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5525 Commits

Author SHA1 Message Date
Uli Baum
80ecef8e4b pythonPackages.pydub: fix build and tests 
- remove obsolete patch that caused build failure
- no tests were run because required data files were missing in pypi
  version; use github version instead
 2018-09-10 18:05:40 +02:00
Uli Baum
d2a885a3b5 pythonPackages.pyfakefs: 3.4.1 -> 3.4.3, fix build 
Update and disable some failing test cases
 2018-09-10 17:43:18 +02:00
Uli Baum
bb1f3422e0 pythonPackages.readme_renderer: fix build 
Disable one test case that has failed since last bleach update.
 2018-09-10 17:19:05 +02:00
Uli Baum
a7166cdc35 pythonPackages.us: fix build 
Required jellyfish==0.5.6 but we have 0.6.1. Loosen requirements.
 2018-09-10 17:06:54 +02:00
Timo Kaufmann
2b6144d1ad
Merge pull request #46368 from Ma27/fix-mahotas 
pythonPackages.mahotas: fix build, move expression
 2018-09-10 11:56:50 +02:00
Maximilian Bosch
ee897b64ff
pythonPackages.mahotas: fix build, move expression 
See https://hydra.nixos.org/build/80828287

Moves `mahotas` out of `python-packages.nix` into its own file and fixes
broken test cases by skipping them using nosetest's `@nottest`
annotation.

These tests broke from time to time in a sandbox and are therefore
considered impure.

Addresses #45960
 2018-09-10 11:32:58 +02:00
Josef Kemetmüller
6f891ff66e pythonPackages.joblib: Disable flaky test (#46439) 
The test `test_nested_parallelism_limit` fails on darwin.
 2018-09-09 22:42:17 +02:00
Josef Kemetmüller
5e0c468737 pythonPackages.fiona: Fix darwin build (#46435) 2018-09-09 22:40:49 +02:00
xeji
12fae6e5c7
Merge pull request #46440 from knedlsepp/fix-pythonPackages.libusb1 
pythonPackages.libusb1: Fix darwin build
 2018-09-09 22:25:06 +02:00
Josef Kemetmüller
b633fc4fb4 pythonPackages.libusb1: Disable flaky test 2018-09-09 22:09:34 +02:00
xeji
d18aaceda6
Merge pull request #46438 from knedlsepp/fix-pythonPackages.flask_ldap_login 
pythonPackages.flask_ldap_login: Fix build
 2018-09-09 22:00:59 +02:00
Josef Kemetmüller
b667a76eac pythonPackages.flask_ldap_login: Disable on python3 2018-09-09 21:48:54 +02:00
Josef Kemetmüller
a4b040e69f pythonPackages.cozy: Disable on python2 (#46436) 
Cozy does not support python2.
 2018-09-09 21:33:45 +02:00
Josef Kemetmüller
063aa389df pythonPackages.libusb1: Fix darwin build 2018-09-09 20:56:34 +02:00
Josef Kemetmüller
25f8753bf4 pythonPackages.flask_ldap_login: 0.3.0 -> 0.3.4 2018-09-09 20:39:46 +02:00
Josef Kemetmüller
d4e89680d2 pythonPackages.flask_ldap_login: Fix build 2018-09-09 20:39:15 +02:00
Jörg Thalheim
201ee19758
Merge pull request #46377 from dasJ/nonhttp 
treewide: Use http/https for homepages
 2018-09-09 15:50:25 +01:00
xeji
17c51ef436
Merge pull request #45925 from markuskowa/ompi-up 
slurm: 17.11.9-2 -> 18.08.0-1
 2018-09-09 14:20:00 +02:00
Maximilian Bode
c020a59ccd pythonPackages.tifffile: fix python 2 build (#46415) 2018-09-09 12:13:36 +02:00
Maximilian Bode
dfcf07d9d3 pythonPackages.django-raster: fix build (#46413) 2018-09-09 11:34:18 +02:00
Markus Kowalewski
7dd2f4ec9c
pyslurm: 20180811 -> 20180908 2018-09-08 23:16:37 +02:00
xeji
113f4d7b44
pythonPackages.persistent: fix build (#46364) 
Documentation-related tests failed, the docs didn't build correctly
because of missing dependencies sphinx and manuel. Add them.
 2018-09-08 21:35:33 +02:00
Maximilian Bode
73e75a7d16 pythonPackages.confluent-kafka: fix build (#46380) 
cc #45960
 2018-09-08 21:32:04 +02:00
Janne Heß
9ef77854f7 treewide: Use http/https for homepages 2018-09-08 18:30:00 +02:00
Maximilian Bosch
a02002deba pythonPackages.pycaption: fix build (#46356) 
The `beaitufulsoup4` package distributed by `nixpkgs` is now at `4.6.3`.

