From e46a043ecd9f9ef46d1d44393362bb7016454544 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 12 Dec 2016 00:25:27 +0100 Subject: [PATCH 001/150] build-system/python: Make sure 'check' returns failures. * guix/build/python-build-system.scm (check): Wrap 'call-setuppy' in 'if' so that it actually fails when the tests fail. Print informational message when skipped. --- guix/build/python-build-system.scm | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) 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 #\-))) From dcb0da7bff9dd35a65769e8f6a3b542306a115ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 01:19:07 +0100 Subject: [PATCH 002/150] gnu: python-py: Disable tests. * gnu/packages/python.scm (python-py, python2-py)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6d6d880bb8..fe96f0f392 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1625,6 +1625,12 @@ 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 From 4fd129ee86b7f2f76fa705327925b7b6c54bb069 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 05:34:25 +0100 Subject: [PATCH 003/150] gnu: python-six: Fix test dependencies. * gnu/packages/python.scm (python-six, python2-six)[native-inputs]: Add python-py and python-pytest. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fe96f0f392..3f816bc1f0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -946,6 +946,9 @@ 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 From bd10e677d1ff5650ea5a13c604a083824f12b238 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 09:50:08 +0100 Subject: [PATCH 004/150] gnu: python-coverage: Disable tests. * gnu/packages/python.scm (python-coverage, python2-coverage)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 3f816bc1f0..bc0a82b3a3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2123,6 +2123,9 @@ 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 From 995cb99e4b9852c497d73a130430e5c96bb74ef7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 10:47:59 +0100 Subject: [PATCH 005/150] gnu: python-pygments: Disable tests. * gnu/packages/python.scm (python-pygments, python2-pygments)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index bc0a82b3a3..65a8076363 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2782,6 +2782,9 @@ reStructuredText.") (base32 "0lagrwifsgn0s8bzqahpr87p7gd38xja8f06akscinp6hj89283k")))) (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 From 03cb5f9edbe67c93d235060c877f6a135a418c9f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 12:01:52 +0100 Subject: [PATCH 006/150] gnu: python-sphinx: Disable tests. * gnu/packages/python.scm (python-sphinx, python2-sphinx)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 65a8076363..e9ec52271e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2808,6 +2808,9 @@ reStructuredText.") (base32 "011xizm3jnmf4cvs5i6kgf6c5nn046h79i8j0vd0f27yw9j3p4wl")))) (build-system python-build-system) + (arguments + ;; FIXME: Missing dependencies. + '(#:tests? #f)) (propagated-inputs `(("python-jinja2" ,python-jinja2) ("python-docutils" ,python-docutils) From 3fe2c209e0e69660164b5484a2d9f9d946006e36 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 12:48:04 +0100 Subject: [PATCH 007/150] gnu: python-tornado: Disable tests. * gnu/packages/python.scm (python-tornado, python2-tornado)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e9ec52271e..28ead167d8 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5458,6 +5458,17 @@ 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 From 97be1bc23128cf42c49867d984c43f6fea3820d6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 18:51:01 +0100 Subject: [PATCH 008/150] gnu: python-click: Fix tests. * gnu/packages/python.scm (python-click, python2-click)[arguments]: Replace 'check' with custom phase. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 28ead167d8..1a8a9a407c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2301,7 +2301,12 @@ 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 From cff0ccf9dce5bb0c6c504909be7dfc581f3068a9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:07:30 +0100 Subject: [PATCH 009/150] gnu: python-requests: Disable tests. * gnu/packages/python.scm (python-requests, python2-requests, python-requests-2.7)[native-inputs]: Remove field. [arguments]: New field. Set #:tests? #f. --- gnu/packages/python.scm | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1a8a9a407c..200ba30498 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2365,12 +2365,11 @@ installed with a newer @code{pip} or with wheel's own command line utility.") (sha256 (base32 "0zsqrzlybf25xscgi7ja4s48y2abf9wvjkn47wh984qgs1fq2xy5")))) + ;; 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 From c8cd850c87f50b476dc87166e09207426efd8409 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:15:21 +0100 Subject: [PATCH 010/150] gnu: python-xcffib: Use 'modify-phases' syntax. * gnu/packages/python.scm (python-xcffib)[arguments]: Use 'modify-phases'. --- gnu/packages/python.scm | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 200ba30498..6aee72cf70 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4230,15 +4230,15 @@ a front-end for C compilers or analysis tools.") ("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))) + (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 From e2816ac72d6225ecb5ab740b7313bfc28c9d7764 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:25:49 +0100 Subject: [PATCH 011/150] gnu: python-xcffib: Disable tests. * gnu/packages/python.scm (python-xcffib, python2-xcffib)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6aee72cf70..bed8124b55 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4229,7 +4229,9 @@ a front-end for C compilers or analysis tools.") `(("python-cffi" ,python-cffi) ; used at run time ("python-six" ,python-six))) (arguments - `(#: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) From 6734c7bae34888756eb40ed13a8c16f3e35cc53d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:28:27 +0100 Subject: [PATCH 012/150] gnu: python-cairocffi: Use 'modify-phases' syntax. * gnu/packages/python.scm (python-cairocffi)[arguments]: Use 'modify-phases'. --- gnu/packages/python.scm | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index bed8124b55..37a595f7cb 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4278,24 +4278,24 @@ support for Python 3 and PyPy. It is based on cffi.") `(("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))) + (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 From a792e1aa8dd6818f6fce942aa0efa9dc1076a99c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 13 Dec 2016 19:30:21 +0100 Subject: [PATCH 013/150] gnu: python-cairocffi: Disable tests. * gnu/packages/python.scm (python-cairocffi, python2-cairocffi)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 37a595f7cb..31f0651d72 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4277,7 +4277,9 @@ support for Python 3 and PyPy. It is based on cffi.") (propagated-inputs `(("python-xcffib" ,python-xcffib))) ; used at run time (arguments - `(#: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) From 2b9e4bead983167aeca375a26d5ddf6a6a5877eb Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 13 Dec 2016 20:45:50 -0500 Subject: [PATCH 014/150] gnu: python-zope-schema: Build with python-zope-exceptions. * gnu/packages/python.scm (python-zope-schema, python2-zope-schema)[propagated-inputs]: Add python-zope-schema. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 31f0651d72..2f3d2b36ac 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7330,6 +7330,7 @@ internationalized messages within program source text.") (build-system python-build-system) (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) From 9d3a15b4962612b8975e68a28f3b13d66b71c18d Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 13 Dec 2016 20:51:26 -0500 Subject: [PATCH 015/150] gnu: python-sphinx-rtd-theme: Build with python-sphinx. * gnu/packages/python.scm (python-sphinx-rtd-theme, python2-sphinx-rtd-theme)[propagated-inputs]: Add python-sphinx. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 2f3d2b36ac..700e792143 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2843,6 +2843,8 @@ 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.") From fb08c4fedc33bb8b7d8c89314b8e4da870d85438 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 10:18:33 +0100 Subject: [PATCH 016/150] gnu: python-psutil: Disable tests. * gnu/packages/python.scm (python-psutil, python2-psutil): Disable tests. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 700e792143..080d3fccc9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -437,6 +437,9 @@ 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 From f6c1ef180459a525c1b38a5a7c37fec3cfb45ab9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 10:38:26 +0100 Subject: [PATCH 017/150] gnu: python-fixtures: Fix test suite. * gnu/packages/python.scm (python-fixtures, python2-fixtures): Replace 'check' with custom phase. [native-inputs]: Add python-mock. --- gnu/packages/python.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 080d3fccc9..ceb4896d34 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2068,10 +2068,18 @@ 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") From 90110ef95616f2fe71e2247aec636824676f0b54 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 10:46:47 +0100 Subject: [PATCH 018/150] gnu: python-testrepository: Disable tests. * gnu/packages/python.scm (python-testrepository, python2-testrepository): Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ceb4896d34..cea60b27e6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2105,6 +2105,9 @@ 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) From 0d84e1ef22f46f27948887fcac56742dcde5fd23 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 11:19:11 +0100 Subject: [PATCH 019/150] gnu: python-pyflakes-0.8.1: Disable tests. * gnu/packages/python.scm (python-pyflakes-0.8.1, python2-pyflakes-0.8.1)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index cea60b27e6..a971e8bc3b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5721,7 +5721,10 @@ 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)) From 73e3060d576effa1064bd89f23010ded6188ffd4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 11:21:50 +0100 Subject: [PATCH 020/150] gnu: python-pep8-1.5.7: Disable tests. * gnu/packages/python.scm (python-pep8-1.5.7, python2-pep8-1.5.7)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a971e8bc3b..ee5cbc5e77 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5702,7 +5702,10 @@ 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)) From a717e8a698319424dfce58ce496d5bfb055753d8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 11:25:02 +0100 Subject: [PATCH 021/150] gnu: python-flake8-2.2.4: Disable tests. * gnu/packages/python.scm (python-flake8-2.2.4, python2-flake8-2.2.4)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ee5cbc5e77..6c58403dd6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5795,7 +5795,10 @@ 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)) From 2ff4559b49b325252ef921be254f2ee800d212ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 11:27:11 +0100 Subject: [PATCH 022/150] gnu: python-hacking: Disable tests. * gnu/packages/openstack.scm (python-hacking, python2-hacking)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index e2672668d8..e4610c150b 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -113,6 +113,9 @@ 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) From ea8907c5d5df89b26d67a7b067cb8c341714ed9b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:02:45 +0100 Subject: [PATCH 023/150] gnu: python-mox3: Disable tests. * gnu/packages/openstack.scm (python-mox3, python2-mox3)[arguments]: Disable tests. [native-inputs]: Add python-oslosphinx and python-sphinx. --- gnu/packages/openstack.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index e4610c150b..a91759faa0 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -149,9 +149,14 @@ guidelines}.") (base32 "0njmh40i1lg5mzn9hc2ax83adj6dli455j6xifilrw27c4wlkjzx")))) (build-system python-build-system) + (arguments + ;; TODO: Requires newer version of testtools (>=1.4.0). + '(#:tests? #f)) (native-inputs `(("python-fixtures" ,python-fixtures) + ("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") From 281cc11c8e33c1e1a558cc2bf4af924881f55c40 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:40:13 +0100 Subject: [PATCH 024/150] gnu: python-django-simple-math-captcha: Disable tests. * gnu/packages/django.scm (python-django-simple-math-captcha, python2-django-simple-math-captcha)[arguments]: Set #:tests? #f. --- gnu/packages/django.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index bbb2d71db1..93fc42f96f 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") From 55ab64516bf8bcb27833479fb3c0df2a7ed06d6b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:43:36 +0100 Subject: [PATCH 025/150] gnu: python-django-filter: Fix test suite. * gnu/packages/django.scm (python-django-filter, python2-django-filter)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/django.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 93fc42f96f..415ee60a20 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -167,6 +167,12 @@ 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))) From 63b02364aa259e58169b0c4af7e860f7b1ceebd2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:47:22 +0100 Subject: [PATCH 026/150] gnu: python-iso8601: Fix test dependencies. * gnu/packages/python.scm (python-iso8601, python2-iso8601)[native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6c58403dd6..9b7d5d99a0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6155,6 +6155,8 @@ 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 From 497355dc09449426ef4fda521433002ec93c4796 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 12:59:40 +0100 Subject: [PATCH 027/150] gnu: python-nbconvert: Disable tests. * gnu/packages/python.scm (python-nbconvert, python2-nbconvert)[arguments]: Set #:tests? #f. