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-rw-r--r--gnu/local.mk1
-rw-r--r--gnu/packages/admin.scm22
-rw-r--r--gnu/packages/bioinformatics.scm31
-rw-r--r--gnu/packages/calendar.scm2
-rw-r--r--gnu/packages/django.scm13
-rw-r--r--gnu/packages/enlightenment.scm12
-rw-r--r--gnu/packages/jrnl.scm2
-rw-r--r--gnu/packages/music.scm2
-rw-r--r--gnu/packages/openstack.scm84
-rw-r--r--gnu/packages/patches/python-pyopenssl-skip-network-test.patch50
-rw-r--r--gnu/packages/pdf.scm4
-rw-r--r--gnu/packages/python.scm926
-rw-r--r--gnu/packages/rdf.scm22
-rw-r--r--gnu/packages/terminals.scm3
-rw-r--r--gnu/packages/version-control.scm2
-rw-r--r--gnu/packages/vpn.scm8
-rw-r--r--guix/build/python-build-system.scm14
17 files changed, 913 insertions, 285 deletions
diff --git a/gnu/local.mk b/gnu/local.mk
index 0e8d901104..8615d12b08 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -861,6 +861,7 @@ dist_patch_DATA = \
%D%/packages/patches/python-configobj-setuptools.patch \
%D%/packages/patches/python-paste-remove-website-test.patch \
%D%/packages/patches/python-paste-remove-timing-test.patch \
+ %D%/packages/patches/python-pyopenssl-skip-network-test.patch \
%D%/packages/patches/python-pycrypto-CVE-2013-7459.patch \
%D%/packages/patches/python2-pygobject-2-gi-info-type-error-domain.patch \
%D%/packages/patches/python-pygpgme-fix-pinentry-tests.patch \
diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index b2207a1205..e12cfd23e3 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1698,15 +1698,29 @@ throughput (in the same interval).")
(base32
"04q2cn8c83f6z6wn1scla1ilrpi5ssjc64987hvmwfvwvb82bvkp"))))
(build-system python-build-system)
- (inputs
+ (arguments
+ '(#:tests? #f))
+ ;; FIXME: 10 test failures. Some require newer pytest (> 2.9.2).
+ ;; Others need more work. Un-comment the below to run the tests.
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; ;; Some tests need write access to $HOME.
+ ;; (setenv "HOME" "/tmp")
+ ;; (zero? (system* "py.test" "-v")))))))
+ (propagated-inputs
`(("python-colorama" ,python-colorama)
("python-decorator" ,python-decorator)
("python-psutil" ,python-psutil)
("python-six" ,python-six)))
(native-inputs
- ;; Requires setuptools >= 17.1 due to some features used, while our
- ;; python currently only includes 12.0. TODO: Remove this input.
- `(("python-setuptools" ,python-setuptools)))
+ `(("python-mock" ,python-mock)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-mock" ,python-pytest-mock)
+ ;; Requires setuptools >= 17.1 due to some features used, while our
+ ;; python currently only includes 12.0. TODO: Remove this input.
+ ("python-setuptools" ,python-setuptools)))
(home-page "https://github.com/nvbn/thefuck")
(synopsis "Correct mistyped console command")
(description
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a448b51c6c..5a1738b936 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -604,6 +604,8 @@ Python.")
("python-future" ,python-future)
("python-click" ,python-click)
("python-h5py" ,python-h5py)))
+ (native-inputs
+ `(("python-nose" ,python-nose)))
(home-page "http://www.biom-format.org")
(synopsis "Biological Observation Matrix (BIOM) format utilities")
(description
@@ -1602,6 +1604,7 @@ databases.")
("python-scipy" ,python2-scipy)))
(native-inputs
`(("python-mock" ,python2-mock) ; for tests
+ ("python-nose" ,python2-nose) ; for tests
("python-pytz" ,python2-pytz))) ; for tests
(home-page "https://github.com/YeoLab/clipper")
(synopsis "CLIP peak enrichment recognition")
@@ -2030,6 +2033,7 @@ trees (phylogenies) and characters.")
("python-pybigwig" ,python2-pybigwig)))
(native-inputs
`(("python-mock" ,python2-mock) ;for tests
+ ("python-nose" ,python2-nose) ;for tests
("python-pytz" ,python2-pytz))) ;for tests
(home-page "https://github.com/fidelram/deepTools")
(synopsis "Tools for normalizing and visualizing deep-sequencing data")
@@ -2969,28 +2973,10 @@ data. It also provides the bgzip, htsfile, and tabix utilities.")
"1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
(build-system python-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after
- 'install 'wrap-program
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((out (assoc-ref outputs "out"))
- (python-version (string-take (string-take-right
- (assoc-ref inputs "python") 5) 3))
- (path (string-join
- (map (lambda (name)
- (string-append (assoc-ref inputs name)
- "/lib/python" python-version
- "/site-packages"))
- '("python-scipy"
- "python-numpy"
- "python-matplotlib"))
- ":")))
- (wrap-program (string-append out "/bin/idr")
- `("PYTHONPATH" ":" prefix (,path))))
- #t)))))
- (inputs
+ `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'"
+ (propagated-inputs
`(("python-scipy" ,python-scipy)
+ ("python-sympy" ,python-sympy)
("python-numpy" ,python-numpy)
("python-matplotlib" ,python-matplotlib)))
(native-inputs
@@ -3679,6 +3665,9 @@ the phenotype as it models the data.")
(build-system python-build-system)
(arguments
`(#:python ,python-2
+ ;; FIXME: Tests fail with "No such file or directory:
+ ;; pbtools/pbtranscript/modified_bx_intervals/intersection_unique.so"
+ #:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-directory
diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm
index 70d9991659..bc044918a8 100644
--- a/gnu/packages/calendar.scm
+++ b/gnu/packages/calendar.scm
@@ -125,7 +125,7 @@ data units.")
`(("sqlite" ,sqlite)))
(propagated-inputs
`(("python-configobj" ,python-configobj)
- ("python-dateutil-2" ,python-dateutil-2)
+ ("python-dateutil" ,python-dateutil)
("python-icalendar" ,python-icalendar)
("python-tzlocal" ,python-tzlocal)
("python-urwid" ,python-urwid)
diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index 9a3c66c45e..185fbf8e62 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -106,6 +106,10 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
(base32
"0906hms6y6znjhpd0g4wmzv9vcla4brkdpsm4zha9zdj8g5vq2hd"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: Upstream uses a 'runtests.py' script that is not
+ ;; present in the pypi tarball.
+ '(#:tests? #f))
(propagated-inputs
`(("python-django" ,python-django)))
(home-page "https://github.com/alsoicode/django-simple-math-captcha")
@@ -131,7 +135,8 @@ with arguments to the field constructor.")
"1mmc7zsz3dlhs6sx4sppkj1vgshabi362r1a8b8wpj1qfximpqcb"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:tests? #f ; FIXME: How to run tests?
+ #:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-setuppy
(lambda _
@@ -163,6 +168,12 @@ useful tools for testing Django applications and projects.")
(base32
"0f78hmk8c903zwfzlsiw7ivgag81ymmb5hi73rzxbhnlg2v0l3fx"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (zero? (system* "python" "runtests.py")))))))
(native-inputs
`(("python-django" ,python-django)
("python-mock" ,python-mock)))
diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm
index a34578afe7..d9eef54b88 100644
--- a/gnu/packages/enlightenment.scm
+++ b/gnu/packages/enlightenment.scm
@@ -253,7 +253,17 @@ embedded systems.")
(lambda _
(setenv "CFLAGS"
(string-append "-I" (assoc-ref %build-inputs "python-dbus")
- "/include/dbus-1.0")))))))
+ "/include/dbus-1.0"))
+ #t))
+ (add-before 'check 'set-environment
+ (lambda _
+ ;; Some tests require write access to HOME.
+ (setenv "HOME" "/tmp")
+ #t)))
+ ;; FIXME: Some tests require a running D-Bus server or a network
+ ;; connection and should be disabled. Other test failures looks
+ ;; legitimate. Disabled for now, needs work!
+ #:tests? #f))
(native-inputs
`(("pkg-config" ,pkg-config)
("python-cython" ,python-cython)))
diff --git a/gnu/packages/jrnl.scm b/gnu/packages/jrnl.scm
index ef1f52956c..f26de0d4ab 100644
--- a/gnu/packages/jrnl.scm
+++ b/gnu/packages/jrnl.scm
@@ -48,7 +48,7 @@
("python-pytz" ,python-pytz)
("python-tzlocal" ,python-tzlocal)
("python-six" ,python-six)
- ("python-dateutil" , python-dateutil-2)
+ ("python-dateutil" ,python-dateutil)
("python-parsedatetime" ,python-parsedatetime)))
(home-page "http://maebert.github.io/jrnl/")
(synopsis "Personal journal application")
diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm
index ce874ac436..b603b0580e 100644
--- a/gnu/packages/music.scm
+++ b/gnu/packages/music.scm
@@ -2061,6 +2061,8 @@ detailed track info including timbre, pitch, rhythm and loudness information.
(base32
"0bml11gfkxqd3i2jxkn5k2xllc4rvxjcyhs8an05gcyy1zp2bwvb"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Requires unpackaged python-flaky.
(native-inputs
`(("python-coverage" ,python-coverage)
("python-mock" ,python-mock)
diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm
index e2672668d8..5bb83095a0 100644
--- a/gnu/packages/openstack.scm
+++ b/gnu/packages/openstack.scm
@@ -19,6 +19,7 @@
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages openstack)
+ #:use-module (gnu packages gnupg)
#:use-module (gnu packages python)
#:use-module (gnu packages ssh)
#:use-module (gnu packages tls)
@@ -81,6 +82,8 @@ all the files it generates a report.")
(base32
"0g4dfskaiy47rhsh4gh66l5vmdsrgq0qk68pl3ix1cj3ffvfndzv"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ;FIXME: Requires packaging python-doc8.
(propagated-inputs
`(("python-six" ,python-six)
("python-wrapt" ,python-wrapt)))
@@ -113,6 +116,9 @@ manner.")
(base32
"1a310k3dv04jg7zvmk37h2ql7y9kf4hvdxb74bjlwdxgmy6h4wap"))))
(build-system python-build-system)
+ (arguments
+ ;; TODO: Requires unpackaged 'eventlet'.
+ '(#:tests? #f))
(propagated-inputs
`(("python-flake8-2.2.4" ,python-flake8-2.2.4)
("python-mccabe-0.2.1" ,python-mccabe-0.2.1)
@@ -146,9 +152,14 @@ guidelines}.")
