X-Git-Url: http://git.hcoop.net/jackhill/guix/guix.git/blobdiff_plain/483cdf36a56e90d1a0a8ab77a59827f7382e6358..f928abac369f699f425ddee925d0d0c2dc0a635d:/gnu/packages/serialization.scm diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 366f7d56f2..79c55e2b2f 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -1,15 +1,17 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015, 2017, 2019, 2021 Ricardo Wurmus +;;; Copyright © 2015, 2017, 2019, 2020, 2021 Ricardo Wurmus ;;; Copyright © 2016 Lukas Gradl ;;; Copyright © 2016 David Craven -;;; Copyright © 2016, 2019, 2020 Marius Bakke -;;; Copyright © 2016, 2018, 2019 Efraim Flashner +;;; Copyright © 2016, 2019, 2020, 2022 Marius Bakke +;;; Copyright © 2016, 2018, 2019, 2021 Efraim Flashner ;;; Copyright © 2017 Corentin Bocquillon ;;; Copyright © 2017 Gregor Giesen ;;; Copyright © 2017 Frederick M. Muriithi ;;; Copyright © 2017 Nikita -;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice +;;; Copyright © 2017–2019, 2022 Tobias Geerinckx-Rice ;;; Copyright © 2018 Joshua Sierles, Nextjournal +;;; Copyright © 2020 Martin Becze +;;; Copyright © 2020 Alexandros Theodotou ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,14 +31,19 @@ (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) @@ -45,6 +52,7 @@ #: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) @@ -70,8 +78,7 @@ (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: @@ -87,10 +94,46 @@ Code generation is not required to read or write data files nor to use or 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 "1.3.0") + (version "1.3.2") (source (origin (method git-fetch) @@ -100,44 +143,68 @@ implement RPC protocols.") (file-name (git-file-name name version)) (sha256 (base32 - "0hc8wh9dwpc1w1zf5lfss4vg5hmgpblqxbrpp1rggicpx9ar831p")))) + "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_BINARY_DIR@") ".") - (("@CMAKE_CURRENT_SOURCE_DIR@") ".")) - (with-directory-excursion "doc" - (invoke "doxygen" "doxygen.in")))) - ;; 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))))))) + (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 @@ -160,10 +227,9 @@ such as compact binary encodings, XML, or JSON.") (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 . However, 'guix gc --references' ;; does not detect a store reference to zlib since these headers are not ;; compiled. @@ -196,7 +262,7 @@ serialization.") (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 @@ -248,7 +314,7 @@ that implements both the msgpack and msgpack-rpc specifications.") "mpack-src") #t))))) (inputs - `(("lua" ,lua))) + (list lua)) (native-inputs `(("pkg-config" ,pkg-config) ("libmpack" ,(package-source libmpack)))) @@ -295,6 +361,71 @@ that implements both the msgpack and msgpack-rpc specifications.") (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") @@ -312,7 +443,7 @@ that implements both the msgpack and msgpack-rpc specifications.") (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.") @@ -321,16 +452,17 @@ that implements both the msgpack and msgpack-rpc specifications.") (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" @@ -364,6 +496,51 @@ it a convenient format to store user input files.") (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") @@ -386,9 +563,9 @@ it a convenient format to store user input files.") ;; /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\"") @@ -414,7 +591,7 @@ RPC system. Think JSON, except binary. Or think Protocol Buffers, except faste (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 @@ -425,21 +602,23 @@ it is comparable to protobuf.") (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 @@ -449,8 +628,43 @@ and has round-trip loaders and dumpers. It supports comments. Block 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 @@ -477,22 +691,28 @@ to generate and parse. The two primary functions are @code{cbor.loads} and (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++, @@ -513,8 +733,7 @@ game development and other performance-critical applications.") "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