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Author SHA1 Message Date
Hartmut Goebel f2516de2fc
gnu: Fix python inputs, part 7: Ensure python-cython is a native-input. 
* gnu/packages/audio.scm (python-pyliblo): [inputs] Move python-cyton to
  [native-inputs].
* gnu/packages/bioinformatics.scm (python2-pybedtools): dito.
* gnu/packages/music.scm (beast, python-pyportmidi): dito.
* gnu/packages/python.scm (python2-fastlmm, python-kivy): dito.
 2016-11-15 22:31:07 +01:00
Hartmut Goebel 328bb95d35
gnu: Fix python inputs, part 6: some inputs become native-inputs. 
This patch handles the inputs which are native-inputs almost always like nose,
sphinx, and pytest.

* gnu/packages/python.scm
  (python-jsonschema, python-numpydoc, python-mccabe, python-mistune,
  python-ptyprocess, python-webob, python-apipkg, python-flake8-2.2.4)[inputs]
  change to [native-inputs].
  (python-flake8, tox) Likewise, add a comment.
  (python-scikit-learn, python-numpy)[native-inputs] New element, move
  python-nose here.
  (python2-kombu)[inputs] change to [native-inputs], use python-kombu's
  package-native-inputs.
 2016-11-15 22:31:06 +01:00
Hartmut Goebel 482d95918e
gnu: Fix python inputs, part 5: some inputs become propagated-inputs 
* gnu/packages/openstack.scm
  (python-os-client-config)[inputs] change to
  [native-inputs]. [propagated-inputs]: New element, move python-appdirs,
  python-pyyaml here.
  (python-git-review)[propagated-inputs]: New element, move python-requests
  here.
* gnu/packages/python.scm
  (python-rpy2)[propagated-inputs]: New element, move python-six here.
  (python-xcffib)[inputs] move python-six to [propagated-inputs].
  (python-flake8)[propagated-inputs]: New element, move python-pep8,
  python-pyflakes, python-mccabe here.
  (python-flake8-2.2.4)[propagated-inputs]: New element, move python-pep8,
  python-pyflakes, python-mccabe here.
  (python-pytest)[propagated-inputs]: New element, move python-py here.
  (python-tox)[propagated-inputs]: New element, move all inputs except of
  python-pytest here.
  (python-botocore)[propagated-inputs]: New element, move python-dateutil,
  python-docutils, python-jmespath here.
  (awscli)[propagated-inputs]: New element, move python-colorama,
  python-botocore, python-s3transfer, python-docutils, python-rsa here.
  (python-mako)[propagated-inputs]: New element, move python-markupsafe here.
* gnu/packages/qemu.scm(python-libvirt)[propagated-inputs]: New element, move
  python-lxml here.
 2016-11-15 22:31:05 +01:00
Hartmut Goebel dae73d9b9a
gnu: Fix python inputs, part 3: all native-inputs become propagated-inputs. 
This patch contains the changes in python.scm where all [native-inputs]
are changed to [propagated-inputs].

* gnu/packages/python.scm.scm (python-feedgenerator): All [native-inputs] are
  changed to [propagated-inputs].
 2016-11-15 22:31:04 +01:00
Hartmut Goebel e7881f3db4
gnu: Fix python inputs, part 2: all inputs become native-inputs. 
This patch contains the changes where all [inputs] are changed to
[native-inputs].

* gnu/packages/python.scm (python-pytest, python-fixtures,
  python-testrepository, python-virtualenv): All [inputs] are changed to
  [native-inputs].
* gnu/packages/openstack.scm (python-bandit, python-debtcollector,
  python-hacking, python-tempest-lib, python-oslo.config, python-oslo.context,
  python-oslo.i18n, python-oslo.log, python-oslo.serialization,
  python-oslosphinx, python-oslotest, python-oslo.utils): Likewise.
 2016-11-15 22:31:03 +01:00
Hartmut Goebel f22efa0152
gnu: Fix python inputs, part 1: all inputs become propagated-inputs. 
This patch contains the changes where all [inputs] are changed to
[propagated-inputs]

