;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2015, 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2017, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2016 Lukas Gradl <lgradl@openmailbox.org>
;;; Copyright © 2016 David Craven <david@craven.ch>
-;;; Copyright © 2016, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
-;;; Copyright © 2016, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2019, 2020, 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2016, 2018, 2019, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017 Corentin Bocquillon <corentin@nybble.fr>
;;; Copyright © 2017 Gregor Giesen <giesen@zaehlwerk.net>
;;; Copyright © 2017 Frederick M. Muriithi <fredmanglis@gmail.com>
;;; Copyright © 2017 Nikita <nikita@n0.is>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017–2019, 2022 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
+;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
+;;; Copyright © 2020 Alexandros Theodotou <alex@zrythm.org>
;;;
;;; This file is part of GNU Guix.
;;;
(define-module (gnu packages serialization)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
+ #:use-module (guix gexp)
#:use-module (guix download)
+ #:use-module (guix hg-download)
#:use-module (guix git-download)
#:use-module (guix utils)
#:use-module (guix build-system cmake)
+ #:use-module (guix build-system copy)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
+ #:use-module (gnu packages base)
+ #:use-module (gnu packages bash)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
#:use-module (gnu packages documentation)
#:use-module (gnu packages gcc)
+ #:use-module (gnu packages llvm)
#:use-module (gnu packages lua)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
(add-after 'unpack 'chdir
(lambda _ (chdir "lang/c++"))))))
(inputs
- `(("boost" ,boost)
- ("snappy" ,snappy)))
+ (list boost snappy))
(home-page "https://avro.apache.org/")
(synopsis "Data serialization system")
(description "Apache Avro is a data serialization system. Avro provides:
implement RPC protocols.")
(license license:asl2.0)))
+(define-public avro-cpp-1.9-for-irods
+ (package
+ (inherit avro-cpp-1.9)
+ (properties `((hidden? . #true)))
+ (arguments
+ `(#:configure-flags
+ '("-DCMAKE_CXX_COMPILER=clang++"
+ "-DCMAKE_CXX_FLAGS=-stdlib=libc++"
+ "-DCMAKE_EXE_LINKER_FLAGS=-lc++abi -lz")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'chdir
+ (lambda _ (chdir "lang/c++")))
+ (add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (cons* (search-input-directory inputs "include/c++/v1")
+ ;; Hide GCC's C++ headers so that they do not interfere with
+ ;; the Clang headers.
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
+ #\:)))
+ ":"))
+ (format #true
+ "environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
+ (getenv "CPLUS_INCLUDE_PATH"))))))))
+ (inputs
+ `(("boost" ,boost-for-irods)
+ ("clang" ,clang-toolchain-6)
+ ("libcxx+libcxxabi" ,libcxx+libcxxabi-6)
+ ("libcxxabi" ,libcxxabi-6)
+ ("snappy" ,snappy-with-clang6)
+ ("zlib" ,zlib)))))
+
(define-public cereal
(package
(name "cereal")
- (version "1.2.1")
+ (version "1.3.2")
(source
(origin
(method git-fetch)
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1vxkrsnxkiblzi1z61vfix167c184fy868sgwj2dxxgbgjcq2nrh"))))
+ (base32
+ "02sd90ynya7wg013zwzjr79fsv4bzqgfg9l2mapd4j38rv06gahx"))))
(build-system cmake-build-system)
(arguments
- `(;; The only included tests are portability tests requiring
- ;; cross-compilation and boost. Since we are building cereal on more
- ;; platforms anyway, there is no compelling reason to build the tests.
- #:tests? #f
- #:out-of-source? #f
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (replace 'build
- (lambda _
- (substitute* "doc/doxygen.in"
- (("@CMAKE_CURRENT_SOURCE_DIR@") "."))
- (invoke "doxygen" "doc/doxygen.in")
- #t))
- ;; There is no "install" target, so we have to provide our own
- ;; "install" phase.
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (doc (string-append out "/share/cereal/docs"))
- (include (string-append out "/include/cereal")))
- (mkdir-p doc)
- (mkdir-p include)
- (copy-recursively "include/cereal" include)
- (copy-recursively "doc/html" doc))
- #t)))))
+ (list
+ #:configure-flags #~'("-DSKIP_PORTABILITY_TEST=ON"
+ ;; Don't bother building the sandbox examples.