Additionally it fixes `gnomecaption` which depends on the broken
`pycaption` package.

See https://hydra.nixos.org/build/81000247
See https://hydra.nixos.org/build/80723223

Addresses #45960
 2018-09-08 11:20:47 +02:00
Maximilian Bosch
218ac50fd4 pythonPackages.trio: fix build (#46342) 
Fixes the build for `python3Packages.trio' for the next ZHF iteration.
Please refer to the Hydra build for further reference: https://hydra.nixos.org/build/80617356

`python3Packages.sniffio` is needed for the build, otherwise the build
aborts with an error like this:

```
  Could not find a version that satisfies the requirement sniffio (from trio==0.6.0) (from versions: )
No matching distribution found for sniffio (from trio==0.6.0)
```

See #45960
 2018-09-08 01:02:55 +02:00
Alexey Shmalko
e5e4fd8ede
Merge pull request #46327 from costrouc/costrouc/markerlib 
pythonPackages.markerlib: init at 0.6.0
 2018-09-07 23:38:16 +03:00
Chris Ostrouchov
2895560f4f
pythonPackages.markerlib: init at 0.6.0 2018-09-07 14:08:35 -04:00
xeji
6f3ff5acc7
Merge pull request #46186 from costrouc/costrouc/python-ncclient 
pythonPackages.ncclient: refactor + init pythonPackages.selectors2
 2018-09-07 17:33:58 +02:00
Chris Ostrouchov
a726956b42
pythonPackages.ncclient: refactor 
adding selectors2 as dependency of ncclient. Added recently 20 days
ago in August. 8ef20f2828
 2018-09-07 10:22:22 -04:00
Chris Ostrouchov
11c3fe2258
pythonPackages.selectors2: init at 2.0.1 
Added package becuase now dependency of ncclient.
 2018-09-07 10:22:22 -04:00
Andrey Golovizin
2bec98ae06 pythonPackages.psycopg2: 2.7.1 -> 2.7.5 2018-09-07 15:40:34 +02:00
Daniël de Kok
d261df5fc1 python2Packages.spacy_models: update all models to version 2.0.0 (#46182) 
Update the model list to those models that are compatibly with the
latest spaCy version:

https://github.com/explosion/spacy-models/blob/master/compatibility.json

The updated model file evaluates to the following packages:

python2Packages.spacy_models.de_core_news_sm
python2Packages.spacy_models.en_core_web_lg
python2Packages.spacy_models.en_core_web_md
python2Packages.spacy_models.en_core_web_sm
python2Packages.spacy_models.en_vectors_web_lg
python2Packages.spacy_models.es_core_news_md
python2Packages.spacy_models.es_core_news_sm
python2Packages.spacy_models.fr_core_news_md
python2Packages.spacy_models.fr_core_news_sm
python2Packages.spacy_models.it_core_news_sm
python2Packages.spacy_models.nl_core_news_sm
python2Packages.spacy_models.pt_core_news_sm
python2Packages.spacy_models.xx_ent_wiki_sm
python3Packages.spacy_models.de_core_news_sm
python3Packages.spacy_models.en_core_web_lg
python3Packages.spacy_models.en_core_web_md
python3Packages.spacy_models.en_core_web_sm
python3Packages.spacy_models.en_vectors_web_lg
python3Packages.spacy_models.es_core_news_md
python3Packages.spacy_models.es_core_news_sm
python3Packages.spacy_models.fr_core_news_md
python3Packages.spacy_models.fr_core_news_sm
python3Packages.spacy_models.it_core_news_sm
python3Packages.spacy_models.nl_core_news_sm
python3Packages.spacy_models.pt_core_news_sm
python3Packages.spacy_models.xx_ent_wiki_sm
 2018-09-07 12:58:53 +02:00
Christopher Ostrouchov
66e1288962 pythonPackages.kubernetes: add missing dependency (#46179) 
fix build issue from missing dependency `adal`. This is due to `adal`
being added as a dependency in July
23rd. 9afec55f4a (diff-b4ef698db8ca845e5845c4618278f29a)
 2018-09-07 11:25:53 +02:00
Christopher Ostrouchov
427e4910ec pythonPackages.ordered-set: add missing dependency (#46183) 
missing dependency for doing tests (pytestrunner) added three months
ago June c0b9308988.
 2018-09-07 09:26:07 +02:00
Christopher Ostrouchov
6586765a8f pythonPackages.phonopy: refactor (#46161) 
Fixing phonopy not building. Tests were moved on Jul 30.
 2018-09-07 08:41:24 +02:00
Christopher Ostrouchov
b5b48c0a91 pythonPackages.locustio: 0.8.1 -> 0.9.0 (#46191) 
Fixing build issue. Additionally fetching from github becuase pypi
packge does not come with README which is a buildtime dependency.
 2018-09-07 08:38:41 +02:00
Christopher Ostrouchov
b1d6d159aa pythonPackages.pyslurm: 20180604 -> 20180811 (#46187) 
Update version to support latest version of slurm. Fixes since
previously did not build.
 2018-09-07 08:28:12 +02:00
Christopher Ostrouchov
7bcc2870c7 pythonPackages.jupyterlab_launcher: refactor (#46178) 
jupyterlab_launcher does not support python version < 3.5. Disabled
for older versions
 2018-09-06 20:40:43 +02:00
Chris Ostrouchov
1d6fd65957 pythonPackages.geopandas: 0.3.0 -> 0.4.0 
Additionally fix issue with tests failing for 18.09 release.