* gnu/packages/python.scm (python-passlib, python-paramiko, python-ccm,
  python-babel, python-keyring python-pandas, python-tzlocal,
  python-parse-type, python-nose2, python-pytest, python-pytest-mock,
  python-pytest-xdist, python-scripttest, python-testtools, python-pytest-cov,
  python-testscenarios, python-pbr-0.11, python-oauthlib, python-jinja2,
  python-sphinx, python-tzlocal, python-bugz, python2-pytest-mock, behave,
  pelican, sqlalchemy-utils, python-pygridtools, python-urwidtrees,
  python-tornado, python2-tornado, python-debian, python-execnet,
  python-pytest-cache, pytest-localserver, python-clint, python-rply,
  python-hy, python-rauth, python-rsa, python-celery, python-vobject, s3cmd,
  python-prompt-toolkit, ptpython, python-requests-oauthlib, python-stem,
  python-binaryornot, python2-binaryornot, python-nltk, python-pymongo,
  python-schematics, python-url, python2-url, python-freezegun,
  python-glances, python-graphql-core, python-graphql-relay, python-graphene,
  python-nautilus, python-s3transfer): All [inputs] become
  [propagated-inputs].
* gnu/packages/bioinformatics.scm (python-biopython): Likewise.
* gnu/packages/django.scm (pytest-django): Likewise.
* gnu/packages/mail.scm (python-mailmanclient): Likewise.
* gnu/packages/password-utils.scm (python-bcrypt): Likewise.
* gnu/packages/propbuf.scm (python-protobuf): Likewise.
* gnu/packages/rdf.scm (python-rdflib): Likewise.

SQACH all become propagated
 2016-11-15 22:31:03 +01:00
Hartmut Goebel b41a05ce49
gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs). 
Bug 20765 is solved since we build all Python packages using
option "--single-version-externally-managed".

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove
  configure-flags. (pepr): remove phase "disable-egg-generation".
* gnu/packages/pdf.scm (reportlab): Remove configure-flags.
* gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl,
  python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove
  configure-flags. (python-pillow) remove phase
  "disable-egg-generation". (python-libarchive-c) Remove patching
  setup.cfg.
* gnu/packages/statistics.scm (python-patsy): remove phase
  "prevent-generation-of-egg-archive".
* gnu/packages/tls.scm (python-acme): remove phase
  "disable-egg-compression".
* gnu/packages/tor.scm (onionshare): Remove configure-flags.
 2016-11-15 22:31:02 +01:00
Hartmut Goebel d8013ee221
gnu: Remove needless inputs python-pip and python2-pip. 
This is installed together with Python 3 anyway and for our build
of Python 2.

* gnu/packages/python.scm (python2-fixtures): [inputs] remove "python-pip".
* gnu/packages/pdf.scm (python2-reportlab): [native-inputs] remove
  "python2-pip". (python-reportlab)[properties]: remove "python2-variant".
 2016-11-15 22:31:01 +01:00
Hartmut Goebel f210e94432
gnu: Remove python-setuptools and python2-setuptools from inputs (part 4b) 
This patch contains the changes in python.scm where
setuptools are used in an inherited package and removing this input also
removes the need for inheriting the package. This is the case if adding
setuptools in the inherited packge was the only change.

Change this to not inherit and remove the new needless call to
"strip-python2-variant (where applicable).