+ "-DSKIP_PERFORMANCE_COMPARISON=ON"
+ "-DBUILD_SANDBOX=OFF")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'install 'install-doc
+ (lambda _
+ (let ((doc (string-append #$output "/share/doc/html")))
+ (invoke "make" "doc")
+ (mkdir-p doc)
+ (copy-recursively "doc/html" doc)))))))
(native-inputs
- `(("doxygen" ,doxygen)))
+ (list doxygen))
(home-page "https://uscilab.github.io/cereal/")
(synopsis "C++11 library for serialization")
(description
"Cereal is a header-only C++11 serialization library. Cereal takes
arbitrary data types and reversibly turns them into different representations,
such as compact binary encodings, XML, or JSON.")
- (license license:bsd-3)))
+ ;; Note: Cereal bundles forked versions of rapidxml and rapidjson
+ ;; (see include/cereal/external/), so list their licenses too.
+ (license (list license:bsd-3 ;Cereal itself
+ ;; The bundled RapidXML is dual Boost/Expat (users choice).
+ ;; RapidJSON is Expat licensed, and further bundles a
+ ;; stdint.h with BSD-3.
+ license:boost1.0 license:expat
+ ;; Finally, include/cereal/external/base64.hpp has a
+ ;; home-grown BSD-like license.
+ (license:non-copyleft
+ "file://include/cereal/external/LICENSE")))))
+
+;; Some packages fail with the latest version. Remove this variable
+;; when unused.
+(define-public cereal-1.3.0
+ (package
+ (inherit cereal)
+ (version "1.3.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/USCiLab/cereal")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name "cereal" version))
+ (sha256
+ (base32
+ "0hc8wh9dwpc1w1zf5lfss4vg5hmgpblqxbrpp1rggicpx9ar831p"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments cereal)
+ ((#:configure-flags flags #~'())
+ #~'("-DSKIP_PORTABILITY_TEST=ON"))
+ ((#:phases phases #~%standard-phases)
+ #~(modify-phases #$phases
+ (add-before 'configure 'skip-sandbox
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("add_subdirectory\\(sandbox\\)") ""))))))))))
(define-public msgpack
(package
(name "msgpack")
- (version "3.2.1")
+ (version "3.3.0")
(source
(origin
(method url-fetch)
(close-output-port p)
#t))
(sha256
- (base32 "1ljqmgscdb0f8w8kx2lnswnisyxchcmijbjbmswkv0g187bvqg23"))))
+ (base32 "0yzhq50ijvwrfkr97knhvn54lj3f4hr3zy39yq8wpf6xll94s4bf"))))
(build-system cmake-build-system)
(native-inputs
- `(("googletest" ,googletest-1.8)
- ("pkg-config" ,pkg-config)))
+ (list googletest-1.8 pkg-config))
(propagated-inputs
- `(("zlib" ,zlib))) ;; Msgpack installs two headers (zbuffer.h,
+ (list zlib)) ;; Msgpack installs two headers (zbuffer.h,
;; zbuffer.hpp) which #include <zlib.h>. However, 'guix gc --references'
;; does not detect a store reference to zlib since these headers are not
;; compiled.
(modify-phases %standard-phases
(delete 'configure))))
(native-inputs
- `(("libtool" ,libtool)))
+ (list libtool))
(home-page "https://github.com/tarruda/libmpack")
(synopsis "Small binary serialization library")
(description "Libmpack is a small binary serialization and RPC library
"mpack-src")
#t)))))
(inputs
- `(("lua" ,lua)))
+ (list lua))
(native-inputs
`(("pkg-config" ,pkg-config)
("libmpack" ,(package-source libmpack))))
(inputs
`(("lua" ,lua-5.2)))))
+(define-public libyaml
+ (package
+ (name "libyaml")
+ (version "0.2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://pyyaml.org/download/libyaml/yaml-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1x4fcw13r3lqy8ndydr3ili87wicplw2awbcv6r21qgyfndswhn6"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:configure-flags '("--disable-static")))
+ (home-page "https://pyyaml.org/wiki/LibYAML")
+ (synopsis "YAML 1.1 parser and emitter written in C")
+ (description
+ "LibYAML is a YAML 1.1 parser and emitter written in C.")