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9b7d5d99a0..540a988234 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6911,9 +6911,19 @@ 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) From bd100c7112b1717881ff6efcaa514be5cfeb5349 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 17:35:28 +0100 Subject: [PATCH 028/150] gnu: python-hypothesis: Don't propagate test inputs. * gnu/packages/python.scm (python-hypothesis, python2-hypothesis)[propagated-inputs]: Move everything from here ... [native-inputs]: ... to here. (python2-hypothesis)[native-inputs]: Append inherited native-inputs. --- gnu/packages/python.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 540a988234..cd6ed1c240 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8544,7 +8544,7 @@ 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") @@ -8561,7 +8561,8 @@ 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 From 30e0229a1713e77dc0397dfb4ee6af4ac6a00443 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 18:34:48 +0100 Subject: [PATCH 029/150] gnu: python-pyopenssl: Disable tests. * gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl)[arguments]: Set #:tests? #f. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index cd6ed1c240..ebe0194aa4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6585,11 +6585,16 @@ message digests and key derivation functions.") (base32 "0vji4yrfshs15xpczbhzhasnjrwcarsqg87n98ixnyafnyxs6ybp")))) (build-system python-build-system) + (arguments + ;; FIXME: Some tests fail with "NameError: name 'long' is not defined". + '(#:tests? #f)) (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 From da5ebd1007488209ba82ef02f0cb7f097f2b9106 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:18:26 +0100 Subject: [PATCH 030/150] gnu: python-biom-format: Fix tests. * gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3d84a44e4c..5f56551526 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -562,6 +562,8 @@ 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 From 1b6d7c3f3f9a19cb899058a586afc0f16afc5e5a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:38:50 +0100 Subject: [PATCH 031/150] gnu: python2-fastlmm: Fix test requirements. * gnu/packages/python.scm (python2-fastlmm)[native-inputs]: Add python2-nose. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index ebe0194aa4..77240ff36d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3290,7 +3290,8 @@ capabilities.") (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 From 52a75a83f970b62eb285067b454a1c25a8669491 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:45:46 +0100 Subject: [PATCH 032/150] gnu: python-jmespath: Fix tests. * gnu/packages/python.scm (python-jmespath, python2-jmespath)[native-inputs]: Add python-nose. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 77240ff36d..1bf3af100a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8468,6 +8468,8 @@ 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 From 877fdac9e3afba664b5c6f66858c98750aa98694 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:49:35 +0100 Subject: [PATCH 033/150] gnu: python-botocore: Disable tests. * gnu/packages/python.scm (python-botocore, python2-botocore): Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1bf3af100a..8e94b52429 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8492,6 +8492,9 @@ document.") (base32 "1zxczlwqy9bl27d9bc5x99mb5mcsxm350240lp5nx7014xb311lj")))) (build-system python-build-system) + (arguments + ;; FIXME: Many tests are failing. + '(#:tests? #f)) (propagated-inputs `(("python-dateutil" ,python-dateutil-2) ("python-docutils" ,python-docutils) From e91275256717a5325020a9a36749adbe759371d3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:50:44 +0100 Subject: [PATCH 034/150] gnu: python-inflection: Fix test requirements. * gnu/packages/python.scm (python-inflection, python2-inflection)[native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8e94b52429..0ee533d007 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10314,6 +10314,8 @@ 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 From f620311a39a9a7dd8bd2637251e448824423a17f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 19:53:21 +0100 Subject: [PATCH 035/150] gnu: python-pyaml: Fix tests. * gnu/packages/python.scm (python-pyaml, python2-pyaml)[native-inputs]: Add python-unidecode. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0ee533d007..de11cd558d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10520,6 +10520,8 @@ 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") From b7f3ea9532c0bf764228b3b7ecbd66d579a2517f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 22:01:36 +0100 Subject: [PATCH 036/150] gnu: python-fake-factory: Fix tests. * gnu/packages/python.scm (python-fake-factory, python2-fake-factory)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index de11cd558d..d6ea07de34 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10484,6 +10484,12 @@ 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) From 6145b604629c071fba8b55b7e0e3a45ed68fa3cc Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 22:07:38 +0100 Subject: [PATCH 037/150] gnu: python-clint: Fix tests. * gnu/packages/python.scm (python-clint, python2-clint)[native-inputs]: Add python-pytest. [arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d6ea07de34..17469036a3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8125,6 +8125,14 @@ 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") From ee4722411fb71f90deb63e7976207f84ecae7360 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 22:24:50 +0100 Subject: [PATCH 038/150] gnu: python-rdflib: Disable tests. * gnu/packages/rdf.scm (python-rdflib)[arguments]: Set #:tests? #f. [native-inputs]: Add python-nose. (python2-rdflib)[inputs]: Remove field. Use 'package-with-python2'. --- gnu/packages/rdf.scm | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) 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)) From bfce8a344d446d7601c1a60adc7b13b66bc75030 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 22:59:56 +0100 Subject: [PATCH 039/150] gnu: python-jedi: Disable tests. * gnu/packages/python.scm (python-jedi, python2-jedi)[arguments]: Disable tests. [native-inputs]: Add python-pytest. --- gnu/packages/python.scm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 17469036a3..90b0b575cc 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10650,6 +10650,11 @@ 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") From 9026e6890a829fa2713cd1dcca407f19adf82802 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 14 Dec 2016 23:01:40 +0100 Subject: [PATCH 040/150] gnu: python-scikit-image: Disable tests. * gnu/packages/python.scm (python-scikit-image, python2-scikit-image)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 90b0b575cc..9bcdb30820 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3060,6 +3060,9 @@ 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) From 972cf9be524535fee3999021a68537039e204ee6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 10:02:11 +0100 Subject: [PATCH 041/150] gnu: python-ly: Disable tests. * gnu/packages/python.scm (python-ly): Set #:tests? #f. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9bcdb30820..04ee836c6c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5991,6 +5991,9 @@ 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 From 7b93d866708d1fae54aee86473ffde5bd64be055 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 10:12:38 +0100 Subject: [PATCH 042/150] gnu: snakemake: Update to 3.9.0. * gnu/packages/python.scm (snakemake): Update to 3.9.0. [source]: Use 'pypi-uri'. [arguments]: Disable tests. [home-page]: Update. --- gnu/packages/python.scm | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 04ee836c6c..cbe770db39 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5306,17 +5306,18 @@ 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 From 385871e5f7a69ed1c473501be22d0338984a932c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:12:13 +0100 Subject: [PATCH 043/150] gnu: python-zope-testrunner: Disable tests. * gnu/packages/python.scm (python-zope-testrunner, python2-zope-testrunner)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index cbe770db39..0646e9739b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7318,6 +7318,8 @@ 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) From 22dba2eff978999a907dfa8b4e2da5cdbb357de4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:35:26 +0100 Subject: [PATCH 044/150] gnu: python-zope-interface: Disable tests. * gnu/packages/python.scm (python-zope-schema, python2-zope-schema)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0646e9739b..9e47d7cf1c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7380,6 +7380,8 @@ 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) From 7e8b1bfa4b6e1003f2b80c049d89c70cc9e28d84 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:38:04 +0100 Subject: [PATCH 045/150] gnu: python-zope-configuration: Disable tests. * gnu/packages/python.scm (python-zope-configuration, python2-zope-configuration)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9e47d7cf1c..9afb37cdd1 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7412,6 +7412,8 @@ 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))) From 66b3aadb73af76c366803e1cd619a9d5d20571c1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:40:10 +0100 Subject: [PATCH 046/150] gnu: python-zope-proxy: Disable tests. * gnu/packages/python.scm (python-zope-proxy, python2-zope-proxy)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9afb37cdd1..47729db02b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7439,6 +7439,8 @@ 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") From 40bb8e07aedb011de863657f6cec29d86d525375 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:42:39 +0100 Subject: [PATCH 047/150] gnu: python-zope-location: Disable tests. * gnu/packages/python.scm (python-zope-location, python2-zope-location)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 47729db02b..7109860f5b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7468,6 +7468,8 @@ 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))) From a74f9b12ae3937cd75c4dba4715cf55387c507c8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 12:45:26 +0100 Subject: [PATCH 048/150] gnu: python-zope-security: Disable tests. * gnu/packages/python.scm (python-zope-security, python2-zope-security)[arguments]: Set #:tests? #f. [native-inputs]: Add python-six. --- gnu/packages/python.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7109860f5b..aca2f3c92d 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7495,12 +7495,15 @@ 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) From a960e73fadda9e3d594775197a20f52177c96b43 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:11:53 +0100 Subject: [PATCH 049/150] gnu: python-twisted: Disable tests. * gnu/packages/python.scm (python-twisted, python2-twisted)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index aca2f3c92d..e640a777c4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10078,6 +10078,13 @@ 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/") From 7917a1355456a924ca85992b4216cf6dc437873a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:17:29 +0100 Subject: [PATCH 050/150] gnu: python-termstyle: Fix tests. * gnu/packages/python.scm (python-termstyle)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e640a777c4..47d7c6a7d9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11940,6 +11940,12 @@ 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.") From 767c7e0ed1d9f8bec64fa5254570a1f2d75ce847 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:23:56 +0100 Subject: [PATCH 051/150] gnu: python-debtcollector: Disable tests. * gnu/packages/openstack.scm (python-debtcollector, python2-debtcollector)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index a91759faa0..7ffd9a2325 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -81,6 +81,8 @@ 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))) From f30e53369bd64b572c1195a53a28d294da160336 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:31:31 +0100 Subject: [PATCH 052/150] gnu: python-oslo.context: Disable tests. * gnu/packages/openstack.scm (python-oslo.context, python2-oslo.context)[arguments]: Set #:tests? #f. [native-inputs]: Add python-coverage, python-hacking, python-mock, python-os-client-config, python-oslosphinx and python-sphinx. --- gnu/packages/openstack.scm | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 7ffd9a2325..ad0c028af8 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -405,11 +405,19 @@ 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 From bb56d9a18ce0f91131b202351a0496ad39103483 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:35:57 +0100 Subject: [PATCH 053/150] gnu: python-oslo.i18n: Disable tests. * gnu/packages/openstack.scm (python-oslo.i18n, python2-oslo.i18n)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index ad0c028af8..4bd44d005a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -441,6 +441,8 @@ 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))) From 130f68ec3bc2efb6895986435c2ff8043bbaa417 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:45:07 +0100 Subject: [PATCH 054/150] gnu: python-stevedore: Fix tests. * gnu/packages/openstack.scm (python-stevedore, python2-stevedore)[native-inputs]: Add python-discover, python-oslosphinx, python-sphinx and python-testrepository. --- gnu/packages/openstack.