* gnu/packages/python.scm.scm: Remove inheriting Python 2 packages inheriting
  from a Python 3 package if adding python-setuptools respective
  python2-setuptools to [inputs], [native-inputs] and [propagated-inputs] have
  been the sole reason for inheriting. Remove now needless [properties]
  "python2-variant" where applicable.
  (python2-lockfile, python2-keyring, python2-dateutil-2,
  python2-parsedatetime, python2-pandas, python2-pyicu, python2-pytest-cov,
  python2-pytest-runner, python2-pytest-xdist, python2-cov-core,
  python2-itsdangerous, python2-numexpr, python2-q, python2-sqlalchemy-utils,
  python2-alembic, python2-beautifulsoup4, python2-msgpack, python2-ipaddress,
  python2-atomicwrites, python2-apipkg, python2-execnet, python2-pytest-cache,
  python2-wtforms, python2-mako, python2-waitress, python2-wsgiproxy2,
  python2-pyquery, python2-webtest, python2-translitcodec, python2-editor,
  python2-sphinxcontrib-programoutput, python2-psycopg2, python2-vobject,
  python2-flask, python2-cookies, python2-responses, python2-future,
  python2-ply, python2-wcwidth, python2-prompt-toolkit, python2-jedi,
  python2-requests-oauthlib, python2-pyserial, python2-nltk, python2-pymongo,
  python2-sh, python2-schematics, python2-publicsuffix, python2-publicsuffix2,
  python2-url, python2-freezegun, python2-cachecontrol, python2-lit,
  python2-pytest-pep8, python2-pytest-flakes, python2-glances,
  python2-betamax, python2-file, python2-flask-babel, python2-furl,
  python2-imagesize python2-orderedmultidict, python2-pycodestyle,
  python2-vcversioner, python2-graphql-core, python2-graphql-relay,
  python2-validictory): Remove neesless input "python2-setuptools", don't
  inherit, don't call strip-python2-variant.
  (python-lockfile, python-keyring, python-dateutil-2, python-parsedatetime,
  python-pandas, python-pyicu, python-pytest-cov, python-pytest-runner,
  python-pytest-xdist, python-cov-core, python-itsdangerous, python-numexpr,
  python-q, python-sqlalchemy-utils, python-alembic, python-beautifulsoup4,
  python-msgpack, python-ipaddress, python-atomicwrites, python-apipkg,
  python-execnet, python-pytest-cache, python-wtforms, python-mako,
  python-waitress, python-wsgiproxy2, python-pyquery, python-webtest,
  python-translitcodec, python-editor, python-sphinxcontrib-programoutput,
  python-psycopg2, python-vobject, python-flask, python-cookies,
  python-responses, python-future, python-ply, python-wcwidth,
  python-prompt-toolkit, python-jedi, python-requests-oauthlib,
  python-pyserial, python-nltk, python-pymongo, python-sh, python-schematics,
  python-nltk, python-publicsuffix2, python-cachecontrol, python-lit,
  python-pytest-pep8, python-pytest-flakes, python-glances, python-betamax,
  python-file, python-flask-babel, python-furl, python-imagesize,
  python-orderedmultidict, python-pycodestyle, python-vcversioner,
  python-graphql-core, python-graphql-relay, python-validictory): Remove
  "python2-variant" property.
 2016-11-15 22:29:00 +01:00
Hartmut Goebel 5c31f4aa7c
gnu: Remove python-setuptools and python2-setuptools from inputs (part 4a) 
This patch contains the changes for all modules beside python.scm where
setuptools are used in an inherited package and removing this input also
removes the need for inheriting the package. This is the case if adding
setuptools in the inherited package was the only change.

Change this to not inherit and remove the new needless call to
"strip-python2-variant (if applicable).

* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython,
  python-twobitreader, python2-twobitreader,
  python-plastid, python2-plastid,
  python2-pybigwig,
  python2-screed,
  sra-tools): No longer "inherit" Python 2 packages
  inheriting from a Python 3 package if the sole reason for inheriting was
  adding python-setuptools respective python2-setuptools to [inputs],
  [native-inputs] or [propagated-inputs]. Remove now needless [properties]
  "python2-variant" where applicable.
* gnu/packages/django.scm (python-pytest-django, python2-pytest-django,
  python-django-filter, python2-django-filter): Likewise.
* gnu/packages/gnupg.scm (python2-pygpgme): Likewise.
* gnu/packages/mail.scm (python-mailmanclient, python2-mailmanclient):
  Likewise.
* gnu/packages/mpd.scm (python-msp, python2-mpd2): Likewise.
* gnu/packages/music.scm (python-pylast, python2-pylast): Likewise.
* gnu/packages/openstack.scm (python-requests-mock, python2-requests-mock,
  python2-git-review): Likewise.
* gnu/packages/password-utils.scm (python2-bcrypt): Likewise.
* gnu/packages/protobuf.scm (python-protobuf, python2-protobuf): Likewise.
* gnu/packages/statistics.scm (python-patsy, python2-patsy): Likewise.
* gnu/packages/web.scm (python2-feedparser): Likewise.
 2016-11-15 22:28:59 +01:00
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 5d85493284
gnu: Remove python-setuptools and python2-setuptools from inputs (part 1b) 
This patch contains the changes in all modules beside python.scm where
removing setuptools from the inputs could be achieved by removing complete
lines.

