Add many julia packages (separate this in multiple commits)

gnu/packages/graphics.scm

@@ -1071,7 +1071,7 @@ and GPU architectures.")
 (define-public gr
   (package
     (name "gr")
-    (version "0.41.4")
+    (version "0.41.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1081,7 +1081,7 @@ and GPU architectures.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1r3f0vqw85i9g3awzfh20zzjcc71h8r7nld2qv4rmqf3gigck2kr"))
+                "1iymzpa6wbbn3vh7n11ax859bmxwq74n2n3y012fd5ad369yflcj"))
               (modules '((guix build utils)))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/maths.scm

@@ -3426,6 +3426,42 @@ packages.")
     ;;  GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
     (license (list license:gpl2+ license:lgpl2.1+))))
 
+(define-public suitesparse-wrapper
+  (package
+    (name "suitesparse-wrapper")
+    (version "5.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url
+              "https://github.com/JuliaLinearAlgebra/SuiteSparseBuilder.git")
+             (commit (string-append "v" version "-0.2.20-1"))))
+       (file-name "SuiteSparse")
+       (sha256
+        (base32 "0wj4ipjv415aib5h398b1qxmwjk54f577n8h7dn68dkybpd2rnp3"))))
+    (native-inputs `(("suitesparse" ,suitesparse)))
+    (arguments
+     `(#:tests? #f                      ; no "check" target
+       #:make-flags (list "CC=gcc"
+                          (string-append "prefix=" (assoc-ref %outputs "out")))
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'build 'make-output
+           (lambda* (#:key outputs #:allow-other-keys)
+             (mkdir-p (string-append (assoc-ref outputs "out") "/lib"))
+             #t))
+         (add-before 'build 'change-directory
+           (lambda _
+             (chdir "src/SuiteSparse_wrapper/")
+             #t)))))
+    (build-system gnu-build-system)
+    (home-page "https://julialinearalgebra.github.io/SuiteSparse.jl/latest/")
+    (synopsis "SuiteSparse wrappers used by Julia SuiteSparse.jl")
+    (description "Binary wrappes for the Julia SuiteSparse.")
+    (license license:expat)))
+
 (define-public atlas
   (package
     (name "atlas")

gnu/packages/statistics.scm

@@ -58,6 +58,7 @@
   #:use-module (gnu packages icu4c)
   #:use-module (gnu packages image)
   #:use-module (gnu packages java)
+  #:use-module (gnu packages julia)
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
@@ -395,6 +396,50 @@ available, greatly increasing its breadth and scope.")
     (description
      "This package provides the R math library as an independent package.")))
 
+(define-public rmath-julia
+  (package
+    (name "rmath-julia")
+    (version "0.2.2")
+    (source
+     ;; This ships it's own version of Rmath sources, version 3.4.1
+     ;; Not sure if we should move our own there
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaStats/Rmath-julia.git")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32 "107l5fgd7m1dx5wl53zvjxq8qnb5smzsnpganrhxycjgw708manj"))))
+    (build-system gnu-build-system)
+    (inputs `(("julia" ,julia)))
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'install)
+         (delete 'check)
+         (add-after 'build 'check
+           (lambda _
+             ;; test.jl is a bit outdated
+             (substitute* "test.jl"
+               ;; Random required for randexp
+               (("using Base.Test") "using Test; using Random")
+               (("Void") "Cvoid")
+               (("cfunction") "@cfunction"))
+             (invoke "julia" "test.jl") #t))
+         (add-after 'check 'install
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             (let ((out (string-append (assoc-ref outputs "out") "/lib/")))
+               (mkdir-p out)
+               (copy-file "src/libRmath-julia.so"
+                          (string-append out "libRmath-julia.so")))
+             #t)))))
+    (home-page "https://github.com/JuliaStats/Rmath-julia")
+    (synopsis "The Rmath library from R, for Julia")
+    (description
+     "This is a slightly modified version of the standalone Rmath library from R, built to be used with the Rmath.jl Julia package.")
+    (license license:gpl2)))
+
 (define-public r-boot
   (package
     (name "r-boot")

guix/build-system/julia.scm

@@ -75,7 +75,7 @@
 
 (define* (julia-build store name inputs
                       #:key source
-                      (tests? #t)
+                      (tests? #f)
                       (phases '(@ (guix build julia-build-system)
                                   %standard-phases))
                       (outputs '("out"))

guix/build/julia-build-system.scm

@@ -79,16 +79,21 @@
   #t)
 
 (define* (check #:key tests? source inputs outputs #:allow-other-keys)
+  (display "Running tests")
   (when tests?
-      (let* ((out (assoc-ref outputs "out"))
+    (let* ((out (assoc-ref outputs "out"))
-             (package (strip-store-file-name source))
+           (package (strip-store-file-name source))
-             (builddir (string-append out "/share/julia/")))
+           (builddir (string-append out "/share/julia/")))
-        (setenv "JULIA_DEPOT_PATH" builddir)
+      (setenv "JULIA_DEPOT_PATH" builddir)
-        (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
+      (setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
-        (display builddir)
+      ;; Sometimes tests require files in the current directory
-        (invoke "julia" (string-append builddir
+      (with-directory-excursion
-                                       "packages/"
+          (string-append builddir "packages/" package "/test")
-                                       package "/test/runtests.jl"))))
+        (invoke "julia"
+                ;; Force bound checking even when annotated not to
+                ;; This appears to be the default on travis
+                "--check-bounds=yes"
+                "runtests.jl"))))
   #t)
 
 (define (julia-create-package-toml outputs source
@@ -123,7 +128,7 @@ 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)