(base32
"0njmh40i1lg5mzn9hc2ax83adj6dli455j6xifilrw27c4wlkjzx"))))
(build-system python-build-system)
+ (arguments
+ ;; TODO: Resolve dependency cycle and re-enable.
+ '(#:tests? #f))
(native-inputs
`(("python-fixtures" ,python-fixtures)
+ ; TODO re-add ("python-oslosphinx" ,python-oslosphinx)
("python-pbr" ,python-pbr)
+ ("python-sphinx" ,python-sphinx)
("python-testtools" ,python-testtools)))
(home-page "http://www.openstack.org/")
(synopsis "Mock object framework for Python")
@@ -282,10 +293,13 @@ portions of your testing code.")
(native-inputs
`(("python-pbr" ,python-pbr)
;; Tests
+ ("python-discover" ,python-discover)
("python-docutils" ,python-docutils)
("python-mock" ,python-mock)
+ ("python-oslosphinx" ,python-oslosphinx)
("python-oslotest" ,python-oslotest)
- ("python-sphinx" ,python-sphinx)))
+ ("python-sphinx" ,python-sphinx)
+ ("python-testrepository" ,python-testrepository)))
(home-page "https://github.com/dreamhost/stevedore")
(synopsis "Manage dynamic plugins for Python applications")
(description
@@ -315,7 +329,8 @@ extensions.")
"1cpp2vwmawpd29hjsklsps181lq2ah91cl412qvpnz228nf9sqn5"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:tests? #f ; FIXME: Requires oslo.log >= 1.14.0.
+ #:phases
(modify-phases %standard-phases
(add-before
'check 'pre-check
@@ -362,6 +377,8 @@ common features used in Tempest.")
(base32
"13r778jfb0fhna37c2pd1f2xipnsbd7zli7qhn96acrzymrwj5k1"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Requires packaging python-argparse.
(propagated-inputs
`(("python-netaddr" ,python-netaddr)
("python-six" ,python-six)
@@ -395,11 +412,19 @@ common features used in Tempest.")
(base32
"0kvha0rs9295njyl2z6n6zm5dapi5mrl5zwjm0m6ldqrvccyf8c3"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Requires python-mock >= 1.2.
(native-inputs
`(("python-babel" ,python-babel)
("python-pbr" ,python-pbr)
;; Tests.
- ("python-oslotest" ,python-oslotest)))
+ ("python-coverage" ,python-coverage)
+ ("python-hacking" ,python-hacking)
+ ("python-mock" ,python-mock)
+ ("python-os-client-config" ,python-os-client-config)
+ ("python-oslotest" ,python-oslotest)
+ ("python-oslosphinx" ,python-oslosphinx)
+ ("python-sphinx" ,python-sphinx)))
(home-page "http://launchpad.net/oslo")
(synopsis "Oslo context library")
(description
@@ -423,6 +448,8 @@ pipeline and used by various modules such as logging.")
(base32
"0bpb1c20sm8my650gl824nzaip83bfn8hr91s65k5ncmyh8hb6pl"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Circular dependency on python-oslo.config.
(propagated-inputs
`(("python-babel" ,python-babel)
("python-six" ,python-six)))
@@ -459,6 +486,8 @@ in an application or library.")
(base32
"1fhy6yvbd565nv4x4i3ppyrlbmz3yy9d0xsvw5nkqsa7g43nmf8z"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Requires oslo.utils >= 3.2.0.
(propagated-inputs
`(("python-debtcollector" ,python-debtcollector)
("python-oslo.config" ,python-oslo.config)
@@ -496,6 +525,8 @@ handlers and support for context specific logging (like resource id’s etc).")
(base32
"00s03krhf833gs76aw5ns32w9m1i4hx6x6d9g82m0j5wyqk0sci4"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Requires python-oslo.utils >= 3.2.0.
(propagated-inputs
`(("python-iso8601" ,python-iso8601)
("python-netaddr" ,python-netaddr)
@@ -520,6 +551,47 @@ in transmittable and storable formats, such as JSON and MessagePack.")
(define-public python2-oslo.serialization
(package-with-python2 python-oslo.serialization))
+(define-public python-reno
+ (package
+ (name "python-reno")
+ (version "2.0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "reno" version))
+ (sha256
+ (base32 "1i2wnn5fnm3jm5774pahg000q0lma5i913hml91bbbm2mybphndd"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'init-git
+ (lambda _
+ ;; reno expects a git repo
+ (zero? (system* "git" "init")))))))
+ (propagated-inputs
+ `(("python-babel" ,python-babel)
+ ("python-dulwich" ,python-dulwich)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-six" ,python-six)))
+ (native-inputs
+ `(("python-testtools" ,python-testtools)
+ ("python-pbr" ,python-pbr)
+ ("python-testscenarios" ,python-testscenarios)
+ ("python-testrepository" ,python-testrepository)
+ ("python-mock" ,python-mock)
+ ("python-oslotest" ,python-oslotest)
+ ("gnupg" ,gnupg)
+ ("git" ,git)))
+ (home-page "http://docs.openstack.org/developer/reno/")
+ (synopsis "Release notes manager")
+ (description "Reno is a tool for storing release notes in a git repository
+and building documentation from them.")
+ (license asl2.0)))
+
+(define-public python2-reno
+ (package-with-python2 python-reno))
+
(define-public python-oslosphinx
(package
(name "python-oslosphinx")
@@ -603,6 +675,8 @@ and better support for mocking results.")
;; phase.
(delete-file "oslo_utils/tests/test_netutils.py")))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Requires oslo.config >= 2.7.0.
(propagated-inputs
`(("python-debtcollector" ,python-debtcollector)
("python-oslo.i18n" ,python-oslo.i18n)
@@ -616,6 +690,8 @@ and better support for mocking results.")
`(("python-babel" ,python-babel)
("python-pbr" ,python-pbr)
;; Tests.
+ ("python-bandit" ,python-bandit)
+ ("python-oslo.config" ,python-oslo.config)
("python-oslotest" ,python-oslotest)
("python-mock" ,python-mock)
("python-mox3" ,python-mox3)
@@ -643,6 +719,8 @@ handling.")
(base32
"1w4csvkah67rfpxylxnvs2s3594i0f9isy8pf4gnsqs5zirvjaa4"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Many tests are failing.
(native-inputs
`(("python-sphinx" ,python-sphinx)
;; and some packages for the tests
diff --git a/gnu/packages/patches/python-pyopenssl-skip-network-test.patch b/gnu/packages/patches/python-pyopenssl-skip-network-test.patch
new file mode 100644
index 0000000000..a24eaf69a0
--- /dev/null
+++ b/gnu/packages/patches/python-pyopenssl-skip-network-test.patch
@@ -0,0 +1,50 @@
+This test tries connecting to an external server which is not supported
+in the build environment. See discussion at:
+
+https://lists.gnu.org/archive/html/guix-devel/2016-12/msg00650.html
+
+diff --git a/tests/test_ssl.py b/tests/test_ssl.py
+index ee849fd..60048b8 100644
+--- a/tests/test_ssl.py
++++ b/tests/test_ssl.py
+@@ -1180,40 +1180,6 @@ class ContextTests(TestCase, _LoopbackMixin):
+ TypeError, context.load_verify_locations, None, None, None
+ )
+
+- @pytest.mark.skipif(
+- platform == "win32",
+- reason="set_default_verify_paths appears not to work on Windows. "
+- "See LP#404343 and LP#404344."
+- )
+- def test_set_default_verify_paths(self):
+- """
+- :py:obj:`Context.set_default_verify_paths` causes the
+- platform-specific CA certificate locations to be used for
+- verification purposes.
+- """
+- # Testing this requires a server with a certificate signed by one
+- # of the CAs in the platform CA location. Getting one of those
+- # costs money. Fortunately (or unfortunately, depending on your
+- # perspective), it's easy to think of a public server on the
+- # internet which has such a certificate. Connecting to the network
+- # in a unit test is bad, but it's the only way I can think of to
+- # really test this. -exarkun
+-
+- # Arg, verisign.com doesn't speak anything newer than TLS 1.0
+- context = Context(SSLv23_METHOD)
+- context.set_default_verify_paths()
+- context.set_verify(
+- VERIFY_PEER,
+- lambda conn, cert, errno, depth, preverify_ok: preverify_ok)
+-
+- client = socket()
+- client.connect(("encrypted.google.com", 443))
+- clientSSL = Connection(context, client)
+- clientSSL.set_connect_state()
+- clientSSL.do_handshake()
+- clientSSL.send(b"GET / HTTP/1.0\r\n\r\n")
+- self.assertTrue(clientSSL.recv(1024))
+-
+ def test_set_default_verify_paths_signature(self):
+ """
+ :py:obj:`Context.set_default_verify_paths` takes no arguments and
diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm
index 2ea48e5999..58416ee66c 100644
--- a/gnu/packages/pdf.scm
+++ b/gnu/packages/pdf.scm
@@ -643,6 +643,10 @@ using a stylus.")
(base32
"0rz2pg04wnzjjm2f5a8ik9v8s54mv4xrjhv5liqjijqv6awh12gl"))))
(build-system python-build-system)
+ (arguments
+ '(;; FIXME: There is one test failure, but it does not cause the
+ ;; build to fail. No time to investigate right now.
+ #:test-target "tests"))
(propagated-inputs
`(("python-pillow" ,python-pillow)))
(home-page "http://www.reportlab.com")
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 22a4c590b0..1492e0f369 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -69,6 +69,7 @@
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages gl)
#:use-module (gnu packages glib)
+ #:use-module (gnu packages graphviz)
#:use-module (gnu packages gstreamer)
#:use-module (gnu packages gtk)
#:use-module (gnu packages icu4c)
@@ -77,6 +78,7 @@
#:use-module (gnu packages libevent)
#:use-module (gnu packages libffi)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages man)
#:use-module (gnu packages maths)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages networking)
@@ -89,6 +91,7 @@
#:use-module (gnu packages protobuf)
#:use-module (gnu packages readline)
#:use-module (gnu packages sdl)
+ #:use-module (gnu packages shells)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tex)
#:use-module (gnu packages texinfo)
@@ -440,6 +443,9 @@ instead of @command{python3}.")))
(base32
"1w4r09fvn6kd80m5mx4ws1wz100brkaq6hzzpwrns8cgjzjpl6c6"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: some tests does not return and times out.
+ '(#:tests? #f))
(home-page "https://www.github.com/giampaolo/psutil")
(synopsis "Library for retrieving information on running processes")
(description
@@ -540,6 +546,14 @@ John the Ripper).")