* gnu/packages/admin.scm (graphios, thefuck): 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 (rdiff-backup): Likewise.
* gnu/packages/bioinformatics.scm (htseq, macs, python2-pbcore, rseqc,
  multiqc): Likewise.
* gnu/packages/django.scm (python-django, python2-django,
  python-django-simple-math-captcha, python2-django-simple-math-captcha):
  Likewise.
* gnu/packages/docker.scm (python-docker-py, docker-compose): Likewise.
* gnu/packages/game-development.scm (python-pygame): Likewise.
* gnu/packages/key-mon.scm (key-mon): Likewise.
* gnu/packages/mail.scm (khard): Likewise.
* gnu/packages/music.scm (beets, python2-pyechonest): Likewise.
* gnu/packages/openstack.scm (python-bandit, python2-bandit,
  python-debtcollector, python2-debtcollector,
  python-mox3, python2-mox3,
  python-os-client-config, python2-os-client-config,
  python-oslo.config, python2-oslo.config,
  python-oslo.context, python2-oslo.context,
  python-oslo.i18n, python2-oslo.i18n,
  python-oslo.serialization, python2-oslo.serialization,
  python-oslosphinx, python2-oslosphinx,
  python-oslotest, python2-oslotest,
  python-oslo.utils, python2-oslo.utils,
  python-swiftclient, python2-swiftclient): Likewise.
* gnu/packages/pdf.scm (pdfposter): Likewise.
* gnu/packages/tls.scm (python-acme, python2-acme): Likewise.
 2016-11-15 21:58:44 +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 b02b9a520e
gnu: libmicrohttpd: Update to 0.9.52. 
* gnu/packages/gnunet.scm (libmicrohttpd): Update to 0.9.52.
[home-page]: Use https.
 2016-11-15 15:25:15 +02:00
Efraim Flashner f5a077b10f
gnu: octave: Update to 4.2.0. 
* gnu/packages/maths.scm (octave): Update to 4.2.0.
[native-inputs]: Add lzip.
[home-page]: Use https.
 2016-11-15 15:21:15 +02:00
Efraim Flashner fccab9931c
gnu: parallel: Update to 20161022. 
* gnu/packages/parallel.scm (parallel): Update to 20161022.
[home-page]: Use https.
 2016-11-15 11:45:53 +02:00
Efraim Flashner 6312043ca5
gnu: libcdio: Update to 0.94. 
* gnu/packages/cdrom.scm (libcdio): Update to 0.94.
[home-page]: Use https.
 2016-11-15 11:13:24 +02:00
Efraim Flashner 3ded2761ab
gnu: gvpe: Update to 3.0. 
* gnu/packages/vpn.scm (gvpe): Update to 3.0.
 2016-11-15 11:06:15 +02:00
Efraim Flashner 336f830961
gnu: cryptsetup: Update to 1.7.3. 
* gnu/packages/cryptsetup.scm (cryptsetup): Update to 1.7.3.
 2016-11-15 09:45:37 +02:00
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
Tobias Geerinckx-Rice 1f781865fb
gnu: fish: Update to 2.4.0. 
* gnu/packages/shells.scm (fish): Update to 2.4.0.
 2016-11-15 01:17:01 +01:00
Tomáš Čech e25c904f2c
services: Require wpa-supplicant-service for connman-service. 
* gnu/services/networking.scm (connman-shepherd-service): Add
  wpa-supplicant among list of requirements.
 2016-11-15 00:19:23 +01:00
Tomáš Čech 2cccbc2af2
services: Add wpa-supplicant-service. 
* gnu/services/networking.scm (wpa-supplicant-service): New procedure.
(wpa-supplicant-service-type): New variable.
* doc/guix.texi (Networking Services): Document it.
 2016-11-15 00:19:17 +01:00
Tomáš Čech 028bf3c0b2
gnu: connman: Use localstatedir outside of store. 
* gnu/packages/connman.scm (connman): Use localstatedir outside of store.
 2016-11-15 00:13:29 +01:00
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
Efraim Flashner 571ffdebc3
gnu: accountsservice: Update to 0.6.43. 
* gnu/packages/freedesktop.scm (accountsservice): Update to 0.6.43.
 2016-11-14 21:02:10 +02:00
Ludovic Courtès a4cb821791
gnu: guix-devel: Update development snapshot. 
* gnu/packages/package-management.scm (guix-devel): Update to commit
7ca37da855.
 2016-11-14 15:39:32 +01:00
Ludovic Courtès 198eac2bca
gnu: guix: Really skip all the container tests. 
* gnu/packages/package-management.scm (guix-0.11.0)[arguments]: Update
pattern in 'disable-container-tests' to match 'test-equal'.
 2016-11-14 15:39:32 +01:00
Tobias Geerinckx-Rice 88eaed6174
gnu: libpsl: Update to 0.15.0. 
* gnu/packages/web.scm (libpsl): Update to 0.15.0.
 2016-11-14 14:12:50 +01:00
Efraim Flashner 7ca37da855
gnu: libinput: Enable GUI event tool. 
* gnu/packages/freedesktop.scm (libinput)[inputs]: Add glib.
[native-inputs]: Add cairo, gtk+-3.
(libinput-minimal)[native-inputs]: Only pkg-config.
 2016-11-14 13:06:02 +02:00
Efraim Flashner 73bb984ec4
gnu: freedesktop.scm: Reorder modules alphabetically. 
* gnu/packages/freedesktop.scm: Reorder modules alphabetically.
 2016-11-14 12:15:40 +02:00
Efraim Flashner 8c5cdf5f20
gnu: libinput: Update to 1.5.1. 
* gnu/packages/freedesktop.scm (libinput): Update to 1.5.1.
 2016-11-14 12:12:26 +02:00
Efraim Flashner b231b057cd
gnu: wayland-protocols: Update to 1.7. 
* gnu/packages/freedesktop.scm (wayland-protocols): Update to 1.7.
 2016-11-14 11:55:01 +02:00
Andy Patterson e66f0dd232
gnu: mpv: Use lua@5.2. 
* gnu/packages/video.scm (mpv)[inputs]: Change 'lua' to 'lua-5.2'.
 2016-11-14 09:03:55 +00:00
Leo Famulari d9721bcf27
gnu: readline-6.2: Fix CVE-2014-2524. 
* gnu/packages/patches/readline-6.2-CVE-2014-2524.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/readline.scm (readline-6.2): Use it.
 2016-11-13 17:01:01 -05:00
Leo Famulari 27d7c4e93a
gnu: signify: Update to 20. 
* gnu/packages/crypto.scm (signify): Update to 20.
 2016-11-13 17:01:01 -05:00
Ludovic Courtès 142530178d
gnu: mailutils: Update to 3.0. 
* gnu/packages/mail.scm (mailutils): Update to 3.0.
[arguments]: Adjust 'pre-build' phase.
* gnu/packages/patches/m4-gets-undeclared.patch: Remove.
* gnu/local.mk (dist_patch_DATA): Adjust accordingly.
 2016-11-13 21:12:32 +01:00
Efraim Flashner d81850d438
gnu: guile-ncurses: Update to 2.1. 
* gnu/packages/guile.scm (guile-ncurses): Update to 2.1.
[home-page]: Use https.
 2016-11-13 22:02:05 +02:00
Tobias Geerinckx-Rice 927d850512
gnu: btrfs-progs: Update to 4.8.3. 
* gnu/packages/linux.scm (btrfs-progs): Update to 4.8.3.
 2016-11-13 13:34:00 +01:00
Tobias Geerinckx-Rice 917239ff99
gnu: tidy: Use ‘modify-phases’. 
* gnu/packages/web.scm (tidy)[arguments]: Use the ‘modify-phases’ syntax.
 2016-11-13 13:34:00 +01:00
Tobias Geerinckx-Rice 3b0ac79500
gnu: protobuf: Replace dead Google Code home-page. 
* gnu/packages/protobuf.scm (protobuf)[home-page]: Update it.
 2016-11-13 13:33:59 +01:00
Tobias Geerinckx-Rice 3b0f2ba46b
gnu: exfat-utils: Update to 1.2.4. 
* gnu/packages/mtools.scm (exfat-utils): Update to 1.2.4.
[source, home-page]: Move away from dead Google Code project.
[arguments, native-inputs]: Remove.
 2016-11-13 13:33:59 +01:00
Andy Patterson c25a51d5c6
gnu: clisp: Use readline@6.2. 
* gnu/packages/lisp.scm (clisp)[inputs]: Use readline-6.2.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-11-13 13:00:44 +01:00
Ludovic Courtès 2cab1dd58b
Merge branch 'core-updates' 2016-11-13 00:34:16 +01:00
Efraim Flashner 15abcabe4e
gnu: Add newsbeuter. 
* gnu/packages/syndication.scm: New file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
 2016-11-12 20:50:48 +02:00
Efraim Flashner c76dab7b36
gnu: Add stfl. 
* gnu/packages/ncurses.scm (stfl): New variable.
 2016-11-12 20:50:47 +02:00
Alex Sassmannshausen 8883b30165
gnu: Add perl-modern-perl. 
* gnu/packages/perl.scm (perl-modern-perl): New variable.
 2016-11-12 18:26:28 +01:00
Leo Famulari 5c66314bd9
gnu: libtiff: Fix CVE-2016-9273. 
* gnu/packages/patches/libtiff-CVE-2016-9273.patch: New patch.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/image.scm (libtiff/fixed): Use it.
 2016-11-12 11:05:19 -05:00
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
Ludovic Courtès 998f9ac56d
gnu: guix: Update development snapshot. 
This is a followup to 166ba5b102.