Tests required url fetch. Disabled with "not web".
 2018-09-06 18:50:11 +02:00
Matthieu Coudron
13050ccc0b python3Packages.genanki: init at 0.6.0 
Library to generate anki flashcards.
 2018-09-06 18:31:57 +02:00
Jörg Thalheim
89571b255e
Merge pull request #45996 from teto/alot_completion 
[rdy] pythonPackages.alot: install zsh completion
 2018-09-06 11:28:09 +01:00
Jörg Thalheim
9a585658e2
Merge pull request #46132 from costrouc/costrouc/pymatgen-networkx-dependency 
pythonPackages.pymatgen: 2018.8.10 -> 2018.9.1
 2018-09-06 09:55:18 +01:00
Sarah Brofeldt
a59f244b2c
Merge pull request #46126 from flokli/gmpy-phe 
pythonPackages: cleanup gmpy[2], add phe
 2018-09-06 10:31:56 +02:00
Sarah Brofeldt
574f893507
Merge pull request #46124 from erosennin/pymetar-1.0 
pythonPackages.pymetar: 0.21 -> 1.0
 2018-09-06 10:26:32 +02:00
Jörg Thalheim
df2cc4121b
Merge pull request #46125 from ashgillman/nipype-futures-py2-only 
python.pkgs.nipype: Futures is python 2 only. Also fix building.
 2018-09-06 08:25:33 +01:00
Chris Ostrouchov
63cf879d6c
pythonPackages.pymatgen: 2018.8.10 -> 2018.9.1 
Also 2018.8.10 does not build in previous state because auto updating
from pypi did not account for a new requirement `networkx`. This has
been added.
 2018-09-06 00:04:28 -04:00
Christopher Ostrouchov
ed130935c8
Merge branch 'master' into costrouc/dask-distributed 2018-09-05 23:53:23 -04:00
Chris Ostrouchov
4f70170f8a
pythonPackages.distributed: 1.15.1 -> 1.22.1 
The github repository was downloaded instead of the pypi repository
for testing (needed `conftest.py`). Major work was done on the
underlying dependencies to make distributed work on python 2.7,
3+. Note that the test **do** take a significant amount of time (10-15
minutes).

 - moved to `python-modules`
 - compatible with 2.7, 3+
 - all tests pass (previously tests were not run)
 2018-09-05 23:46:28 -04:00
Chris Ostrouchov
7b920172db
pythonPackages.pytest-repeat: init at 0.6.0 
- compatible with 2.7, 3+
 - all tests pass and running
 2018-09-05 23:46:28 -04:00
Chris Ostrouchov
05890dda3d
pythonPackages.joblib: 0.12.1 -> 0.12.2 
In order to get all the tests passing the Github repository was
downloaded instead of from pypi so that the `conftest.py` is
available.

In addition to updating the version:

  - compatible with 2.7, 3+ now
  - all tests are running and passing
 2018-09-05 23:46:28 -04:00
Chris Ostrouchov
3a56e314b8
pythonPackages.python-lz4: init at 2.1.0 
Fetching from github repository instead of pypi so that all tests can
be run.

