Commit Graph

887 Commits

Author SHA1 Message Date
Hartmut Goebel 00e10c6e67
gnu: Remove python-setuptools and python2-setuptools from inputs (part 3)
This patch contains the changes where setuptools are used in an inherited
package and removing this input keeps the need for inheriting the package.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove
  python-setuptools respective python2-setuptools from [inputs],
  [native-inputs] and [propagated-inputs] in Python 2 packages inheriting from
  a Python 3 package.
* gnu/packages/python.scm (python2-pytest-mock,
  python2-oauthlib,
  python2-seaborn,
  python2-tornado,
  python2-terminado,
  python2-rauth,
  python2-anyjson,
  python2-amqp,
  python2-kombu,
  python2-billiard,
  python2-celery,
  python2-jellyfish,
  python2-binaryornot,
  python2-natsort,
  python2-graphene): Likewise.
* gnu/packages/statistics.scm (python2-statsmodels): Likewise.
2016-11-15 22:28:38 +01:00
Hartmut Goebel f3b98f4fec
gnu: Remove python-setuptools and python2-setuptools from inputs (part 2)
This patch contains the changes where removing setuptools from the inputs
affected some code-lines beside.

* gnu/packages/admin.scm (ansible): Remove all [inputs], [native-inputs] and
  [propagated-inputs] where python-setuptools or python2-setuptools are the
  sole entries. Remove python-setuptools and python2-setuptools listed on a
  line by its own from [inputs], [native-inputs] and [propagated-inputs].

* gnu/packages/backup.scm (duplicity): Likewise.
* gnu/packages/bioinformatics.scm (bamm, python2-pybedtools,
  python2-bx-python, python2-dendropy, python-pysam, python2-pysam, clipper,
  crossmap, cutadapt, deeptools, grit, idr, python2-warpedlmm,
  pbtranscript-tofu, seqmagick): Likewise.
* gnu/packages/docbook.scm (dblatex): Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg, python2-pyxdg): Likewise.
* gnu/packages/lirc.scm (python2-lirc): Likewise.
* gnu/packages/mp3.scm (eyed3): Likewise.
* gnu/packages/nutrition.scm (gourmet): Likewise.
* gnu/packages/openstack.scm (python-hacking, python2-hacking,
  python-os-testr, python2-os-testr,
  python-stevedore, python2-stevedore,
  python-tempest-lib, python2-tempest-lib,
  python-oslo.log, python2-oslo.log,
  python-keystoneclient, python2-keystoneclient): Likewise.
* gnu/packages/password-utils.scm (assword): Likewise.
* gnu/packages/python.scm (python-passlib, python2-passlib,
  python-babel, python2-babel,
  python-parse-type,
  python-pytest, python2-pytest,
  python-scripttest, python2-scripttest,
  python-testtools, python2-testtools,
  python-testscenarios, python2-testscenarios,
  python-subunit, python2-subunit,
  python-pbr-0.11,
  python-pbr, python2-pbr,
  python-testrepository, python2-testrepository,
  behave,
  python-wheel, python2-wheel,
  python-requests, python2-requests,
  python-jsonschema, python2-jsonschema,
  python-pyjwt, python2-pyjwt,
  python-virtualenv, python2-virtualenv,
  python-jinja2, python2-jinja2,
  python-joblib, python2-joblib,
  python-sphinx, python2-sphinx,
  python-feedgenerator, python2-feedgenerator,
  python-scikit-image, python2-scikit-image,
  python-redis, python2-redis,
  python2-fastlmm,
  python-numpydoc, python2-numpydoc,
  python-matplotlib, python2-matplotlib,
  python2-pysnptools,
  python-rpy2, python2-rpy2,
  python-pillow, python2-pillow,
  python-pycparser, python2-pycparser,
  python-cffi, python2-cffi,
  python-cairocffi, python2-cairocffi,
  python-drmaa, python2-drmaa,
  python-pathpy, python2-pathpy,
  python-simplegeneric, python2-simplegeneric,
  python-ipython, python2-ipython,
  python-apsw, python2-apsw,
  python-lxml, python2-lxml,
  python-networkx, python2-networkx,
  python-pyzmq, python2-pyzmq,
  python-mccabe, python2-mccabe,
  python-mccabe-0.2.1,
  python-flake8, python2-flake8,
  python-flake8-2.2.4,
  python-mistune, python2-mistune,
  python-ptyprocess, python2-ptyprocess,
  python-llfuse, python2-llfuse,
  python-webob, python2-webob,
  python-xlrd, python2-xlrd,
  python-tables, python2-tables,
  python-pip, python2-pip,
  python-libarchive-c, python2-libarchive-c,
  python-docopt, python2-docopt,
  python-pyrfc3339, python2-pyrfc3339,
  python-configobj, python2-configobj,
  python-clint, python2-clint,
  python-rply, python2-rply,
  python2-rpython,
  python-widgetsnbextension, python2-widgetsnbextension
  jupyter,
  python-jupyter-console, python2-jupyter-console,
  python-hy, python2-hy,
  python-urllib3, python2-urllib3,
  python-rsa, python2-rsa,
  python-tox, python2-tox,
  python2-hypothesis,
  python-paste, python2-paste,
  python-pastescript, python2-pastescript,
  python2-unicodecsv,
  python-pkgconfig, python2-pkgconfig,
  python2-rope,
  python-sqlparse, python2-sqlparse,
  python-gevent, python2-gevent,
  python-tabulate, python2-tabulate,
  python-arrow, python2-arrow,
  python-cleo, python2-cleo,
  python-fake-factory, python2-fake-factory,
  ptpython): Likewise.
