diff options
Diffstat (limited to 'gnu/packages/databases.scm')
| -rw-r--r-- | gnu/packages/databases.scm | 335 |
1 files changed, 291 insertions, 44 deletions
diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index 7ef211be37..92ab94f453 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2018 Ludovic Courtès <[email protected]> +;;; Copyright © 2012-2016, 2018, 2022 Ludovic Courtès <[email protected]> ;;; Copyright © 2012, 2013, 2014, 2015, 2016 Andreas Enge <[email protected]> ;;; Copyright © 2013, 2017 Cyril Roelandt <[email protected]> ;;; Copyright © 2014, 2016 David Thompson <[email protected]> @@ -1160,7 +1160,7 @@ developed in C/C++ to MariaDB and MySQL databases.") (define-public galera (package (name "galera") - (version "26.4.10") + (version "26.4.12") (source (origin (method git-fetch) (uri (git-reference @@ -1169,7 +1169,7 @@ developed in C/C++ to MariaDB and MySQL databases.") (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 "1n6zhzwj713ixyqvcjn4ldlq0y9fxqgvmqv3cj3h4207v9lwlxxz")))) + (base32 "0n4272mvr8a6h5prbhvl376asdp89ipix5yx5n6i1iiw9bs3v76l")))) (build-system cmake-build-system) (inputs (list check boost openssl)) @@ -1184,14 +1184,14 @@ and high-availability (HA).") (define-public postgresql-14 (package (name "postgresql") - (version "14.2") + (version "14.3") (source (origin (method url-fetch) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "0ylpka64wli72jvjyqcayvlw44zk1hsbapb93l8gh4l98qp8pxrc")) + "0f5gm43hx8j67nfad8mrfhzb9aq4brfgka5d0nf936pmicv5g417")) (patches (search-patches "postgresql-disable-resolve_symlinks.patch")))) (build-system gnu-build-system) (arguments @@ -1247,6 +1247,7 @@ pictures, sounds, or video.") (package (inherit postgresql-14) (version "13.6") + (replacement postgresql-13/replacement) (source (origin (inherit (package-source postgresql-14)) (uri (string-append "https://ftp.postgresql.org/pub/source/v" @@ -1256,37 +1257,70 @@ pictures, sounds, or video.") "1z37ix80hb2bqa2smh1hbj9r507ypnl3pil43gkqznnlv6ipzz5s")) (patches (search-patches "postgresql-riscv-spinlocks.patch")))))) +;; The merge of commit ... +;; 781dd2de230e3 gnu: postgresql-13: Fix building on riscv64-linux. +;; ... in ... +;; 49b350fafc2c3 Merge branch 'master' into staging. +;; ... lost the inherited patch from postgresql-14, causing problems such as ... +;; 05fef7bfc6005 gnu: timescaledb: Adjust test preparation to PostgreSQL 13.6. +;; +;; While at it, remove the RISC-V spinlock patch, which has been upstreamed +;; in a different form (so the old patch still applies). +;; TODO: Remove in the next rebuild cycle. +(define postgresql-13/replacement + (package + (inherit postgresql-13) + (version "13.7") + (source + (origin + (inherit (package-source postgresql-13)) + (uri (string-append "https://ftp.postgresql.org/pub/source/v" + version "/postgresql-" version ".tar.bz2")) + (sha256 + (base32 + "16b3ljid7zd1v5l4l4pmwihx43wi8p9izidkjfii8dnqygs5p40v")) + (patches (search-patches "postgresql-disable-resolve_symlinks.patch")))))) + (define-public postgresql-11 (package (inherit postgresql-13) (name "postgresql") - (version "11.15") + (version "11.16") (source (origin (inherit (package-source postgresql-13)) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "1qvrm0vhwnc5nijfbqybhwfjbq4r7vmk445sz7s6fiagpn78xxf8")))))) + "1983a7y4y6zhbgh0qcdfkf99445j1zm5q1ncrbkrx555y08y3n9d")) + (patches (search-patches + "postgresql-disable-resolve_symlinks.patch")))) + (native-inputs + (modify-inputs (package-native-inputs postgresql-13) + (replace "docbook-xml" docbook-xml-4.2))))) (define-public postgresql-10 (package (inherit postgresql-11) - (version "10.20") + (version "10.21") (source (origin (inherit (package-source postgresql-11)) (uri (string-append "https://ftp.postgresql.org/pub/source/v" version "/postgresql-" version ".tar.bz2")) (sha256 (base32 - "17v51a9vnz6lgbfmbdmcwsiyi572wndwa4n30nk2zr6gkgaidpl7")))))) + "1la5dx4hhy5yaznwk9gwdsymih3sd23fyhh6spssdaajdn2rh8fk")))) + (native-inputs + (modify-inputs (package-native-inputs postgresql-11) + (append opensp docbook-sgml-4.2) + (delete "docbook-xml"))))) -(define-public postgresql postgresql-13) +(define-public postgresql postgresql-14) (define-public timescaledb (package (name "timescaledb") - (version "2.5.1") + (version "2.7.0") (source (origin (method git-fetch) (uri (git-reference @@ -1295,14 +1329,18 @@ pictures, sounds, or video.") (file-name (git-file-name name version)) (sha256 (base32 - "174dm3higa0i7al9r2hdv5hk36pd0d5fnqj57w5a350kxshxyvyw")) + "18wszj8ia5rs4y4zkyfb0f5z4y1g7ac3jym748nbkbszhxmq7nc7")) + (patches (search-patches "timescaledb-flaky-test.patch")) (modules '((guix build utils))) (snippet ;; Remove files carrying the proprietary TIMESCALE license. '(begin (delete-file-recursively "tsl") (for-each delete-file - '("test/perl/AccessNode.pm" + '("scripts/c_license_header-timescale.h" + "scripts/license_tsl.spec" + "scripts/sql_license_tsl.sql" + "test/perl/AccessNode.pm" "test/perl/DataNode.pm" "test/perl/TimescaleNode.pm")))))) (build-system cmake-build-system) @@ -1347,12 +1385,28 @@ pictures, sounds, or video.") (pg-union (string-append (getcwd) "/../pg-union"))) (match inputs (((names . directories) ...) - (union-build pg-union (cons #$output directories)))) + ;; PG will only load extensions from its own $libdir, + ;; which it calculates based on argv[0]. As of + ;; PostgreSQL 13.6, it calls 'canonicalize_path' on + ;; argv[0] so a merge symlink is not enough to trick + ;; it; thus, the code below makes a full copy of PG + ;; and friends such that 'pg_config --libdir', for + ;; instance, points to PG-UNION, allowing it to load + ;; the timescaledb extension. + ;; TODO: The above comment and the #:symlink trick can + ;; be removed in the next rebuild cycle. + (union-build pg-union (cons #$output directories) + #:symlink + (lambda (old new) + (if (file-is-directory? old) + (copy-recursively old new) + (copy-file old new)))))) (setenv "PATH" (string-append pg-union "/bin:" (getenv "PATH"))) (invoke "initdb" "-D" pg-data) (copy-file "test/postgresql.conf" (string-append pg-data "/postgresql.conf")) + (invoke "pg_ctl" "-D" pg-data "-o" (string-append "-k " pg-data) "-l" (string-append pg-data "/db.log") @@ -1363,7 +1417,7 @@ pictures, sounds, or video.") (home-page "https://www.timescale.com/") (synopsis "Time-series extension for PostgreSQL") (description - "TimescaleDB is an database designed to make SQL scalable for + "TimescaleDB is a database designed to make SQL scalable for time-series data. It is engineered up from PostgreSQL and packaged as a PostgreSQL extension, providing automatic partitioning across time and space (partitioning key), as well as full SQL support.") @@ -1868,7 +1922,7 @@ extremely small.") "1yinx39960y241vf2sknxj0dfz82a5m9gvklq5rw78k0nlyrjawa")))) (build-system perl-build-system) (synopsis "Database independent interface for Perl") - (description "This package provides an database interface for Perl.") + (description "This package provides a database interface for Perl.") (home-page "https://metacpan.org/release/DBI") (license license:perl-license))) @@ -2035,7 +2089,7 @@ columns, primary keys, unique constraints and relationships.") (define-public perl-dbd-pg (package (name "perl-dbd-pg") - (version "3.14.2") + (version "3.15.1") (source (origin (method url-fetch) @@ -2043,7 +2097,7 @@ columns, primary keys, unique constraints and relationships.") "DBD-Pg-" version ".tar.gz")) (sha256 (base32 - "0kcfqq7g3832wiix0sbyvlc885qghjrp2ah3akn7h2lnb22fjwy9")))) + "0zn17xb6bmixkmv53p576igzw1jd43cwql35r19m56jwahxm9iqk")))) (build-system perl-build-system) (native-inputs (list perl-dbi)) @@ -2814,13 +2868,13 @@ can autogenerate peewee models using @code{pwiz}, a model generator.") (define-public python-pypika-tortoise (package (name "python-pypika-tortoise") - (version "0.1.1") + (version "0.1.5") (source (origin (method url-fetch) (uri (pypi-uri "pypika-tortoise" version)) (sha256 - (base32 "0g4z0lz739nk04b405ynqpd3y1z5nfyxjz9hqgxcw3jydsjx0cb8")))) + (base32 "0j20574s2yrq8d7fav3816vj1nfpihkm2mj8jzh2ank4zixp8brf")))) (build-system python-build-system) (home-page "https://github.com/tortoise/pypika-tortoise") (synopsis "Pypika fork for tortoise-orm") @@ -2851,24 +2905,19 @@ coroutine-specific markup.") (define-public python-asyncpg (package (name "python-asyncpg") - (version "0.24.0") + (version "0.25.0") (source (origin (method url-fetch) (uri (pypi-uri "asyncpg" version)) (sha256 - (base32 "1in0q6iffpl8ag6ady4bvwnn40igh10cpp4xgm426j1lqdis0byx")))) + (base32 "0h1573lp4607nppflnnjrhn7yrfy6i54cm98gi4qbcikjykfdy33")))) (build-system python-build-system) (propagated-inputs (list python-typing-extensions)) (native-inputs (list postgresql python-cython - python-flake8 - python-pycodestyle python-pytest - python-sphinx - python-sphinx-rtd-theme - python-sphinxcontrib-asyncio python-uvloop)) (home-page "https://github.com/MagicStack/asyncpg") (synopsis "Fast PostgreSQL database client library for Python") @@ -2921,13 +2970,13 @@ of PyMySQL. @code{aiomysql} tries to preserve the same API as the (define-public python-tortoise-orm (package (name "python-tortoise-orm") - (version "0.17.8") + (version "0.19.1") (source (origin (method url-fetch) (uri (pypi-uri "tortoise-orm" version)) (sha256 - (base32 "1gzgiypln7lck3p95vk3i8rdx1bjbmmlcpb8xpba8cjdjvlj0l0z")))) + (base32 "17yk71dlx5ai98i6ivqgsplkwivdxackz9jfn6z42bpcdgbpiwhg")))) (build-system python-build-system) ;; The test suite relies on asynctest, which is abandoned and doesn't ;; support Python >= 3.8. @@ -3004,44 +3053,58 @@ development.") (define-public python-pyodbc-c (package (name "python-pyodbc-c") - (version "3.1.4") + (version "3.1.5") (source (origin - (method url-fetch) - (uri (string-append "https://gitlab.com/daym/pyodbc-c/repository/" - "archive.tar.gz?ref=v" version)) + (method git-fetch) + (uri (git-reference + (url "https://gitlab.com/daym/pyodbc-c/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 - "05aq2297k779xidmxcwkrrxjvj1bh2q7d9a1rcjv6zr15y764ga9")) - (file-name (string-append name "-" version ".tar.gz")))) + (base32 "08y60c5sx0k953zfx0s2a155l8py968sb17ap9a9fg8bjnj783k8")))) (build-system python-build-system) (inputs (list unixodbc)) (arguments - `(;; No unit tests exist. + `(;; The tests require a running SQL server that they don't help set up. #:tests? #f)) - (home-page "https://github.com/mkleehammer/pyodbc") - (synopsis "Python ODBC Library") + (home-page "https://gitlab.com/daym/pyodbc-c") + (synopsis "Python ODBC Library written in C") (description "@code{python-pyodbc-c} provides a Python DB-API driver -for ODBC.") +for ODBC, similar to python-pyodbc but written in C. + +It's designed to stand alone and not have other dependencies on other packages +or languages. It uses only Python's built-in data types.") (license (license:x11-style "file://LICENSE.TXT")))) (define-public python-pyodbc (package (name "python-pyodbc") - (version "4.0.30") + (version "4.0.32") (source (origin (method url-fetch) (uri (pypi-uri "pyodbc" version)) (sha256 - (base32 "0skjpraar6hcwsy82612bpj8nw016ncyvvq88j5syrikxgp5saw5")) - (file-name (string-append name "-" version ".tar.gz")))) + (base32 "0sqs0x2l5mk3yv0wwz3ya8yh5f4babihyhc8hjbf2m86b71z1rcv")) + (modules '((guix build utils))) + (snippet + ;; Delete precompiled binaries. The corresponding source is included. + #~(for-each delete-file (find-files "." "\\.pyc$"))))) (build-system python-build-system) (inputs (list unixodbc)) (arguments - `(#:tests? #f)) ; no unit tests exist + ;; XXX Tests fail with ‘Can't open lib 'SQL Server Native Client 10.0' : + ;; file not found (0) (SQLDriverConnect)")’. + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python3" "tests3/test.py"))))))) (home-page "https://github.com/mkleehammer/pyodbc") (synopsis "Python ODBC Library") (description "@code{python-pyodbc} provides a Python DB-API driver @@ -4195,6 +4258,132 @@ language-bindings for structure manipulation. It also provides IPC and common algorithm implementations.") (license license:asl2.0))) +(define-public apache-arrow-0.16 + (package + (name "apache-arrow") + (version "0.16.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/apache/arrow") + (commit (string-append "apache-arrow-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "15bplqy5708bxy1mynzjkd3d2g8v2wd36z8l0ap8yyyq54l3gdvy")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'configure 'enter-source-directory + (lambda _ + (chdir "cpp") + (substitute* "src/parquet/CMakeLists.txt" + ((" parquet_constants.cpp") "") + (("set\\(THRIFT_OUTPUT_FILES \\$\\{THRIFT_OUTPUT_FILES\\}.*") "") + ((".*\"\\$\\{THRIFT_OUTPUT_DIR\\}/parquet_constants.cpp\"\\).*") "")))) + (add-after 'unpack 'set-env + (lambda _ + (setenv "BOOST_ROOT" (assoc-ref %build-inputs "boost")) + (setenv "BROTLI_HOME" (assoc-ref %build-inputs "brotli")) + (setenv "FLATBUFFERS_HOME" (assoc-ref %build-inputs "flatbuffers")) + (setenv "RAPIDJSON_HOME" (assoc-ref %build-inputs "rapidjson"))))) + #:build-type "Release" + #:configure-flags + (list "-DARROW_PYTHON=ON" + "-DARROW_GLOG=ON" + "-DARROW_SSE42=OFF" + "-DARROW_BOOST_USE_SHARED=ON" + ;; Parquet options + "-DARROW_PARQUET=ON" + + ;; The maintainers disallow using system versions of + ;; jemalloc: + ;; https://issues.apache.org/jira/browse/ARROW-3507. This + ;; is unfortunate because jemalloc increases performance: + ;; https://arrow.apache.org/blog/2018/07/20/jemalloc/. + "-DARROW_JEMALLOC=OFF" + + ;; The CMake option ARROW_DEPENDENCY_SOURCE is a global + ;; option that instructs the build system how to resolve + ;; each dependency. SYSTEM = Finding the dependency in + ;; system paths using CMake's built-in find_package + ;; function, or using pkg-config for packages that do not + ;; have this feature + "-DARROW_DEPENDENCY_SOURCE=SYSTEM" + + ;; Split output into its component packages. + (string-append "-DCMAKE_INSTALL_PREFIX=" + (assoc-ref %outputs "out")) + (string-append "-DCMAKE_INSTALL_RPATH=" + (assoc-ref %outputs "out") + "/lib") + (string-append "-DCMAKE_INSTALL_BINDIR=" + (assoc-ref %outputs "out") + "/bin") + (string-append "-DCMAKE_INSTALL_INCLUDEDIR=" + (assoc-ref %outputs "include") + "/share/include") + + + "-DARROW_WITH_SNAPPY=ON" + "-DARROW_WITH_ZLIB=ON" + "-DARROW_WITH_ZSTD=ON" + "-DARROW_WITH_LZ4=ON" + "-DARROW_COMPUTE=ON" + "-DARROW_CSV=ON" + "-DARROW_DATASET=ON" + "-DARROW_FILESYSTEM=ON" + "-DARROW_HDFS=ON" + "-DARROW_JSON=ON" + ;; Arrow Python C++ integration library (required for + ;; building pyarrow). This library must be built against + ;; the same Python version for which you are building + ;; pyarrow. NumPy must also be installed. Enabling this + ;; option also enables