(base32
"14k8z7ndc3zk5xivnm4d8lncchx475ll5izpf8vmfbq7rp9yp5rj"))))
(build-system python-build-system)
+ (arguments
+ '(;; FIXME: One test fails with "EOFError not raised by connect".
+ #:tests? #f))
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; (zero? (system* "python" "test.py")))))))
(propagated-inputs
`(("python-pycrypto" ,python-pycrypto)
("python-ecdsa" ,python-ecdsa)))
@@ -1048,6 +1062,9 @@ password storage.")
(base32
"0snmb8xffb3vsma0z67i0h0w2g2dy0p3gsgh9gi4i0kgc5l8spqh"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-py" ,python-py)
+ ("python-pytest" ,python-pytest)))
(home-page "http://pypi.python.org/pypi/six/")
(synopsis "Python 2 and 3 compatibility utilities")
(description
@@ -1061,7 +1078,7 @@ Python file, so it can be easily copied into your project.")
(define-public python2-six
(package-with-python2 python-six))
-(define-public python-dateutil-2
+(define-public python-dateutil
(package
(name "python-dateutil")
(version "2.5.3")
@@ -1082,29 +1099,6 @@ Python file, so it can be easily copied into your project.")
datetime module, available in Python 2.3+.")
(license license:bsd-3)))
-(define-public python2-dateutil-2
- (package-with-python2 python-dateutil-2))
-
-(define-public python-dateutil
- (package
- (name "python-dateutil")
- (version "1.5") ; last version for python < 3
- (source
- (origin
- (method url-fetch)
- (uri (string-append "http://labix.org/download/python-dateutil/"
- "python-dateutil-" version ".tar.gz"))
- (sha256
- (base32
- "0fqfglhy5khbvsipr3x7m6bcaqljh8xl5cw33vbfxy7qhmywm2n0"))))
- (build-system python-build-system)
- (home-page "https://dateutil.readthedocs.io/en/stable/")
- (synopsis "Extensions to the standard datetime module")
- (description
- "The dateutil module provides powerful extensions to the standard
-datetime module, available in Python 2.3+.")
- (license license:psfl)))
-
(define-public python2-dateutil
(package-with-python2 python-dateutil))
@@ -1150,7 +1144,7 @@ datetime module, available in Python 2.3+.")
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-pytz" ,python-pytz)
- ("python-dateutil" ,python-dateutil-2)))
+ ("python-dateutil" ,python-dateutil)))
(native-inputs
`(("python-nose" ,python-nose)
("python-cython" ,python-cython)))
@@ -1726,6 +1720,12 @@ standard library.")
(base32
"0561gz2w3i825gyl42mcq14y3dcgkapfiv5zv9a2bz15qxiijl56"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: "ImportError: 'test' module incorrectly imported from
+ ;; '/gnu/store/...-python-pytest-mimimal-3.0.5/lib/python3.5/site-packages'.
+ ;; Expected '/tmp/guix-build-python-py-1.4.31.drv-0/py-1.4.31/py'.
+ ;; Is this module globally installed?"
+ '(#:tests? #f))
(home-page "http://pylib.readthedocs.org/")
(synopsis "Python library for parsing, I/O, instrospection, and logging")
(description
@@ -1924,6 +1924,15 @@ same arguments.")
(for-each delete-file (find-files "." "\\.pyc$"))
#t))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ;FIXME: Some tests are failing.
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (delete 'check)
+ ;; (add-after 'install 'check
+ ;; (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; (add-installed-pythonpath inputs outputs)
+ ;; (zero? (system* "py.test" "-v")))))
(native-inputs
`(("unzip" ,unzip)
("python-setuptools-scm" ,python-setuptools-scm)))
@@ -1976,17 +1985,36 @@ subprocess and see the output as well as any file modifications.")
(define-public python-testtools
(package
(name "python-testtools")
- (version "1.0.0")
+ (version "1.4.0")
(source
(origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/t/testtools/testtools-"
- version ".tar.gz"))
+ (uri (pypi-uri "testtools" version))
(sha256
(base32
- "1dyml28ykpl5jb9khdmcdvhy1cxqingys6qvj2k04fzlaj6z3bbx"))))
+ "1vw8yljnd75d396hhw6s2hrf4cclzy845ifd5am0lxsl235z3i8c"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-module-imports
+ (lambda _
+ (substitute* "setup.py"
+ (("'unittest2>=0.8.0',") ""))
+ (substitute* '("testtools/testcase.py"
+ "testtools/testsuite.py"
+ "testtools/run.py"
+ "testtools/tests/test_run.py"
+ "testtools/tests/test_testsuite.py"
+ "testtools/tests/test_deferredruntest.py")
+ ;; unittest2 is a backport of Python2.7 features to Python 2.4.
+ (("import unittest2 as unittest") "import unittest")
+ (("import unittest2") "import unittest as unittest2")
+ (("from unittest2 import") "from unittest import"))
+ (substitute* "testtools/tests/test_testresult.py"
+ ;; NUL in source code is not allowed (raises ValueError).
+ (("\\x00\\x04") "\\x04"))
+ #t)))))
(propagated-inputs
`(("python-mimeparse" ,python-mimeparse)
("python-extras" ,python-extras)))
@@ -2157,10 +2185,18 @@ from git information.
(base32
"0djxvdwm8s60dbfn7bhf40x6g818p3b3mlwijm1c3bqg7msn271y"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (zero? (system* "python" "-m" "testtools.run"
+ "fixtures.test_suite")))))))
(propagated-inputs
`(("python-six" ,python-six)))
(native-inputs
- `(("python-pbr-minimal" ,python-pbr-minimal)
+ `(("python-mock" ,python-mock)
+ ("python-pbr-minimal" ,python-pbr-minimal)
("python-testtools" ,python-testtools)))
(home-page "https://launchpad.net/python-fixtures")
(synopsis "Python test fixture library")
@@ -2186,6 +2222,9 @@ Python tests.")
(base32
"1ssqb07c277010i6gzzkbdd46gd9mrj0bi0i8vn560n2k2y4j93m"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: Many tests are failing.
+ '(#:tests? #f))
(propagated-inputs
`(("python-fixtures" ,python-fixtures)
("python-subunit" ,python-subunit)
@@ -2215,6 +2254,9 @@ have failed since the last commit or what tests are currently failing.")
(base32
"01rbr4br4lsk0lwn8fb96zwd2xr4f0mg1w7iq3j11i8f5ig2nqs1"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: 95 tests failed, 539 passed, 6 skipped, 2 errors.
+ '(#:tests? #f))
(home-page "http://nedbatchelder.com/code/coverage")
(synopsis "Code coverage measurement for Python")
(description
@@ -2390,7 +2432,12 @@ is used by the Requests library to verify HTTPS requests.")
(substitute* "click/_unicodefun.py"
(("'locale'")
(string-append "'" glibc "/bin/locale'"))))
- #t)))))
+ #t))
+ (replace 'check
+ (lambda _
+ (zero? (system* "make" "test")))))))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "http://click.pocoo.org")
(synopsis "Command line library for Python")
(description
@@ -2442,19 +2489,18 @@ installed with a newer @code{pip} or with wheel's own command line utility.")
(define-public python-requests
(package
(name "python-requests")
- (version "2.9.1")
+ (version "2.12.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "requests" version))
(sha256
(base32
- "0zsqrzlybf25xscgi7ja4s48y2abf9wvjkn47wh984qgs1fq2xy5"))))
+ "0d5fwxmw4ibynk3imph3n4n84m0n3ib1vj339fxhkqri0qd4767d"))))
+ ;; TODO: unbundle urllib3 and chardet.
(build-system python-build-system)
- (native-inputs
- `(("python-py" ,python-py)
- ("python-pytest" ,python-pytest)
- ("python-pytest-cov" ,python-pytest-cov)
- ("python-wheel" ,python-wheel)))
+ (arguments
+ ;; FIXME: Some tests require network access.
+ '(#:tests? #f))
(home-page "http://python-requests.org/")
(synopsis "Python HTTP library")
(description
@@ -2627,6 +2673,7 @@ somewhat intelligeble.")
(build-system python-build-system)
(native-inputs
`(("python-nose" ,python-nose)
+ ("python-mock" ,python-mock)
("python-cryptography" ,python-cryptography)
("python-pyjwt" ,python-pyjwt)
("python-blinker" ,python-blinker)))
@@ -2643,7 +2690,6 @@ OAuth request-signing logic.")
(package
(inherit base)
(native-inputs `(("python2-unittest2" ,python2-unittest2)
- ("python2-mock" ,python2-mock)
,@(package-native-inputs base))))))
(define-public python-itsdangerous
@@ -2790,15 +2836,26 @@ written in pure Python.")
(base32
"0nmqsfmiw4arjxqkmf9z66ml950pcdjk6aq4gin4sywmzdjw5fzp"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Python 3 tests are failing.
(home-page "http://defunkt.io/pystache/")
(synopsis "Python logic-less template engine")
(description
"Pystache is a Python implementation of the framework agnostic,
logic-free templating system Mustache.")
- (license license:expat)))
+ (license license:expat)
+ (properties `((python2-variant . ,(delay python2-pystache))))))
(define-public python2-pystache
- (package-with-python2 python-pystache))
+ (package (inherit (package-with-python2
+ (strip-python2-variant python-pystache)))
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (zero? (system* "python" "test_pystache.py")))))))))
(define-public python-joblib
(package
@@ -2895,6 +2952,9 @@ reStructuredText.")
(base32
"10axnp2wpjnq9g8wg53fx0c70dfxqrz498jyz8mrdx9a3flwir48"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: Tests require sphinx, which depends on this.
+ '(#:tests? #f))
(home-page "http://pygments.org/")
(synopsis "Syntax highlighting")
(description
@@ -2907,30 +2967,74 @@ reStructuredText.")
(define-public python-sphinx
(package
(name "python-sphinx")
- (version "1.2.3")
+ (version "1.5.1")
(source
(origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/S/Sphinx/Sphinx-"
- version ".tar.gz"))
+ (uri (pypi-uri "Sphinx" version))
(sha256
(base32
- "011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl"))))
+ "1i8p9idnli4gr0y4x67yakbdk5w6a0xjzhrg6bg51y9d1fi7fslf"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ ;; Requires Internet access.