* gnu/packages/rdf.scm (python-rdflib, python2-rdflib): Likewise.
* gnu/packages/terminals.scm (asciinema): Likewise.
* gnu/packages/version-control.scm (git-annex-remote-hubic): Likewise.
* gnu/packages/xdisorg.scm (arandr): Likewise.
2016-11-15 22:27:31 +01:00
Hartmut Goebel f54d6bacbf
gnu: Remove python-setuptools and python2-setuptools from inputs (part 1a)
This patch contains the changes in python.scm where removing setuptools from
the inputs could be achieved by removing complete lines.

* gnu/packages/python.scm (python-psutil, python2-psutil,
  python-py-bcrypt, python2-py-bcrypt,
  python-paramiko, python2-paramiko,
  python-httplib2, python2-httplib2,
  python-ecdsa, python2-ecdsa,
  python-ccm, python2-ccm,
  python2-backport-ssl-match-hostname,
  python-pycrypto, python2-pycrypto,
  python-six, python2-six,
  python-dateutil, python2-dateutil,
  python2-mechanize,
  python-extras, python2-extras,
  python-mimeparse, python2-mimeparse,
  python-nose, python2-nose,
  python-nose2, python2-nose2,
  python-unittest2, python2-unittest2,
  python-py, python2-py,
  python-testresources, python2-testresources,
  python-fixtures-0.3.16,
  python-fixtures, python2-fixtures,
  python-coverage, python2-coverage,
  python-discover, python2-discover,
  python-exif-read, python2-exif-read,
  python-pyld, python2-pyld,
  python-certifi, python2-certifi,
  python-click, python2-click,
  python-vcversioner, python2-vcversioner,
  python-unidecode, python2-unidecode,
  python-pyyaml, python2-pyyaml,
  python-markupsafe, python2-markupsafe,
  python-pystache, python2-pystache,
  python-docutils, python2-docutils,
  python-pygments, python2-pygments,
  python-sphinx-rtd-theme, python2-sphinx-rtd-theme,
  python-blinker, python2-blinker,
  python-rq, python2-rq,
  python-numpy, python2-numpy,
  python-distutils-extra, python2-distutils-extra,
  python2-elib.intl,
  python-pillow, python2-pillow,
  python-xcffib, python2-xcffib,
  python-decorator, python2-decorator,
  python-gridmap, python2-gridmap,
  python-pickleshare, python2-pickleshare,
  python-isodate, python2-isodate,
  python-html5lib, python2-html5lib,
  python2-cssutils,
  python-cssselect, python2-cssselect,
  python-netifaces, python2-netifaces,
  python-sympy, python2-sympy,
  python-testlib, python2-testlib,
  python2-xlib,
  python-singledispatch, python2-singledispatch,
  python-backports-abc, python2-backports-abc,
  python-pep8, python2-pep8,
  python-pyflakes, python2-pyflakes,
  python-fonttools, python2-fonttools,
  python-ly,
  python-appdirs, python2-appdirs,
  python-netaddr, python2-netaddr,
  python-wrapt, python2-wrapt,
  python-iso8601, python2-iso8601,
  python-monotonic, python2-monotonic,
  python-prettytable, python2-prettytable,
  python-pyasn1-modules, python2-pyasn1-modules,
  python-idna, python2-idna,
  python-pretend, python2-pretend,
  python-cryptography-vectors, python2-cryptography-vectors,
  python-cryptography, python2-cryptography,
  python-pyopenssl, python2-pyopenssl,
  python-debian, python2-debian,
  python-chardet, python2-chardet,
  python-zope-event, python2-zope-event,
  python-zope-i18nmessageid, python2-zope-i18nmessageid,
  python-websocket-client, python2-websocket-client,
  python-args, python2-args,
  python-astor, python2-astor,
  python2-functools32,
  python2-futures,
  python2-promise,
  python-colorama, python2-colorama,
  python-pluggy, python2-pluggy,
  python-jmespath, python2-jmespath,
  python-botocore, python2-botocore,
  awscli,
