             (commit (string-append "v" version))))
+       (file-name "BufferedStreams")
+       (sha256
+        (base32 "0sf4sxbq55mg2pwxyxf0c839z1lk0yxg8nmb7617bfbvw31cp88z"))))
+    (build-system julia-build-system)
+    ;; tests are freezing, see
+    ;; https://travis-ci.org/BioJulia/BufferedStreams.jl/jobs/491050182
+    (arguments '(#:tests? #f))
+    (propagated-inputs `(("julia-compat" ,julia-compat)))
+    (home-page "https://github.com/BioJulia/BufferedStreams.jl")
+    (synopsis "Fast composable IO streams")
+    (description "@code{BufferedStreams} provides buffering for IO
+operations.  It can wrap any IO type automatically making incremental reading
+and writing faster.")
+    (license license:expat)))
+
 (define-public julia-compat
   (package
     (name "julia-compat")
-- 
2.25.0

>From 5a906605765854b7955a8530e89f63959f3cc2ff Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:48:25 +0100
Subject: [PATCH 10/16] gnu: Add julia-parsers.

* gnu/packages/julia-xyz.scm (julia-parsers): New variable.
---
 gnu/packages/julia-xyz.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index c26765f2a4..22b1cc9914 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -168,6 +168,26 @@ allows to interface with @file{.ini} files.")
 cryptography C libary for Julia.")
     (license license:expat)))
 
+(define-public julia-parsers
+  (package
+    (name "julia-parsers")
+    (version "0.3.11")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaData/Parsers.jl")
+             (commit (string-append "v" version))))
+       (file-name "Parsers")
+       (sha256
+        (base32 "07dgcy12206a3lw55h00znq3yq4faczng6bbdn3lhc0l6jmclsly"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaData/Parsers.jl")
+    (synopsis "Fast parsing machinery for basic types in Julia")
+    (description "@code{Parsers} is a collection of type parsers and utilities
+for Julia")
+    (license license:expat)))
+
 (define-public julia-sha
   (package
     (name "julia-sha")
-- 
2.25.0

>From 68f095c392924936f59c7df9ec2363f6054651ab Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:51:21 +0100
Subject: [PATCH 11/16] gnu: Add julia-offsetarrays.

* gnu/packages/julia-xyz.scm (julia-offsetarrays): New variable.
---
 gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 22b1cc9914..5cc7529c20 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -168,6 +168,30 @@ allows to interface with @file{.ini} files.")
 cryptography C libary for Julia.")
     (license license:expat)))
 
+(define-public julia-offsetarrays
+  (package
+    (name "julia-offsetarrays")
+    (version "1.0.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaArrays/OffsetArrays.jl")
+             (commit (string-append "v" version))))
+       (file-name "OffsetArrays")
+       (sha256
+        (base32 "0x86px7gynyzqqwan88z3lkq8yj0id4pa718l8xqj4yp9fbz440c"))))
+    (build-system julia-build-system)
+    ;; tests require Catindices, introducing a circular dependency
+    (arguments '(#:tests? #f))
+    (home-page "https://github.com/JuliaArrays/OffsetArrays.jl")
+    (synopsis "Fortran-like arrays with arbitrary, zero or negative starting
+indices")
+    (description "OffsetArrays provides Julia users with arrays that have
+arbitrary indices, similar to those found in some other programming languages
+like Fortran.")
+    (license license:expat)))
+
 (define-public julia-parsers
   (package
     (name "julia-parsers")
-- 
2.25.0

>From 3a0f60d4e21dd893ee11ddde0947c0323c9b5537 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 15:54:30 +0100
Subject: [PATCH 12/16] gnu: Add julia-fixedpointnumbers.

