diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 1 | ||||
| -rw-r--r-- | gnu/packages/compression.scm | 173 | ||||
| -rw-r--r-- | gnu/packages/java-compression.scm | 3 | ||||
| -rw-r--r-- | gnu/packages/python-compression.scm | 206 | ||||
| -rw-r--r-- | gnu/packages/xorg.scm | 1 |
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) |