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695 Commits
Author SHA1 Message Date
peterjc 7e5d99ebb2 Update check_python.py now dropping Python 2.6 
Closes #1596
 2016-03-07 15:50:05 +00:00
Nicola Soranzo 501a10c3f1 Do not import dumps and loads from galaxy.util.json . 2016-03-02 19:04:24 +00:00
John Chilton 94f847b3b2 Merge pull request #1755 from nsoranzo/flake8_fixes 
Fix the remaining 1334 flake8 errors in scripts/ .
 2016-02-25 08:11:55 -05:00
Nate Coraor 8943a0f86b Add the script I used to create security patches 2016-02-24 16:54:30 -05:00
Nicola Soranzo d85db9daa6 Use __file__ when adding paths to sys.path instead of os.getcwd() . 
Also insert additional paths in position 1 unless strictly necessary.
 2016-02-18 15:45:15 +00:00
Nicola Soranzo 196d174716 Python 3 support for 3 files. 2016-02-18 15:45:15 +00:00
Nicola Soranzo 93348e7199 Fix the remaining 1334 flake8 errors in scripts/ . Close #391. 2016-02-18 15:45:15 +00:00
Martin Cech db1bb2f191 Merge pull request #1556 from jmchilton/datatype_imports 
Code design and legacy cleanup of datatypes and metadata.
 2016-02-09 12:44:59 -05:00
Nate Coraor 9551fc07b4 Add the scientific platform (Scientific Linux) as binary compatible 
with RHEL.
 2016-02-03 13:33:42 -05:00
Nate Coraor 04af1ae1c6 Always use the python hashlib for verifying the virtualenv download in 
common_startup.sh rather than attempting to use sha256sum. Older
versions of coreutils (such as in RHEL 6) did not include the --strict
argument to sha256sum.
 2016-02-03 13:16:27 -05:00
Dannon Baker 6635e91170 Bump gx pip version to fix OSX platform issues. 2016-02-02 10:45:14 -05:00
Mark Einon 50ea4694af Change python print() format to be backward compatible with older versions 
In python versions prior to 3.1, the print("{}", .format(x)) form throws
an error, use the more compatible print("{0}", .format(x)) form
instead.
 2016-02-02 10:25:16 +00:00
Nicola Soranzo 685fd1560e Merge pull request #1595 from natefoo/fix-pip-wheel-version 
[16.01] Always install a specific version of Galaxy pip in common_startup.sh.
 2016-01-28 19:56:14 +00:00
Nate Coraor 60062b020d pip 1.6 -> 6.0, thanks @nsoranzo 2016-01-28 12:46:14 -05:00
Nate Coraor 46471d61e4 pip < 1.6 cannot parse requirement specifiers to the install command 
that contain a `+` in the version. For these older versions, directly
install the wheel or install from the sdist. Technically 1.4 and later
can install wheels, but in testing, only 1.5+ was able to install them
properly with their scripts.

The new heredoc execute and redirect syntax is Bourne-compatible.

pip --pre is no longer necessary since the Galaxy pip version is no
longer a development version of pip.
 2016-01-28 10:45:54 -05:00
Nate Coraor 390c1fc275 Always install a specific version of Galaxy pip in common_startup.sh. 2016-01-27 09:57:41 -05:00
John Chilton bc9f9b9bf1 Adapt release notes boot strap to new issues. 2016-01-26 10:03:08 +00:00
Nate Coraor 8ceb4d8ee4 Force --skip-venv if we can detect that Python is Conda Python. 2016-01-21 11:49:51 -05:00
John Chilton df5a3a6da7 Eliminate legacy set metadata entry points. 2016-01-21 14:31:41 +00:00
Mark Einon efa1334d45 Change python print() format to be backward compatible with older versions 
In python versions prior to 3.1, the print("{}", .format(x)) form throws
an error, use the more compatible print("{0}", .format(x)) form
instead.
 2016-01-15 12:58:36 +00:00
John Chilton 8fd83df665 Allow override of location of virtual env Galaxy manages. 2016-01-13 13:55:36 +00:00
John Chilton 9dc9ddf8cd Add --replace-pip option to common_startup.sh. 
Needed to restore correct functionality to planemo.
 2016-01-13 13:55:35 +00:00
Dannon Baker 2f1dbeee68 Address W503 and E721 errors now enforced by pep8 1.7. 2016-01-13 10:41:27 -05:00
Nate Coraor 4eefd885ec Improve startup options related to wheel/dependency/virtualenv 
management. Drop hard requirement on lzo (doubt anyone other than
usegalaxy.org is using it, but it will be added as a extras option for
bxlab/bx-python for anyone who is).