* gnu/packages/julia-xyz.scm (julia-fixedpointnumbers): New variable.
---
 gnu/packages/julia-xyz.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 5cc7529c20..046c365b08 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -96,6 +96,32 @@ provides a macro that lets you use the latest syntax in a backwards-compatible
 way.")
     (license license:expat)))
 
+(define-public julia-fixedpointnumbers
+  (package
+    (name "julia-fixedpointnumbers")
+    (version "0.8.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaMath/FixedPointNumbers.jl")
+             (commit (string-append "v" version))))
+       (file-name "FixedPointNumbers")
+       (sha256
+        (base32 "0zi0va64vhnhqga62j7116m5alrkfzlv7qady4bq6v9sfrwfzvw1"))))
+    (build-system julia-build-system)
+    (propagated-inputs `(("julia-compat" ,julia-compat)))
+    (home-page "https://github.com/JuliaMath/FixedPointNumbers.jl")
+    (synopsis "Fixed point types for julia")
+    (description "This library implements fixed-point number types.  A
+fixed-point number represents a fractional, or non-integral, number.  In
+contrast with the more widely known floating-point numbers, with fixed-point
+numbers the decimal point doesn't \"float\": fixed-point numbers are
+effectively integers that are interpreted as being scaled by a constant
+factor.  Consequently, they have a fixed number of digits (bits) after the
+decimal (radix) point.")
+    (license license:expat)))
+
 (define-public julia-inifile
   (package
     (name "julia-inifile")
-- 
2.25.0

>From 8582ad38d348dae41be96b5c9ff9512748c6ee7b Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 16:08:00 +0100
Subject: [PATCH 13/16] gnu: Add julia-orderedcollections.

* gnu/packages/julia-xyz.scm (julia-orderedcollections): New variable.
---
 gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 046c365b08..797c61ce6f 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -218,6 +218,30 @@ arbitrary indices, similar to those found in some other programming languages
 like Fortran.")
     (license license:expat)))
 
+(define-public julia-orderedcollections
+  (package
+    (name "julia-orderedcollections")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaCollections/OrderedCollections.jl")
+             ;; They added Package.toml after the 1.1.0 tag
+             (commit "7a789d72a40f4c446f59575f5d77a63df4391a24")))
+       (file-name "OrderedCollections")
+       (sha256
+        (base32 "09b3mlzkxcbc8wn0pji73591865li07q4kvvfzn9x4256mw47riq"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaCollections/OrderedCollections.jl")
+    (synopsis "Julia implementation of associative containers that preserve
+insertion order")
+    (description "This package implements OrderedDicts and OrderedSets, which
+are similar to containers in base Julia.  However, during iteration the
+Ordered* containers return items in the order in which they were added to the
+collection.")
+    (license license:expat)))
+
 (define-public julia-parsers
   (package
     (name "julia-parsers")
-- 
2.25.0

>From 3b122c28d94bd0bdd149a0e7d1031d81bc85face Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 16:08:25 +0100
Subject: [PATCH 14/16] gnu: Add julia-datastructures.

* gnu/packages/julia-xyz.scm (julia-datastructures): New variable.
---
 gnu/packages/julia-xyz.scm | 43 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 797c61ce6f..a4a9939894 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -96,6 +96,49 @@ provides a macro that lets you use the latest syntax in a backwards-compatible
 way.")
     (license license:expat)))
 
+(define-public julia-datastructures
+  (package
+    (name "julia-datastructures")
+    (version "0.17.9")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaCollections/DataStructures.jl")
+             (commit (string-append "v" version))))
+       (file-name "DataStructures")
+       (sha256
+        (base32 "1gp5n99c1llwp2zfsh1iw9jr5hhjswrq7v8iwkp2vj7yp5vvy5lw"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     `(("julia-orderedcollections" ,julia-orderedcollections)))
+    (home-page "https://github.com/JuliaCollections/DataStructures.jl")
+    (synopsis "Julia implementation of Data structures")
+    (description "This package implements a variety of data structures,
+including:
+
+@enumerate
+@item Deque (implemented with an unrolled linked list)
+@item CircularBuffer
+@item CircularDeque
+@item Stack
+@item Queue
+@item Accumulators and Counters (i.e. Multisets / Bags)
+@item Disjoint Sets
+@item Binary Heap
+@item Mutable Binary Heap
+@item Ordered Dicts and Sets
+@item Dictionaries with Defaults
+@item Trie
+@item Linked List and Mutable Linked List
+@item Sorted Dict, Sorted Multi-Dict and Sorted Set
+@item DataStructures.IntSet
+@item Priority Queue
+@item Fenwick Tree
+@item SparseIntSet
+@end enumerate")
+    (license license:expat)))
+
 (define-public julia-fixedpointnumbers
   (package
     (name "julia-fixedpointnumbers")
-- 
2.25.0

>From e29caaaf651b750f8fcc734dab06921c81f4b226 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 16:09:38 +0100
Subject: [PATCH 15/16] gnu: Add julia-json.