 - compatible with 2.7, 3+
 - all tests pass
 2018-09-05 23:46:28 -04:00
Chris Ostrouchov
5704642a3f
pythonPackages.pytest-faulthandler: init at 1.5.0 
- compatible with 2.7 and 3+
 - all test pass.
 2018-09-05 23:46:28 -04:00
Florian Klink
e053386c92 gmpy2: 2.0.6 -> 2.0.8 
Also move outside python-packages.nix
 2018-09-05 23:56:20 +02:00
Florian Klink
7339a4004c gmpy: move outside python-packages.nix 2018-09-05 23:56:20 +02:00
Florian Klink
f051f66c9a phe: init at 1.4.0 2018-09-05 23:56:20 +02:00
Robert Schütz
041043420f python.pkgs.py3status: fix build 2018-09-05 23:28:31 +02:00
Ashley Gillman
12c0dd5432 python.pkgs.nipype: Futures is python 2 only. Also fix building. 2018-09-05 22:26:34 +01:00
Andrey Golovizin
7de5708e9e pythonPackages.pymetar: enable tests 2018-09-05 23:08:47 +02:00
Andrey Golovizin
ee841c57bf pythonPackages.pymetar: 0.21 -> 1.0 2018-09-05 22:32:57 +02:00
Andrey Golovizin
085cc29323 pythonPackages.pymetar: fix license 2018-09-05 22:32:49 +02:00
Jethro Kuan
a9a380b259 pythonPackages.tflearn: 0.2.1 -> 0.3.2 (#46102) 2018-09-05 17:38:23 +01:00
Daniël de Kok
348a153781 pythonPackages.thinc: fix darwin build (#46092) 
thinc uses Accelerate on macOS as a blas library. Add the necessary
dependencies to allow building on unsandboxed Darwin machines.
 2018-09-05 16:22:52 +02:00
Daniël de Kok
da8475736e spacy: relax dependency versions 2018-09-05 10:39:03 +02:00
Daniël de Kok
ffb094f939 thinc: relax dependency version requirements 2018-09-05 10:29:01 +02:00
Andreas Rammhold
d814c98ec8 python.pkgs.pytest-fixture-config: disable tests (#46021) 
Tests seem to fail on all recent versions even outside of our build
system. The upstream CI tests seem to somehow succeed but I wasn't able
to reproduce that locally. For not it is probably best to disable them.
 2018-09-05 01:02:06 +02:00
xeji
d22e22e2dd
Merge pull request #45987 from danieldk/fix-vowpalwabbit 
vowpalwabbit: fix build against boost-python.
 2018-09-04 08:54:00 +02:00
Daniël de Kok
69d418aeac vowpalwabbit: mark broken on aarch64. 2018-09-04 07:43:53 +02:00
Michiel Leenaars
9692b7997c pythonPackages.authres: fix broken homepage 2018-09-03 23:52:27 +02:00
Daniël de Kok
e33be2ab56 Keras: fix build by updating expected dependencies. (#45992) 
Keras expects keras_preprocessing 1.0.2 and 1.0.4. 1.0.3 and 1.0.5
are respectively in nixpkgs.