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 4bd44d005a..9c43ea9c6a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -292,10 +292,13 @@ 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 From d9184f4f76443011130944f7a2ca7fa75bad7aea Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:49:08 +0100 Subject: [PATCH 055/150] gnu: python-oslo.config: Disable tests. * gnu/packages/openstack.scm (python-oslo.config, python2-oslo.config)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 9c43ea9c6a..2a1313c4bd 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -375,6 +375,8 @@ 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) From ad59ebda5350b94885475980dfdb1a6be8eda2d5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:50:55 +0100 Subject: [PATCH 056/150] gnu: python-oslo.utils: Disable tests. * gnu/packages/openstack.scm (python-oslo.utils, python2-oslo.utils)[arguments]: Set #:tests? #f. [native-inputs]: Add python-bandit and python-oslo.config. --- gnu/packages/openstack.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 2a1313c4bd..d05d9caf48 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -628,6 +628,8 @@ 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) @@ -641,6 +643,8 @@ 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) From 5ae31b547cda78025a5a9f4d29b0cda511ec66d6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 13:55:54 +0100 Subject: [PATCH 057/150] gnu: python-oslo.serialization: Disable tests. * gnu/packages/openstack.scm (python-oslo.serialization, python2-oslo.serialization)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index d05d9caf48..97fdabffa7 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -521,6 +521,8 @@ 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) From 49910e6a7c14702502124efd70cc40227dc9df46 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 14:01:27 +0100 Subject: [PATCH 058/150] gnu: python-paramiko: Disable tests. * gnu/packages/python.scm (python-paramiko, python2-paramiko)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 47d7c6a7d9..4472e7832f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -540,6 +540,14 @@ 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))) From 73b494a11de3eb59fdbcd73f2c90e74c4fc08924 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 15:22:16 +0100 Subject: [PATCH 059/150] gnu: python-oslo.log: Disable tests. * gnu/packages/openstack.scm (python-oslo.log, python2-oslo.log)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 97fdabffa7..080f283b2a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -484,6 +484,8 @@ 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) From f959495ba06d77194d843ea729c39aaa8a168051 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 15:23:39 +0100 Subject: [PATCH 060/150] gnu: python-tempest-lib: Disable tests. * gnu/packages/openstack.scm (python-tempest-lib, python2-tempest-lib)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 080f283b2a..33a54e3ab9 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -328,7 +328,8 @@ 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 From c616b5d3b5aefc00485f03f756871a2d87714268 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 16:49:14 +0100 Subject: [PATCH 061/150] gnu: python-oauthlib: Fix tests. * gnu/packages/python.scm (python-oauthlib)[native-inputs]: Add python-mock. (python2-oauthlib)[native-inputs]: Inherit python-mock. --- gnu/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 4472e7832f..55274783ff 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2536,6 +2536,7 @@ 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))) @@ -2552,7 +2553,6 @@ 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 From bfba083684e80d2bc23e3c07205e3d63910e978f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 16:53:55 +0100 Subject: [PATCH 062/150] gnu: python-keystoneclient: Disable tests. * gnu/packages/openstack.scm (python-keystoneclient, python2-keystoneclient)[arguments]: Set #:tests? #f. --- gnu/packages/openstack.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 33a54e3ab9..b3e3f08c23 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -677,6 +677,8 @@ 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 From 35d56b7b607f6de615d5e13eb05273c649ee4543 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 17:26:42 +0100 Subject: [PATCH 063/150] gnu: python-sqlalchemy-utils: Disable tests. * gnu/packages/python.scm (python-sqlalchemy-utils, python2-sqlalchemy-utils)[arguments]: Set #:tests? #f. [native-inputs]: Add python-dateutil-2, python-flexmock, python-pcycopg2 and python-pytz. --- gnu/packages/python.scm | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 55274783ff..011483d897 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3988,11 +3988,22 @@ 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-2) + ("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 From 6f976df6771a3eb90c3b16de45a861856bcde52e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 17:31:29 +0100 Subject: [PATCH 064/150] gnu: python-seaborn: Disable tests. * gnu/packages/python.scm (python-seaborn, python2-seaborn)[arguments]: Disable tests. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 011483d897..610785bc59 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5355,6 +5355,8 @@ Python style, together with a fast and comfortable execution environment.") (sha256 (base32 "0ibi3xsfm2kysph61mnfy0pf8d5rkgxgrdb0z9nbizgcgdsb5a0m")))) (build-system python-build-system) + (arguments + '(#:tests? #f)) ; Tests requires a running X11 server. (propagated-inputs `(("python-pandas" ,python-pandas) ("python-matplotlib" ,python-matplotlib) From 444464ec28fe63a8162d6b7d8ef5b408082df91b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 17:42:22 +0100 Subject: [PATCH 065/150] gnu: python-rpy2: Fix tests. * gnu/packages/python.scm (python-rpy2, python2-rpy2)[arguments]: Replace check phase with custom post-install command. --- gnu/packages/python.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 610785bc59..f79073470a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3674,6 +3674,16 @@ 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 From 9e378e6a5c0477cc0cb8cdbc06be8dd1fd4a8091 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 17:53:49 +0100 Subject: [PATCH 066/150] gnu: python-reportlab: Fix tests. * gnu/packages/pdf.scm (python-reportlab, python2-reportlab)[arguments]: Set #:test-target. --- gnu/packages/pdf.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/pdf.scm b/gnu/packages/pdf.scm index 3f329c5426..1c04824ea6 100644 --- a/gnu/packages/pdf.scm +++ b/gnu/packages/pdf.scm @@ -628,6 +628,10 @@ 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") From 4eb385fb33a324ee87724d43131b40d0c371f72f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 18:11:43 +0100 Subject: [PATCH 067/150] gnu: python-pytest-xdist: Disable tests. * gnu/packages/python.scm (python-pytest-xdist, python2-pytest-xdist)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f79073470a..086890ec32 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1843,6 +1843,15 @@ 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))) From 1f31a5e0bfd0287e5dcc6bcccd0e70474904e3cf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 18:19:34 +0100 Subject: [PATCH 068/150] gnu: python-pytest-django: Disable tests. * gnu/packages/django.scm (python-pytest-django, python2-pytest-django)[arguments]: Set #:tests? #f. --- gnu/packages/django.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm index 415ee60a20..106d18a8d7 100644 --- a/gnu/packages/django.scm +++ b/gnu/packages/django.scm @@ -135,7 +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 _ From 8bd5164b4ac1ec625cdbb45ddf8c539253c75b3d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 18:35:21 +0100 Subject: [PATCH 069/150] gnu: python-pystache: Disable tests for python3 variant. * gnu/packages/python.scm (python-pystache)[arguments]: Disable tests. [properties]: New field. Delay python2 variant. (python2-pystache)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 086890ec32..f99df753e5 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2710,15 +2710,26 @@ 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 From 0a7020095185c6b5aaac42bc04449c39c3673e38 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 18:42:22 +0100 Subject: [PATCH 070/150] gnu: python-pyserial: Disable tests. * gnu/packages/python.scm (python-pyserial, python2-pyserial)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index f99df753e5..81e085f2d7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10861,6 +10861,13 @@ 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") From 810f89839cdbc8c73fdc40024465f1d12fdcaf4a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:06:12 +0100 Subject: [PATCH 071/150] gnu: python-pylast: Disable tests. * gnu/packages/music.scm (python-pylast, python2-pylast)[arguments]: Set #:tests? #f. --- gnu/packages/music.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/music.scm b/gnu/packages/music.scm index 4297f846f9..8b1644ca4c 100644 --- a/gnu/packages/music.scm +++ b/gnu/packages/music.scm @@ -2035,6 +2035,8 @@ 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) From 8653c1d5574d43bba0ecc7efbbdf0b0ee8264a6c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:09:18 +0100 Subject: [PATCH 072/150] gnu: python-py3status: Disable tests. * gnu/packages/python.scm (python-py3status)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 81e085f2d7..d438e5c6d4 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9975,6 +9975,8 @@ 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 From 15c37077bc3801317c9e40ee3552f6aac67baaa7 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:47:47 +0100 Subject: [PATCH 073/150] gnu: python-hy: Fix test suite. * gnu/packages/python.scm (python-hy, python2-hy)[arguments]: Replace 'check' phase with custom command. [native-inputs]: Add python-coverage and python-nose. --- gnu/packages/python.scm | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index d438e5c6d4..c45afbc2ff 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8273,6 +8273,17 @@ 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) From ad348f9f39434dfce5e778b678fba586a7cae670 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:50:12 +0100 Subject: [PATCH 074/150] gnu: python-gridmap: Disable tests. * gnu/packages/python.scm (python-gridmap, python2-gridmap)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c45afbc2ff..2dc2ba3b36 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4447,6 +4447,8 @@ 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) From 59f74825d60ec46d387edcc24f7d256d5c2c602d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 19:56:44 +0100 Subject: [PATCH 075/150] gnu: python-flask-restplus: Disable tests. * gnu/packages/python.scm (python-flask-restplus)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 2dc2ba3b36..91cee71d62 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12069,6 +12069,13 @@ 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) From 22d7360b1660faeae42ca382b3dc3f999a56d3ca Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 00:54:48 +0100 Subject: [PATCH 076/150] gnu: Remove python-dateutil@1.5. * gnu/packages/python.scm (python-dateutil-2, python2-dateutil-2): Rename to ... (python-dateutil, python2-dateutil): ... this. Remove 1.5 version. (python-tzlocal, python2-tzlocal): Adjust variable name. (python-rst.linker, python2-rst.linker): Likewise. (pelican): Likewise. (python-matplotlib, python2-matplotlib): Likewise. (python-sqlalchemy-utils, python2-sqlalchemy-utils): Likewise. (python-icalendar, python2-icalendar): Likewise. (python-botocore, python2-botocore): Likewise. (python-vobject, python2-vobject): Likewise. (python-arrow, python2-arrow): Likewise. (python-fake-factory, python2-fake-factory): Likewise. (python-freezegun, python2-freezegun): Likewise. (python-aniso8601, python2-aniso8601): Likewise. * gnu/packages/jrnl.scm (jrnl): Likewise. * gnu/packages/calendar.scm (limnoria): Likewise. --- gnu/packages/calendar.scm | 2 +- gnu/packages/jrnl.scm | 2 +- gnu/packages/python.scm | 49 +++++++++++---------------------------- 3 files changed, 15 insertions(+), 38 deletions(-) diff --git a/gnu/packages/calendar.scm b/gnu/packages/calendar.scm index 447dcd698e..00e908109b 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/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/python.scm b/gnu/packages/python.scm index 91cee71d62..57275ac5d2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -973,7 +973,7 @@ 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 "2.5.2") @@ -994,29 +994,6 @@ 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)) @@ -1062,7 +1039,7 @@ 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))) @@ -2908,7 +2885,7 @@ 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))) @@ -3002,7 +2979,7 @@ 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 @@ -3530,7 +3507,7 @@ 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) @@ -4029,7 +4006,7 @@ both of which are installed automatically if you install this library.") `(("python-six" ,python-six) ("python-sqlalchemy" ,python-sqlalchemy))) (native-inputs - `(("python-dateutil" ,python-dateutil-2) + `(("python-dateutil" ,python-dateutil) ("python-flexmock" ,python-flexmock) ("python-psycopg2" ,python-psycopg2) ("python-pytest" ,python-pytest) @@ -8140,7 +8117,7 @@ processes across test runs.") "01v2f3swd5s72x65cdihw83dx1z799b4i49a6ncg7vqmcm20wapd")))) (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 @@ -8588,7 +8565,7 @@ document.") ;; 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 @@ -9352,7 +9329,7 @@ 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 @@ -10392,7 +10369,7 @@ 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 @@ -10597,7 +10574,7 @@ parsing UK postcodes.") ("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") @@ -11202,7 +11179,7 @@ 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 @@ -11785,7 +11762,7 @@ 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 From 01fb9f6638bf6a77e5323ed63b3462976aa318f0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 01:07:41 +0100 Subject: [PATCH 077/150] gnu: python-axolotl: Remove workaround for bug #20765. * gnu/packages/python.scm (python-axolotl, python2-axolotl)[arguments]: Remove #:configure-flags. --- gnu/packages/python.scm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 57275ac5d2..326f5ee1b3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11959,10 +11959,7 @@ 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) From ed11804309a1fba077ae44bde83bc84c5f2b1b12 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 02:10:58 +0100 Subject: [PATCH 078/150] gnu: python-pexpect: Update to 4.2.1. * gnu/packages/python.scm (python-pexpect, python2-pexpect): Update to 4.2.1. [source]: Use 'pypi-uri'. [arguments]: Add 'prepare-tests' phase to patch paths and delete network test. [native-inputs]: Add python-pytest, man-db and which. [propagated-inputs]: Add python-ptyprocess. --- gnu/packages/python.scm | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 326f5ee1b3..52f242df33 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -74,6 +74,7 @@ #: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) @@ -4444,21 +4445,39 @@ 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 From 58f5fae7c40f1bca9adfe63c2e6a134f89da0c0c Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 02:14:54 +0100 Subject: [PATCH 079/150] gnu: python-widgetsnbextension: Fix tests. * gnu/packages/python.scm (python-widgetsnbextension, python2-widgetsnbextension)[native-inputs]: Add python-certifi. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 52f242df33..10f295fe93 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -7086,7 +7086,8 @@ 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 From 80ce42bdbf3f795ba6b91cebd472261b1e141a4a Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 02:16:23 +0100 Subject: [PATCH 080/150] gnu: python-argcomplete: Fix tests. * gnu/packages/python.scm (python-argcomplete, python2-argcomplete)[native-inputs]: Add python-pexpect and tcsh. --- gnu/packages/python.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 10f295fe93..90c9ecd413 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -87,6 +87,7 @@ #: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) @@ -12150,6 +12151,9 @@ 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 From 154d207c435a5a16d44bcb98dbb31c124dc87574 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 02:45:49 +0100 Subject: [PATCH 081/150] gnu: python-apsw: Fix tests. * gnu/packages/python.scm (python-apsw, python2-apsw)[arguments]: Use 'modify-phases'. Add installed PYTHONPATH before running tests. --- gnu/packages/python.scm | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 90c9ecd413..7e7e54f54f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5155,13 +5155,12 @@ 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 From d281be18bca2437ff27f8c045c5dd5a3e5b77e57 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 04:26:32 +0100 Subject: [PATCH 082/150] gnu: clipper: Fix test dependency. * gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5f56551526..3a7bffba79 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1562,6 +1562,7 @@ 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") From aaffb9c97b8daae7dd81547e8b808ac73fd65f4f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 04:27:35 +0100 Subject: [PATCH 083/150] gnu: deeptools: Fix test dependency. * gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3a7bffba79..e160015b1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2002,6 +2002,7 @@ 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") From 1c10a1d75c78afc85f5709743b1ac5f83e1897f4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:08:57 +0100 Subject: [PATCH 084/150] gnu: idr: Disable tests. * gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f. --- gnu/packages/bioinformatics.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e160015b1f..fc75fd1abd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2879,7 +2879,8 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) (build-system python-build-system) (arguments - `(#:phases + `(#:tests? #f ; FIXME: "ImportError: No module named 'utility'" + #:phases (modify-phases %standard-phases (add-after 'install 'wrap-program From b7a820fc97485a7bdf7703d3b627871d6a6be6c6 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:11:20 +0100 Subject: [PATCH 085/150] gnu: idr: Correct inputs. * gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ... [propagated-inputs]: ... to here. Add python-sympy. --- gnu/packages/bioinformatics.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fc75fd1abd..a2191d060b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2900,8 +2900,9 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") (wrap-program (string-append out "/bin/idr") `("PYTHONPATH" ":" prefix (,path)))) #t))))) - (inputs + (propagated-inputs `(("python-scipy" ,python-scipy) + ("python-sympy" ,python-sympy) ("python-numpy" ,python-numpy) ("python-matplotlib" ,python-matplotlib))) (native-inputs From 14386fc7d9192b35a81dedb7616a44651807ee19 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:16:39 +0100 Subject: [PATCH 086/150] gnu: idr: Remove explicit wrapper. This is now done implicitly. * gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases. --- gnu/packages/bioinformatics.scm | 22 +--------------------- 1 file changed, 1 insertion(+), 21 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a2191d060b..3fb9bbc35d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2879,27 +2879,7 @@ data. It also provides the bgzip, htsfile, and tabix utilities.") "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r")))) (build-system python-build-system) (arguments - `(#:tests? #f ; FIXME: "ImportError: No module named 'utility'" - #: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))))) + `(#:tests? #f)) ; FIXME: "ImportError: No module named 'utility'" (propagated-inputs `(("python-scipy" ,python-scipy) ("python-sympy" ,python-sympy) From 58a35665d98386d98e7fbb84812d2b2282990eca Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 15:59:23 +0100 Subject: [PATCH 087/150] gnu: Add python-mpmath. * gnu/packages/python.scm (python-mpmath, python2-mpmath): New variables. --- gnu/packages/python.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7e7e54f54f..0414e889fe 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5406,6 +5406,36 @@ 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") From 52f622ef9fd315945f37de921c9d46997d176692 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 15 Dec 2016 16:47:13 +0100 Subject: [PATCH 088/150] gnu: python-sympy: Update to 1.0. * gnu/packages/python.scm (python-sympy, python2-sympy): Update to 1.0. [propagated-inputs]: Add python-mpmath. --- gnu/packages/python.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 0414e889fe..18a8b58873 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5439,7 +5439,7 @@ more advanced mathematics.") (define-public python-sympy (package (name "python-sympy") - (version "0.7.6") + (version "1.0") (source (origin (method url-fetch) @@ -5447,8 +5447,10 @@ more advanced mathematics.") "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 From 0d9087597467c3e34cf614a5475bfb0ea75b133b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:28:49 +0100 Subject: [PATCH 089/150] gnu: multiqc: Fix test dependencies. * gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose. --- gnu/packages/bioinformatics.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3fb9bbc35d..e37226b275 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7843,6 +7843,8 @@ replacement for strverscmp.") (base32 "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy")))) (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose))) (propagated-inputs `(("python-jinja2" ,python-jinja2) ("python-simplejson" ,python-simplejson) From 329553482d0632e35b3c0028548b004f8cb32aec Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 13:39:07 +0100 Subject: [PATCH 090/150] gnu: ptpython: Disable tests. * gnu/packages/python.scm (ptpython, ptpython2)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 18a8b58873..fece7cdb75 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10798,6 +10798,8 @@ 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) From 7c6bf660d8a455090f4c140c5b2849f1b58f2fe3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 14:32:34 +0100 Subject: [PATCH 091/150] gnu: python-pyopenssl: Enable tests. * gnu/packages/patches/python-pyopenssl-skip-network-test.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-pyopenssl, python2-pyopenssl)[source]: Use it. [arguments]: Replace 'check' with custom phase. --- gnu/local.mk | 1 + .../python-pyopenssl-skip-network-test.patch | 50 +++++++++++++++++++ gnu/packages/python.scm | 13 +++-- 3 files changed, 61 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/python-pyopenssl-skip-network-test.patch diff --git a/gnu/local.mk b/gnu/local.mk index a06f359435..89d1e83b4b 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -815,6 +815,7 @@ 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/python2-pygobject-2-gi-info-type-error-domain.patch \ %D%/packages/patches/qemu-CVE-2016-8576.patch \ %D%/packages/patches/qemu-CVE-2016-8577.patch \ 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/python.scm b/gnu/packages/python.scm index fece7cdb75..dce46cec34 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6672,11 +6672,18 @@ 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 - ;; FIXME: Some tests fail with "NameError: name 'long' is not defined". - '(#:tests? #f)) + '(#: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))) From 752eb9e0d86931de9eb42d1a60069e48ac1fbfd8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 15:33:13 +0100 Subject: [PATCH 092/150] gnu: python2-kombu: Disable tests. * gnu/packages/python.scm (python2-kombu)[arguments]: Set #:tests? #f. --- gnu/packages/python.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index dce46cec34..8af6965b1e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9165,6 +9165,10 @@ 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)))))) From ee94ca11a1d695871c11cd5cf521089d5bcdb34f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 16:15:41 +0100 Subject: [PATCH 093/150] gnu: python-beautifulsoup4: Fix python2 variant. This is a followup to 5f37f0b66e301210698ab0c0af24453c826ba18a. * gnu/packages/python.scm (python-beautifulsoup4)[properties]: New field. Delay python2 variant. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8af6965b1e..9388534c98 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5232,7 +5232,8 @@ 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 From cdc2bb50b29422e8edfb00cabb5edd632f6ebe07 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 16 Dec 2016 18:15:47 +0100 Subject: [PATCH 094/150] gnu: pbtranscript-tofu: Disable tests. * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f. --- gnu/packages/bioinformatics.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e37226b275..50b0bfaa03 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3572,6 +3572,9 @@ 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 From 39d0de3375071b240f6a4d617e48d8449bc50e5e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 17 Dec 2016 12:19:41 +0100 Subject: [PATCH 095/150] gnu: asciinema: Fix test requirements. * gnu/packages/terminals.scm (asciinema)[native-inputs]: Add python-requests. --- gnu/packages/terminals.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/terminals.scm b/gnu/packages/terminals.scm index efedba480f..79da6c7127 100644 --- a/gnu/packages/terminals.scm +++ b/gnu/packages/terminals.scm @@ -164,6 +164,9 @@ 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 From 7b6ff42aa3cf9398213d3c1f0e5f87c45a9730df Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sun, 18 Dec 2016 00:44:09 +0100 Subject: [PATCH 096/150] gnu: git-annex-remote-hubic: Fix python-dateutil dependency. This is a followup to 22d7360b1660faeae42ca382b3dc3f999a56d3ca. * gnu/packages/version-control.scm (git-annex-remote-hubic)[propagated-inputs]: Change python-dateutil-2 to python-dateutil. --- gnu/packages/version-control.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 7918b90ca6..cc958281c7 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -1172,7 +1172,7 @@ 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))) From 1c1b67a3c91cd46241dee9c556d326e11b1d9ce2 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2016 01:05:52 +0100 Subject: [PATCH 097/150] gnu: thefuck: Correct inputs and disable tests. * gnu/packages/admin.scm (thefuck)[arguments]: Set #:tests? #f. [inputs]: Move everything to ... [propagated-inputs]: ... here. Remove duplicate [inputs] and python-setuptools. [native-inputs]: Add python-pytest, python-pytest-mock and python-mock. --- gnu/packages/admin.scm | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 69c04dc139..6e913d2cd0 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1697,15 +1697,26 @@ 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))) - (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))) + (native-inputs + `(("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-mock" ,python-pytest-mock))) (home-page "https://github.com/nvbn/thefuck") (synopsis "Correct mistyped console command") (description From c0b12a606b6af07e739b8326e032774245f38297 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2016 04:13:59 +0100 Subject: [PATCH 098/150] gnu: sshoot: Fix tests. * gnu/packages/vpn.scm (sshoot)[arguments]: Add 'patch-paths' phase. --- gnu/packages/vpn.scm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index a32ac206ac..9a08ad4f41 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -247,6 +247,14 @@ 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) From a25b6880f1398ad36aea1d0e4e4105936a8b7e70 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 19 Dec 2016 17:01:48 +0100 Subject: [PATCH 099/150] gnu: python-efl: Disable tests. * gnu/packages/enlightenment.scm (python-efl, python2-efl)[arguments]: Add phase to set test environment. And set #:tests? #f. --- gnu/packages/enlightenment.scm | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/gnu/packages/enlightenment.scm b/gnu/packages/enlightenment.scm index 77814960ee..5ec3ec5a88 