Merge branch 'master' into core-updates

1 files changed, 242 insertions, 18 deletions

diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 9a1b628809..b3377a2fb4 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -19,6 +19,7 @@
 ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
 ;;; Copyright © 2017 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2017 Petter <petter@mykolab.ch>
+;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -41,6 +42,7 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
@@ -53,6 +55,8 @@
   #:use-module (gnu packages check)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages file)
+  #:use-module (gnu packages java)
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -1035,6 +1039,38 @@ well as bzip2.")
     (license (list license:gpl3+
                    license:public-domain)))) ; most files in lzma/
 
+(define-public bitshuffle
+  (package
+    (name "bitshuffle")
+    (version "0.3.2")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "bitshuffle" version))
+              (sha256
+               (base32
+                "01vcjrvsxjvv47y5hf9rps69zwv0vwd4ydhhms2jfs4rpcnlak6v"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'make-required-dir
+           (lambda _
+             (mkdir-p "bitshuffle/plugin")
+             #t)))))
+    (inputs
+     `(("numpy" ,python-numpy)
+       ("h5py" ,python-h5py)
+       ("hdf5" ,hdf5)))
+    (native-inputs
+     `(("cython" ,python-cython)))
+    (home-page "https://github.com/kiyo-masui/bitshuffle")
+    (synopsis "Filter for improving compression of typed binary data")
+    (description "Bitshuffle is an algorithm that rearranges typed, binary data
+for improving compression, as well as a python/C package that implements this
+algorithm within the Numpy framework.")
+    (license license:expat)))
+
 (define-public snappy
   (package
     (name "snappy")
@@ -1058,6 +1094,177 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
 100% bigger.")
     (license license:asl2.0)))
 
+(define bitshuffle-for-snappy
+  (package
+    (inherit bitshuffle)
+    (name "bitshuffle-for-snappy")
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'configure
+           (lambda* (#:key outputs #:allow-other-keys)
+             (with-output-to-file "Makefile"
+               (lambda _
+                 (format #t "\
+libbitshuffle.so: src/bitshuffle.o src/bitshuffle_core.o src/iochain.o lz4/lz4.o
+\tgcc -O3 -ffast-math -std=c99 -o $@ -shared -fPIC $^
+
+%.o: %.c
+\tgcc -O3 -ffast-math -std=c99 -fPIC -Isrc -Ilz4 -c $< -o $@
+
+PREFIX:=~a
+LIBDIR:=$(PREFIX)/lib
+INCLUDEDIR:=$(PREFIX)/include
+
+install: libbitshuffle.so
+\tinstall -dm755 $(LIBDIR)
+\tinstall -dm755 $(INCLUDEDIR)
+\tinstall -m755 libbitshuffle.so $(LIBDIR)
+\tinstall -m644 src/bitshuffle.h $(INCLUDEDIR)
+\tinstall -m644 src/bitshuffle_core.h $(INCLUDEDIR)
+\tinstall -m644 src/iochain.h $(INCLUDEDIR)
+\tinstall -m644 lz4/lz4.h $(INCLUDEDIR)
+" (assoc-ref outputs "out"))))
+             #t)))))
+    (inputs '())
+    (native-inputs '())))
+
+(define-public java-snappy
+  (package
+    (name "java-snappy")
+    (version "1.1.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/xerial/snappy-java/archive/"
+                                  version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "1w58diryma7qz7aa24yv8shf3flxcbbw8jgcn2lih14wgmww58ww"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "snappy.jar"
+       #:source-dir "src/main/java"
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'remove-binaries
+           (lambda _
+             (delete-file "lib/org/xerial/snappy/OSInfo.class")
+             (delete-file-recursively "src/main/resources/org/xerial/snappy/native")
+             #t))
+         (add-before 'build 'build-jni
+           (lambda _
+             ;; Rebuild one of the binaries we removed earlier
+             (system* "javac" "src/main/java/org/xerial/snappy/OSInfo.java"
+                      "-d" "lib")
+             ;; Link to the dynamic bitshuffle and snappy, not the static ones
+             (substitute* "Makefile.common"
+               (("-shared")
+                "-shared -lbitshuffle -lsnappy"))
+             (substitute* "Makefile"
+               ;; Don't try to use git, don't download bitshuffle source
+               ;; and don't build it.
+               (("\\$\\(SNAPPY_GIT_UNPACKED\\) ")
+                "")
+               ((": \\$\\(SNAPPY_GIT_UNPACKED\\)")
+                ":")
+               (("\\$\\(BITSHUFFLE_UNPACKED\\) ")
+                "")
+               ((": \\$\\(SNAPPY_SOURCE_CONFIGURED\\)") ":")
+               ;; What we actually want to build
+               (("SNAPPY_OBJ:=.*")
+                "SNAPPY_OBJ:=$(addprefix $(SNAPPY_OUT)/, \
+                 SnappyNative.o BitShuffleNative.o)\n")
+               ;; Since we removed the directory structure in "native" during
+               ;; the previous phase, we need to recreate it.
+               (("NAME\\): \\$\\(SNAPPY_OBJ\\)")
+                "NAME): $(SNAPPY_OBJ)\n\t@mkdir -p $(@D)"))
+             ;; Finally we can run the Makefile to build the dynamic library.
+             (zero? (system* "make" "native"))))
+         ;; Once we have built the shared library, we need to place it in the
+         ;; "build" directory so it can be added to the jar file.
+         (add-after 'build-jni 'copy-jni
+           (lambda _
+             (copy-recursively "src/main/resources/org/xerial/snappy/native"
+                               "build/classes/org/xerial/snappy/native")))
+         (add-before 'check 'fix-failing
+           (lambda _
+             ;; This package assumes maven build, which puts results in "target".
+             ;; We put them in "build" instead, so fix that.
+             (substitute* "src/test/java/org/xerial/snappy/SnappyLoaderTest.java"
+               (("target/classes") "build/classes"))
+             ;; FIXME: probably an error
+             (substitute* "src/test/java/org/xerial/snappy/SnappyOutputStreamTest.java"
+               (("91080") "91013")))))))
+    (inputs
+     `(("osgi-framework" ,java-osgi-framework)))
+    (propagated-inputs
+     `(("bitshuffle" ,bitshuffle-for-snappy)
+       ("snappy" ,snappy)))
+    (native-inputs
+     `(("junit" ,java-junit)
+       ("hamcrest" ,java-hamcrest-core)
+       ("xerial-core" ,java-xerial-core)
+       ("classworlds" ,java-plexus-classworlds)
+       ("perl" ,perl)))
+    (home-page "https://github.com/xerial/snappy-java")
+    (synopsis "Compression/decompression algorithm in Java")
+    (description "Snappy-java is a Java port of the snappy, a fast C++
+compresser/decompresser.")
+    (license license:asl2.0)))
+
+(define-public java-iq80-snappy
+  (package
+    (name "java-iq80-snappy")
+    (version "0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/dain/snappy/archive/snappy-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "0rb3zhci7w9wzd65lfnk7p3ip0n6gb58a9qpx8n7r0231gahyamf"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:jar-name "iq80-snappy.jar"
+       #:source-dir "src/main/java"
+       #:test-dir "src/test"
+       #:jdk ,icedtea-8
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             (define (test class)
+               (zero? (system* "java" "-cp" (string-append (getenv "CLASSPATH")
+                                                           ":build/classes"
+                                                           ":build/test-classes")
+                               "-Dtest.resources.dir=src/test/resources"
+                               "org.testng.TestNG" "-testclass"
+                               class)))
+             (system* "ant" "compile-tests")
+             (and
+               (test "org.iq80.snappy.SnappyFramedStreamTest")
+               (test "org.iq80.snappy.SnappyStreamTest"))))
+         (add-before 'build 'remove-hadoop-dependency
+           (lambda _
+             ;; We don't have hadoop
+             (delete-file "src/main/java/org/iq80/snappy/HadoopSnappyCodec.java")
+             (delete-file "src/test/java/org/iq80/snappy/TestHadoopSnappyCodec.java")
+             #t)))))
+    (home-page "https://github.com/dain/snappy")
+    (native-inputs
+     `(("guava" ,java-guava)
+       ("java-snappy" ,java-snappy)
+       ("hamcrest" ,java-hamcrest-core)
+       ("testng" ,java-testng)))
+    (synopsis "Java port of snappy")
+    (description "Iq80-snappy is a rewrite (port) of Snappy writen in pure
+Java.  This compression code produces a byte-for-byte exact copy of the output
+created by the original C++ code, and extremely fast.")
+    (license license:asl2.0)))
+
 (define-public p7zip
   (package
     (name "p7zip")
@@ -1294,24 +1501,6 @@ or junctions, and always follows hard links.")
  archives from InstallShield installers.")
     (license license:expat)))
 