ZHF #45960
 2018-09-03 21:59:36 +02:00
Daniël de Kok
fe7e89ba3b vowpal-wabbit: fix Darwin build. 
- Follow the same logic for finding boost-python as for Linux.
- Set DYLD_LIBRARY_PATH so that ctypes find_library can find
  boost-python.
- Do not use '-mt' suffix when linking against boost-serialization
  and boost-program_options on Darwin.
 2018-09-03 21:48:13 +02:00
Matthieu Coudron
97816bed33 pythonPackages.alot: install zsh completion 2018-09-04 02:22:58 +09:00
Daniël de Kok
875bb6bcb9 vowpalwabbit: fix build against boost-python. 
Patch setup.py to look for libboost_python{Major}{Minor}.
 2018-09-03 15:47:04 +02:00
Jörg Thalheim
d1c6c32230
Merge pull request #45964 from Mic92/irc 
python.pkgs.irc: 14.2.2 -> 16.4
 2018-09-03 01:36:07 +01:00
Jörg Thalheim
35c9408ca4 python.pkgs.irc: 14.2.2 -> 16.4 2018-09-03 01:25:03 +01:00
Jörg Thalheim
9bc1b13983 python.pkgs.jaraco_logging: 1.5 -> 1.5.2 2018-09-03 01:25:03 +01:00
Jörg Thalheim
7cd2bf48f7 python.pkgs.jaraco_text: 1.7 -> 1.10.1 2018-09-03 01:25:02 +01:00
Jörg Thalheim
c4bf056c08 python.pkgs.jaraco.collections: 1.3.2 -> 1.5.3 2018-09-03 01:25:02 +01:00
Jörg Thalheim
6b1b6c84bf python.pkgs.jaraco.itertools: 1.7.1 -> 2.4 2018-09-03 01:25:02 +01:00
Jörg Thalheim
b3e9520a0c python.pkgs.jaraco.classes: 1.4 -> 1.5 2018-09-03 01:25:01 +01:00
Jörg Thalheim
97b73d6a58 python.pkgs.jaraco.stream: 1.1.1 -> 1.2 2018-09-03 01:25:01 +01:00
Jörg Thalheim
8e15622cf3 python.pkgs.inflect: 0.2.5 -> 1.0.0 2018-09-03 01:25:01 +01:00
Ryan Mulligan
7b54a50e97
Merge pull request #45730 from Helkafen/snakemake 
snakemake: init at 5.2.2
 2018-09-02 07:54:13 -07:00
Tobias Happ
e6a3ad775f pythonPackages.dependency-injector: init at 3.13.1 (#45871) 2018-09-01 17:29:47 +02:00
Vladimír Čunát
355f19653c
pythonPackages.more-itertools: avoid doCheck on i686 
I expect noone will want to spend time really fixing these,
but it blocks wine from building...
 2018-09-01 15:08:53 +02:00
Frederik Rietdijk
4134048b6f Merge master into staging-next 2018-09-01 10:41:58 +02:00
Frederik Rietdijk
43f6ceabb8 pythonPackages.pandas: fix build 2018-09-01 10:41:37 +02:00
Robert Schütz
5a9270fe57 python.pkgs.h5py: disable tests 2018-09-01 10:41:37 +02:00
Robert Schütz
de151625f2 python.pkgs.natsort: no pyflakes and pep8 checks 2018-09-01 10:41:37 +02:00
Robert Schütz
6c9f7e2742 python.pkgs.cairocffi: remove superfluous patch 2018-09-01 10:41:37 +02:00
Robert Schütz
5a7e9c8237 python.pkgs.celery: fix tests 2018-09-01 10:41:37 +02:00
Robert Schütz
30970aa039 python.pkgs.keyrings-alt: fix tests 2018-09-01 10:41:37 +02:00
Frederik Rietdijk
0840e427e6 pythonPackages.bottleneck: get rid of warnings during tests 2018-09-01 10:41:37 +02:00
Frederik Rietdijk
39ca3eb666 pythonPackages.cmd2: fix build 2018-09-01 10:41:37 +02:00
Frederik Rietdijk
1c66e6d76d pythonPackages.moto: fix build 2018-09-01 10:41:37 +02:00
Frederik Rietdijk
32492d9189 Python: fix botocore/boto3/awscli mess 
Revert "pythonPackages.boto3: 1.7.84 -> 1.8.4"

This reverts commit 06b37899300e0800e7a0ea632fcb5bf0f291e003.

Revert "python: botocore: 1.11.1 -> 1.11.4"

This reverts commit 3b0242d4c014a440b8c1c58cae812dc84496cc95.

Revert "python: botocore: 1.10.75 -> 1.11.1"

This reverts commit 996fd79967.

Revert "awscli: 1.16.1 -> 1.16.4"

This reverts commit 4880df9078bf024fd5a98afa8c6f28833e13f3d3.

Revert "awscli: 1.15.66 -> 1.16.1"

This reverts commit 6923bc8d23.

awscli: fix build

pythonPackages.botocore: 1.10.75 -> 1.10.84
 2018-09-01 10:41:37 +02:00
Frederik Rietdijk
f823ca5752 pythonPackages.scipy: disable tests 
We should try to get these enabled again asap.
https://github.com/scipy/scipy/pull/8871#issuecomment-417391433
 2018-09-01 10:41:37 +02:00
Frederik Rietdijk
ee5bff207f Revert "python.pkgs.python-jose: 2.0.2 -> 3.0.0" 
This breaks moto.

This reverts commit a6d3577d3d.
 2018-09-01 10:41:37 +02:00
Frederik Rietdijk
7f50451d3c Revert "python: shippai: 0.2.3 -> 0.3.1" 
This broke vdirsyncer.

This reverts commit 0bca28c890.
 2018-09-01 10:41:37 +02:00
Frederik Rietdijk
5918fc4601 pythonPackages.cement: disable Python 2 2018-09-01 10:41:37 +02:00