+ (delete-file "tests/test_build_linkcheck.py")
+ (zero? (system* "make" "test")))))))
(propagated-inputs
- `(("python-jinja2" ,python-jinja2)
+ `(("python-imagesize" ,python-imagesize)
+ ("python-sphinx-alabaster-theme"
+ ,python-sphinx-alabaster-theme)
+ ("python-babel" ,python-babel)
+ ("python-snowballstemmer" ,python-snowballstemmer)
("python-docutils" ,python-docutils)
- ("python-pygments" ,python-pygments)))
+ ("python-jinja2" ,python-jinja2)
+ ("python-pygments" ,python-pygments)
+ ("python-six" ,python-six)))
+ (native-inputs
+ `(("graphviz" ,graphviz)
+ ("python-html5lib" ,python-html5lib)
+ ("python-mock" ,python-mock)
+ ("python-nose" ,python-nose)
+ ("python-requests" ,python-requests)))
(home-page "http://sphinx-doc.org/")
(synopsis "Python documentation generator")
(description "Sphinx is a tool that makes it easy to create documentation
for Python projects or other documents consisting of multiple reStructuredText
sources.")
- (license license:bsd-3)))
+ (license license:bsd-3)
+ (properties `((python2-variant . ,(delay python2-sphinx))))))
(define-public python2-sphinx
- (package-with-python2 python-sphinx))
+ (let ((base (package-with-python2 (strip-python2-variant python-sphinx))))
+ (package
+ (inherit base)
+ (native-inputs `(("python2-mock" ,python2-mock)
+ ("python2-enum34" ,python2-enum34)
+ ,@(package-native-inputs base)))
+ (propagated-inputs `(("python2-pytz" ,python2-pytz)
+ ,@(package-propagated-inputs base))))))
+
+;; This is needed for python-matplotlib@1.4 and python-scipy@0.16, at least.
+;; Try removing this when they are updated.
+(define-public python-sphinx-1.2.3
+ (package (inherit python-sphinx)
+ (version "1.2.3")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "Sphinx" version))
+ (sha256
+ (base32
+ "011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl"))))
+ ;; XXX: "'NoneType' object has no attribute 'split'".
+ (arguments '(#:tests? #f))))
+
+(define-public python2-sphinx-1.2.3
+ (package (inherit (package-with-python2
+ (strip-python2-variant python-sphinx-1.2.3)))))
(define-public python-sphinx-rtd-theme
(package
@@ -2946,6 +3050,8 @@ sources.")
(base32
"19nw3rn7awplcdrz63kg1njqwkbymfg9lwn7l2grhdyhyr2gaa8g"))))
(build-system python-build-system)
+ (propagated-inputs
+ `(("python-sphinx" ,python-sphinx)))
(home-page "https://github.com/snide/sphinx_rtd_theme/")
(synopsis "ReadTheDocs.org theme for Sphinx")
(description "A theme for Sphinx used by ReadTheDocs.org.")
@@ -2967,7 +3073,7 @@ sources.")
"0bh4lnj2p1nh0wf5pgxgfbrp27xhb1rinahkb5j7s3qprq6qn0sr"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-dateutil" ,python-dateutil-2)
+ `(("python-dateutil" ,python-dateutil)
("python-six" ,python-six)))
(native-inputs
`(("python-setuptools-scm" ,python-setuptools-scm)))
@@ -3061,7 +3167,7 @@ interested parties to subscribe to events, or \"signals\".")
("python-blinker" ,python-blinker)
("python-unidecode" ,python-unidecode)
("python-six" ,python-six)
- ("python-dateutil-2" ,python-dateutil-2)))
+ ("python-dateutil" ,python-dateutil)))
(home-page "http://getpelican.com/")
(arguments
`(;; XXX Requires a lot more packages to do unit tests :P
@@ -3138,6 +3244,9 @@ mining and data analysis.")
(sha256
(base32 "0jz416fqvpahqyffw8plmszzfj669w8wvf3y9clnr5lr6a7md3kn"))))
(build-system python-build-system)
+ (arguments
+ ;; TODO: Some tests require running X11 server. Disable them?
+ '(#:tests? #f))
;; See DEPENDS.txt for the list of build and run time requiremnts
(propagated-inputs
`(("python-matplotlib" ,python-matplotlib)
@@ -3387,7 +3496,8 @@ objects.")
(native-inputs
`(("unzip" ,unzip)
("python2-cython" ,python2-cython)
- ("python2-mock" ,python2-mock)))
+ ("python2-mock" ,python2-mock)
+ ("python2-nose" ,python2-nose)))
(home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
(synopsis "Perform genome-wide association studies on large data sets")
(description
@@ -3622,7 +3732,7 @@ transcendental functions).")
("python-pygobject" ,python-pygobject)
("gobject-introspection" ,gobject-introspection)
("python-tkinter" ,python "tk")
- ("python-dateutil" ,python-dateutil-2)
+ ("python-dateutil" ,python-dateutil)
("python-numpy" ,python-numpy-bootstrap)
("python-pillow" ,python-pillow)
("python-pytz" ,python-pytz)
@@ -3655,7 +3765,7 @@ transcendental functions).")
("tk" ,tk)))
(native-inputs
`(("pkg-config" ,pkg-config)
- ("python-sphinx" ,python-sphinx)
+ ("python-sphinx" ,python-sphinx-1.2.3)
("python-numpydoc" ,python-numpydoc)
("python-nose" ,python-nose)
("python-mock" ,python-mock)
@@ -3663,62 +3773,65 @@ transcendental functions).")
("texinfo" ,texinfo)))
(arguments
`(#:phases
- (alist-cons-before
- 'build 'configure-environment
- (lambda* (#:key outputs inputs #:allow-other-keys)
- (let ((cairo (assoc-ref inputs "cairo"))
- (gtk+ (assoc-ref inputs "gtk+")))
- ;; Setting these directories in the 'basedirlist' of 'setup.cfg'
- ;; has not effect.
- (setenv "LD_LIBRARY_PATH"
- (string-append cairo "/lib:" gtk+ "/lib"))
- (setenv "HOME" (getcwd))
- (call-with-output-file "setup.cfg"
- (lambda (port)
- (format port "[directories]~%
+ (modify-phases %standard-phases
+ (add-before 'build 'configure-environment
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let ((cairo (assoc-ref inputs "cairo"))
+ (gtk+ (assoc-ref inputs "gtk+")))
+ ;; Setting these directories in the 'basedirlist' of 'setup.cfg'
+ ;; has not effect.
+ (setenv "LD_LIBRARY_PATH"
+ (string-append cairo "/lib:" gtk+ "/lib"))
+ (setenv "HOME" (getcwd))
+ (call-with-output-file "setup.cfg"
+ (lambda (port)
+ (format port "[directories]~%
basedirlist = ~a,~a~%
[rc_options]~%
backend = TkAgg~%"
- (assoc-ref inputs "tcl")
- (assoc-ref inputs "tk"))))))
- (alist-cons-after
- 'install 'install-doc
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
- (doc (string-append data "/doc/" ,name "-" ,version))
- (info (string-append data "/info"))
- (html (string-append doc "/html")))
- ;; Make installed package available for building the
- ;; documentation
- (add-installed-pythonpath inputs outputs)
- (with-directory-excursion "doc"
- ;; Produce pdf in 'A4' format.
- (substitute* (find-files "." "conf\\.py")
- (("latex_paper_size = 'letter'")
- "latex_paper_size = 'a4'"))
- (mkdir-p html)
- (mkdir-p info)
- ;; The doc recommends to run the 'html' target twice.
- (system* "python" "make.py" "html")
- (system* "python" "make.py" "html")
- (copy-recursively "build/html" html)
- (system* "python" "make.py" "latex")
- (system* "python" "make.py" "texinfo")
- (symlink (string-append html "/_images")
- (string-append info "/matplotlib-figures"))
- (with-directory-excursion "build/texinfo"
- (substitute* "matplotlib.texi"
- (("@image\\{([^,]*)" all file)
- (string-append "@image{matplotlib-figures/" file)))
+ (assoc-ref inputs "tcl")
+ (assoc-ref inputs "tk"))))
+ #t)))
+ (add-after 'install 'install-doc
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (doc (string-append data "/doc/" ,name "-" ,version))
+ (info (string-append data "/info"))
+ (html (string-append doc "/html")))
+ ;; Make installed package available for building the
+ ;; documentation
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "doc"
+ ;; Produce pdf in 'A4' format.
+ (substitute* (find-files "." "conf\\.py")
+ (("latex_paper_size = 'letter'")
+ "latex_paper_size = 'a4'"))
+ (substitute* "users/intro.rst"
+ ;; Fix reST markup error (see <https://github.com/sphinx-doc/sphinx/issues/3044>)
+ (("[[][*][]]") "[#]"))
+ (mkdir-p html)
+ (mkdir-p info)
+ ;; The doc recommends to run the 'html' target twice.
+ (system* "python" "make.py" "html")
+ (system* "python" "make.py" "html")
+ (copy-recursively "build/html" html)
+ (system* "python" "make.py" "latex")
+ (system* "python" "make.py" "texinfo")
(symlink (string-append html "/_images")
- "./matplotlib-figures")
- (system* "makeinfo" "--no-split"
- "-o" "matplotlib.info" "matplotlib.texi"))
- (copy-file "build/texinfo/matplotlib.info"
- (string-append info "/matplotlib.info"))
- (copy-file "build/latex/Matplotlib.pdf"
- (string-append doc "/Matplotlib.pdf")))))
- %standard-phases))))
+ (string-append info "/matplotlib-figures"))
+ (with-directory-excursion "build/texinfo"
+ (substitute* "matplotlib.texi"
+ (("@image\\{([^,]*)" all file)
+ (string-append "@image{matplotlib-figures/" file)))
+ (symlink (string-append html "/_images")
+ "./matplotlib-figures")
+ (system* "makeinfo" "--no-split"
+ "-o" "matplotlib.info" "matplotlib.texi"))
+ (copy-file "build/texinfo/matplotlib.info"
+ (string-append info "/matplotlib.info"))
+ (copy-file "build/latex/Matplotlib.pdf"
+ (string-append doc "/Matplotlib.pdf")))
+ #t))))))
(home-page "http://matplotlib.org")
(synopsis "2D plotting library for Python")
(description
@@ -3736,6 +3849,10 @@ toolkits.")
(package (inherit matplotlib)
;; Make sure to use special packages for Python 2 instead
;; of those automatically rewritten by package-with-python2.
+ (native-inputs
+ `(("python2-sphinx" ,python2-sphinx-1.2.3)
+ ,@(fold alist-delete (package-native-inputs matplotlib)
+ '("python-sphinx"))))
(propagated-inputs
`(("python2-pycairo" ,python2-pycairo)
("python2-pygobject-2" ,python2-pygobject-2)
@@ -3786,6 +3903,16 @@ operators such as union, intersection, and difference.")