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))) From 9a8acd00da3ad44ac6ef423f3d9cba87645cc022 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 13 Jan 2017 22:58:54 +0100 Subject: [PATCH 100/150] gnu: python-sphinx: Update to 1.4.8. * gnu/packages/python.scm (python-sphinx)[version]: Update to 1.4.8. [source]: Use pypi-uri. [propagated-inputs]: Add python-imagesize, python-sphinx-alabaster-theme, python-babel, python-snowballstemmer, python-six. [properties]: Add python2-variant. (python2-sphinx)[native-inputs]: Add python2-mock. [propagated-inputs]: Add python2-pytz. --- gnu/packages/python.scm | 29 ++++++++++++++++++++--------- 1 file changed, 20 insertions(+), 9 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index bfd003ba3e..c540d7b5a0 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2945,33 +2945,44 @@ reStructuredText.") (define-public python-sphinx (package (name "python-sphinx") - (version "1.2.3") + (version "1.4.8") (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")))) + "0zvh8wwhm6gy21rr0cg42znsy4zzv2mnsxxk9gmn5y1ycn7rgbs1")))) (build-system python-build-system) (arguments ;; FIXME: Missing dependencies. '(#:tests? #f)) (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))) (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) + ,@(package-native-inputs base))) + (propagated-inputs `(("python2-pytz" ,python2-pytz) + ,@(package-propagated-inputs base)))))) (define-public python-sphinx-rtd-theme (package From 42b7009a004178332f761c64c4363549e5743714 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 14 Jan 2017 22:03:54 +0100 Subject: [PATCH 101/150] gnu: python-matplotlib: Use 'modify-phases' syntax. * gnu/packages/python.scm (python-matplotlib)[arguments]: Use 'modify-phases'. --- gnu/packages/python.scm | 102 ++++++++++++++++++++-------------------- 1 file changed, 50 insertions(+), 52 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c540d7b5a0..40b65012d3 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3723,62 +3723,60 @@ 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"))))))) + (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'")) + (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"))))))))) (home-page "http://matplotlib.org") (synopsis "2D plotting library for Python") (description From 84e0f8c1ed48614a636f4462ec50d52597624861 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 14 Jan 2017 22:05:35 +0100 Subject: [PATCH 102/150] gnu: python-matplotlib: Fix reST markup error. * gnu/packages/python.scm (python-matplotlib)[arguments]: Fix reST markup error. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 40b65012d3..a5220e05e7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3755,6 +3755,9 @@ backend = TkAgg~%" (substitute* (find-files "." "conf\\.py") (("latex_paper_size = 'letter'") "latex_paper_size = 'a4'")) + (substitute* "users/intro.rst" + ;; Fix reST markup error (see ) + (("[[][*][]]") "[#]")) (mkdir-p html) (mkdir-p info) ;; The doc recommends to run the 'html' target twice. From fdcbf10b700e58c5d527254c2624a9b624f32cfc Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 14 Jan 2017 22:33:46 +0100 Subject: [PATCH 103/150] gnu: python-matplotlib: Make sure that phases end with #t. * gnu/packages/python.scm (python-matplotlib)[arguments]: Make sure that phases end with #t. --- gnu/packages/python.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a5220e05e7..6518006aa2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3740,7 +3740,8 @@ basedirlist = ~a,~a~% [rc_options]~% backend = TkAgg~%" (assoc-ref inputs "tcl") - (assoc-ref inputs "tk"))))))) + (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")) @@ -3779,7 +3780,8 @@ backend = TkAgg~%" (copy-file "build/texinfo/matplotlib.info" (string-append info "/matplotlib.info")) (copy-file "build/latex/Matplotlib.pdf" - (string-append doc "/Matplotlib.pdf"))))))))) + (string-append doc "/Matplotlib.pdf"))) + #t)))))) (home-page "http://matplotlib.org") (synopsis "2D plotting library for Python") (description From d1ba1d6bfd05bbf7e5855d43a2bdfcb0a9742cc9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 17 Jan 2017 21:56:31 +0100 Subject: [PATCH 104/150] gnu: python-requests: Update to 2.12.4. * gnu/packages/python.scm (python-requests, python2-requests): Update to 2.12.4. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6518006aa2..7f72ed13da 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2467,13 +2467,13 @@ 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) (arguments From c9a1812527f97ca2963dad6be9a9792120cdb99b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 17 Jan 2017 23:13:19 +0100 Subject: [PATCH 105/150] gnu: Add python-geventhttpclient. * gnu/packages/python.scm (python-geventhttpclient, python2-geventhttpclient): New variables. --- gnu/packages/python.scm | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7f72ed13da..9a44b5881a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10487,6 +10487,51 @@ 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-twisted (package (name "python-twisted") From c227458ac84273c12c254827e3311e9df2798767 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:05 +0100 Subject: [PATCH 106/150] gnu: python-sphinx: Update to 1.5.1 and enable tests. * gnu/packages/python.scm (python-sphinx): Update to 1.5.1. [arguments]: New field. [native-inputs]: Add graphviz, python-html5lib, python-mock, python-nose, python-requests. (python2-sphinx)[native-inputs]: Add python2-enum34. --- gnu/packages/python.scm | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 9a44b5881a..75c3bc8574 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -67,6 +67,7 @@ #: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) @@ -2945,18 +2946,23 @@ reStructuredText.") (define-public python-sphinx (package (name "python-sphinx") - (version "1.4.8") + (version "1.5.1") (source (origin (method url-fetch) (uri (pypi-uri "Sphinx" version)) (sha256 (base32 - "0zvh8wwhm6gy21rr0cg42znsy4zzv2mnsxxk9gmn5y1ycn7rgbs1")))) + "1i8p9idnli4gr0y4x67yakbdk5w6a0xjzhrg6bg51y9d1fi7fslf")))) (build-system python-build-system) (arguments - ;; FIXME: Missing dependencies. - '(#:tests? #f)) + `(#: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-imagesize" ,python-imagesize) ("python-sphinx-alabaster-theme" @@ -2967,6 +2973,12 @@ reStructuredText.") ("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 @@ -2980,6 +2992,7 @@ sources.") (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)))))) From 376c4619cf8ad683fba5d04513a5298c0a77cfdb Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:04 +0100 Subject: [PATCH 107/150] gnu: python-mox3: Remove python-oslosphinx dependency (since the tests don't run anyway). * gnu/packages/openstack.scm (python-mox3)[native-inputs]: Remove python-oslosphinx. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index b3e3f08c23..2500590b2f 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -152,11 +152,11 @@ guidelines}.") "0njmh40i1lg5mzn9hc2ax83adj6dli455j6xifilrw27c4wlkjzx")))) (build-system python-build-system) (arguments - ;; TODO: Requires newer version of testtools (>=1.4.0). + ;; TODO: Resolve dependency cycle and re-enable. '(#:tests? #f)) (native-inputs `(("python-fixtures" ,python-fixtures) - ("python-oslosphinx" ,python-oslosphinx) + ; TODO re-add ("python-oslosphinx" ,python-oslosphinx) ("python-pbr" ,python-pbr) ("python-sphinx" ,python-sphinx) ("python-testtools" ,python-testtools))) From b585e361844e0ab527d10880698ee0489347b1c6 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:01 +0100 Subject: [PATCH 108/150] gnu: Add python-fastimport. * gnu/packages/python.scm (python-fastimport, python2-fastimport): New variables. --- gnu/packages/python.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 75c3bc8574..b0601da4db 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10545,6 +10545,27 @@ concurrent HTTP client library for python using @code{gevent}.") (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") From d83d87225980cec4926aec03280ad3533b778281 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:02 +0100 Subject: [PATCH 109/150] gnu: Add python-dulwich. * gnu/packages/python.scm (python-dulwich, python2-dulwich): New variables. --- gnu/packages/python.scm | 46 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b0601da4db..7c4996ce4b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12734,3 +12734,49 @@ Features: @item Compiles templates into optimized, yet readable, Python code. @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)) From 7adb90311f8ce5e44c5bd1ecba28dcb26bfabebe Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:00 +0100 Subject: [PATCH 110/150] gnu: python-testtools: Update to 1.4.0. * gnu/packages/python.scm (python-testtools): Update to 1.4.0. [source]: Use pypi-uri. [arguments]: New field. --- gnu/packages/python.scm | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 7c4996ce4b..80d03f6b0a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1983,17 +1983,36 @@ 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))) From c8d7e063d0b576615fb481e0abc55c0aeab609b8 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Wed, 18 Jan 2017 08:53:03 +0100 Subject: [PATCH 111/150] gnu: Add python-reno. * gnu/packages/openstack.scm (python-reno, python-reno2): New variables. --- gnu/packages/openstack.scm | 42 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 2500590b2f..5bb83095a0 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -19,6 +19,7 @@ ;;; along with GNU Guix. If not, see . (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) @@ -550,6 +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") From 16ca6aaac867862ea6d84c5888bfc59099f335a0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 19 Jan 2017 16:59:28 +0100 Subject: [PATCH 112/150] gnu: python-scipy: Use 'modify-phases' syntax. * gnu/packages/python.scm (python-scipy)[arguments]: Use 'modify-phases'. --- gnu/packages/python.scm | 104 +++++++++++++++++++--------------------- 1 file changed, 50 insertions(+), 54 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 80d03f6b0a..6d1a04ce88 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3946,13 +3946,18 @@ 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 @@ -3962,53 +3967,44 @@ 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 From db967b646292e3517fc11f98ea0d4c19fd2191a9 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 19 Jan 2017 17:46:48 +0100 Subject: [PATCH 113/150] gnu: python-scipy: Fix expression after changing to 'modify-phases'. This is a followup to 16ca6aaac867862ea6d84c5888bfc59099f335a0. * gnu/packages/python.scm (python-scipy)[arguments]: Fix parens. --- gnu/packages/python.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 6d1a04ce88..007c18206e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3951,7 +3951,7 @@ functions.") (lambda _ (substitute* "scipy/integrate/tests/test_quadpack.py" (("libm.so") "libm.so.6")) - #t) + #t)) (add-before 'build 'configure-openblas (lambda* (#:key inputs #:allow-other-keys) (call-with-output-file "site.cfg" @@ -3970,7 +3970,7 @@ atlas_libs = openblas (assoc-ref inputs "openblas") (assoc-ref inputs "openblas") (assoc-ref inputs "openblas")))) - #t) + #t)) (delete 'check) (add-after 'install 'install-doc (lambda* (#:key inputs outputs #:allow-other-keys) @@ -4004,7 +4004,7 @@ atlas_libs = openblas ;; 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()")))))))))) + (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 From a50e03014177d2f00b5b85d3e1c295406f842016 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 20 Jan 2017 19:03:08 +0100 Subject: [PATCH 114/150] gnu: python-scipy, python-matplotlib: Fix build after Sphinx update. * gnu/packages/python.scm (python-sphinx-1.2.3, python2-sphinx-1.2.3): New variables. (python-matplotlib)[native-inputs]: Change 'python-sphinx' to 'python-sphinx-1.2.3'. (python2-matplotlib)[native-inputs]: New field. (python-scipy)[native-inputs]: Change 'python-sphinx' to 'python-sphinx-1.2.3'. (python2-scipy)[native-inputs]: New field. --- gnu/packages/python.scm | 36 +++++++++++++++++++++++++++++++++--- 1 file changed, 33 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 007c18206e..fd423d3112 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3016,6 +3016,24 @@ sources.") (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 (name "python-sphinx-rtd-theme") @@ -3747,7 +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) @@ -3831,6 +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) @@ -3938,7 +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) @@ -4013,7 +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 From 97b62eb0bfcf5eb7e1e5a320f779839d13052ad0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 13 Feb 2017 22:58:03 +0100 Subject: [PATCH 115/150] gnu: python-trollius-redis: Disable tests. * gnu/packages/python.scm (python-trollius-redis, python2-trollius-redis)[arguments]: New field. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1492e0f369..13dc698341 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8488,6 +8488,8 @@ minimal and fast API targetting the following uses: (base32 "0k3vypszmgmaipgw9xscvgm79h2zd6p6ci8gdp5sxl6g5kbqr9fy")))) (build-system python-build-system) + ;; TODO: Tests require packaging 'hiredis'. + (arguments '(#:tests? #f)) (home-page "https://github.com/benjolitz/trollius-redis") (synopsis "Port of asyncio-redis to trollius") (description "@code{trollius-redis} is a Redis client for Python From bb6043fe9f0198c1e253ae2a8adeea1337830265 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:01:59 +0100 Subject: [PATCH 116/150] gnu: python-pygit2: Skip tests requiring network access. * gnu/packages/python.scm (python-pygit2, python2-pygit2)[source](patches): New field. * gnu/packages/patches/python-pygit2-disable-network-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. --- gnu/local.mk | 1 + .../python-pygit2-disable-network-tests.patch | 64 +++++++++++++++++++ gnu/packages/python.scm | 4 +- 3 files changed, 68 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-pygit2-disable-network-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 8615d12b08..0b9b5b1a1e 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-pygit2-disable-network-tests.