gnu: Move Python compression packages to new module.

* gnu/packages/compression.scm (python-lzo, python2-lzo, python-lz4,
python2-lz4, python-lzstring, python2-lzstring, bitshuffle,
bitshuffle-for-snappy): Move variables from here...
* gnu/packages/python-compression.scm: ...to this new module.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/bioinformatics.scm,
gnu/packages/java-compression.scm,
gnu/packages/xorg.scm: Adjust module references.

6 files changed, 211 insertions, 174 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index 7ee41de644..fb8e0e1eb0 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -367,6 +367,7 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/pure.scm				\
   %D%/packages/pv.scm				\
   %D%/packages/python.scm			\
+  %D%/packages/python-compression.scm		\
   %D%/packages/python-crypto.scm		\
   %D%/packages/python-web.scm			\
   %D%/packages/python-xyz.scm			\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1254d21c87..28dbdca13b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -98,6 +98,7 @@
   #:use-module (gnu packages popt)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-compression)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages readline)
diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm
index 956cac7a1f..327951fded 100644
--- a/gnu/packages/compression.scm
+++ b/gnu/packages/compression.scm
@@ -47,7 +47,6 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages assembly)
   #:use-module (gnu packages autotools)
@@ -61,7 +60,6 @@
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages valgrind)
   #:use-module (ice-9 match)
@@ -462,44 +460,6 @@ LZO is written in ANSI C.  Both the source code and the compressed data
 format are designed to be portable across platforms.")
     (license license:gpl2+)))
 
-(define-public python-lzo
-  (package
-    (name "python-lzo")
-    (version "1.12")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "python-lzo" version))
-       (sha256
-        (base32
-         "0iakqgd51n1cd7r3lpdylm2rgbmd16y74cra9kcapwg84mlf9a4p"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:test-target "check"
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'patch-setuppy
-           (lambda _
-             (substitute* "setup.py"
-               (("include_dirs.append\\(.*\\)")
-                (string-append "include_dirs.append('"
-                               (assoc-ref %build-inputs "lzo")
-                               "/include/lzo"
-                               "')")))
-             #t)))))
-    (inputs
-     `(("lzo" ,lzo)))
-    (home-page "https://github.com/jd-boyd/python-lzo")
-    (synopsis "Python bindings for the LZO data compression library")
-    (description
-     "Python-LZO provides Python bindings for LZO, i.e. you can access
-the LZO library from your Python scripts thereby compressing ordinary
-Python strings.")
-    (license license:gpl2+)))
-
-(define-public python2-lzo
-  (package-with-python2 python-lzo))
-
 (define-public lzop
   (package
     (name "lzop")
@@ -741,54 +701,6 @@ time for compression ratio.")
     ;; line interface programs (lz4, fullbench, fuzzer, datagen) are GPL2+.
     (license (list license:bsd-2 license:gpl2+))))
 
-(define-public python-lz4
-  (package
-    (name "python-lz4")
-    (version "0.10.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "lz4" version))
-       (sha256
-        (base32
-         "0ghv1xbaq693kgww1x9c22bplz479ls9szjsaa4ig778ls834hm0"))))
-    (build-system python-build-system)
-    (native-inputs
-     `(("python-nose" ,python-nose)
-       ("python-setuptools-scm" ,python-setuptools-scm)))
-    (home-page "https://github.com/python-lz4/python-lz4")
-    (synopsis "LZ4 bindings for Python")
-    (description
-     "This package provides python bindings for the lz4 compression library
-by Yann Collet.  The project contains bindings for the LZ4 block format and
-the LZ4 frame format.")
-    (license license:bsd-3)))
-
-(define-public python2-lz4
-  (package-with-python2 python-lz4))
-
-(define-public python-lzstring
-  (package
-    (name "python-lzstring")
-    (version "1.0.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "lzstring" version))
-       (sha256
-        (base32
-         "18ly9pppy2yspxzw7k1b23wk77k7m44rz2g0271bqgqrk3jn3yhs"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-future" ,python-future)))
-    (home-page "https://github.com/gkovacs/lz-string-python")
-    (synopsis "String compression")
-    (description "Lz-string is a string compressor library for Python.")
-    (license license:expat)))
-
-(define-public python2-lzstring
-  (package-with-python2 python-lzstring))
-
 (define-public squashfs-tools
   (package
     (name "squashfs-tools")
@@ -1118,54 +1030,6 @@ well as bzip2.")
     (license (list license:gpl3+
                    license:public-domain)))) ; most files in lzma/
 
-(define-public bitshuffle
-  (package
-    (name "bitshuffle")
-    (version "0.3.5")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "bitshuffle" version))
-              (sha256
-               (base32
-                "1823x61kyax4dc2hjmc1xraskxi1193y8lvxd03vqv029jrj8cjy"))
-              (modules '((guix build utils)))
-              (snippet
-               '(begin
-                  ;; Remove generated Cython files.
-                  (delete-file "bitshuffle/h5.c")
-                  (delete-file "bitshuffle/ext.c")
-                  #t))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f             ; fail: https://github.com/h5py/h5py/issues/769
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-neon-detection
-           ;; Neon is only for aarch64 ATM
-           ;; see: https://github.com/kiyo-masui/bitshuffle/pull/73
-           (lambda _
-             (substitute* "src/bitshuffle_core.c"
-               (("#define USEARMNEON")
-                "#ifdef __aarch64__\n#define USEARMNEON\n#endif"))
-             #t))
-         (add-after 'unpack 'dont-build-native
-           (lambda _
-             (substitute* "setup.py"
-               (("'-march=native', ") ""))
-             #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")
@@ -1192,43 +1056,6 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
 100% bigger.")
     (license license:asl2.0)))
 