(base32
"0nhan2qvrw7b7gg5zddwa22kybdv3x1g26vkd7q8lvnkgzrs4dga"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ ;; It's easier to run tests after install.
+ ;; Make installed package available for running the tests
+ (add-installed-pythonpath inputs outputs)
+ (zero? (system* "python" "-m" "rpy2.tests" "-v")))))))
(propagated-inputs
`(("python-six" ,python-six)))
(inputs
@@ -3833,7 +3960,7 @@ functions.")
("openblas" ,openblas)))
(native-inputs
`(("python-nose" ,python-nose)
- ("python-sphinx" ,python-sphinx)
+ ("python-sphinx" ,python-sphinx-1.2.3)
("python-numpydoc" ,python-numpydoc)
("gfortran" ,gfortran)
("texlive" ,texlive)
@@ -3841,13 +3968,18 @@ functions.")
(outputs '("out" "doc"))
(arguments
`(#:phases
- (alist-cons-before
- 'build 'configure-openblas
- (lambda* (#:key inputs #:allow-other-keys)
- (call-with-output-file "site.cfg"
- (lambda (port)
- (format port
- "[blas]
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* "scipy/integrate/tests/test_quadpack.py"
+ (("libm.so") "libm.so.6"))
+ #t))
+ (add-before 'build 'configure-openblas
+ (lambda* (#:key inputs #:allow-other-keys)
+ (call-with-output-file "site.cfg"
+ (lambda (port)
+ (format port
+ "[blas]
libraries = openblas
library_dirs = ~a/lib
include_dirs = ~a/include
@@ -3857,53 +3989,44 @@ include_dirs = ~a/include
library_dirs = ~a/lib
atlas_libs = openblas
"
- (assoc-ref inputs "openblas")
- (assoc-ref inputs "openblas")
- (assoc-ref inputs "openblas"))))
- #t)
- (alist-cons-after
- 'install 'install-doc
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
- (doc (string-append data "/doc/" ,name "-" ,version))
- (html (string-append doc "/html"))
- (pyver ,(string-append "PYVER=")))
- ;; Make installed package available for building the
- ;; documentation
- (add-installed-pythonpath inputs outputs)
- (with-directory-excursion "doc"
- ;; Fix generation of images for mathematical expressions.
- (substitute* (find-files "source" "conf\\.py")
- (("pngmath_use_preview = True")
- "pngmath_use_preview = False"))
- (mkdir-p html)
- (system* "make" "html" pyver)
- (system* "make" "latex" "PAPER=a4" pyver)
- (system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver)
- (copy-file "build/latex/scipy-ref.pdf"
- (string-append doc "/scipy-ref.pdf"))
- (with-directory-excursion "build/html"
- (for-each (lambda (file)
- (let* ((dir (dirname file))
- (tgt-dir (string-append html "/" dir)))
- (install-file file html)))
- (find-files "." ".*"))))))
- ;; Tests can only be run after the library has been installed and not
- ;; within the source directory.
- (alist-cons-after
- 'install 'check
- (lambda _
- (with-directory-excursion "/tmp"
- (zero? (system* "python" "-c" "import scipy; scipy.test()"))))
- (alist-delete
- 'check
- (alist-cons-after
- 'unpack 'fix-tests
- (lambda _
- (substitute* "scipy/integrate/tests/test_quadpack.py"
- (("libm.so") "libm.so.6"))
- #t)
- %standard-phases)))))))
+ (assoc-ref inputs "openblas")
+ (assoc-ref inputs "openblas")
+ (assoc-ref inputs "openblas"))))
+ #t))
+ (delete 'check)
+ (add-after 'install 'install-doc
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (doc (string-append data "/doc/" ,name "-" ,version))
+ (html (string-append doc "/html"))
+ (pyver ,(string-append "PYVER=")))
+ ;; Make installed package available for building the
+ ;; documentation
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "doc"
+ ;; Fix generation of images for mathematical expressions.
+ (substitute* (find-files "source" "conf\\.py")
+ (("pngmath_use_preview = True")
+ "pngmath_use_preview = False"))
+ (mkdir-p html)
+ (system* "make" "html" pyver)
+ (system* "make" "latex" "PAPER=a4" pyver)
+ (system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver)
+ (copy-file "build/latex/scipy-ref.pdf"
+ (string-append doc "/scipy-ref.pdf"))
+ (with-directory-excursion "build/html"
+ (for-each (lambda (file)
+ (let* ((dir (dirname file))
+ (tgt-dir (string-append html "/" dir)))
+ (install-file file html)))
+ (find-files "." ".*"))))
+ #t)))
+ (add-after 'install-doc 'check
+ (lambda _
+ ;; Tests can only be run after the library has been installed and not
+ ;; within the source directory.
+ (with-directory-excursion "/tmp"
+ (zero? (system* "python" "-c" "import scipy; scipy.test()"))))))))
(home-page "http://www.scipy.org/")
(synopsis "The Scipy library provides efficient numerical routines")
(description "The SciPy library is one of the core packages that make up
@@ -3912,7 +4035,15 @@ routines such as routines for numerical integration and optimization.")
(license license:bsd-3)))
(define-public python2-scipy
- (package-with-python2 python-scipy))
+ (let ((scipy (package-with-python2
+ (strip-python2-variant python-scipy))))
+ (package (inherit scipy)
+ ;; Make sure to use special packages for Python 2 instead
+ ;; of those automatically rewritten by package-with-python2.
+ (native-inputs
+ `(("python2-sphinx" ,python2-sphinx-1.2.3)
+ ,@(fold alist-delete (package-native-inputs scipy)
+ '("python-sphinx")))))))
(define-public python-socksipy-branch
(package
@@ -4100,11 +4231,22 @@ both of which are installed automatically if you install this library.")
(base32
"1wghyvk73cmq3iqyg3fczw128fv2pan2v76m0xg1bw05h8fhvnk3"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Many tests require a running database server.
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; (zero? (system* "py.test" "sqlalchemy_utils" "tests")))))
(propagated-inputs
`(("python-six" ,python-six)
("python-sqlalchemy" ,python-sqlalchemy)))
(native-inputs
- `(("python-pytest" ,python-pytest)))
+ `(("python-dateutil" ,python-dateutil)
+ ("python-flexmock" ,python-flexmock)
+ ("python-psycopg2" ,python-psycopg2)
+ ("python-pytest" ,python-pytest)
+ ("python-pytz" ,python-pytz)))
(home-page "https://github.com/kvesteri/sqlalchemy-utils")
(synopsis "Various utility functions for SQLAlchemy")
(description
@@ -4395,16 +4537,18 @@ a front-end for C compilers or analysis tools.")
`(("python-cffi" ,python-cffi) ; used at run time
("python-six" ,python-six)))
(arguments
- `(#:phases
- (alist-cons-after
- 'install 'install-doc
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((doc (string-append (assoc-ref outputs "out") "/share"
- "/doc/" ,name "-" ,version)))
- (mkdir-p doc)
- (copy-file "README.md"
- (string-append doc "/README.md"))))
- %standard-phases)))
+ `(;; FIXME: Tests cannot load libxcb.so.1
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'install-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((doc (string-append (assoc-ref outputs "out") "/share"
+ "/doc/" ,name "-" ,version)))
+ (mkdir-p doc)
+ (copy-file "README.md"
+ (string-append doc "/README.md"))
+ #t))))))
(home-page "https://github.com/tych0/xcffib")
(synopsis "XCB Python bindings")
(description
@@ -4441,25 +4585,27 @@ support for Python 3 and PyPy. It is based on cffi.")
(propagated-inputs
`(("python-xcffib" ,python-xcffib))) ; used at run time
(arguments
- `(#:phases
- (alist-cons-after
- 'install 'install-doc
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
- (doc (string-append data "/doc/" ,name "-" ,version))
- (html (string-append doc "/html")))
- (setenv "LD_LIBRARY_PATH"
- (string-append (assoc-ref inputs "cairo") "/lib" ":"
- (assoc-ref inputs "gdk-pixbuf") "/lib"))
- (setenv "LANG" "en_US.UTF-8")
- (mkdir-p html)
- (for-each (lambda (file)
- (copy-file (string-append "." file)
- (string-append doc file)))
- '("/README.rst" "/CHANGES" "/LICENSE"))
- (system* "python" "setup.py" "build_sphinx")
- (copy-recursively "docs/_build/html" html)))
- %standard-phases)))
+ `(;; FIXME: Tests cannot find 'libcairo.so.2'.
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'install-doc
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (doc (string-append data "/doc/" ,name "-" ,version))
+ (html (string-append doc "/html")))
+ (setenv "LD_LIBRARY_PATH"
+ (string-append (assoc-ref inputs "cairo") "/lib" ":"
+ (assoc-ref inputs "gdk-pixbuf") "/lib"))
+ (setenv "LANG" "en_US.UTF-8")
+ (mkdir-p html)
+ (for-each (lambda (file)
+ (copy-file (string-append "." file)
+ (string-append doc file)))
+ '("/README.rst" "/CHANGES" "/LICENSE"))
+ (system* "python" "setup.py" "build_sphinx")
+ (copy-recursively "docs/_build/html" html)
+ #t))))))
(home-page "https://github.com/SimonSapin/cairocffi")
(synopsis "Python bindings and object-oriented API for Cairo")
(description
@@ -4540,6 +4686,8 @@ Python language binding specification.")
(sha256
(base32 "1gzjg2k6f14i1msm2b0ax8d9ds1hvk6qd5nlaivg8m4cxqp4cp1x"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Requires python-cherrypy.
(propagated-inputs
`(("python-psutil" ,python-psutil)
("python-drmaa" ,python-drmaa)
@@ -4558,21 +4706,39 @@ cluster without needing to write any wrapper code yourself.")
(define-public python-pexpect
(package
(name "python-pexpect")
- (version "3.3")
+ (version "4.2.1")
(source
(origin
(method url-fetch)
- (uri (string-append "https://pypi.python.org/packages/source/p/"
- "pexpect/pexpect-" version ".tar.gz"))
+ (uri (pypi-uri "pexpect" version))
(sha256
- (base32 "1fp5gm976z7ghm8jw57463rj19cv06c8zw842prgyg788f6n3snz"))))
+ (base32 "14ls7k99pwvl21zqv65kzrhccv50j89m5ij1hf0slmsvlxjj84rx"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
+ (add-before 'check 'prepare-tests
+ (lambda _
+ (substitute* (find-files "tests")
+ (("/bin/ls") (which "ls"))
+ (("/bin/echo") (which "echo"))
+ (("/bin/which") (which "which"))
+ ;; Many tests try to use the /bin directory which
+ ;; is not present in the build environment.
