Merge branch 'master' into staging

1 files changed, 131 insertions, 36 deletions

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 6237e34dcb..0584fe111a 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -944,7 +944,7 @@ Language.")
      `(("bison" ,bison)
        ;; XXX: On armhf, use GCC 5 to work around <https://bugs.gnu.org/37605>.
        ,@(if (string-prefix? "armhf" (%current-system))
-             `(("gcc@5", gcc-5))
+             `(("gcc@5" ,gcc-5))
              '())
        ("perl" ,perl)))
     (inputs
@@ -970,7 +970,7 @@ as a drop-in replacement of MySQL.")
 (define-public mariadb-connector-c
   (package
     (name "mariadb-connector-c")
-    (version "3.1.9")
+    (version "3.1.10")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -979,7 +979,7 @@ as a drop-in replacement of MySQL.")
                     version "-src.tar.gz"))
               (sha256
                (base32
-                "1izjzf7yzjqzlk8dkp327fa9lawsv2hnnlnr7g5lshyx5azrk38h"))))
+                "13v5z4w1cl890lnr2fbwbziw638lqw2aga45vdq1z0cyrc9mcgmg"))))
     (inputs
      `(("openssl" ,openssl)))
     (build-system cmake-build-system)
@@ -1343,7 +1343,7 @@ for example from a shell script.")
 (define-public sqitch
   (package
     (name "sqitch")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
      (origin
        (method url-fetch)
@@ -1351,7 +1351,7 @@ for example from a shell script.")
              "mirror://cpan/authors/id/D/DW/DWHEELER/App-Sqitch-v"
              version ".tar.gz"))
        (sha256
-        (base32 "0p4wraqiscvwmmsvfqfy65blgsilwpvd9zj4d2zvm2xdx70ncr7l"))))
+        (base32 "1ayiwg9kh3w0nbacbcln7h944z94vq5vnnd5diz86033bpbnq57f"))))
     (build-system perl-build-system)
     (arguments
      '(#:phases
@@ -1383,6 +1383,7 @@ for example from a shell script.")
        ("perl-test-file" ,perl-test-file)
        ("perl-test-file-contents" ,perl-test-file-contents)
        ("perl-test-mockmodule" ,perl-test-mockmodule)
+       ("perl-test-mockobject" ,perl-test-mockobject)
        ("perl-test-nowarnings" ,perl-test-nowarnings)
        ("perl-test-warn" ,perl-test-warn)))
     (inputs
@@ -1391,7 +1392,9 @@ for example from a shell script.")
        ("perl-config-gitlike" ,perl-config-gitlike)
        ("perl-datetime" ,perl-datetime)
        ("perl-datetime-timezone" ,perl-datetime-timezone)
+       ("perl-dbd-mysql" ,perl-dbd-mysql)
        ("perl-dbd-pg" ,perl-dbd-pg)
+       ("perl-dbd-sqlite" ,perl-dbd-sqlite)
        ("perl-dbi" ,perl-dbi)
        ("perl-devel-stacktrace" ,perl-devel-stacktrace)
        ("perl-encode-locale" ,perl-encode-locale)
@@ -1738,7 +1741,7 @@ columns, primary keys, unique constraints and relationships.")
 (define-public perl-dbd-sqlite
   (package
     (name "perl-dbd-sqlite")
-    (version "1.64")
+    (version "1.66")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1746,7 +1749,7 @@ columns, primary keys, unique constraints and relationships.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "00gz5aw3xrr92lf9nfk0dhmy7a8jzmxhznddd9b0a8w4a1xqzbpl"))))
+                "1zljln5nh61gj3k22a1fv2vhx5l83waizmarwkh77hk6kzzmvrw9"))))
     (build-system perl-build-system)
     (inputs `(("sqlite" ,sqlite)))
     (propagated-inputs `(("perl-dbi" ,perl-dbi)))
@@ -1777,7 +1780,7 @@ module, and nothing else.")
     (synopsis "Parse and utilize MySQL's /etc/my.cnf and ~/.my.cnf files")
     (description
      "@code{MySQL::Config} emulates the @code{load_defaults} function from
-libmysqlclient.  It will fill an aray with long options, ready to be parsed by
+libmysqlclient.  It will fill an array with long options, ready to be parsed by
 @code{Getopt::Long}.")
     (license license:perl-license)))
 