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 \ diff --git a/gnu/packages/patches/python-pygit2-disable-network-tests.patch b/gnu/packages/patches/python-pygit2-disable-network-tests.patch new file mode 100644 index 0000000000..e46d244807 --- /dev/null +++ b/gnu/packages/patches/python-pygit2-disable-network-tests.patch @@ -0,0 +1,64 @@ +Disable tests trying to look up remote servers. + +diff --git a/test/test_credentials.py b/test/test_credentials.py +index 92482d9..9a281e5 100644 +--- a/test/test_credentials.py ++++ b/test/test_credentials.py +@@ -68,39 +68,5 @@ class CredentialCreateTest(utils.NoRepoTestCase): + self.assertEqual((username, None, None, None), cred.credential_tuple) + + +-class CredentialCallback(utils.RepoTestCase): +- def test_callback(self): +- class MyCallbacks(pygit2.RemoteCallbacks): +- @staticmethod +- def credentials(url, username, allowed): +- self.assertTrue(allowed & GIT_CREDTYPE_USERPASS_PLAINTEXT) +- raise Exception("I don't know the password") +- +- url = "https://github.com/github/github" +- remote = self.repo.create_remote("github", url) +- +- self.assertRaises(Exception, lambda: remote.fetch(callbacks=MyCallbacks())) +- +- def test_bad_cred_type(self): +- class MyCallbacks(pygit2.RemoteCallbacks): +- @staticmethod +- def credentials(url, username, allowed): +- self.assertTrue(allowed & GIT_CREDTYPE_USERPASS_PLAINTEXT) +- return Keypair("git", "foo.pub", "foo", "sekkrit") +- +- url = "https://github.com/github/github" +- remote = self.repo.create_remote("github", url) +- self.assertRaises(TypeError, lambda: remote.fetch(callbacks=MyCallbacks())) +- +-class CallableCredentialTest(utils.RepoTestCase): +- +- def test_user_pass(self): +- credentials = UserPass("libgit2", "libgit2") +- callbacks = pygit2.RemoteCallbacks(credentials=credentials) +- +- url = "https://bitbucket.org/libgit2/testgitrepository.git" +- remote = self.repo.create_remote("bb", url) +- remote.fetch(callbacks=callbacks) +- + if __name__ == '__main__': + unittest.main() +diff --git a/test/test_repository.py b/test/test_repository.py +index cfdf01e..c0d8de4 100644 +--- a/test/test_repository.py ++++ b/test/test_repository.py +@@ -538,13 +538,6 @@ class CloneRepositoryTest(utils.NoRepoTestCase): + self.assertTrue('refs/remotes/custom_remote/master' in repo.listall_references()) + self.assertIsNotNone(repo.remotes["custom_remote"]) + +- def test_clone_with_credentials(self): +- repo = clone_repository( +- "https://bitbucket.org/libgit2/testgitrepository.git", +- self._temp_dir, callbacks=pygit2.RemoteCallbacks(credentials=pygit2.UserPass("libgit2", "libgit2"))) +- +- self.assertFalse(repo.is_empty) +- + def test_clone_with_checkout_branch(self): + # create a test case which isolates the remote + test_repo = clone_repository('./test/data/testrepo.git', diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 13dc698341..c9cf347373 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3580,7 +3580,9 @@ association studies (GWAS) on extremely large data sets.") (uri (pypi-uri "pygit2" version)) (sha256 (base32 - "0wf5rp0fvrw7j3j18dvwjq6xqlbm611wd55aphrfpps0v1gxh3ny")))) + "0wf5rp0fvrw7j3j18dvwjq6xqlbm611wd55aphrfpps0v1gxh3ny")) + (patches + (search-patches "python-pygit2-disable-network-tests.patch")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six) From 23015b4fb4dd7964d37165687ca1fa6dc796a4f4 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:15:27 +0100 Subject: [PATCH 117/150] gnu: python-oslosphinx: Disable tests. * gnu/packages/openstack.scm (python-oslosphinx, python2-oslosphinx)[arguments]: New field. --- gnu/packages/openstack.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 5bb83095a0..6f7e843e9d 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -604,6 +604,9 @@ and building documentation from them.") (base32 "0cz8ym4i1n4rgljlqhyhfkpgdmid7nkb909k8r8nk186m9cmpla2")))) (build-system python-build-system) + ;; FIXME: Incompatible sphinx version. + (arguments + '(#:tests? #f)) (propagated-inputs `(("python-requests" ,python-requests))) (native-inputs From 019ccdb6c88cb19a6db3b1a4394cd2c2bfcd30c0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:22:06 +0100 Subject: [PATCH 118/150] gnu: python-openid-cla: Disable tests. * gnu/packages/python.scm (python-openid-cla, python2-openid-cla)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index c9cf347373..1c3415988a 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5611,6 +5611,7 @@ another XPath engine to find the matching elements in an XML or HTML document.") (base32 "102hy2qisvjxp5s0v9lvwqi4f2dk0dhns40vjgn008yxc7k0h3cr")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ; No tests. (home-page "https://github.com/puiterwijk/python-openid-cla/") (synopsis "Implementation of the OpenID CLA extension for python-openid") (description "@code{openid-cla} is an implementation of the OpenID From ac72d3d2cca1381a807493763b2e80db5307fdb1 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:38:04 +0100 Subject: [PATCH 119/150] gnu: python-openid-teams: Disable tests. * gnu/packages/python.scm (python-openid-teams, python2-openid-teams)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 1c3415988a..18e55bf6b2 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5633,6 +5633,7 @@ contributor license agreement extension for python-openid.") (base32 "05zrh78alav24rxkbqlpbad6d3x2nljk6z6j7kflxf3vdqa7w969")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ; No tests. (home-page "https://github.com/puiterwijk/python-openid-teams/") (synopsis "Implementation of the OpenID teams extension for python-openid") (description From e435af5c2a9318a65dd4f240c33ba77870e6086d Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 00:48:53 +0100 Subject: [PATCH 120/150] gnu: python-mako: Fix tests. * gnu/packages/python.scm (python-mako, python2-mako)[native-inputs]: Add PYTHON-PYTEST. --- gnu/packages/python.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 18e55bf6b2..85704d3eee 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9271,7 +9271,8 @@ available in Django, but is a standalone package.") `(("python-markupsafe" ,python-markupsafe))) (native-inputs `(("python-mock" ,python-mock) - ("python-nose" ,python-nose))) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) (home-page "http://www.makotemplates.org/") (synopsis "Templating language for Python") (description "Mako is a templating language for Python that compiles From 619bfd811eb778998101cf3d72d7fba9447813e3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 14 Feb 2017 16:09:49 +0100 Subject: [PATCH 121/150] gnu: awscli: Explicitly disable tests. * gnu/packages/python.scm (awscli)[arguments]: New field. [native-inputs]: Remove. --- gnu/packages/python.scm | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 85704d3eee..421291d7de 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9108,12 +9108,9 @@ interface to the Amazon Web Services (AWS) API.") ("python-s3transfer" ,python-s3transfer) ("python-docutils" ,python-docutils) ("python-rsa" ,python-rsa))) - (native-inputs - `(("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-sphinx" ,python-sphinx) - ("python-tox" ,python-tox) - ("python-wheel" ,python-wheel))) + (arguments + ;; FIXME: The 'pypi' release does not contain tests. + '(#:tests? #f)) (home-page "https://aws.amazon.com/cli/") (synopsis "Command line client for AWS") (description "AWS CLI provides a unified command line interface to the From fe2ba3a888f78669cc4abe6a9bf2db73c390a4c8 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 08:28:03 +0100 Subject: [PATCH 122/150] gnu: python-tabulate: Disable tests. * gnu/packages/python.scm (python-tabulate)[arguments]: New field. [native-inputs]: Remove. [source]: Remove test substitution snippet. --- gnu/packages/python.scm | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 421291d7de..87066fc88e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -10824,18 +10824,12 @@ It uses LR parsing and does extensive error checking.") (uri (pypi-uri "tabulate" version)) (sha256 (base32 - "1inqhspd4frxnp08c32yndr0lc4px1xfkqah184i5w09gkhvi843")) - ;; Fix tests - (modules '((guix build utils))) - (snippet '(substitute* '("test/test_cli.py" - "test/test_input.py" - "test/test_output.py" - "test/test_regression.py") - (("from common") "from nose.tools"))))) + "1inqhspd4frxnp08c32yndr0lc4px1xfkqah184i5w09gkhvi843")))) (build-system python-build-system) - (native-inputs - `(;; For testing - ("python-nose" ,python-nose))) + (arguments + ;; FIXME: The pypi release tarball is missing a 'test/common.py' + ;; and the latest release is not tagged in the upstream repository. + '(#:tests? #f)) (home-page "https://bitbucket.org/astanin/python-tabulate") (synopsis "Pretty-print tabular data") (description From 2010af55b98b1cbe6295b7f8b066fed04696a4ba Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 08:39:15 +0100 Subject: [PATCH 123/150] gnu: python-requests-mock: Update to 1.3.0. * gnu/packages/openstack.scm (python-requests-mock, python2-requests-mock): Update to 1.3.0. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 6f7e843e9d..1e8a840e9a 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -245,14 +245,14 @@ tested on Python version 3.2, 2.7 and 2.6.") (define-public python-requests-mock (package (name "python-requests-mock") - (version "1.0.0") + (version "1.3.0") (source (origin (method url-fetch) (uri (pypi-uri "requests-mock" version)) (sha256 (base32 - "0gcjjwsckhqixyffflc54i59x41jnbb37bli077vabii1bjmkin6")))) + "0jr997dvk6zbmhvbpcv3rajrgag69mcsm1ai3w3rgk2jdh6rg1mx")))) (build-system python-build-system) (propagated-inputs `(("python-requests" ,python-requests) From e2cb140efb43a56b1cdf2253564490a0f5be26ff Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 08:51:17 +0100 Subject: [PATCH 124/150] gnu: python-sphinxcontrib-programoutput: Disable tests. * gnu/packages/python.scm (python-sphinxcontrib-programoutput, python2-sphinxcontrib-programoutput)[arguments]: New field. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 87066fc88e..5c6dda0fbf 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9763,6 +9763,9 @@ programmatically interfacing with your system's $EDITOR.") (base32 "098as6z1s0gb4dh5xcr1fd2vpm91zj93jzvgawspxf5s4hqs0xhp")))) (build-system python-build-system) + (arguments + ;; FIXME: Many tests are failing and the upstream is gone. + '(#:tests? #f)) (propagated-inputs `(("python-sphinx" ,python-sphinx))) (synopsis "Sphinx extension to include program output") From 3d2a544c6901622ca30c507028532734f0f52040 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:03:05 +0100 Subject: [PATCH 125/150] gnu: python-sphinxcontrib-newsfeed: Disable tests. * gnu/packages/python.scm (python-sphinxcontrib-newsfeed python2-sphinxcontrib-newsfeed)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5c6dda0fbf..a80daeea73 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -8642,6 +8642,7 @@ files for use with Python.") (sha256 (base32 "1d7gam3mn8v4in4p16yn3v10vps7nnaz6ilw99j4klij39dqd37p")))) + (arguments '(#:tests? #f)) ; No tests. (build-system python-build-system) (propagated-inputs `(("python-sphinx" ,python-sphinx))) From 9893cff37695dbe99eb3d776d405f90607e86d37 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:05:56 +0100 Subject: [PATCH 126/150] gnu: python-sphinx-rtd-theme: Disable tests. * gnu/packages/python.scm (python-sphinx-rtd-theme, python2-sphinx-rtd-theme)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index a80daeea73..196fe2c833 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3050,6 +3050,7 @@ sources.") (base32 "19nw3rn7awplcdrz63kg1njqwkbymfg9lwn7l2grhdyhyr2gaa8g")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ; No tests. (propagated-inputs `(("python-sphinx" ,python-sphinx))) (home-page "https://github.com/snide/sphinx_rtd_theme/") From 5b3c3d4b5a7a775a407b97f044c93cc151b3103f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:08:11 +0100 Subject: [PATCH 127/150] gnu: python-sphinx-repoze-autointerface: Disable tests. * gnu/packages/python.scm (python-sphinx-repoze-autointerface, python2-sphinx-repoze-autointerface)[arguments]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 196fe2c833..315d741b7f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9790,6 +9790,7 @@ commands into documents, helping you to keep your command examples up to date.") (base32 "08ycivzf7bh4a1zcyp31hbyqs1b2c9r26raa3vxjwwmbfqr3iw4f")))) (build-system python-build-system) + (arguments '(#:tests? #f)) ; No tests. (propagated-inputs `(("python-sphinx" ,python-sphinx) ("python-zope-interface" ,python-zope-interface))) From a31e2f1a56ed0495698ad0355db7f6caef3cc8b3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:11:05 +0100 Subject: [PATCH 128/150] gnu: python-sphinx-cloud-sptheme: Explicitly disable tests. * gnu/packages/python.scm (python-sphinx-cloud-sptheme, python2-sphinx-cloud-sptheme)[arguments]: New field. --- gnu/packages/python.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 315d741b7f..39fd58716e 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12240,6 +12240,8 @@ English stemmer.") (base32 "0zm9ap4p5dzln8f1m2immadaxv2xpg8jg4w53y52rhfl7pdb58vy")))) (build-system python-build-system) + ;; FIXME: The 'pypi' release archive does not contain tests. + (arguments '(#:tests? #f)) (native-inputs `(("python-sphinx" ,python-sphinx))) (home-page "https://bitbucket.org/ecollins/cloud_sptheme") From 6925cd788b5a36481dd261c78fb954a9825e3041 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 09:23:01 +0100 Subject: [PATCH 129/150] gnu: python-qrcode: Disable tests. * gnu/packages/python.scm (python-qrcode, python2-qrcode)[arguments]: New field. --- gnu/packages/python.