+ ;; Use one that's non-empty and unlikely to change.
+ (("/bin'") "/dev'"))
+ ;; XXX: Socket connection test gets "Connection reset by peer".
+ ;; Why does it not work? Delete for now.
+ (delete-file "tests/test_socket.py")
+ #t))
(replace 'check (lambda _ (zero? (system* "nosetests")))))))
(native-inputs
- `(("python-nose" ,python-nose)))
+ `(("python-nose" ,python-nose)
+ ("python-pytest" ,python-pytest)
+ ("man-db" ,man-db)
+ ("which" ,which)))
+ (propagated-inputs
+ `(("python-ptyprocess" ,python-ptyprocess)))
(home-page "http://pexpect.readthedocs.org/")
(synopsis "Controlling interactive console applications")
(description
@@ -5288,13 +5454,12 @@ implementation of D-Bus.")
`(("sqlite" ,sqlite)))
(arguments
`(#:phases
- ;; swap check and install phases
- (alist-cons-after
- 'install 'check
- (assoc-ref %standard-phases 'check)
- (alist-delete
- 'check
- %standard-phases))))
+ (modify-phases %standard-phases
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (zero? (system* "python" "setup.py" "test")))))))
(home-page "https://github.com/rogerbinns/apsw/")
(synopsis "Another Python SQLite Wrapper")
(description "APSW is a Python wrapper for the SQLite
@@ -5366,7 +5531,8 @@ screen-scraping projects. It offers Pythonic idioms for navigating,
searching, and modifying a parse tree, providing a toolkit for
dissecting a document and extracting what you need. It automatically
converts incoming documents to Unicode and outgoing documents to UTF-8.")
- (license license:expat)))
+ (license license:expat)
+ (properties `((python2-variant . ,(delay python2-beautifulsoup4))))))
(define-public python2-beautifulsoup4
(package
@@ -5530,17 +5696,18 @@ of the structure, dynamics, and functions of complex networks.")
(define-public snakemake
(package
(name "snakemake")
- (version "3.2.1")
+ (version "3.9.0")
(source
(origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/s/snakemake/snakemake-"
- version ".tar.gz"))
+ (uri (pypi-uri "snakemake" version))
(sha256
- (base32 "0fi4b63sj60hvi7rfydvmz2icl4wj74djw5sn2gl8hxd02qw4b91"))))
+ (base32 "1d48ql0010v9ls6mac7fz6j391gm4h74a64hqgw89s0vfqgdyzdl"))))
(build-system python-build-system)
- (home-page "https://bitbucket.org/johanneskoester/snakemake")
+ (arguments
+ ;; TODO: Package missing test dependencies.
+ '(#:tests? #f))
+ (home-page "https://bitbucket.org/snakemake/snakemake/wiki/Home")
(synopsis "Python-based execution environment for make-like workflows")
(description
"Snakemake aims to reduce the complexity of creating workflows by
@@ -5559,6 +5726,8 @@ Python style, together with a fast and comfortable execution environment.")
(sha256
(base32 "0pawrqc3mxpwd5g9pvi9gba02637bh5c8ldpp8izfwpfn52469zs"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; Tests requires a running X11 server.
(propagated-inputs
`(("python-pandas" ,python-pandas)
("python-matplotlib" ,python-matplotlib)
@@ -5580,10 +5749,40 @@ and statistical routines from scipy and statsmodels.")
(propagated-inputs `(("python2-pytz" ,python2-pytz)
,@(package-propagated-inputs base))))))
+(define-public python-mpmath
+ (package
+ (name "python-mpmath")
+ (version "0.19")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://mpmath.org/files/mpmath-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "08ijsr4ifrqv3cjc26mkw0dbvyygsa99in376hr4b96ddm1gdpb8"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (zero?
+ (system* "python" "mpmath/tests/runtests.py" "-local")))))))
+ (home-page "http://mpmath.org")
+ (synopsis "Arbitrary-precision floating-point arithmetic in python")
+ (description
+ "@code{mpmath} can be used as an arbitrary-precision substitute for
+Python's float/complex types and math/cmath modules, but also does much
+more advanced mathematics.")
+ (license license:bsd-3)))
+
+(define-public python2-mpmath
+ (package-with-python2 python-mpmath))
+
(define-public python-sympy
(package
(name "python-sympy")
- (version "0.7.6")
+ (version "1.0")
(source
(origin
(method url-fetch)
@@ -5591,8 +5790,10 @@ and statistical routines from scipy and statsmodels.")
"https://github.com/sympy/sympy/releases/download/sympy-"
version "/sympy-" version ".tar.gz"))
(sha256
- (base32 "19yp0gy4i7p4g6l3b8vaqkj9qj7yqb5kqy0qgbdagpzgkdz958yz"))))
+ (base32 "1bpzjwr9hrr7w88v4vgnj9lr6vxcldc94si13n8xpr1rv08d5b1y"))))
(build-system python-build-system)
+ (propagated-inputs
+ `(("python-mpmath" ,python-mpmath)))
(home-page "http://www.sympy.org/")
(synopsis "Python library for symbolic mathematics")
(description
@@ -5710,6 +5911,17 @@ It is written entirely in Python.")
(sha256
(base32 "1gzgwayl6hmc9jfcl88bni4jcsk2jcca9dn1rvrfsvnijcjx7hn9"))))
(build-system python-build-system)
+ (arguments
+ '(;; FIXME: Two tests error out with:
+ ;; AssertionError: b'Error in atexit._run_exitfuncs:\nFileNotF[44 chars]ry\n' != b''
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; ;; 'setup.py test' hits an AssertionError on BSD-specific
+ ;; ;; "tornado/platform/kqueue.py". This is the supported method:
+ ;; (zero? (system* "python" "-m" "tornado.test")))))
+ #:tests? #f))
(native-inputs
`(("python-certifi" ,python-certifi)))
(propagated-inputs
@@ -5919,7 +6131,10 @@ complexity of Python source code.")
".tar.gz"))
(sha256
(base32
- "12b9bbdbwnspxgak14xg58c130x2n0blxzlms5jn2dszn8qj3d0m"))))))
+ "12b9bbdbwnspxgak14xg58c130x2n0blxzlms5jn2dszn8qj3d0m"))))
+ (arguments
+ ;; XXX Tests not compatible with Python 3.5.
+ '(#:tests? #f))))
(define-public python2-pep8-1.5.7
(package-with-python2 python-pep8-1.5.7))
@@ -5938,7 +6153,10 @@ complexity of Python source code.")
".tar.gz"))
(sha256
(base32
- "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z"))))))
+ "0sbpq6pqm1i9wqi41mlfrsc5rk92jv4mskvlyxmnhlbdnc80ma1z"))))
+ (arguments
+ ;; XXX Tests not compatible with Python 3.5.
+ '(#:tests? #f))))
(define-public python2-pyflakes-0.8.1
(package-with-python2 python-pyflakes-0.8.1))
@@ -6006,7 +6224,10 @@ complexity of Python source code.")
(for-each delete-file-recursively
(find-files "." "__pycache__" #:directories? #t))
(for-each delete-file (find-files "." "\\.pyc$"))
- #t))))))
+ #t))))
+ (arguments
+ ;; XXX Fails with Python 3.5.
+ '(#:tests? #f))))
(define-public python2-flake8-2.2.4
(package-with-python2 python-flake8-2.2.4))
@@ -6295,6 +6516,9 @@ from an XML-based format.")
(base32
"0g6n288l83sfwavxh1aryi0aqvsr3sp7v6f903mckwqa4scpky62"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: Some tests need network access.
+ '(#:tests? #f))
(synopsis "Tool and library for manipulating LilyPond files")
(description "This package provides a Python library to parse, manipulate
or create documents in LilyPond format. A command line program ly is also
@@ -6463,6 +6687,8 @@ and MAC network addresses.")
(base32
"0c7gh3lsdjds262h0v1sqc66l7hqgfwbakn96qrhdbl0i3vm5yz8"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "https://bitbucket.org/micktwomey/pyiso8601")
(synopsis "Module to parse ISO 8601 dates")
(description
@@ -6875,13 +7101,25 @@ message digests and key derivation functions.")
(uri (pypi-uri "pyOpenSSL" version))
(sha256
(base32
- "0vji4yrfshs15xpczbhzhasnjrwcarsqg87n98ixnyafnyxs6ybp"))))
+ "0vji4yrfshs15xpczbhzhasnjrwcarsqg87n98ixnyafnyxs6ybp"))
+ (patches
+ (search-patches "python-pyopenssl-skip-network-test.patch"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (zero? (system* "py.test" "-v")))))))
(propagated-inputs
`(("python-cryptography" ,python-cryptography)
("python-six" ,python-six)))
(inputs
`(("openssl" ,openssl)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "https://github.com/pyca/pyopenssl")
(synopsis "Python wrapper module around the OpenSSL library")
(description
@@ -7196,9 +7434,19 @@ functions to find and load entry points.")
(base32
"0brclbb18l4nmd5qy3dl9wn05rjdh1fz4rmzdlfqacj12rcdvdgp"))))
(build-system python-build-system)
- ;; The "bdist_egg" target is disabled by default, causing the installation
- ;; to fail.
- (arguments `(#:configure-flags (list "bdist_egg")))
+ (arguments
+ `(;; The "bdist_egg" target is disabled by default, causing the installation
+ ;; to fail.
+ #:configure-flags (list "bdist_egg")
+ ;; FIXME: 5 failures, 40 errors.
+ #:tests? #f))
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; (zero? (system* "py.test" "-v")))))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(propagated-inputs
`(("python-bleach" ,python-bleach)
("python-entrypoints" ,python-entrypoints)
@@ -7299,7 +7547,8 @@ interactive computing.")
(propagated-inputs
`(("python-notebook" ,python-notebook)))
(native-inputs
- `(("python-nose" ,python-nose)))
+ `(("python-certifi" ,python-certifi)
+ ("python-nose" ,python-nose)))
(home-page "http://ipython.org")
(synopsis "IPython HTML widgets for Jupyter")
(description "This package provides interactive HTML widgets for Jupyter
@@ -7580,6 +7829,8 @@ forms, HTTP servers, regular expressions, and more.")
(base32
"1r7iqknhh55y45f64mz5hghgvzx34h1i11k350s0avx6q8gznja1"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Tests can't find zope.interface.
(native-inputs
`(("python-six" ,python-six)
;("python-zope-interface" ,python-zope-interface)
@@ -7640,8 +7891,11 @@ internationalized messages within program source text.")
(base32
"1p943jdxb587dh7php4vx04qvn7b2877hr4qs5zyckvp5afhhank"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Tests can't find zope.event.