@@ -2120,14 +2123,14 @@ database.")
 (define-public perl-db-file
  (package
   (name "perl-db-file")
-  (version "1.853")
+  (version "1.854")
   (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cpan/authors/id/P/PM/PMQS/DB_File-"
                           version ".tar.gz"))
       (sha256
-        (base32 "1y967si45vj0skip1hnhicbv9da29fv6qcfwnsbnvj06n36mkj6h"))))
+        (base32 "0fv0any5am6vr6h1wcwhnraj70hd55fs4d8c2y7chsc9alf9di5y"))))
   (build-system perl-build-system)
   (inputs `(("bdb" ,bdb)))
   (native-inputs `(("perl-test-pod" ,perl-test-pod)))
@@ -2140,8 +2143,7 @@ database.")
                        (("/usr/local/BerkeleyDB") (assoc-ref inputs "bdb")))
                      #t)))))
   (home-page "https://metacpan.org/release/DB_File")
-  (synopsis
-    "Perl5 access to Berkeley DB version 1.x")
+  (synopsis "Perl5 access to Berkeley DB version 1.x")
   (description
     "The DB::File module provides Perl bindings to the Berkeley DB version 1.x.")
   (license license:perl-license)))
@@ -2450,13 +2452,13 @@ etc., and an SQL engine for performing simple SQL queries.")
 (define-public python-lmdb
   (package
     (name "python-lmdb")
-    (version "0.99")
+    (version "1.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lmdb" version))
               (sha256
                (base32
-                "12fwlzfd82471ss9xzbqwcqc6f5miy51y72y2yya9j5cm9589szr"))
+                "1di1gj2agbxwqqwrpk4w58dpfah0kl10ha20s63dlqdd1bgzydj1"))
               (modules '((guix build utils)))
               (snippet
                ;; Delete bundled lmdb source files.
@@ -2475,6 +2477,7 @@ etc., and an SQL engine for performing simple SQL queries.")
          (add-before 'build 'use-system-lmdb
            (lambda* (#:key inputs #:allow-other-keys)
              (let ((lmdb (assoc-ref inputs "lmdb")))
+               (setenv "LMDB_PURE" "set") ; don't apply env-copy-txn.patch
                (setenv "LMDB_FORCE_SYSTEM" "set")
                (setenv "LMDB_INCLUDEDIR" (string-append lmdb "/include"))
                (setenv "LMDB_LIBDIR" (string-append lmdb "/lib"))
@@ -2712,16 +2715,57 @@ You might also want to install the following optional dependencies:
 (define-public python2-sqlalchemy-utils
   (package-with-python2 python-sqlalchemy-utils))
 
+(define-public python-alchemy-mock
+  (package
+    (name "python-alchemy-mock")
+    (version "0.4.3")
+    (home-page "https://github.com/miki725/alchemy-mock")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "alchemy-mock" version))
+              (sha256
+               (base32
+                "0ylxygl3bcdapzz529n8wgk7vx9gjwb3ism564ypkpd7dbsw653r"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (replace 'check
+                    (lambda _
+                      ;; Create pytest.ini that adds doctest options to
+                      ;; prevent test failure.  Taken from tox.ini.
+                      (call-with-output-file "pytest.ini"
+                        (lambda (port)
+                          (format port "[pytest]
+doctest_optionflags=IGNORE_EXCEPTION_DETAIL
+")))
+                      (invoke "pytest" "-vv" "--doctest-modules"
+                              "alchemy_mock/"))))))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)))
+    (propagated-inputs
+     `(("python-six" ,python-six)
+       ("python-sqlalchemy" ,python-sqlalchemy)))
+    (synopsis "Mock helpers for SQLAlchemy")
+    (description
+     "This package provides mock helpers for SQLAlchemy that makes it easy
+to mock an SQLAlchemy session while preserving the ability to do asserts.
+
+Normally Normally SQLAlchemy's expressions cannot be easily compared as
+comparison on binary expression produces yet another binary expression, but
+this library provides functions to facilitate such comparisons.")
+    (license license:expat)))
+
 (define-public python-alembic
   (package
     (name "python-alembic")
-    (version "1.4.2")
+    (version "1.4.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "alembic" version))
        (sha256
-        (base32 "1gsdrzx9h7wfva200qvvsc9sn4w79mk2vs0bbnzjhxi1jw2b0nh3"))))
+        (base32 "0if2dgb088clk738p26bwk50735h6jpd2kacdgc5capv2hiz6d2k"))))
     (build-system python-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
@@ -2897,13 +2941,13 @@ designed to be easy and intuitive to use.")
 (define-public python-psycopg2
   (package
     (name "python-psycopg2")
-    (version "2.8.5")
+    (version "2.8.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "psycopg2" version))
        (sha256
-        (base32 "06081jk9srkd4ra9j8b93x9ld3a2yxsbsf5bbbcivbm1yx065m7p"))))
+        (base32 "0hzmk6b1hb5riqkljr5xics6p4zbvmis6knbczb7zhq7273zc8zv"))))
     (build-system python-build-system)
     (arguments
      ;; Tests would require a postgresql database "psycopg2_test"
@@ -2951,24 +2995,19 @@ database).")
 (define-public python-mysqlclient
   (package
     (name "python-mysqlclient")
-    (version "1.3.13")
+    (version "2.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mysqlclient" version))
        (sha256
         (base32
-         "0kv4a1icwdav8jpl7qvnr931lw5h3v22ids6lwq6qpi1hjzf33pz"))))
+         "1rf5l8hazs3v18hmcrm90z3hi9wxv553ipwd5l6kj8j7l6p7abzv"))))
     (build-system python-build-system)
-    (native-inputs
-     `(("nose" ,python-nose)
-       ("mock" ,python-mock)
-       ("py.test" ,python-pytest)))
+    (arguments '(#:tests? #f))          ;XXX: requires a live database
     (inputs
      `(("mysql" ,mariadb "lib")
-       ("mysql-dev" ,mariadb "dev")
-       ("libz" ,zlib)
-       ("openssl" ,openssl)))
+       ("mysql-dev" ,mariadb "dev")))
     (home-page "https://github.com/PyMySQL/mysqlclient-python")
     (synopsis "MySQLdb is an interface to the popular MySQL database server for Python")
     (description "MySQLdb is an interface to the popular MySQL database server
@@ -2980,9 +3019,6 @@ for Python.  The design goals are:
 @end enumerate")
     (license license:gpl2)))
 