-(define-public unrar
-  (package
-    (name "unrar")
-    (version "0.0.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "http://download.gna.org/unrar/unrar-" version ".tar.gz"))
-              (sha256
-               (base32
-                "1fgmjaxffj3shyxgy765jhxwz1cq88hk0fih1bsdzyvymyyz6mz7"))))
-    (build-system gnu-build-system)
-    (home-page "http://download.gna.org/unrar")
-    (synopsis "RAR archive extraction tool")
-    (description "Unrar is a simple command-line program to list and extract
-RAR archives.")
-    (license license:gpl2+)))
-
 (define-public zstd
   (package
     (name "zstd")
@@ -1634,3 +1823,38 @@ of archives.")
 without having to worry how it does so, or use different interfaces for each
 type by using either Perl modules, or command-line tools on your system.")
     (license license:perl-license)))
+
+(define-public java-tukaani-xz
+  (package
+    (name "java-tukaani-xz")
+    (version "1.6")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://tukaani.org/xz/xz-java-" version ".zip"))
+              (sha256
+               (base32
+                "1z3p1ri1gvl07inxn0agx44ck8n7wrzfmvkz8nbq3njn8r9wba8x"))))
+    (build-system ant-build-system)
+    (arguments
+     `(#:tests? #f; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'chdir
+           (lambda _
+             ;; Our build system enters the first directory in the archive, but
+             ;; the package is not contained in a subdirectory
+             (chdir "..")))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Do we want to install *Demo.jar?
+             (install-file "build/jar/xz.jar"
+                           (string-append
+                             (assoc-ref outputs "out")
+                             "/share/java/xz.jar")))))))
+    (native-inputs
+     `(("unzip" ,unzip)))
+    (home-page "https://tukaani.org")
+    (synopsis "XZ in Java")
+    (description "Tukaani-xz is an implementation of xz compression/decompression
+algorithms in Java.")
+    (license license:public-domain)))