  python-pytest-subtesthack, python2-pytest-subtesthack,
  python-pastedeploy, python2-pastedeploy,
  python-magic, python2-magic,
  python2-s3cmd,
  python2-bz2file,
  python-cysignals, python2-cysignals,
  python-py3status,
  python-tblib, python2-tblib,
  python-greenlet, python2-greenlet,
  python-twisted, python2-twisted,
  python-kazoo, python2-kazoo,
  python-pykafka, python2-pykafka,
  python2-jsonrpclib,
  python-chai, python2-chai,
  python-inflection, python2-inflection,
  python-pylev, python2-pylev,
  python-lazy-object-proxy, python2-lazy-object-proxy,
  python-dnspython, python2-dnspython,
  python-email-validator, python2-email-validator,
  python-ukpostcodeparser, python2-ukpostcodeparser,
  python-pyaml, python2-pyaml,
  python-flexmock, python2-flexmock,
  python-orator, python2-orator,
  python-bleach, python2-bleach,
  python-ipywidgets, python2-ipywidgets,
  python-nbconvert, python2-nbconvert,
  python-nbformat, python2-nbformat,
  python-axolotl-curve25519, python-axolotl2-curve25519,
  python-axolotl, python2-axolotl,
  python-nautilus, python-s3transfer): Remove python-setuptools and
  python2-setuptools from [inputs], [native-inputs] or [propagated-inputs].
  Remove [inputs], [native-inputs] and [propagated-inputs] where
  python-setuptools or python2-setuptools were the sole entry.
2016-11-15 21:54:58 +01:00
Hartmut Goebel 15e57f5762
gnu: python-2.7: Add all guix prefixes in PYTHONPATH to site-prefixes.
* gnu/packages/patches/python-2.7-site-prefixes.patch: New file.
* gnu/packages/python.scm (python-2)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Add patch.
2016-11-15 17:37:48 +01:00
Hartmut Goebel aaf75c890b
gnu: ensure pip and setuptools are installed even for Python 2.
* gnu/packages/python.scm (python-2.7): Add "--with-ensurepip=install" to
  configure-flags.
* doc/guix.texi (Python Modules): Document it.
2016-11-15 17:37:40 +01:00
Efraim Flashner 538fe01934
gnu: python-vcversioner: Update to 2.16.0.0.
* gnu/packages/python.scm (python-vcversioner): Update to 2.16.0.0.
[inputs]: Remove python-setuptools.
[properties]: New field.
(python2-vcversioner): Use 'strip-python2-variant'.
[native-inputs]: Add python2-setuptools.
2016-11-15 09:45:28 +02:00
Efraim Flashner 8bcd6b91ff
gnu: python-jsonschema: Use 'nosetests'.
* gnu/packages/python.scm (python-jsonschema)[arguments]: Replace 'check
phase with python nosetests.
[native-inputs]: Add python-nose.
[home-page]: Use https.
(python2-jsonschema)[native-inputs]: Add python2-mock.
2016-11-14 22:49:50 +02:00
Ludovic Courtès 2cab1dd58b
Merge branch 'core-updates' 2016-11-13 00:34:16 +01:00
Danny Milosavljevic 0a7f17f0e0
gnu: Add python-flask-restplus.
* gnu/packages/python.scm (python-flask-restplus): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-11-12 16:17:40 +01:00
Danny Milosavljevic 1e6112d89f
gnu: Add python-rednose.
* gnu/packages/python.scm (python-rednose): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-11-12 16:15:08 +01:00
Danny Milosavljevic e2fca4906e
gnu: Add python-termstyle.
* gnu/packages/python.scm (python-termstyle): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-11-12 16:10:23 +01:00
Leo Famulari aba5182c69
gnu: python-pillow: Update to 3.3.3 [fixes CVE-2016-{9189,9190}].
* gnu/packages/python.scm (python-pillow, python2-pillow): Update to 3.3.3.
2016-11-10 18:17:50 -05:00
Marius Bakke eaba9d6670
gnu: python-jsonschema: Correct inputs.
* gnu/packages/python.scm (python-jsonschema)[inputs]: Remove
python-setuptools. Move python-vcversioner to ...
