E Rasche
e4518ff3e3
Rebase hardening commits from dev
2017-10-12 17:04:55 -04:00
Dave Bouvier
2c8a5d9d58
Correct import order.
2016-09-23 12:13:10 -04:00
Dave Bouvier
b83f0a1024
Fix whoosh indexing.
2016-09-21 14:40:12 -04:00
Ben
6516f20602
Update common_startup.sh to require python2.7 in .venv
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by changing the .venv creation to 'virtualenv -p python2.7' we force the python version we need.
The current suggestion on getgalaxy is: https://wiki.galaxyproject.org/Admin/Python
% mkdir ~/galaxy-python
% ln -s /path/to/python2.7 ~/galaxy-python/python
% export PATH=~/galaxy-python:$PATH
Which break lots of things, since we are working in a virtual environment anyway we can build it from the start with the version we want.
This will require that python 2.7 used in the virtual environment, and prevent breakage from multi-python deployed hosts. This simple change makes the software more accessible.
This edit built fine on OS X 10.10.5
python installed: 2.6, 2.7, 3.2, 3.5
galaxy.queue_worker INFO 2016-08-08 22:14:15,624 Binding and starting galaxy control worker for main
Starting server in PID 69210.
serving on http://127.0.0.1:8080
/Users/benc/Code/github/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
'storage.' % (dialect.name, dialect.driver))
127.0.0.1 - - [08/Aug/2016:22:39:18 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/52.0.2743.116 Safari/537.36"
2016-08-08 22:40:06 -04:00
Nicola Soranzo
5e7f0c4b18
Fix unit tests exit status
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Broken in https://github.com/galaxyproject/galaxy/pull/2564
Also update scripts/nosetests.py
2016-07-29 19:47:08 +01:00
Bjoern Gruening
6b8b0cde5b
make client
2016-07-22 22:47:13 +02:00
John Chilton
8dbf987e10
Merge pull request #2455 from erasche/grt
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Galactic Radio Telescope
2016-07-21 20:06:12 -04:00
John Chilton
76628c7203
Refactor grt.py method names to be clear public interface is only main().
2016-07-21 14:59:29 -04:00
John Chilton
bbe1d7bed0
Remove custom Galaxy config parsing in grt.py.
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Use existing abstractions - so things like environment variable based configuration will work.
2016-07-21 14:59:29 -04:00
John Chilton
1f292824a1
Fix some obvious Python 2isms in grt client...
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... and one instance of bare exception.
2016-07-21 14:59:27 -04:00
John Chilton
a93874fe7b
Define a main() function for grt client.
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This is purely stylistic - but I prefer to structure code to allow testing even if there are no actual test cases yet.
For more information see discussion here - http://stackoverflow.com/questions/4041238/why-use-def-main .
2016-07-21 14:59:05 -04:00
John Chilton
6432eae251
Give grt a top-level docstring.
2016-07-21 14:33:58 -04:00
John Chilton
0280daebef
grt.ini.sample is a YAML file, git it a YAML extension.