Fixes #1150
 2015-12-22 14:03:50 -05:00
Nate Coraor 43e38414e6 --pre does not exist on pip < 1.4, but on pip < 1.4, the default 
behavior was the same as using --pre on pip >= 1.4. Therefore, detect
the version of pip and add --pre if necessary.

Fixes #1134
 2015-12-18 12:27:12 -05:00
Dannon Baker f35bd9ae02 Merge pull request #1181 from souravsingh/rename_file 
Renames reports_wsgi.ini
 2015-11-30 11:49:41 -05:00
Sourav Singh 9fceddf8a2 Changed reports_wsgi.ini to reports.ini 2015-11-27 23:50:46 +05:30
John Chilton c408b0ec65 Do not check for tool migrations when running tests. 
This is an inappropriate time for the check and causes slow down when running tests.
 2015-11-25 15:19:30 +00:00
Nicola Soranzo 4f6aad473d Merge branch 'master' into dev 2015-11-25 16:18:37 +00:00
Nate Coraor dc10ac7e3e Add stub fetch_eggs.py/check_eggs.py for people whose build/test/run 
pipelines may have been running these by hand. Print hopefully helpful
information and return 1. Fixes #1030
 2015-11-06 11:06:11 -05:00
Nate Coraor f406cdefc7 Merge pull request #990 from nsoranzo/post_eggs_smash 
Remove remaining references to galaxy.eggs . flake8 some tools.
 2015-11-01 21:58:27 -05:00
Nate Coraor 7010e38b6f Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs 2015-10-27 17:07:28 -04:00
Nate Coraor 9563f121e8 binary_compatibility.py shouldn't fail on platforms that don't return 
anything for get_specific_platform() (e.g. things other than Linux).
 2015-10-27 16:41:27 -04:00
Nate Coraor b7c8a6d334 Rename lib/galaxy/main.py to scripts/galaxy-main since that makes more 
sense and doesn't result in lib/galaxy/ being added to sys.path.

Create a symlink at lib/galaxy/main.py for backward compatibility.
 2015-10-27 16:03:33 -04:00
Nate Coraor 1a3a594d4e Allow CentOS to install RHEL wheels. 2015-10-26 15:47:51 -04:00
Nicola Soranzo 69cda48690 Remove remaining references to galaxy.eggs . flake8 some files in tools/ . 2015-10-26 19:29:13 +00:00
Nate Coraor d90ba82e92 Add a --dev-wheels arg to common_startup.sh (called by run_tests.sh by 
default) that will install things in dev-requirements.txt.
 2015-10-26 14:07:00 -04:00
Nate Coraor 88683c3c40 Unset $PYTHONPATH in run.sh and common_startup.sh unless --skip-env is 
provided.
 2015-10-22 18:42:06 -04:00
Nate Coraor 4a5f5f44dc Install our modified pip as a wheel from wheels.galaxyproject.org rather 
than an editable directly from github.

Also, use `set -e` in scripts/common_startup.sh to fail if anything
fails, rather than chaining a bunch of things with `&&` but not properly
handling failure cases.
 2015-10-22 15:02:14 -04:00
Nate Coraor 4a05d5ea12 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs 2015-10-20 18:59:06 -04:00
Nate Coraor 27ab6fe8f9 Use the database temp directory store the Mako template cache when 
running framework tests.
 2015-10-20 13:56:28 -04:00
Nate Coraor c893afda00 Merge branch 'dev' into smash_eggs 2015-10-19 11:46:58 -04:00
Eric Rasche 8a66701d4f Don't re-upload if already there 2015-10-15 16:02:05 -05:00
Nate Coraor d92787557a Move vvers and vurl vars to a more relevant scope. 2015-10-15 11:00:50 -04:00
Eric Rasche 2cca823a78 Prepopulate memoization cache 2015-10-14 16:05:44 -05:00
Eric Rasche 6be301ca8a Support local/non local data and paths including root 2015-10-14 15:02:27 -05:00
Eric Rasche 33925747b8 Allow linking only 2015-10-14 14:50:35 -05:00
Eric Rasche aec9961407 Strip newlines 2015-10-14 14:43:08 -05:00
Eric Rasche decca0e96a Refactor to accept output of find 2015-10-14 14:37:21 -05:00
Eric Rasche 61f1cdf5d7 Added script to upload a directory to a data library 2015-10-14 14:16:45 -05:00