John Chilton
807586ace8
Merge release_16.01 into dev.
2016-01-26 09:06:52 +00:00
Mark Einon
efa1334d45
Change python print() format to be backward compatible with older versions
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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.
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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
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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
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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
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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.
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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
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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
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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
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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
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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
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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
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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
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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
John Chilton
bbef5ed737
Improvements to release notes generation.
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- Add last commit for 15.10 (need to automate finding that).
- Generate next release annoucement.
- Generate annoucement for this release.
- Respect the minor tag.
2015-10-14 17:04:49 +01:00
Nate Coraor
433b79de2b
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into smash_eggs
2015-10-13 16:54:18 -04:00
Dannon Baker
b77496ec63
Update other quota manipulations to use the new user.adjust_quota_usage function.
2015-10-13 13:53:15 -04:00
Nate Coraor
744835bbfe
Allow the use of common_startup.sh's --skip-eggs from run_tests.sh, and
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have tox pass this flag (so that dependencies are installed in the tox
envs)
2015-10-13 12:47:01 -04:00
Nate Coraor
665c4c299d
Handle the case where there are no conditional (heh) requirements
2015-10-01 15:38:58 -04:00
Dannon Baker
7f3ee5b167
Merge pull request #612 from lparsons/manual_builds
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Move manual_builds.txt to manual_builds.txt.sample
2015-09-24 17:10:49 -04:00
Nate Coraor
a44b2c2170
Rename galaxy.wheels to the more generalized galaxy.dependencies (since
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technically we don't care whether they are wheels), handle optional deps
more correctly. Add error handling to common_startup.sh.
2015-09-22 12:54:03 -04:00
Nate Coraor
93410ecf25
Fix additional lint errors created by modifying stuff in scripts/
2015-09-21 16:01:22 -04:00
Nate Coraor
0469ed29e0
Remove egg cruft from scripts/
2015-09-21 15:55:07 -04:00
Nate Coraor
97ad53f570
Merge remote-tracking branch 'upstream/dev' into smash_eggs
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Conflicts:
eggs.ini
lib/galaxy/__init__.py
lib/galaxy/datatypes/binary.py
lib/galaxy/datatypes/converters/bgzip.py
lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
lib/galaxy/datatypes/converters/interval_to_bed_converter.py
lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
lib/galaxy/datatypes/converters/interval_to_coverage.py
lib/galaxy/datatypes/converters/interval_to_fli.py
lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
lib/galaxy/datatypes/converters/maf_to_interval_converter.py
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py
lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py
lib/galaxy/datatypes/coverage.py
lib/galaxy/eggs/__init__.py
lib/galaxy/eggs/dist.py
lib/galaxy/eggs/scramble.py
lib/galaxy/exceptions/__init__.py
lib/galaxy/jobs/runners/pbs.py
lib/galaxy/jobs/transfer_manager.py
lib/galaxy/model/__init__.py
lib/galaxy/model/migrate/check.py
lib/galaxy/model/orm/__init__.py
lib/galaxy/model/tool_shed_install/migrate/check.py
lib/galaxy/web/framework/__init__.py
lib/galaxy/web/framework/helpers/__init__.py
lib/galaxy/web/framework/middleware/sentry.py
lib/galaxy/web/framework/openid_manager.py
lib/galaxy/web/framework/webapp.py
lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py
lib/galaxy/webapps/galaxy/controllers/dataset.py
lib/galaxy/webapps/galaxy/controllers/library_common.py
lib/galaxy/webapps/reports/controllers/workflows.py
lib/galaxy/webapps/tool_shed/controllers/repository.py
lib/galaxy/webapps/tool_shed/search/repo_search.py
lib/galaxy/webapps/tool_shed/search/tool_search.py
lib/galaxy_ext/metadata/set_metadata.py
lib/pulsar/client/config_util.py
lib/tool_shed/galaxy_install/install_manager.py
lib/tool_shed/galaxy_install/migrate/check.py
lib/tool_shed/grids/admin_grids.py
lib/tool_shed/grids/repository_grids.py
lib/tool_shed/repository_types/repository_suite_definition.py
lib/tool_shed/repository_types/tool_dependency_definition.py
lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py
lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py
lib/tool_shed/scripts/check_repositories_for_functional_tests.py
lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py
lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py
lib/tool_shed/util/basic_util.py
lib/tool_shed/util/encoding_util.py
lib/tool_shed/util/hg_util.py
scripts/check_eggs.py
scripts/dist-scramble.py
scripts/fetch_eggs.py
scripts/make_egg_packager.py
scripts/scramble.py
scripts/scramble/lib/scramble_lib.py
scripts/scramble/scripts/DRMAA_python-macosx.py
scripts/scramble/scripts/DRMAA_python-solaris.py
scripts/scramble/scripts/DRMAA_python.py
scripts/scramble/scripts/MySQL_python-solaris.py
scripts/scramble/scripts/MySQL_python.py
scripts/scramble/scripts/PyRods.py
scripts/scramble/scripts/bx_python-solaris.py
scripts/scramble/scripts/generic.py
scripts/scramble/scripts/pbs_python.py
scripts/scramble/scripts/psycopg2-linux.py
scripts/scramble/scripts/psycopg2-macosx.py
scripts/scramble/scripts/psycopg2-solaris.py
scripts/scramble/scripts/psycopg2.py
scripts/scramble/scripts/pysam-solaris.py
scripts/scramble/scripts/pysqlite.py
scripts/test_dist_egg.py
2015-09-21 15:02:47 -04:00
Nate Coraor
40bde6e102
Install required dependencies from requirements.txt rather than
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convoluted galaxy.wheels method. Not sure why I was doing that.
Hackathons are dangerous places.
2015-09-21 13:21:13 -04:00
Nate Coraor
150c17b9e8
Do not explicitly require pexpect. If anyone wants to use the old and
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mostly unused features that depend on it (namely remote sequencer
transfers via scp) they can pip install pexpect.
2015-09-17 13:56:44 -04:00
John Chilton
bd55650f06
Add testing environment variable GALAXY_TEST_LOGGING_CONFIG.
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Unifies logging through the testing process. Requires adding a Galaxy option to disable its own attempts to configure a different root logger.
2015-09-16 16:24:53 +01:00
Nicola Soranzo
cd456e186d
Print to stderr when calling sys.exit(1)
2015-09-11 19:05:37 +01:00
Nicola Soranzo
2625bc4bc0
Fix flake8 broken when merging 041c94bf78 from release_15.07 .
2015-09-02 16:30:50 +01:00
Nicola Soranzo
bcbeb75a68
Merge branch 'master' into dev
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Conflicts:
lib/tool_shed/dependencies/tool/tag_attribute_handler.py
2015-09-02 16:10:03 +01:00
John Chilton
4a05c07aa5
Fixup end of release items for release notes.
2015-08-27 13:04:17 +01:00
John Chilton
041c94bf78
Release notes for 15.07.
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This includes a script to boot strap the notes for future releases, updated announcement page for 15.07, and new announcement page for 15.10.
2015-08-27 12:00:18 +01:00
John Chilton