* gnu/packages/package-management.scm (guix-devel): Update to commit
166ba5b102.
 2016-11-12 14:49:04 +01:00
Clément Lassieur 4a38422157
gnu: prosody: fix SSL/TLS. 
* gnu/packages/lua.scm (lua5.1-sec-0.5): New variable.
* gnu/packages/messaging.scm (prosody):
[inputs]: Change lua5.1-sec to lua5.1-sec-0.5.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-11-12 13:04:45 +01:00
Ben Woodcroft 8be62d3f20
gnu: ruby-lumberjack: Update to 1.0.10. 
* gnu/packages/ruby.scm (ruby-lumberjack): Update to 1.0.10.
[native-inputs]: Add 'ruby-timecop'.
 2016-11-11 22:56:13 +10:00
Ben Woodcroft e87dfdee86
gnu: ruby-arel: Update to 7.1.4. 
* gnu/packages/ruby.scm (ruby-arel): Update to 7.1.4.
 2016-11-11 22:48:22 +10:00
Ben Woodcroft 16d8d8b289
gnu: ruby-rake-compiler: Update to 1.0.1. 
* gnu/packages/ruby.scm (ruby-rake-compiler): Update to 1.0.1.
 2016-11-11 22:45:38 +10:00
Ben Woodcroft 81d0bd2f44
gnu: ruby-hoe: Update to 3.15.2. 
* gnu/packages/ruby.scm (ruby-hoe): Update to 3.15.2.
 2016-11-11 22:44:03 +10:00
Ben Woodcroft c59491183a
gnu: ruby-rspec-core: Update to 3.5.4. 
* gnu/packages/ruby.scm (ruby-rspec-core): Update to 3.5.4.
 2016-11-11 22:40:39 +10:00
Ben Woodcroft bb4bcb02c2
gnu: bundler: Update to 1.13.6. 
* gnu/packages/ruby.scm (bundler): Update to 1.13.6.
 2016-11-11 22:38:13 +10:00
Ben Woodcroft e2bb2e1780
gnu: ruby-yard: Update to 0.9.5-1.d816482a. 
* gnu/packages/ruby.scm (ruby-yard): Update to 0.9.5-1.d816482a.
[source]: Update source URL.
[arguments]: Remove unneeded substitutions.  Change test target.
* gnu/packages/patches/ruby-yard-fix-skip-of-markdown-tests.patch (New
file)
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-11-11 22:15:37 +10:00
Ricardo Wurmus 7c45670b32
gnu: r-org-mm-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus 0cfac6f270
gnu: r-org-dm-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus f04a3eff98
gnu: r-org-ce-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus 83f9a6fb60
gnu: r-org-hs-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.4.0.
 2016-11-11 09:08:07 +01:00
Leo Famulari 071c223bfa
gnu: linux-libre@4.4: Update to 4.4.31. 
* gnu/packages/linux.scm (linux-libre-4.4): Update to 4.4.31.
 2016-11-11 01:31:19 -05:00
Leo Famulari 86fc6fe777
gnu: linux-libre: Update to 4.8.7. 
* gnu/packages/linux.scm (%linux-libre-version, %linux-libre-hash)
(linux-libre): Update to 4.8.7.
 2016-11-11 01:31:15 -05:00
Ludovic Courtès 472fc855bc
gnu: Add guile-aspell. 
* gnu/packages/guile.scm (guile-aspell): New variable.
 2016-11-11 00:23:16 +01:00
Ludovic Courtès 2c5ab05bff
gnu: wordnet: Build with gcc@6 to prevent chunked literal strings. 
* gnu/packages/wordnet.scm (wordnet)[arguments]: Remove
-fno-builtin-strcpy.
[native-inputs]: New field.
 2016-11-11 00:23:16 +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
Ricardo Wurmus b8deffe2b2
gnu: r-rmarkdown: Remove phase "copy-files-without-mode". 
This phase is no longer needed as upstream has merged the fix in the
current release.