[native-inputs]: ... here.
* gnu/packages/python.scm (python2-jsonschema)[inputs]: Move
python2-functools32 to ...
[propagated-inputs]: ... here.
[native-inputs]: Add python2-setuptools.
2016-11-08 18:22:07 +00:00
Marius Bakke 912dcbad86
gnu: python-cryptography, python-cryptography-vectors: Update to 1.5.3.
* gnu/packages/python.scm (python-cryptography, python2-cryptography):
Update to 1.5.3.
[native-inputs]: Add python-pytz. Change python-pytest to python-pytest-2.9.2.
(python-cryptography-vectors, python2-cryptography-vectors): Update to 1.5.3.
2016-11-08 16:14:15 +00:00
Leo Famulari fca4ff3559
gnu: Add python-pytest-2.9.2.
* gnu/packages/python.scm (python-pytest-2.9.2): New variable.
2016-11-08 16:14:04 +00:00
Danny Milosavljevic 6a686b18e0
gnu: python-sqlalchemy-utils: Mention optional dependencies in description.
* gnu/packages/python.scm (python-sqlalchemy-utils,
python2-sqlalchemy-utils)[description]: Mention optional dependencies.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-11-07 12:49:03 -05:00
Mark H Weaver 71e21fb26d
Merge branch 'master' into core-updates 2016-11-07 00:33:16 -05:00
Danny Milosavljevic 26d07efb79
gnu: python-sqlalchemy-utils: Use python-pytest.
* gnu/packages/python.scm (python-sqlalchemy-utils)[native-inputs]: Add
python-pytest.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-06 19:53:15 +00:00
Danny Milosavljevic c22b4f87c2
gnu: python-sqlalchemy-utils: Propagate existing inputs.
* gnu/packages/python.scm (python-sqlalchemy-utils)[inputs]: Move to ...
[propagated-inputs]: ... here.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-06 19:53:14 +00:00
Danny Milosavljevic 462bf27157
gnu: Add python-flask-babel.
* gnu/packages/python.scm (python-flask-babel, python2-flask-babel):
  New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-06 19:53:14 +00:00
Danny Milosavljevic 9dede065ba
gnu: Add python-furl.
* gnu/packages/python.scm (python-furl, python2-furl): New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-06 19:53:14 +00:00
Danny Milosavljevic b91912c42a
gnu: Add python-orderedmultidict.
* gnu/packages/python.scm (python-orderedmultidict, python2-orderedmultidict):
  New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-06 19:53:13 +00:00
Danny Milosavljevic 4a0933307e
gnu: Add python-pycodestyle.
* gnu/packages/python.scm (python-pycodestyle, python2-pycodestyle):
  New variables.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-06 19:53:13 +00:00
Mark H Weaver 8b6ad165d1
Merge branch 'master' into core-updates 2016-11-06 03:29:06 -05:00
Leo Famulari 683cdbf51b
gnu: python-axolotl-curve25519: Fix license.
* gnu/packages/python.scm (python-axolotl-curve25519,
python2-axolotl-curve25519)[license]: Replace ISC with BSD-3.
2016-11-05 16:34:14 -04:00
Arun Isaac 06ff083754
gnu: Add python-axolotl.
* gnu/packages/python.scm (python-axolotl, python2-axolotl): New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-11-05 16:32:19 -04:00
Arun Isaac 2f6dd9cdef
gnu: Add python-axolotl-curve25519.
* gnu/packages/python.scm (python-axolotl-curve25519,
  python2-axolotl-curve25519): New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-11-05 16:32:15 -04:00
Leo Famulari 9422c98a0a
gnu: python-imagesize: Disable the test suite.
* gnu/packages/python.scm (python-imagesize, python2-imagesize)[arguments]:
Disable the tests.
2016-11-05 14:13:39 -04:00
ng0 02f8f804f0
gnu: Add python-pafy.
* gnu/packages/python.scm (python-pafy): New variable.

Signed-off-by: Marius Bakke <mbakke@fastmail.com>
2016-11-05 12:27:12 +00:00
Ricardo Wurmus c27ae827da
gnu: Add jupyter.
* gnu/packages/python.scm (jupyter): New variable.
2016-11-04 21:23:08 +01:00
Ricardo Wurmus accd5f996e
gnu: python-ipython: Update to 4.0.0.
* gnu/packages/python.scm (python-ipython): Update to 4.0.0.
[inputs]: Keep only "readline" and "which"; move the remaining inputs
to propagated-inputs, except for "python-requests" and "python-nose"
which are moved to native-inputs.