+ (license license:expat)))
+
+(define-public libyaml+static
+ (package
+ (inherit libyaml)
+ (name "libyaml+static")
+ (arguments
+ '(#:configure-flags '("--enable-static")))))
+
+(define-public libcyaml
+ (package
+ (name "libcyaml")
+ (version "1.3.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/tlsa/libcyaml")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (patches (search-patches "libcyaml-libyaml-compat.patch"))
+ (sha256
+ (base32 "0gvf3h8r8300wdwfjgxw3nzlj7w14q63m67p8wdm5fvpha017n4y"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+ #:make-flags
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ (string-append "CC=" ,(cc-for-target)))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)))) ; no configure script
+ (inputs
+ (list libyaml))
+ (native-inputs
+ (list pkg-config))
+ (synopsis "C library for reading and writing YAML")
+ (description
+ "LibCYAML is a C library written in ISO C11 for reading and writing
+structured YAML documents. The fundamental idea behind CYAML is to allow
+applications to construct schemas which describe both the permissible
+structure of the YAML documents to read/write, and the C data structure(s)
+in which the loaded data is arranged in memory.")
+ (home-page "https://github.com/tlsa/libcyaml")
+ (license license:isc)))
+
(define-public yaml-cpp
(package
(name "yaml-cpp")
(arguments
'(#:configure-flags '("-DYAML_BUILD_SHARED_LIBS=ON")))
(native-inputs
- `(("python" ,python)))
+ (list python))
(home-page "https://github.com/jbeder/yaml-cpp")
(synopsis "YAML parser and emitter in C++")
(description "YAML parser and emitter in C++ matching the YAML 1.2 spec.")
(define-public jsoncpp
(package
(name "jsoncpp")
- (version "1.9.2")
+ (version "1.9.4")
(home-page "https://github.com/open-source-parsers/jsoncpp")
(source (origin
(method git-fetch)
(uri (git-reference (url home-page) (commit version)))
(file-name (git-file-name name version))
- (patches (search-patches "jsoncpp-fix-inverted-case.patch"))
+ (patches
+ (search-patches "jsoncpp-pkg-config-version.patch"))
(sha256
(base32
- "037d1b1qdmn3rksmn1j71j26bv4hkjv7sn7da261k853xb5899sg"))))
+ "0qnx5y6c90fphl9mj9d20j2dfgy6s5yr5l0xnzid0vh71zrp6jwv"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
(base32
"1180ln8blrb0mwzpcf78k49hlki6di65q77rsvglf83kfcyh4d7z"))))))
+(define-public json.sh
+ (let ((commit "0d5e5c77365f63809bf6e77ef44a1f34b0e05840") ;no releases
+ (revision "1"))
+ (package
+ (name "json.sh")
+ (version (git-version "0.0.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dominictarr/JSON.sh")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "14lxvp5xbdk0dcwkjbdp098z1108j8z48zaibndh4i731kkcz43i"))))
+ (build-system copy-build-system)
+ (arguments
+ `(#:install-plan '(("JSON.sh" "bin/"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'install 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests? (invoke "./all-tests.sh"))
+ #t))
+ (add-after 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (wrap-program (string-append (assoc-ref outputs "out") "/bin/JSON.sh")
+ `("PATH" ":" prefix
+ (,(string-join
+ (map (lambda (in) (string-append (assoc-ref inputs in) "/bin"))
+ '("grep" "sed"))
+ ":"))))
+ #t)))))
+ (inputs
+ (list bash-minimal grep sed))
+ (synopsis "Pipeable JSON parser written in shell")
+ (description
+ "This package provides a JSON parser written in shell, compatible with
+ash, Bash, Dash and Zsh. Pipe JSON to it, and it traverses the JSON objects
+and prints out the path to the current object (as a JSON array) and then the
+object, without whitespace.")
+ (home-page "https://github.com/dominictarr/JSON.sh")
+ (license (list license:expat license:asl2.0))))) ;dual-licensed
+
(define-public capnproto
(package
(name "capnproto")
;; /etc/services, which is not present in build environment.
(substitute* "src/kj/async-io-test.c++" ((":http") ":80"))
#t))
- (add-before 'check 'use-tmp-for-tempory-files
+ (add-before 'check 'use-tmp-for-temporary-files
(lambda _
- ;; Use /tmp for tempory files, as the default /var/tmp directory
+ ;; Use /tmp for temporary files, as the default /var/tmp directory
;; doesn't exist.