* gnu/packages/statistics.scm (r-rmarkdown)[arguments]: Remove build
phase "copy-files-without-mode".
 2016-11-10 18:49:49 +01:00
Ricardo Wurmus 3f62fa2b81
gnu: inkscape: Use modify-phases syntax. 
* gnu/packages/inkscape.scm (inkscape)[arguments]: Use modify-phases
syntax.
 2016-11-10 18:49:48 +01:00
Marius Bakke 65d2f396f7
gnu: vim: Update to 8.0.0073. 
* gnu/packages/vim.scm (vim, vim-full): Update to 8.0.0073.
 2016-11-10 17:30:08 +00:00
Ludovic Courtès 5970e8e248
container: Pass a list of <file-system> objects as things to mount. 
* gnu/build/linux-container.scm (mount-file-systems): 'mounts' is now a
list of <file-system> objects instead of a list of lists ("specs").
Add call to 'file-system->spec' as the argument to 'mount-file-system'.
(run-container, call-with-container): Adjust docstring accordingly.
* gnu/system/file-systems.scm (spec->file-system): New procedure.
* gnu/system/linux-container.scm (container-script)[script]: Call
'spec->file-system' inside gexp.
* guix/scripts/environment.scm (launch-environment/container): Remove
call to 'file-system->spec'.
* tests/containers.scm ("call-with-container, mnt namespace")
("call-with-container, mnt namespace, wrong bind mount"): Pass a list of
<file-system> objects.
 2016-11-10 18:01:44 +01:00
Ludovic Courtès 5e7eaccb14
linux-container: Use 'source-module-closure' when generating the script. 
* gnu/system/linux-container.scm (container-script)[script]: Use
'source-module-closure' in 'with-imported-modules' form.
 2016-11-10 18:01:44 +01:00
Ludovic Courtès 9e4e431e04
gnu: guix: Update development snapshot. 
* gnu/packages/package-management.scm (guix-devel): Update to commit
324a2ba56c.
 2016-11-10 18:01:44 +01:00
Paul Garlick 1c79e0861a
gnu: gmsh: Update to 2.14.1 
* gnu/packages/maths.scm (gmsh): Update to 2.14.1.
[source]: Use new uri.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2016-11-10 18:57:57 +02:00
Marius Bakke 1b35fea19f
gnu: milkytracker: Update upstream location. 
* gnu/packages/music.scm (milkytracker)[source]: Update source uri.
[home-page]: Change to new domain.