(propagated-inputs
`(("python-zope-event" ,python-zope-event)
+ ("python-zope-exceptions", python-zope-exceptions)
("python-zope-interface" ,python-zope-interface)))
(native-inputs
`(("python-zope-testing" ,python-zope-testing)
@@ -7669,6 +7923,8 @@ defining data schemas.")
(base32
"1x9dfqypgympnlm25p9m43xh4qv3p7d75vksv9pzqibrb4cggw5n"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Tests can't find zope.interface.
(propagated-inputs
`(("python-zope-i18nmessageid" ,python-zope-i18nmessageid)
("python-zope-schema" ,python-zope-schema)))
@@ -7694,6 +7950,8 @@ Markup Language.")
(base32
"0pqwwmvm1prhwv1ziv9lp8iirz7xkwb6n2kyj36p2h0ppyyhjnm4"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Tests can't find zope.interface.
(propagated-inputs
`(("python-zope-interface" ,python-zope-interface)))
(home-page "http://pypi.python.org/pypi/zope.proxy")
@@ -7721,6 +7979,8 @@ brokering, etc.) for which the proxy is responsible.")
(base32
"1nj9da4ksiyv3h8n2vpzwd0pb03mdsh7zy87hfpx72b6p2zcwg74"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Tests can't find zope.interface.
(propagated-inputs
`(("python-zope-proxy" ,python-zope-proxy)
("python-zope-schema" ,python-zope-schema)))
@@ -7746,12 +8006,15 @@ Zope3, which are are special objects that have a structural location.")
(base32
"14zmf684amc0x32kq05yxnhfqd1cmyhafkw05gn81rn90zjv6ssy"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Tests can't find zope.testrunner.
(propagated-inputs
`(("python-zope-i18nmessageid" ,python-zope-i18nmessageid)
("python-zope-proxy" ,python-zope-proxy)
("python-zope-schema" ,python-zope-schema)))
- (native-inputs
- `(("python-zope-component" ,python-zope-component)
+ (native-inputs
+ `(("python-six" ,python-six)
+ ("python-zope-component" ,python-zope-component)
("python-zope-configuration" ,python-zope-configuration)
("python-zope-location" ,python-zope-location)
("python-zope-testrunner" ,python-zope-testrunner)
@@ -8355,7 +8618,7 @@ processes across test runs.")
"17rcy6rb9kqjf4p707ivmx7phjq7ngcz3bf7zriwxrqgrjagj7ag"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-dateutil-2" ,python-dateutil-2)
+ `(("python-dateutil" ,python-dateutil)
("python-pytz" ,python-pytz)))
(synopsis "Python library for parsing iCalendar files")
(description "The icalendar package is a parser/generator of iCalendar
@@ -8413,6 +8676,14 @@ Blog, News or Announcements section to a Sphinx website.")
(base32
"1an5lkkqk1zha47198p42ji3m94xmzx1a03dn7866m87n4r4q8h5"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (zero? (system* "py.test" "-v")))))))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(propagated-inputs
`(("python-args" ,python-args)))
(home-page "https://github.com/kennethreitz/clint")
@@ -8482,6 +8753,17 @@ with a new public API, and RPython support.")
(base32
"1msqv747iz12r73mz4qvsmlwkddwjvrahlrk7ysrcz07h7dsscxs"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ ;; Tests require write access to HOME.
+ (setenv "HOME" "/tmp")
+ (zero? (system* "nosetests")))))))
+ (native-inputs
+ `(("python-coverage" ,python-coverage)
+ ("python-nose" ,python-nose)))
(propagated-inputs
`(("python-astor" ,python-astor)
("python-clint" ,python-clint)
@@ -8756,6 +9038,8 @@ servers.")
(base32
"0g9xvl69y7nr3w7ag4fsp6sm4fqf6vrqjw7504x2hzrrsh3ampq8"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-nose" ,python-nose)))
(synopsis "JSON Matching Expressions")
(description "JMESPath (pronounced “james path”) is a Python library that
allows one to declaratively specify how to extract elements from a JSON
@@ -8778,8 +9062,11 @@ document.")
(base32
"1zxczlwqy9bl27d9bc5x99mb5mcsxm350240lp5nx7014xb311lj"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: Many tests are failing.
+ '(#:tests? #f))
(propagated-inputs
- `(("python-dateutil" ,python-dateutil-2)
+ `(("python-dateutil" ,python-dateutil)
("python-docutils" ,python-docutils)
("python-jmespath" ,python-jmespath)))
(native-inputs
@@ -8838,7 +9125,7 @@ Amazon Web Services (AWS) API.")
(base32
"0qyqq9akm4vshhn8cngjc1qykcvsn7cz6dlm6njfsgpbraqrmbbw"))))
(build-system python-build-system)
- (propagated-inputs
+ (native-inputs
`(("python-flake8" ,python-flake8)
("python-pytest" ,python-pytest)))
(synopsis "Library for property based testing")
@@ -8855,7 +9142,8 @@ seamlessly into your existing Python unit testing work flow.")
(strip-python2-variant python-hypothesis))))
(package (inherit hypothesis)
(native-inputs
- `(("python2-enum34" ,python2-enum34))))))
+ `(("python2-enum34" ,python2-enum34)
+ ,@(package-native-inputs hypothesis))))))
(define-public python-pytest-subtesthack
(package
@@ -9321,6 +9609,10 @@ RabbitMQ messaging server is the most popular implementation.")
(strip-python2-variant python-kombu))))
(package
(inherit kombu)
+ (arguments `(;; FIXME: 'TestTransport.test_del_sync' fails on python2.
+ ;; It works fine on the python3 variant.
+ #:tests? #f
+ ,@(package-arguments kombu)))
(native-inputs `(("python2-unittest2" ,python2-unittest2)
,@(package-native-inputs kombu))))))
@@ -9544,7 +9836,7 @@ introspection of @code{zope.interface} instances in code.")
'(;; The test suite relies on some non-portable Windows interfaces.
#:tests? #f))
(propagated-inputs
- `(("python-dateutil-2" ,python-dateutil-2)
+ `(("python-dateutil" ,python-dateutil)
("python-pyicu" ,python-pyicu)))
(synopsis "Parse and generate vCard and vCalendar files")
(description "Vobject is intended to be a full featured Python package for
@@ -10230,6 +10522,8 @@ to occurences in strings and comments.")
(base32
"0i283z1pivmir61z8kbiycigc94l61v33ygzkhczf1ifq7cppyds"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; TODO: Requires many libraries not in Guix.
(home-page "https://github.com/ultrabug/py3status")
(synopsis "Extensible i3status wrapper written in Python")
(description "py3status is an i3status wrapper which extends i3status
@@ -10373,6 +10667,72 @@ to provide a high-level synchronous API on top of the libev event loop.")
(define-public python2-gevent
(package-with-python2 python-gevent))
+(define-public python-geventhttpclient
+ (package
+ (name "python-geventhttpclient")
+ (version "1.3.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "geventhttpclient" version))
+ (sha256
+ (base32
+ "07d0q3wzmml75227r6y6mrl5a0zpf4v9gj0ni5rhbyzmaj4az1xx"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete pre-compiled files.
+ (for-each delete-file (find-files "src/geventhttpclient"
+ ".*\\.pyc"))
+ #t))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'delete-network-tests
+ (lambda _
+ (delete-file "src/geventhttpclient/tests/test_client.py")
+ #t))
+ (delete 'check)
+ (add-after 'install 'check
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (add-installed-pythonpath inputs outputs)
+ (zero? (system* "py.test" "src/geventhttpclient/tests" "-v")))))))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (propagated-inputs
+ `(("python-certifi" ,python-certifi)
+ ("python-gevent" ,python-gevent)
+ ("python-six" ,python-six)))
+ (home-page "https://github.com/gwik/geventhttpclient")
+ (synopsis "HTTP client library for gevent")
+ (description "@code{python-geventhttpclient} is a high performance,
+concurrent HTTP client library for python using @code{gevent}.")
+ (license license:expat)))
+
+(define-public python2-geventhttpclient
+ (package-with-python2 python-geventhttpclient))
+
+(define-public python-fastimport
+ (package
+ (name "python-fastimport")
+ (version "0.9.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "fastimport" version))
+ (sha256
+ (base32 "1aqjsin4rmqm7ln4j0p73fzxifws6c6ikgyhav7r137m2ixsxl43"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/jelmer/python-fastimport")
+ (synopsis "VCS fastimport parser and generator in Python")
+ (description "This package provides a parser for and generator of the Git
+@url{https://www.kernel.org/pub/software/scm/git/docs/git-fast-import.html,fastimport}
+format.")
+ (license license:gpl2+)))
+
+(define-public python2-fastimport
+ (package-with-python2 python-fastimport))
+
(define-public python-twisted
(package
(name "python-twisted")
@@ -10384,6 +10744,13 @@ to provide a high-level synchronous API on top of the libev event loop.")
(base32
"0ydxrp9myw1mvsz3qfzx5579y5llmqa82pxvqchgp5syczffi450"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: Some tests are failing.
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; (zero? (system* "./bin/trial" "twisted")))))
(propagated-inputs
`(("python-zope-interface" ,python-zope-interface)))
(home-page "https://twistedmatrix.com/")
@@ -10622,7 +10989,7 @@ objects, patterned after the Mocha library for Ruby.")
("python-chai" ,python-chai)
("python-simplejson" ,python-simplejson)))
(propagated-inputs
- `(("python-dateutil" ,python-dateutil-2)))
+ `(("python-dateutil" ,python-dateutil)))
(home-page "https://github.com/crsmithdev/arrow/")
(synopsis "Dates and times for Python")
(description
@@ -10645,6 +11012,8 @@ datetime type.")
(base32
"1jhnxgnw8y3mbzjssixh6qkc7a3afc4fygajhqrqalnilyvpzshq"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "http://github.com/jpvanhal/inflection")
(synopsis "Python string transformation library")
(description
@@ -10813,13 +11182,19 @@ parsing UK postcodes.")
(base32
"0vs0dkmg0dlaxf8w6q2i3k0i03gmp56ablldv7ci9x3nbadkn71g"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (zero? (system* "python" "-m" "unittest" "-v" "faker.tests")))))))
(native-inputs
`(;; For testing
("python-email-validator" ,python-email-validator)
("python-mock" ,python-mock)
("python-ukpostcodeparser" ,python-ukpostcodeparser)))
(propagated-inputs
- `(("python-dateutil" ,python-dateutil-2)
+ `(("python-dateutil" ,python-dateutil)
("python-six" ,python-six)))
(home-page "https://github.com/joke2k/faker")
(synopsis "Python package that generates fake data")
@@ -10849,6 +11224,8 @@ addresses, and phone numbers.")