(substitute* "src/kj/filesystem-disk-test.c++"
(("VAR\\_TMP \"/var/tmp\"")
(base32
"1fj4554msq0rrz14snbj908dzqj46gh7jg9w9j0akn2b7q911m5a"))))
(build-system gnu-build-system)
- (native-inputs `(("perl" ,perl)))
+ (native-inputs (list perl))
(home-page "http://mongoc.org/libbson/current/index.html")
(synopsis "C BSON library")
(description "Libbson can create and parse BSON documents. It can also
(define-public python-ruamel.yaml
(package
(name "python-ruamel.yaml")
- (version "0.15.83")
+ (version "0.16.13")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ruamel.yaml" version))
(sha256
(base32
- "0p4i8ad28cbbbjja8b9274irkhnphhvhap3aym6yb8xfp1d72kpw"))))
+ "0hm9yg785f46bkrgqknd6fdvmkby9dpzjnm0b63qf0i748acaj5v"))))
(build-system python-build-system)
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ (list python-pytest))
+ (propagated-inputs
+ (list python-ruamel.yaml.clib))
(arguments
`(;; TODO: Tests require packaging "ruamel.std.pathlib".
#:tests? #f))
- (home-page "https://bitbucket.org/ruamel/yaml")
+ (home-page "https://sourceforge.net/projects/ruamel-yaml/")
(synopsis "YAML 1.2 parser/emitter")
(description
"This package provides YAML parser/emitter that supports roundtrip
style and key ordering are kept, so you can diff the source.")
(license license:expat)))
-(define-public python2-ruamel.yaml
- (package-with-python2 python-ruamel.yaml))
+(define-public python-ruamel.yaml.clib
+ (package
+ (name "python-ruamel.yaml.clib")
+ (version "0.2.6")
+ (source
+ (origin
+ ;; pypi release code has cythonized code without corresponding source.
+ (method hg-fetch)
+ (uri (hg-reference
+ (url "http://hg.code.sf.net/p/ruamel-yaml-clib/code")
+ (changeset version)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "05m3y7pjfbaarqbbgw1k6gs6cnnmxnwadjipxvw1aaaqk3s236cs"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ (delete-file "_ruamel_yaml.c")))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ; This package is split from python-ruamel.yaml and
+ ; depends on modules from it for the test suite.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'sanity-check) ; Depends on python-ruamel.yaml
+ (add-after 'unpack 'cythonize-code
+ (lambda _
+ (invoke "cython" "_ruamel_yaml.pyx"))))))
+ (native-inputs
+ (list python-cython))
+ (home-page "https://sourceforge.net/p/ruamel-yaml-clib/code/ci/default/tree")
+ (synopsis "C version of reader, parser and emitter for ruamel.yaml")
+ (description
+ "This package provides a C version of the reader, parser and emitter for
+@code{ruamel.yaml} derived from libyaml.")
+ (license license:expat)))
(define-public python-cbor
(package
(define-public flatbuffers
(package
(name "flatbuffers")
- (version "1.10.0")
+ (version "2.0.0")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/google/flatbuffers/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/google/flatbuffers")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0z4swldxs0s31hnkqdhsbfmc8vx3p7zsvmqaw4l31r2iikdy651p"))))
+ "1zbf6bdpps8369r1ql00irxrp58jnalycc8jcapb8iqg654vlfz8"))))
(build-system cmake-build-system)
(arguments
'(#:build-type "Release"
#:configure-flags
- (list (string-append "-DCMAKE_INSTALL_LIBDIR="
- (assoc-ref %outputs "out") "/lib"))))
+ (list "-DFLATBUFFERS_BUILD_SHAREDLIB=ON"
+ (string-append "-DCMAKE_INSTALL_LIBDIR="
+ (assoc-ref %outputs "out") "/lib"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'make-writable
+ (lambda _ (for-each make-file-writable (find-files ".")))))))
(home-page "https://google.github.io/flatbuffers/")
(synopsis "Memory-efficient serialization library")
(description "FlatBuffers is a cross-platform serialization library for C++,
"00w9hwz7sj3fkdjc378r066vdy6lpxmn6vfac3qx956k8lvpxxj5"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-pandas" ,python-pandas)
- ("python-pyarrow" ,python-pyarrow)))
+ (list python-pandas python-pyarrow))
(home-page "https://github.com/wesm/feather")
(synopsis "Python wrapper to the Feather file format")
(description "This package provides a Python wrapper library to the
HCoop / jackhill / guix / guix.git / blobdiff