[propagated-inputs]: Add "python-pexpect", "python-pickleshare",
"python-simplegeneric", "python-traitlets", "python-ipykernel".
[native-inputs]: Add "python-testpath".
[arguments]: Enable building of HTML documentation.
[source]: Remove patch.
* gnu/packages/patches/python-ipython-inputhook-ctype.patch: Remove
patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2016-11-04 21:23:07 +01:00
Ricardo Wurmus 8ceebf8fa6
gnu: Add python-jupyter-console.
* gnu/packages/python.scm (python-jupyter-console,
python2-jupyter-console): New variable.
2016-11-04 21:23:07 +01:00
Ricardo Wurmus 4fe2e34409
gnu: Add python-ipywidgets.
* gnu/packages/python.scm (python-ipywidgets, python2-ipywidgets): New
variables.
2016-11-04 21:23:06 +01:00
Ricardo Wurmus d55724ed5b
gnu: Add python-widgetsnbextension.
* gnu/packages/python.scm (python-widgetsnbextension,
python2-widgetsnbextension): New variables.
2016-11-04 21:23:06 +01:00
Ricardo Wurmus a0d62280f5
gnu: Add python-notebook.
* gnu/packages/python.scm (python-notebook, python2-notebook): New
variables.
2016-11-04 21:23:05 +01:00
Ricardo Wurmus c60898a845
gnu: Add python-nbconvert.
* gnu/packages/python.scm (python-nbconvert, python2-nbconvert): New
variables.
2016-11-04 21:23:05 +01:00
Ricardo Wurmus 60590a3ae8
gnu: Add python-entrypoints.
* gnu/packages/python.scm (python-entrypoints, python2-entrypoints): New
variables.
2016-11-04 21:23:04 +01:00
Ricardo Wurmus 55436048d8
gnu: Add python-bleach.
* gnu/packages/python.scm (python-bleach, python2-bleach): New
variables.
2016-11-04 11:32:35 +01:00
Ricardo Wurmus 2d321bb2c5
gnu: Add python-nbformat.
* gnu/packages/python.scm (python-nbformat, python2-nbformat): New
variables.
2016-11-04 11:29:16 +01:00
Ricardo Wurmus 8ee62c97f6
gnu: Add python-html5lib-0.9.
* gnu/packages/python.scm (python-html5lib-0.9, python2-html5lib-0.9):
New variables.
2016-11-04 11:26:34 +01:00
Ricardo Wurmus 5ff6effcc0
gnu: Add python-testpath.
* gnu/packages/python.scm (python-testpath, python2-testpath): New
variables.
2016-11-04 11:24:02 +01:00
Ricardo Wurmus ab526102ed
gnu: Add python-ipykernel.
* gnu/packages/python.scm (python-ipykernel, python2-ipykernel): New
variables.
2016-11-04 11:23:19 +01:00
Ricardo Wurmus 9ff01f2d01
gnu: Add python-jupyter-client.
* gnu/packages/python.scm (python-jupyter-client,
python2-jupyter-client): New variables.
2016-11-04 11:22:54 +01:00
Ricardo Wurmus 4263b06fa2
gnu: Add python-jupyter-core.
* gnu/packages/python.scm (python-jupyter-core, python2-jupyter-core):
New variables.
2016-11-04 11:21:37 +01:00
Ricardo Wurmus a5ba14811a
gnu: python-traitlets: Update to 4.2.0.
* gnu/packages/python.scm (python-traitlets): Update to 4.2.0.
2016-11-04 11:19:22 +01:00
Leo Famulari 0bc6ef2a87
gnu: Add python-pytest-2.9.2.
* gnu/packages/python.scm (python-pytest-2.9.2): New variable.
2016-10-31 17:02:34 -04:00
Leo Famulari 205f0107bb
Merge branch 'master' into core-updates 2016-10-30 19:19:21 -04:00
Danny Milosavljevic 45b4f12727
gnu: Add python-imagesize.
* gnu/packages/python.scm (python-imagesize, python2-imagesize): New variables.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-10-30 15:31:11 -04:00
Ricardo Wurmus a8dd960ac0
gnu: python-joblib: Disable failing tests.
* gnu/packages/python.scm (python-joblib)[arguments]: Add phase to
disable failing tests.
2016-10-30 18:54:41 +01:00
Ricardo Wurmus f34ef3317e
gnu: python-joblib: Update to 0.10.3.
* gnu/packages/python.scm (python-joblib): Update to 0.10.3.
[native-inputs]: Add python-sphinx, python-docutils, python-numpydoc.
2016-10-30 17:04:24 +01:00