* gnu/packages/julia-xyz.scm (julia-json): New variable.
---
 gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index a4a9939894..5130663e48 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -185,6 +185,31 @@ decimal (radix) point.")
 allows to interface with @file{.ini} files.")
     (license license:expat)))
 
+(define-public julia-json
+  (package
+    (name "julia-json")
+    (version "0.21.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaIO/JSON.jl")
+             (commit (string-append "v" version))))
+       (file-name "JSON")
+       (sha256
+        (base32 "0knmfjhchd3ggy86dsfyb7l4v3fv5dcr207cgp54mj7rj96caqsm"))))
+    (build-system julia-build-system)
+    (propagated-inputs `(("julia-parsers" ,julia-parsers)))
+    ;; For some reason, the precompile cache for this package is broken,
+    ;; meaning that it will get re-generated at `using'
+    (inputs `(("julia-offsetarrays" ,julia-offsetarrays)
+              ("julia-datastructures" ,julia-datastructures)
+              ("julia-fixedpointnumbers" ,julia-fixedpointnumbers)))
+    (home-page "https://github.com/JuliaIO/JSON.jl")
+    (synopsis "JSON parsing and printing in Julia")
+    (description "Parsing and printing JSON in pure Julia.")
+    (license license:expat)))
+
 (define-public julia-mbedtls
   (package
     (name "julia-mbedtls")
-- 
2.25.0

>From 238554a69cab1f7b1eedb93d453e78587b0e4597 Mon Sep 17 00:00:00 2001
From: nixo <[email-masked]>
Date: Mon, 24 Feb 2020 16:37:10 +0100
Subject: [PATCH 16/16] gnu: Add julia-http.

* gnu/packages/julia-xyz.scm (julia-http): New variable.
---
 gnu/packages/julia-xyz.scm | 45 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 5130663e48..be3c776f49 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -165,6 +165,51 @@ factor.  Consequently, they have a fixed number of digits (bits) after the
 decimal (radix) point.")
     (license license:expat)))
 
+(define-public julia-http
+  (package
+    (name "julia-http")
+    (version "0.8.9")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaWeb/HTTP.jl")
+             (commit (string-append "v" version))))
+       (file-name "HTTP")
+       (sha256
+        (base32 "11g49gnnacvmihnr0p3inqmsdw6wllyfkq5sbka09mwnrf3vahs7"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'install 'disable-network-tests
+           (lambda _
+             (substitute* "test/runtests.jl"
+               (("\"client.jl") "# \"client.jl")
+               (("\"multipart.jl") "# \"multipart.jl")
+               (("\"aws4.jl") "# \"as4.jl")
+               ;; some of those might still be saved
+               (("\"async.jl") "# \"async.jl")
+               (("\"server.jl") "# \"server.jl"))
+             (substitute* "test/websockets.jl"
+               (("for s in socket_type") "for s in []"))
+             (substitute* "test/messages.jl"
+               (("@testset \"Read methods\" ") "return\n"))
+             #t)))))
+    (propagated-inputs
+     `(("julia-inifile" ,julia-inifile)
+       ("julia-mbedtls" ,julia-mbedtls)
+       ("julia-compat" ,julia-compat)))
+    ;; required for tests
+    (inputs
+     `(("julia-json" ,julia-json)
+       ("julia-bufferedstreams" ,julia-bufferedstreams)))
+    (home-page "https://juliaweb.github.io/HTTP.jl/")
+    (synopsis "HTTP support for Julia")
+    (description "@code{HTTP.jl} is a Julia library for HTTP Messages,
+implementing both a client and a server.")
+    (license license:expat)))
+
 (define-public julia-inifile
   (package
     (name "julia-inifile")
-- 
2.25.0

Thanks, Nicolò

>
> On Tue, 11 Feb 2020 at 18:58, zimoun <[email-masked]> wrote:
>>
>> Hi,
>>
>> Please find attach the almost updated julia using 2 patches. The first
>> add a dependency and the second update and patch.
>>
>> I hope that I do not screw up the indentation; sometimes my Emacs does
>> weird stuff. Anyway.
>>
>> If it is fine with you, please ping Ludo or any committer. :-)
>>
>>
>> Cheers,
>> simon