Reported-by: ng0 <ng0@we.make.ritual.n0.is>
 2016-11-10 16:33:57 +00:00
Leo Famulari 8f9c89d13b
gnu: imagemagick: Update to 6.9.6-4. 
* gnu/packages/imagemagick.scm (imagemagick): Update to 6.9.6-4.
 2016-11-10 11:33:20 -05:00
Tobias Geerinckx-Rice f34284abcb
gnu: claws-mail: Update to 3.14.1. 
* gnu/packages/mail.scm (claws-mail): Update to 3.14.1.
 2016-11-10 14:30:09 +01:00
Hartmut Goebel 99abcdbd9b
gnu: Add pdfposter. 
* gnu/packages/pdf.scm(pdfposter): New variable.
 2016-11-10 14:26:04 +01:00
Hartmut Goebel c68e8591d8
gnu: Add python2-pypdf. 
* gnu/packages/pdf.scm (python2-pypdf): New variable.
 2016-11-10 14:26:04 +01:00
Hartmut Goebel ad5a7d49c3
gnu: Add python-pypdf2. 
* gnu/packages/pdf.scm (python-pypdf2, python2-pypdf2): New variables.
 2016-11-10 14:26:04 +01:00
Ludovic Courtès 8033772363
gnu: gcc@5, gcc@6: Work around use of 'movabs' for /gnu/store strings. 
Partly addresses <http://bugs.gnu.org/24703>.
Reported by Mark H Weaver <mhw@netris.org>.