-(define-public python2-mysqlclient
-  (package-with-python2 python-mysqlclient))
-
 (define-public python-hiredis
   (package
     (name "python-hiredis")
@@ -3042,13 +3078,13 @@ reasonable substitute.")
 (define-public python-redis
   (package
     (name "python-redis")
-    (version "3.3.8")
+    (version "3.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "redis" version))
        (sha256
-        (base32 "0fyxzqax7lcwzwhvnz0i0q6v62hxyv1mv52ywx3bpff9a2vjz8lq"))))
+        (base32 "18h5b87g15x3j6pb1h2q27ri37p2qpvc9n2wgn5yl3b6m3y0qzhf"))))
     (build-system python-build-system)
     ;; Tests require a running Redis server.
     (arguments '(#:tests? #f))
@@ -3067,14 +3103,35 @@ reasonable substitute.")
 (define-public python-rq
   (package
     (name "python-rq")
-    (version "0.13.0")
+    (version "1.5.2")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "rq" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rq/rq")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0xvapd2bxnyq480i48bdkddzlqmv2axbsq85rlfy8k3al8zxxxrf"))))
+        (base32 "0ikqmpq0g1qiqwd7ar1286l4hqjb6aj2wr844gihhb8ijzwhp8va"))))
     (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-before 'check 'start-redis
+                    (lambda _
+                      (invoke "redis-server" "--daemonize" "yes")))
+                  (replace 'check
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let ((out (assoc-ref outputs "out")))
+                        ;; Drop test that needs the SDK for Sentry.io.
+                        (delete-file "tests/test_sentry.py")
+                        ;; Ensure 'rq' and 'rqworker' ends up on PATH.
+                        (setenv "PATH" (string-append out "/bin:"
+                                                      (getenv "PATH")))
+                        (invoke "pytest" "-vv")))))))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-pytest" ,python-pytest)
+       ("redis" ,redis)))
     (propagated-inputs
      `(("python-click" ,python-click)
        ("python-redis" ,python-redis)))
@@ -3089,6 +3146,44 @@ is designed to have a low barrier to entry.")
 (define-public python2-rq
   (package-with-python2 python-rq))
 
+(define-public python-rq-scheduler
+  (package
+    (name "python-rq-scheduler")
+    (version "0.10.0")
+    (home-page "https://github.com/rq/rq-scheduler")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url home-page)
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0xg6yazqs5kbr2ayvhvljs1h5vgx5k5dds613fmhswln7gglf9hk"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:phases (modify-phases %standard-phases
+                  (add-before 'check 'start-redis
+                    (lambda _
+                      (invoke "redis-server" "--daemonize" "yes")))
+                  (replace 'check
+                    (lambda _
+                      (substitute* "run_tests.py"
+                        (("/usr/bin/env")
+                         (which "env")))
+                      (invoke "./run_tests.py"))))))
+    (native-inputs
+     `(("redis" ,redis)
+       ("which" ,which)))
+    (propagated-inputs
+     `(("python-croniter" ,python-croniter)
+       ("python-rq" ,python-rq)))
+    (synopsis "Job scheduling capabilities for RQ (Redis Queue)")
+    (description
+     "This package provides job scheduling capabilities to @code{python-rq}
+(Redis Queue).")
+    (license license:expat)))
+
 (define-public python-trollius-redis
   (package
     (name "python-trollius-redis")