(base32
"1f5m28vkh4ksq3d80d8mmd2z8wxvc3mgy2pmrv2751dm2xgznm4w"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-unidecode" ,python-unidecode)))
(propagated-inputs
`(("python-pyyaml" ,python-pyyaml)))
(home-page "https://github.com/mk-fg/pretty-yaml")
@@ -10963,6 +11340,11 @@ characters, mouse support, and auto suggestions.")
(base32
"0c8x962ynpx001fdvp07m2q5jk4igkxbj3rmnydavphvlgxijk1v"))))
(build-system python-build-system)
+ (arguments
+ ;; FIXME: One test fails (use "py.test" instead of 'setup.py test').
+ '(#:tests? #f))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
(home-page "https://github.com/davidhalter/jedi")
(synopsis
"Autocompletion for Python that can be used for text editors")
@@ -10984,6 +11366,8 @@ characters, mouse support, and auto suggestions.")
(base32
"1mmbiyzf0n8hm7z2a562x7w5cbl6jc0zsk6vp40q1z4cyblv1k13"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: No tests in pypi tarball.
(propagated-inputs
`(("python-docopt" ,python-docopt)
("python-jedi" ,python-jedi)
@@ -11089,6 +11473,13 @@ relays publish about themselves.")
(base32
"0k1nfdrxxkdlv4zgaqsdv8li0pj3gbh2pyxw8q2bsg6f9490amyn"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: 3/49 tests are failing.
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; (zero? (system* "python" "test/run_all_tests.py" "loop://")))))))
(home-page
"https://github.com/pyserial/pyserial")
(synopsis "Python Serial Port Bindings")
@@ -11408,7 +11799,7 @@ List. Forked from and using the same API as the publicsuffix package.")
("python-coverage" ,python-coverage)))
(propagated-inputs
`(("python-six" ,python-six)
- ("python-dateutil-2" ,python-dateutil-2)))
+ ("python-dateutil" ,python-dateutil)))
(arguments
`(#:phases (modify-phases %standard-phases
;; The tests are normally executed via `make test`, but the PyPi
@@ -12059,7 +12450,7 @@ useful as a validator for JSON data.")
"1k5mjg9iqbjfslb5prrsfz7dhlvi6s35p1jxq8dm87w1b7dn5i2g"))))
(build-system python-build-system)
(propagated-inputs
- `(("python-dateutil-2" ,python-dateutil-2)))
+ `(("python-dateutil" ,python-dateutil)))
(home-page
"https://bitbucket.org/nielsenb/aniso8601")
(synopsis
@@ -12256,10 +12647,7 @@ python-axolotl.")
(lambda _
(for-each delete-file-recursively
'("axolotl/tests" "build/lib/axolotl/tests"))
- #t)))
- ;; Prevent creation of the egg. This works around
- ;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=20765
- #:configure-flags '("--root=/")))
+ #t)))))
(propagated-inputs
`(("python-axolotl-curve25519" ,python-axolotl-curve25519)
("python-dateutil" ,python-dateutil)
@@ -12287,6 +12675,12 @@ asynchronous messaging environments.")
(base32
"17wzkkcqy5zc0g68xlad3kcv66iw14d2pwqc0h9420gak0vbhx7g"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (zero? (system* "python" "test3.py")))))))
(home-page "http://github.com/gfxmonk/termstyle")
(synopsis "Console text coloring for Python")
(description "This package provides console text coloring for Python.")
@@ -12337,6 +12731,13 @@ asynchronous messaging environments.")
(base32
"11his6ii5brpkhld0d5bwzjjw4q3vmplpd6fmgzjrvvklsbk0cf4"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; FIXME: 35/882 tests failing.
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; (zero? (system* "nosetests")))))))
(propagated-inputs
`(("python-aniso8601" ,python-aniso8601)
("python-flask" ,python-flask)
@@ -12417,6 +12818,9 @@ specs from your Flask-Restful projects.")
(base32
"11bwiw6j0nilgz81xnw6f1npyga3prp8asjqrm87cdr3ria5l03x"))))
(build-system python-build-system)
+ (native-inputs
+ `(("python-pexpect" ,python-pexpect)
+ ("tcsh" ,tcsh)))
(home-page "https://github.com/kislyuk/argcomplete")
(synopsis "Shell tab completion for Python argparse")
(description "argcomplete provides extensible command line tab completion
@@ -12498,6 +12902,52 @@ Features:
@end enumerate")
(license (license:x11-style "file://LICENSE"))))
+(define-public python-dulwich
+ (package
+ (name "python-dulwich")
+ (version "0.16.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (list (string-append "https://www.dulwich.io/releases/"
+ "dulwich-" version ".tar.gz")
+ (pypi-uri "dulwich" version)))
+ (sha256
+ (base32 "0fl47vzfgc3w3rmhn8naii905cjqcp0vc68iyvymxp7567hh6als"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'fix-tests
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; The tests use Popen with a custom environment which doesn't
+ ;; include PATH.
+ (substitute* "dulwich/tests/compat/utils.py"
+ (("'git'") (string-append "'"
+ (which "git")
+ "'")))
+ (substitute* '("dulwich/tests/test_repository.py"
+ "dulwich/tests/test_hooks.py")
+ (("#!/bin/sh") (string-append "#!" (which "sh"))))
+ (setenv "TEST_RUNNER" "unittest")
+ (setenv "PYTHONHASHSEED" "random")
+ #t)))))
+ (propagated-inputs
+ `(("python-fastimport" ,python-fastimport)))
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-geventhttpclient" ,python-geventhttpclient)
+ ("git" ,git)))
+ (home-page "https://www.dulwich.io/")
+ (synopsis "Git implementation in Python")
+ (description "Dulwich is an implementation of the Git file formats and
+protocols written in pure Python.")
+ ;; Can be used with either license.
+ (license (list license:asl2.0 license:gpl2+))))
+
+(define-public python2-dulwich
+ (package-with-python2 python-dulwich))
+
(define-public python-pbkdf2
(package
(name "python-pbkdf2")
diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm
index 1dd23c28e3..97e6b881cc 100644
--- a/gnu/packages/rdf.scm
+++ b/gnu/packages/rdf.scm
@@ -315,6 +315,18 @@ ideal (e.g. in LV2 implementations or embedded applications).")
(base32
"0kvaf332cqbi47rqzlpdx4mbkvw12mkrzkj8n9l19wk713d4py9w"))))
(build-system python-build-system)
+ (arguments
+ '(;; FIXME: Three test failures. Try uncommenting the below next update.
+ #:tests? #f))
+ ;; #:phases
+ ;; (modify-phases %standard-phases
+ ;; (replace 'check
+ ;; (lambda _
+ ;; ;; Run tests from the build directory so python3 only
+ ;; ;; sees the installed 2to3 version.
+ ;; (zero? (system* "nosetests" "--where=./build/src")))))
+ (native-inputs
+ `(("python-nose" ,python-nose)))
(propagated-inputs
`(("python-html5lib" ,python-html5lib)
("python-isodate" ,python-isodate)
@@ -329,12 +341,4 @@ powerful language for representing information.")
"See LICENSE in the distribution."))))
(define-public python2-rdflib
- (let ((base (package-with-python2 python-rdflib)))
- (package
- (inherit base)
- (inputs
- (append (package-inputs base)
- `(("python2-nose" ,python2-nose))))
- (arguments
- `(#:python ,python-2
- #:tests? #f))))) ; 3 tests fail, also outside Guix
+ (package-with-python2 python-rdflib))
diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm
index e90ee6847f..d0d99932c4 100644
--- a/gnu/packages/terminals.scm
+++ b/gnu/packages/terminals.scm
@@ -166,6 +166,9 @@ insert mode and command mode where keybindings have different functions.")
(string-append "'" ncurses "/bin/tput'"))))
#t)))))
(inputs `(("ncurses" ,ncurses)))
+ (native-inputs
+ ;; For tests.
+ `(("python-requests" ,python-requests)))
(home-page "https://asciinema.org")
(synopsis "Terminal session recorder")
(description
diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm
index 5c371b0ba0..e49d6137b5 100644
--- a/gnu/packages/version-control.scm
+++ b/gnu/packages/version-control.scm
@@ -1210,7 +1210,7 @@ Mercurial, Bazaar, Darcs, CVS, Fossil, and Veracity.")
`(;; for the tests
("python2-six" ,python2-six)))
(propagated-inputs
- `(("python2-dateutil" ,python2-dateutil-2)
+ `(("python2-dateutil" ,python2-dateutil)
("python2-futures" ,python2-futures)
("python2-rauth" ,python2-rauth)
("python2-swiftclient" ,python2-swiftclient)))
diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm
index 8c7f07a263..efb46f73d4 100644
--- a/gnu/packages/vpn.scm
+++ b/gnu/packages/vpn.scm
@@ -248,6 +248,14 @@ DNS domain name queries.")
(base32
"0a92lk8790dpp9j64vb6p4sazax0x3nby01lnfll7mxs1hx6n27q"))))
(build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-paths
+ (lambda _
+ (substitute* "sshoot/tests/test_manager.py"
+ (("/bin/sh") (which "sh")))
+ #t)))))
(inputs
`(("python-argcomplete" ,python-argcomplete)
("python-prettytable" ,python-prettytable)
diff --git a/guix/build/python-build-system.scm b/guix/build/python-build-system.scm
index 3f280b0ac0..dd07986b94 100644
--- a/guix/build/python-build-system.scm
+++ b/guix/build/python-build-system.scm
@@ -137,11 +137,15 @@
;; (given with `package_dir`). This will by copied to the output, too,
;; so we need to remove.
(let ((before (find-files "build" "\\.egg-info$" #:directories? #t)))
- (call-setuppy test-target '() use-setuptools?)
- (let* ((after (find-files "build" "\\.egg-info$" #:directories? #t))
- (inter (lset-difference eqv? after before)))
- (for-each delete-file-recursively inter)))
- #t))
+ (if (call-setuppy test-target '() use-setuptools?)
+ (let* ((after (find-files "build" "\\.egg-info$" #:directories? #t))
+ (inter (lset-difference eqv? after before)))
+ (for-each delete-file-recursively inter)
+ #t)
+ #f))
+ (begin
+ (format #t "test suite not run~%")
+ #t)))
(define (get-python-version python)
(let* ((version (last (string-split python #\-)))
generated by cgit v1.2.3 (git 2.25.4) at 2024-07-10 08:53:37 +0000