-(define-public 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 p7zip
   (package
     (name "p7zip")
diff --git a/gnu/packages/java-compression.scm b/gnu/packages/java-compression.scm
index 8cebfc65a5..3102c70d88 100644
--- a/gnu/packages/java-compression.scm
+++ b/gnu/packages/java-compression.scm
@@ -29,7 +29,8 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages java)
-  #:use-module (gnu packages perl))
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python-compression))
 
 (define-public java-snappy
   (package
diff --git a/gnu/packages/python-compression.scm b/gnu/packages/python-compression.scm
new file mode 100644
index 0000000000..3792f37328
--- /dev/null
+++ b/gnu/packages/python-compression.scm
@@ -0,0 +1,206 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
+;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
+;;;
+;;; 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 python-compression)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-xyz))
+
+(define-public python-lzo
+  (package
+    (name "python-lzo")
+    (version "1.12")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "python-lzo" version))
+       (sha256
+        (base32
+         "0iakqgd51n1cd7r3lpdylm2rgbmd16y74cra9kcapwg84mlf9a4p"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:test-target "check"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'patch-setuppy
+           (lambda _
+             (substitute* "setup.py"
+               (("include_dirs.append\\(.*\\)")
+                (string-append "include_dirs.append('"
+                               (assoc-ref %build-inputs "lzo")
+                               "/include/lzo"
+                               "')")))
+             #t)))))
+    (inputs
+     `(("lzo" ,lzo)))
+    (home-page "https://github.com/jd-boyd/python-lzo")
+    (synopsis "Python bindings for the LZO data compression library")
+    (description
+     "Python-LZO provides Python bindings for LZO, i.e. you can access
+the LZO library from your Python scripts thereby compressing ordinary
+Python strings.")
+    (license license:gpl2+)))
+
+(define-public python2-lzo
+  (package-with-python2 python-lzo))
+
+(define-public python-lz4
+  (package
+    (name "python-lz4")
+    (version "0.10.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "lz4" version))
+       (sha256
+        (base32
+         "0ghv1xbaq693kgww1x9c22bplz479ls9szjsaa4ig778ls834hm0"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("python-setuptools-scm" ,python-setuptools-scm)))
+    (home-page "https://github.com/python-lz4/python-lz4")
+    (synopsis "LZ4 bindings for Python")
+    (description
+     "This package provides python bindings for the lz4 compression library
+by Yann Collet.  The project contains bindings for the LZ4 block format and
+the LZ4 frame format.")
+    (license license:bsd-3)))
+
+(define-public python2-lz4
+  (package-with-python2 python-lz4))
+
+(define-public python-lzstring
+  (package
+    (name "python-lzstring")
+    (version "1.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "lzstring" version))
+       (sha256
+        (base32
+         "18ly9pppy2yspxzw7k1b23wk77k7m44rz2g0271bqgqrk3jn3yhs"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-future" ,python-future)))
+    (home-page "https://github.com/gkovacs/lz-string-python")
+    (synopsis "String compression")
+    (description "Lz-string is a string compressor library for Python.")
+    (license license:expat)))
+
+(define-public python2-lzstring
+  (package-with-python2 python-lzstring))
+
+(define-public bitshuffle
+  (package
+    (name "bitshuffle")
+    (version "0.3.5")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "bitshuffle" version))
+              (sha256
+               (base32
+                "1823x61kyax4dc2hjmc1xraskxi1193y8lvxd03vqv029jrj8cjy"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Remove generated Cython files.
+                  (delete-file "bitshuffle/h5.c")
+                  (delete-file "bitshuffle/ext.c")
+                  #t))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f             ; fail: https://github.com/h5py/h5py/issues/769
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-neon-detection
+           ;; Neon is only for aarch64 ATM
+           ;; see: https://github.com/kiyo-masui/bitshuffle/pull/73
+           (lambda _
+             (substitute* "src/bitshuffle_core.c"
+               (("#define USEARMNEON")
+                "#ifdef __aarch64__\n#define USEARMNEON\n#endif"))
+             #t))
+         (add-after 'unpack 'dont-build-native
+           (lambda _
+             (substitute* "setup.py"
+               (("'-march=native', ") ""))
+             #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 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 '())))
diff --git a/gnu/packages/xorg.scm b/gnu/packages/xorg.scm
index a6a2e603aa..67b38246ec 100644
--- a/gnu/packages/xorg.scm
+++ b/gnu/packages/xorg.scm
@@ -71,6 +71,7 @@
   #:use-module (gnu packages perl-check)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-compression)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)