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 39fd58716e..5bcdc6d0c7 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12995,6 +12995,9 @@ a file-like object from which an arbitrarly-sized key can be read.") (base32 "0kljfrfq0c2rmxf8am57333ia41kd0snbm2rnqbdy816hgpcq5a1")))) (build-system python-build-system) + (arguments + ;; FIXME: Tests require packaging 'pymaging'. + '(#:tests? #f)) (propagated-inputs `(("python-lxml" ,python-lxml) ; for SVG output ("python-pillow" ,python-pillow) ; for PNG output From a1e3ed6e8b57c1920d01e357fb2a8e545d4acc33 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 18 Feb 2017 16:43:37 +0100 Subject: [PATCH 130/150] gnu: python-pbr: Support python-sphinx>=1.2.1. * gnu/packages/patches/python-pbr-fix-man-page-support.patch: New file. * gnu/packages/python.scm (python-pbr-minimal): Use the new patch file. --- .../python-pbr-fix-man-page-support.patch | 28 +++++++++++++++++++ gnu/packages/python.scm | 3 +- 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-pbr-fix-man-page-support.patch diff --git a/gnu/packages/patches/python-pbr-fix-man-page-support.patch b/gnu/packages/patches/python-pbr-fix-man-page-support.patch new file mode 100644 index 0000000000..b9036f5b01 --- /dev/null +++ b/gnu/packages/patches/python-pbr-fix-man-page-support.patch @@ -0,0 +1,28 @@ +See: https://bugs.launchpad.net/oslosphinx/+bug/1661861 +diff -ur orig/pbr-1.10.0/pbr/builddoc.py pbr-1.10.0/pbr/builddoc.py +--- orig/pbr-1.10.0/pbr/builddoc.py 2016-05-23 21:38:18.000000000 +0200 ++++ pbr-1.10.0/pbr/builddoc.py 2017-02-18 14:01:37.424434317 +0100 +@@ -138,7 +138,8 @@ + sphinx_config.init_values(warnings.warn) + else: + sphinx_config.init_values() +- if self.builder == 'man' and len(sphinx_config.man_pages) == 0: ++ if self.builder == 'man' and len( ++ getattr(sphinx_config, 'man_pages', '')) == 0: + return + app = application.Sphinx( + self.source_dir, self.config_dir, +diff -ur orig/pbr-1.10.0/pbr/util.py pbr-1.10.0/pbr/util.py +--- orig/pbr-1.10.0/pbr/util.py 2016-05-23 21:38:18.000000000 +0200 ++++ pbr-1.10.0/pbr/util.py 2017-02-18 15:36:32.951196795 +0100 +@@ -211,7 +211,9 @@ + parser.read(path) + config = {} + for section in parser.sections(): +- config[section] = dict(parser.items(section)) ++ config[section] = dict() ++ for k, value in parser.items(section): ++ config[section][k.replace('-', '_')] = value + + # Run setup_hooks, if configured + setup_hooks = has_get_option(config, 'global', 'setup_hooks') diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 5bcdc6d0c7..93e18b2fb9 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2130,7 +2130,8 @@ protocol.") (uri (pypi-uri "pbr" version)) (sha256 (base32 - "177kd9kbv1hvf2ban7l3x9ymzbi1md4hkaymwbgnz7ihf312hr0q")))) + "177kd9kbv1hvf2ban7l3x9ymzbi1md4hkaymwbgnz7ihf312hr0q")) + (patches (search-patches "python-pbr-fix-man-page-support.patch")))) (build-system python-build-system) (arguments `(#:tests? #f)) From 9c4810b47cdf2aeccfbb99a6af427c6c2777c46e Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 18 Feb 2017 16:49:03 +0100 Subject: [PATCH 131/150] gnu: python-oslosphinx: Update to 4.10.0. * gnu/packages/openstack.scm (python-oslosphinx): Update to 4.10.0. --- gnu/packages/openstack.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 1e8a840e9a..fe0dd11eb3 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -595,14 +595,14 @@ and building documentation from them.") (define-public python-oslosphinx (package (name "python-oslosphinx") - (version "4.3.0") + (version "4.10.0") (source (origin (method url-fetch) (uri (pypi-uri "oslosphinx" version)) (sha256 (base32 - "0cz8ym4i1n4rgljlqhyhfkpgdmid7nkb909k8r8nk186m9cmpla2")))) + "09mxqyabi68f3s3arvdhlhq0mn38vf74jbsfcg84151hcj6czhnl")))) (build-system python-build-system) ;; FIXME: Incompatible sphinx version. (arguments From 27693b1e34347c4e2e4d12283c8c825ec6332716 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Sat, 18 Feb 2017 18:12:34 +0100 Subject: [PATCH 132/150] gnu: python-oslosphinx: Re-enable tests. * gnu/packages/openstack.scm (python-oslosphinx): Re-enable tests. --- gnu/packages/openstack.scm | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index fe0dd11eb3..381480b786 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -604,9 +604,15 @@ and building documentation from them.") (base32 "09mxqyabi68f3s3arvdhlhq0mn38vf74jbsfcg84151hcj6czhnl")))) (build-system python-build-system) - ;; FIXME: Incompatible sphinx version. (arguments - '(#:tests? #f)) + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Note: Upstream tests would have also built the release notes. + ;; That only would work if we were in a git checkout. + ;; Therefore, we don't do it here. + (zero? (system* "python" "setup.py" "build_sphinx"))))))) (propagated-inputs `(("python-requests" ,python-requests))) (native-inputs From a10b9810c6abfca006c8f2e0c2f8a4c60753c338 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 08:55:48 +0100 Subject: [PATCH 133/150] gnu: python-sphinx: Propagate python-requests. * gnu/packages/python.scm (python-sphinx)[native-inputs]: Move PYTHON-REQUESTS to ... [propagated-inputs]: ... here. --- gnu/packages/python.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 93e18b2fb9..fff9a666a6 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -2994,13 +2994,13 @@ reStructuredText.") ("python-docutils" ,python-docutils) ("python-jinja2" ,python-jinja2) ("python-pygments" ,python-pygments) + ("python-requests" ,python-requests) ("python-six" ,python-six))) (native-inputs `(("graphviz" ,graphviz) ("python-html5lib" ,python-html5lib) ("python-mock" ,python-mock) - ("python-nose" ,python-nose) - ("python-requests" ,python-requests))) + ("python-nose" ,python-nose))) (home-page "http://sphinx-doc.org/") (synopsis "Python documentation generator") (description "Sphinx is a tool that makes it easy to create documentation From 8ef8de799fcbc7b1a04be0d33e1183c766d0f893 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 21:40:08 +0100 Subject: [PATCH 134/150] gnu: duplicity: Fix tests. * gnu/packages/backup.scm (duplicity)[native-inputs]: Add PAR2CMDLINE. [arguments]: Move /bin/sh substitution to 'patch-source' phase and add one file. --- gnu/packages/backup.scm | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 8dbe32ebdd..809d54a646 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -67,6 +67,7 @@ (build-system python-build-system) (native-inputs `(("util-linux" ,util-linux) ;setsid command, for the tests + ("par2cmdline" ,par2cmdline) ("python-pexpect" ,python2-pexpect) ("mock" ,python2-mock))) (propagated-inputs @@ -83,16 +84,18 @@ #:test-target "test" #:phases (modify-phases %standard-phases - (add-before - 'build 'patch-source ; embed gpg store name - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "duplicity/gpginterface.py" - (("self.call = 'gpg'") - (string-append "self.call = '" (assoc-ref inputs "gnupg") "/bin/gpg'"))))) + (add-before 'build 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + ;; embed gpg store name + (substitute* "duplicity/gpginterface.py" + (("self.call = 'gpg'") + (string-append "self.call = '" (assoc-ref inputs "gnupg") "/bin/gpg'"))) + (substitute* '("testing/functional/__init__.py" + "testing/overrides/bin/lftp") + (("/bin/sh") (which "sh"))) + #t)) (add-before 'check 'check-setup (lambda* (#:key inputs #:allow-other-keys) - (substitute* "testing/functional/__init__.py" - (("/bin/sh") (which "sh"))) (setenv "HOME" (getcwd)) ;gpg needs to write to $HOME (setenv "TZDIR" ;some timestamp checks need TZDIR (string-append (assoc-ref inputs "tzdata") From fffcd8b829d1fbd8bdb6af85385033224c576cec Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 22:19:08 +0100 Subject: [PATCH 135/150] gnu: python-pbkdf2: Fix tests. * gnu/packages/python.scm (python-pbkdf2)[arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index fff9a666a6..70aa8cd665 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -12967,6 +12967,15 @@ protocols written in pure Python.") (base32 "0yb99rl2mbsaamj571s1mf6vgniqh23v98k4632150hjkwv9fqxc")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) "/build/lib:" + (getenv "PYTHONPATH"))) + (zero? (system* "python" "test/test_pbkdf2.py"))))))) (propagated-inputs `(("python-pycrypto" ,python-pycrypto))) ; optional (home-page "http://www.dlitz.net/software/python-pbkdf2/") From d296d30013587722b37aeb0be114e00b15564f3f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 23:55:37 +0100 Subject: [PATCH 136/150] gnu: python-flask-wtf: Drop failing test. * gnu/packages/python.scm (python-flask-wtf, python2-flask-wtf)[arguments]: Add phase to delete file that needs network access. --- gnu/packages/python.scm | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 70aa8cd665..635feb489c 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -9922,6 +9922,16 @@ presume or force a developer to use a particular tool or library.") (base32 "04l5743j2dici46038sqlzvf0xzpg8rf7s9ld2x24xv7f4idg990")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-before 'check 'drop-failing-test + (lambda _ + ;; FIXME: This file tries resolving an external server, which + ;; fails. Try to patch out the offending section instead of + ;; deleting the whole thing. + (delete-file "tests/test_recaptcha.py") + #t))))) (propagated-inputs `(("python-flask-babel" ,python-flask-babel) ("python-babel" ,python-babel) From 2c1cad7ad2f95685be889bdf662ffdf8df87d5cf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 15 Feb 2017 23:59:51 +0100 Subject: [PATCH 137/150] gnu: python-flake8-polyfill: Enable tests. * gnu/packages/python.scm (python-flake8-polyfill, python2-flake8-polyfill)[native-inputs]: Add PYTHON-FLAKE8, PYTHON-MOCK, PYTHON-PYCODESTYLE and PYTHON-PYTEST. New field. [arguments]: Replace 'check' phase with custom command. --- gnu/packages/python.scm | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 635feb489c..89d8c5cb06 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -6250,6 +6250,20 @@ complexity of Python source code.") (base32 "02gn2wxvh9vnf7m7dld7ca4l60mg5c370hv3swwppkngwaqmcw67")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) "/build/lib:" + (getenv "PYTHONPATH"))) + (zero? (system* "py.test" "-v"))))))) + (native-inputs + `(("python-flake8" ,python-flake8) + ("python-mock" ,python-mock) + ("python-pycodestyle" ,python-pycodestyle) + ("python-pytest" ,python-pytest))) (home-page "https://gitlab.com/pycqa/flake8-polyfill") (synopsis "Polyfill package for Flake8 plugins") (description From 9200fe14f70506474cfc178dc8c1066bf00a5e7e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 17 Feb 2017 00:57:11 +0000 Subject: [PATCH 138/150] gnu: python-scipy: Declare python2-variant. This is a followup to a50e03014177d2f00b5b85d3e1c295406f842016. * gnu/packages/python.scm (python-scipy)[properties]: New field. --- gnu/packages/python.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 89d8c5cb06..e7553bb82b 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -4036,6 +4036,7 @@ atlas_libs = openblas (description "The SciPy library is one of the core packages that make up the SciPy stack. It provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization.") + (properties `((python2-variant . ,(delay python2-scipy)))) (license license:bsd-3))) (define-public python2-scipy From 4d25c486a5565e2b3fed1be53bc8b8278204f86e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 17 Feb 2017 02:37:58 +0100 Subject: [PATCH 139/150] gnu: python-scikit-learn: Fix test failure. * gnu/packages/python.scm (python-scikit-learn, python2-scikit-learn)[arguments]: Use 'modify-phases'. Move 'check' phase after 'install' and incorporate 'set-HOME' phase. --- gnu/packages/python.scm | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e7553bb82b..e2bf5f73da 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -3210,11 +3210,20 @@ and is very extensible.") (build-system python-build-system) (arguments `(#:phases - (alist-cons-before - 'check 'set-HOME - ;; some tests require access to "$HOME" - (lambda _ (setenv "HOME" "/tmp")) - %standard-phases))) + (modify-phases %standard-phases + (delete 'check) + (add-after 'install 'check + ;; Running tests from the source directory requires + ;; an "inplace" build with paths relative to CWD. + ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing + ;; Use the installed version instead. + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + ;; some tests require access to "$HOME" + (setenv "HOME" "/tmp") + ;; Step out of the source directory just to be sure. + (chdir "..") + (zero? (system* "nosetests" "-v" "sklearn"))))))) (inputs `(("openblas" ,openblas))) (native-inputs From dc027d401471955a3edd17cdd810357c6c01ca41 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 17 Feb 2017 07:09:46 +0100 Subject: [PATCH 140/150] gnu: python-pyicu: Fix build. * gnu/packages/python.scm (python-pyicu, python2-pyicu)[arguments]: New field. Add phase to delete locale-dependent test. --- gnu/packages/python.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index e2bf5f73da..8353ca178f 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -1288,6 +1288,15 @@ Python 3.3+.") (base32 "16rmxy9y0qhqqna2v49i7nzwm09as699rbyvh4raw7w602w55c3k")))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (add-before 'check 'delete-failing-test + (lambda _ + ;; XXX: These tests require locales that are unavailable + ;; in the build environment. + (delete-file "test/test_DateTimeParserGenerator.py") + #t))))) (inputs `(("icu4c" ,icu4c))) (home-page "http://pyicu.osafoundation.org/") From 42945fb58c4652943a036c99f9bcc59fab61909b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 18:24:06 +0100 Subject: [PATCH 141/150] gnu: python-fake-factory: Fix build on 32bit. * gnu/packages/patches/python-fake-factory-fix-build-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/python.scm (python-fake-factory, python2-fake-factory)[source]: Use it. --- gnu/local.mk | 1 + .../python-fake-factory-fix-build-32bit.patch | 36 +++++++++++++++++++ gnu/packages/python.scm | 5 ++- 3 files changed, 41 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-fake-factory-fix-build-32bit.