2016-07-21 14:31:25 -04:00
anuprulez
0d915ce131
Adding maximize/minimize feature to the communication channel
2016-07-14 14:11:44 +02:00
Dannon Baker
61a11341f9
When CONDA_ALREADY_INSTALLED is undefined there's an error due to the number of arguments in the boolean expression (we actually *do* always want a 1 or 0 there, never empty)
2016-07-08 10:52:08 -04:00
Remi Marenco
de702db55d
s/creation/activation. Thx @nsoranzo
2016-07-07 15:45:40 -04:00
remimarenco
b53a9275d5
Add Warning when Conda is installed because we skip the virtualenv creation
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Fix the case where we could have conda not installed but not setting VirtualEnv still (and have this non relevant warning
2016-07-07 14:34:40 -04:00
Dannon Baker
a946b04316
Merge pull request #2574 from bxlab/python3
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Python3: port 215 files
2016-07-05 09:57:54 -04:00
Eric Enns
417d43fb3e
Added upload1 to tool blacklist
2016-06-26 09:19:57 -05:00
Nicola Soranzo
cd13423953
Python3: small fixes to previous commits
2016-06-26 02:43:57 -04:00
Junzhou Wang
f68a8198da
Python3: scripts/cleanup_datasets scripts/data_libraries
2016-06-25 21:49:25 -04:00
Eric Enns
2fc3ffffff
Removed unused copy import
2016-06-25 20:13:37 -05:00
Eric Enns
0383d47037
Added in params reporting with initial sanitization
2016-06-25 20:09:52 -05:00
Junzhou Wang
e45f8abb54
Python3:script/api/
2016-06-25 20:49:06 -04:00
Junzhou Wang
a04f6589ea
Python3: test/shed_functional/ and test/unit/
2016-06-25 20:00:42 -04:00
Dannon Baker
a0b20a61a2
Initialize objectstore for fix_set_dataset_sizes script (otherwise it doesn't currently run successfully)
2016-06-25 19:04:44 -04:00
Eric Enns
0c24b1c408
Fixed remaining flake8 issues
2016-06-25 14:26:40 -05:00
Eric Enns
db4abace58
Flake8 fixes
2016-06-25 14:08:43 -05:00
Eric Enns
5cd9423677
Added grt_url to grt.ini.sample and removed default from argparse
2016-06-25 14:04:23 -05:00
Eric Enns
c2239b1d9b
Moved almost all cmd line parameters to config file.
2016-06-25 14:00:50 -05:00
Eric Enns
473b7eadc1
Added in tool_blacklist
2016-06-25 13:15:45 -05:00
Eric Enns
bb3f026bfa
Removed call to args.days
2016-06-25 13:00:22 -05:00
Eric Enns
722695a01b
Added in last_job_id_sent and removed days options so no duplicates will be sent.
2016-06-25 12:54:19 -05:00
Eric Rasche
d1d8642756
Change metric captured
2016-06-25 17:16:08 +00:00
Eric Rasche
012101692c
Ignore metadata setting
2016-06-25 16:42:04 +00:00
Bjoern Gruening
1f1c35f708
merge
2016-06-19 21:49:15 +02:00
anuprulez
464e9a4261
Fixed issue with Firefox auto scrolling
2016-06-19 17:45:30 +02:00
anuprulez
008220d88d
Adjusted the vertical position of gravatar icons
2016-06-19 15:47:09 +02:00
anuprulez
feb00567e4
Adjusted the vertical position of gravatar icons
2016-06-19 15:44:20 +02:00
Bjoern Gruening
10c2764f09
add the identicon to gravatar
2016-06-19 13:21:26 +02:00
Bjoern Gruening
e477d728d4
do not show gravatar for server messages
2016-06-19 10:30:45 +02:00
anuprulez
c017b51666
Fixed UI issues and log deletion functionality in main tab
2016-06-19 02:29:20 +02:00
Bjoern Gruening
b690abb46a
make chat view a little bit more compact and fix bug in displaying "me" messages
2016-06-19 00:56:40 +02:00
Bjoern Gruening
4a304b63b1
fix pep8
2016-06-19 00:56:10 +02:00
Eric Rasche
83e61f1ca4
Support gravatar and rework template
2016-06-18 19:12:37 +00:00
anuprulez
b8a92a3f80
Fixing issue with no persistent rooms
2016-06-18 17:20:38 +02:00
Bjoern Gruening
5ed647e34f
release preparation
2016-06-18 10:33:03 +02:00
anuprulez
111a1c6222
Fixing the issue with persistent room names with spaces, adding fancy scroll bar, buttons instead of links for persistent rooms and UI changes for message area
2016-06-14 20:03:58 +02:00
Bjoern Gruening
f034f1778b
make the communication window more packed
2016-06-14 00:00:48 +02:00
anuprulez
074fefeda2
Adding features-space enabled chat room names, ctrl+l for chat log deletion, removing delete icon, smooth transition on window load and code cleanup
2016-06-13 20:48:42 +02:00
E Rasche