* gnu/packages/patches/gcc-strmov-store-file-names.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/gcc.scm (gcc-5)[sources](patches): Add it.
(gcc-6)[sources](patches): Add it.
 2016-11-09 21:24:44 +01:00
Thomas Danckaert 8bb115e0c6
gnu: Add kdevelop-pg-qt. 
* gnu/packages/kde.scm (kdevelop-pg-qt): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-11-09 21:24:44 +01:00
Thomas Danckaert 5a16e1c04e
gnu: Add libkomparediff2. 
* gnu/packages/kde.scm (libkomparediff2): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2016-11-09 21:24:44 +01:00
Ludovic Courtès 28791c1c8d
gnu: hidapi: Fix 'license'. 
* gnu/packages/libusb.scm (hidapi)[license]: Actually call
'non-copyleft'.
 2016-11-09 21:24:44 +01:00
Efraim Flashner 65dccb3a86
gnu: Add vifm. 
* gnu/packages/vim.scm (vifm): New variable.
 2016-11-09 20:56:36 +02:00
Leo Famulari 0b34b58688
gnu: libxslt: Fix CVE-2016-4738. 
* gnu/packages/patches/libxslt-CVE-2016-4738.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/xml.scm (libxslt)[replacement]: New field.
(libxslt/fixed): New variable.
 2016-11-09 10:19:49 -05:00
Efraim Flashner d887f420d2
gnu: postgresql: Update to 9.5.5. 
* gnu/packages/databases.scm (postgresql): Update to 9.5.5.
[home-page]: Use https.
 2016-11-09 11:39:30 +02:00
Efraim Flashner bc332a638b
gnu: mariadb: Update to 10.1.19. 
* gnu/packages/databases.scm (mariadb): Update to 10.1.19.
 2016-11-09 11:04:36 +02:00
Ludovic Courtès de7da4e5d1
gnu: gnome-calculator: Update to 3.22.2. 
* gnu/packages/gnome.scm (gnome-calculator): Update to 3.22.2.
 2016-11-09 09:25:18 +01:00
Ludovic Courtès 7894ea6122
gnu: gcc-arm-none-eabi-4.9: Remove non-applicable patch. 
* gnu/packages/embedded.scm (gcc-arm-none-eabi-4.9)[patches]: Remove
"gcc-arm-bug-71399.patch" from XGCC's patches.
 2016-11-08 23:57:29 +01:00
Ludovic Courtès 946465bbaf
system: Reintroduce 'GUIX_LOCPATH', for compatibility with glibc@2.23. 
* gnu/system.scm (operating-system-environment-variables): Re-add
'GUIX_LOCPATH'.  This reverts part of
9f58fe3d1c.
 2016-11-08 23:31:27 +01:00
Efraim Flashner e3ec6c806a
gnu: mate-themes: Update to 3.20.9. 
* gnu/packages/mate.scm (mate-themes): Update to 3.20.9.
[source]: Update package location.
[inputs]: Remove gtk+-2, add gtk+-3.
[description]: Add note about dual gtk+-2/gtk+-3 support.
 2016-11-08 22:53:43 +02:00
Efraim Flashner 27caff1b5d
gnu: mate-menus: Update to 1.16.0. 
* gnu/packages/mate.scm (mate-menus): Update to 1.16.0.
[propagated-inputs]: Move glib ...
[inputs]: ... to here.
 2016-11-08 22:35:27 +02:00
John Darrington 859e367d07
gnu: Add pam-krb5 service. 
* doc/guix.texi (Kerberos Services): New node.
* gnu/services/kerberos.scm: New file.
* gnu/local.mk: Add it.
 2016-11-08 21:35:26 +01:00
Efraim Flashner 9927943c30
gnu: mate-desktop: Update to 1.16.1. 
* gnu/packages/mate.scm (mate-desktop): Update to 1.16.1.
[arguments]: Build with gtk+-3, enable mpaste.
[propagated-inputs]: Remove gtk+-2, move libxrandr,
startup-notification ...
[inputs]: ... to here.  Add gtk+-3, python-2.
 2016-11-08 22:18:07 +02:00