ARROW_COMPUTE, ARROW_CSV, + ;; ARROW_DATASET, ARROW_FILESYSTEM, ARROW_HDFS, and + ;; ARROW_JSON. + "-DARROW_PYTHON=ON" + + ;; Building the tests forces on all the + ;; optional features and the use of static + ;; libraries. + "-DARROW_BUILD_TESTS=OFF" + "-DBENCHMARK_ENABLE_GTEST_TESTS=OFF" + ;;"-DBENCHMARK_ENABLE_TESTING=OFF" + "-DARROW_BUILD_STATIC=OFF"))) + (inputs + `(("boost" ,boost) + ("brotli" ,google-brotli) + ("double-conversion" ,double-conversion) + ("snappy" ,snappy) + ("gflags" ,gflags) + ("glog" ,glog) + ("apache-thrift" ,apache-thrift "lib") + ("protobuf" ,protobuf) + ("rapidjson" ,rapidjson) + ("zlib" ,zlib) + ("bzip2" ,bzip2) + ("lz4" ,lz4) + ("zstd" ,zstd "lib") + ("re2" ,re2) + ("grpc" ,grpc) + ("python-3" ,python) + ("python-numpy" ,python-numpy))) + (native-inputs + (list pkg-config apache-thrift)) + (outputs '("out" "include")) + (home-page "https://arrow.apache.org/") + (synopsis "Columnar in-memory analytics") + (description "Apache Arrow is a columnar in-memory analytics layer +designed to accelerate big data. It houses a set of canonical in-memory +representations of flat and hierarchical data along with multiple +language-bindings for structure manipulation. It also provides IPC and common +algorithm implementations.") + (license license:asl2.0))) + (define-public python-pyarrow (package (inherit apache-arrow) @@ -4253,6 +4442,64 @@ implementation, along with tools for interoperability with pandas, NumPy, and other traditional Python scientific computing packages.") (license license:asl2.0))) +(define-public python-pyarrow-0.16 + (package + (inherit apache-arrow-0.16) + (name "python-pyarrow") + (build-system python-build-system) + (arguments + '(#:tests? #f ; XXX There are no tests in the "python" directory + #:phases + (modify-phases %standard-phases + (delete 'build) ; XXX the build is performed again during the install phase + (add-after 'unpack 'enter-source-directory + (lambda _ (chdir "python"))) + (add-after 'unpack 'make-git-checkout-writable + (lambda _ + (for-each make-file-writable (find-files ".")))) + (add-before 'install 'patch-cmake-variables + (lambda* (#:key inputs #:allow-other-keys) + ;; Replace cmake locations with hardcoded guix links for the + ;; underlying C++ library and headers. This is a pretty awful + ;; hack. + (substitute* "cmake_modules/FindParquet.cmake" + (("# Licensed to the Apache Software Foundation" m) + (string-append "set(PARQUET_INCLUDE_DIR \"" + (assoc-ref inputs "apache-arrow:include") + "/share/include\")\n" m)) + (("find_package_handle_standard_args" m) + (string-append "set(PARQUET_LIB_DIR \"" + (assoc-ref inputs "apache-arrow:lib") + "/lib\")\n" m))))) + (add-before 'install 'patch-parquet-library + (lambda _ + (substitute* "CMakeLists.txt" + (("parquet_shared") "parquet")))) + (add-before 'install 'set-PYARROW_WITH_PARQUET + (lambda _ + (setenv "PYARROW_WITH_PARQUET" "1")))))) + (propagated-inputs + `(("apache-arrow:lib" ,apache-arrow-0.16) + ("apache-arrow:include" ,apache-arrow-0.16 "include") + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-six" ,python-six))) + (native-inputs + (list cmake-minimal + pkg-config + python-cython + python-pytest + python-pytest-runner + python-setuptools-scm)) + (outputs '("out")) + (home-page "https://arrow.apache.org/docs/python/") + (synopsis "Python bindings for Apache Arrow") + (description + "This library provides a Pythonic API wrapper for the reference Arrow C++ +implementation, along with tools for interoperability with pandas, NumPy, and +other traditional Python scientific computing packages.") + (license license:asl2.0))) + (define-public python-crate (package (name "python-crate") |