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0b9b5b1a1e..63eb56cc51 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -859,6 +859,7 @@ dist_patch_DATA = \ %D%/packages/patches/python2-rdflib-drop-sparqlwrapper.patch \ %D%/packages/patches/python-statsmodels-fix-tests.patch \ %D%/packages/patches/python-configobj-setuptools.patch \ + %D%/packages/patches/python-fake-factory-fix-build-32bit.patch \ %D%/packages/patches/python-paste-remove-website-test.patch \ %D%/packages/patches/python-paste-remove-timing-test.patch \ %D%/packages/patches/python-pygit2-disable-network-tests.patch \ diff --git a/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch b/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch new file mode 100644 index 0000000000..cb60896fad --- /dev/null +++ b/gnu/packages/patches/python-fake-factory-fix-build-32bit.patch @@ -0,0 +1,36 @@ +These tests fail on 32-bit due to an overflow. + +Upstream bug URL: https://github.com/joke2k/faker/issues/408 + +diff --git a/faker/tests/__init__.py b/faker/tests/__init__.py +index 6026772..58b6b83 100644 +--- a/faker/tests/__init__.py ++++ b/faker/tests/__init__.py +@@ -384,7 +384,6 @@ class FactoryTestCase(unittest.TestCase): + provider = Provider + # test century + self.assertTrue(self._datetime_to_time(provider.date_time_this_century(after_now=False)) <= self._datetime_to_time(datetime.datetime.now())) +- self.assertTrue(self._datetime_to_time(provider.date_time_this_century(before_now=False, after_now=True)) >= self._datetime_to_time(datetime.datetime.now())) + # test decade + self.assertTrue(self._datetime_to_time(provider.date_time_this_decade(after_now=False)) <= self._datetime_to_time(datetime.datetime.now())) + self.assertTrue(self._datetime_to_time(provider.date_time_this_decade(before_now=False, after_now=True)) >= self._datetime_to_time(datetime.datetime.now())) +@@ -413,8 +412,6 @@ class FactoryTestCase(unittest.TestCase): + + # ensure all methods provide timezone aware datetimes + with self.assertRaises(TypeError): +- provider.date_time_this_century(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now() +- with self.assertRaises(TypeError): + provider.date_time_this_decade(after_now=False, tzinfo=utc) <= datetime.datetime.now() + with self.assertRaises(TypeError): + provider.date_time_this_year(after_now=False, tzinfo=utc) <= datetime.datetime.now() +@@ -423,7 +420,6 @@ class FactoryTestCase(unittest.TestCase): + + # test century + self.assertTrue(provider.date_time_this_century(after_now=False, tzinfo=utc) <= datetime.datetime.now(utc)) +- self.assertTrue(provider.date_time_this_century(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now(utc)) + # test decade + self.assertTrue(provider.date_time_this_decade(after_now=False, tzinfo=utc) <= datetime.datetime.now(utc)) + self.assertTrue(provider.date_time_this_decade(before_now=False, after_now=True, tzinfo=utc) >= datetime.datetime.now(utc)) +-- +2.11.1 + diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 8353ca178f..e26e442e58 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -11228,7 +11228,10 @@ parsing UK postcodes.") (uri (pypi-uri "fake-factory" version)) (sha256 (base32 - "0vs0dkmg0dlaxf8w6q2i3k0i03gmp56ablldv7ci9x3nbadkn71g")))) + "0vs0dkmg0dlaxf8w6q2i3k0i03gmp56ablldv7ci9x3nbadkn71g")) + (patches + (search-patches + "python-fake-factory-fix-build-32bit.patch")))) (build-system python-build-system) (arguments '(#:phases From ec867b86a0575d049922e074312b36dfb9d71868 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:27:47 +0100 Subject: [PATCH 142/150] gnu: python2-oslotest: Disable tests. * gnu/packages/openstack.scm(python2-oslotest)[arguments]: New field. (python-oslotest)[properties]: Delay it. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 381480b786..8130097c83 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -662,10 +662,16 @@ from the OpenStack project.") (description "The Oslo Test framework provides common fixtures, support for debugging, and better support for mocking results.") + (properties `((python2-variant . ,(delay python2-oslotest)))) (license asl2.0))) (define-public python2-oslotest - (package-with-python2 python-oslotest)) + (package (inherit (package-with-python2 + (strip-python2-variant python-oslotest))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-oslo.utils (package From dc6bedbacadf7d0c9871fe3b22415d12ea266f74 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:45:46 +0100 Subject: [PATCH 143/150] gnu: python2-requests-mock: Disable tests. * gnu/packages/openstack.scm (python2-requests-mock)[arguments]: New field. (python-requests-mock): Delay it. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 8130097c83..d41c9c8916 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -271,10 +271,16 @@ tested on Python version 3.2, 2.7 and 2.6.") (description "This module provides a building block to stub out the HTTP requests portions of your testing code.") + (properties `((python2-variant . ,(delay python2-requests-mock)))) (license asl2.0))) (define-public python2-requests-mock - (package-with-python2 python-requests-mock)) + (package (inherit (package-with-python2 + (strip-python2-variant python-requests-mock))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-stevedore (package From 11a8767b9482f8ff6e89b3ab782b28400e2126d5 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:48:11 +0100 Subject: [PATCH 144/150] gnu: python2-stevedore: Disable tests. * gnu/packages/openstack.scm (python2-stevedore)[arguments]: New field. (python-stevedore)[properties]: New field. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index d41c9c8916..f6a399aa2f 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -317,10 +317,16 @@ mechanism by building on top of setuptools entry points. The code for managing entry points tends to be repetitive, though, so stevedore provides manager classes for implementing common patterns for using dynamically loaded extensions.") + (properties `((python2-variant . ,(delay python2-stevedore)))) (license asl2.0))) (define-public python2-stevedore - (package-with-python2 python-stevedore)) + (package (inherit (package-with-python2 + (strip-python2-variant python-stevedore))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-tempest-lib (package From 041b5932dad0944079118ec97dd0d2317ba1f802 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:51:39 +0100 Subject: [PATCH 145/150] gnu: python2-bandit: Disable tests. * gnu/packages/openstack.scm (python2-bandit)[arguments]: New field. (python-bandit)[properties]: Delay it. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index f6a399aa2f..632534fb3c 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -65,10 +65,16 @@ To do this Bandit processes each file, builds an AST from it, and runs appropriate plugins against the AST nodes. Once Bandit has finished scanning all the files it generates a report.") + (properties `((python2-variant . ,(delay python2-bandit)))) (license asl2.0))) (define-public python2-bandit - (package-with-python2 python-bandit)) + (package (inherit (package-with-python2 + (strip-python2-variant python-bandit))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-debtcollector (package From e1f2e190471ae87bc51f8e9539f4bfbe9f69caa0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 20:56:06 +0100 Subject: [PATCH 146/150] gnu: python2-swiftclient: Disable tests. * gnu/packages/openstack.scm (python2-swiftclient)[arguments]: New field. --- gnu/packages/openstack.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index 632534fb3c..cdd37815de 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -860,6 +860,10 @@ permanence.") (define-public python2-swiftclient (let ((swiftclient (package-with-python2 python-swiftclient))) (package (inherit swiftclient) + (arguments + `(#:python ,python-2 + ;; FIXME: subunit.run discover: error: no such option: --list + #:tests? #f)) (propagated-inputs `(("python2-futures" ,python2-futures) ("python2-requests" ,python2-requests) From d6caebc4d63ac8e7ae5e82b1261557e1b6898c10 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 24 Feb 2017 21:30:22 +0100 Subject: [PATCH 147/150] gnu: python2-reno: Disable tests. * gnu/packages/openstack.scm (python2-reno)[arguments]: New field. (python-reno)[properties]: Delay it. --- gnu/packages/openstack.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/openstack.scm b/gnu/packages/openstack.scm index cdd37815de..51566b65e3 100644 --- a/gnu/packages/openstack.scm +++ b/gnu/packages/openstack.scm @@ -605,10 +605,16 @@ in transmittable and storable formats, such as JSON and MessagePack.") (synopsis "Release notes manager") (description "Reno is a tool for storing release notes in a git repository and building documentation from them.") + (properties `((python2-variant . ,(delay python2-reno)))) (license asl2.0))) (define-public python2-reno - (package-with-python2 python-reno)) + (package (inherit (package-with-python2 + (strip-python2-variant python-reno))) + (arguments + `(#:python ,python-2 + ;; FIXME: 'subunit.run discover: error: no such option: --list' + #:tests? #f)))) (define-public python-oslosphinx (package From 1885bb0c08e943a2e0e37c5c0a83473c8af904d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 21 Feb 2017 18:28:21 +0100 Subject: [PATCH 148/150] gnu: python-dendropy: Fix failing tests. * gnu/packages/patches/python-dendropy-fix-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 3 +- .../patches/python-dendropy-fix-tests.patch | 41 +++++++++++++++++++ 3 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/python-dendropy-fix-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index 63eb56cc51..899dc06b8e 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -853,6 +853,7 @@ dist_patch_DATA = \ %D%/packages/patches/python-3-search-paths.patch \ %D%/packages/patches/python-3.4-fix-tests.patch \ %D%/packages/patches/python-3.5-fix-tests.patch \ + %D%/packages/patches/python-dendropy-fix-tests.patch \ %D%/packages/patches/python-file-double-encoding-bug.patch \ %D%/packages/patches/python-fix-tests.patch \ %D%/packages/patches/python-parse-too-many-fields.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5a1738b936..de6186de27 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1981,7 +1981,8 @@ accessing bigWig files.") (uri (pypi-uri "DendroPy" version)) (sha256 (base32 - "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")))) + "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p")) + (patches (search-patches "python-dendropy-fix-tests.patch")))) (build-system python-build-system) (home-page "http://packages.python.org/DendroPy/") (synopsis "Library for phylogenetics and phylogenetic computing") diff --git a/gnu/packages/patches/python-dendropy-fix-tests.patch b/gnu/packages/patches/python-dendropy-fix-tests.patch new file mode 100644 index 0000000000..30ab618ff1 --- /dev/null +++ b/gnu/packages/patches/python-dendropy-fix-tests.patch @@ -0,0 +1,41 @@ +This patch fixes two test failures. It was downloaded from: +https://github.com/jeetsukumaran/DendroPy/commit/93f984bba7a6c588a28ca87f4e557ce283809453 + +From 93f984bba7a6c588a28ca87f4e557ce283809453 Mon Sep 17 00:00:00 2001 +From: jeetsukumaran +Date: Tue, 21 Feb 2017 16:41:01 -0500 +Subject: [PATCH] Update to Python 3 container and iteration semantics + +--- + dendropy/dataio/newickreader.py | 3 ++- + dendropy/datamodel/treemodel.py | 3 +++ + 2 files changed, 5 insertions(+), 1 deletion(-) + +diff --git a/dendropy/dataio/newickreader.py b/dendropy/dataio/newickreader.py +index 6dcf3c5..f978729 100644 +--- a/dendropy/dataio/newickreader.py ++++ b/dendropy/dataio/newickreader.py +@@ -303,7 +303,8 @@ def tree_iter(self, + taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol) + yield tree + if tree is None: +- raise StopIteration ++ # raise StopIteration ++ return + + def _read(self, + stream, +diff --git a/dendropy/datamodel/treemodel.py b/dendropy/datamodel/treemodel.py +index 0ecfe31..73146f0 100644 +--- a/dendropy/datamodel/treemodel.py ++++ b/dendropy/datamodel/treemodel.py +@@ -772,6 +772,9 @@ def __hash__(self): + def __eq__(self, other): + return self is other + ++ def __lt__(self, other): ++ return id(self) < id(other) ++ + ########################################################################### + ### Basic Structure + From e9eafae289aa70a3e839902ddf48a40d3c97b05b Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 12:54:19 +0100 Subject: [PATCH 149/150] gnu: khard: Disable tests. * gnu/packages/mail.scm (khard)[arguments]: Set #:tests? #f. --- gnu/packages/mail.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index f4f732ec19..8651deefb5 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1509,7 +1509,11 @@ maintained.") (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (doc (string-append out "/share/doc/khard"))) - (copy-recursively "misc/khard" doc))))))) + (copy-recursively "misc/khard" doc) + #t)))) + ;; FIXME: check phase fails with + ;; "Config file /tmp/.config/khard/khard.conf not available" + #:tests? #f)) (propagated-inputs `(("python-vobject" ,python-vobject) ("python-pyyaml" ,python-pyyaml) From 2bb12f5a68f6547b3de295c22c2886aaa0415e47 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 27 Feb 2017 15:30:03 +0100 Subject: [PATCH 150/150] gnu: ribodiff: Fix test failure. * gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK and PYTHON2-NOSE. --- gnu/packages/bioinformatics.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index de6186de27..bdcb5a4010 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -499,6 +499,9 @@ provides the Ribotaper pipeline.") ("python-matplotlib" ,python2-matplotlib) ("python-scipy" ,python2-scipy) ("python-statsmodels" ,python2-statsmodels))) + (native-inputs + `(("python-mock" ,python2-mock) + ("python-nose" ,python2-nose))) (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/") (synopsis "Detect translation efficiency changes from ribosome footprints") (description "RiboDiff is a statistical tool that detects the protein