mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Remove the namespacing of galaxy packages for now, everything will just
live in the `galaxy` package. Install deps at install time.
This commit is contained in:
Nate Coraor
@@ -5,85 +5,11 @@ from setuptools import setup, find_packages
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readme = open('README.rst').read()
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GALAXY_PACKAGE = os.environ.get("GALAXY_PACKAGE", "galaxy-lib")
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VERSION = None
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def _find_packages(base):
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r = []
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for sub in find_packages(os.sep.join(['lib'] + base.split('.'))):
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print 'Found package', '.'.join([base, sub])
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r.append('.'.join([base, sub]))
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return r
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if GALAXY_PACKAGE == "galaxy-lib":
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requirements = []
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base_packages = [
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'galaxy.datatypes',
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'galaxy.exceptions',
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'galaxy.jobs.metrics',
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'galaxy.objectstore',
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'galaxy.tools',
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'galaxy.util',
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]
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package_data = [
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'exceptions/error_codes.json',
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'datatypes/converters/*.xml',
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'datatypes/display_applications/configs/*/*.xml',
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'datatypes/set_metadata_tool.xml',
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'tools/imp_exp/imp_history_from_archive.xml',
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'tools/imp_exp/exp_history_to_archive.xml',
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]
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elif GALAXY_PACKAGE == "galaxy":
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requirements = [
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'galaxy-lib',
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]
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base_packages = [
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'galaxy.actions',
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'galaxy.auth',
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'galaxy.dataset_collections',
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'galaxy.dependencies',
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'galaxy.external_services',
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'galaxy.forms',
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'galaxy.jobs',
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'galaxy.managers',
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'galaxy.model',
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'galaxy.openid',
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'galaxy.quota',
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'galaxy.sample_tracking',
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'galaxy.security',
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'galaxy.tags',
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'galaxy.tours',
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'galaxy.visualization',
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'galaxy.web',
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'galaxy.webapps',
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'galaxy.workflow',
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'galaxy.work',
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]
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package_data = [
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'jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh',
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'jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh',
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'model/migrate/migrate.cfg',
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'dependencies/*.txt',
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]
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elif GALAXY_PACKAGE == 'tool-shed':
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requirements = [
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'galaxy-app',
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]
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packages = ['tool_shed'] + _find_packages('tool_shed')
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package_data = []
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else:
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sys.stderr.write('ERROR: Unknown package name: {}\n'.format(GALAXY_PACKAGE))
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sys.exit(1)
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if GALAXY_PACKAGE.startswith('galaxy'):
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packages = ['galaxy']
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for base_package in base_packages:
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packages.append(base_package)
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packages.extend(_find_packages(base_package))
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# TODO: detect if we are not running from pip (inspect the stack?) and if not,
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# suggest using `pip install -i https://wheels.galaxyproject.org/simple .`
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# sets VERSION (also VERSION_MAJOR and VERSION_MINOR)
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@@ -92,22 +18,32 @@ execfile('lib/galaxy/version.py')
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scripts = ["scripts/galaxy"]
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setup(
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name=GALAXY_PACKAGE,
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name='galaxy',
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version=VERSION,
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description='Galaxy (http://galaxyproject.org/).',
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long_description=readme,
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author='Galaxy Project',
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author_email='galaxy-dev@lists.galaxyproject.org',
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url='https://github.com/galaxyproject/galaxy',
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packages=packages,
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packages=find_packages('lib'),
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entry_points='''
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[console_scripts]
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galaxy-paster=galaxy.util.pastescript.serve:run
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galaxy-main=galaxy.main:main
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''',
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scripts=scripts,
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package_data={
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'galaxy': package_data,
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'galaxy': [
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'exceptions/error_codes.json',
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'datatypes/converters/*.xml',
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'datatypes/display_applications/configs/*/*.xml',
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'datatypes/set_metadata_tool.xml',
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'jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh',
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'jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh',
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'tools/imp_exp/imp_history_from_archive.xml',
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'tools/imp_exp/exp_history_to_archive.xml',
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'model/migrate/migrate.cfg',
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'dependencies/*.txt',
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],
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'tool_shed': [
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'galaxy_install/migrate/migrate.cfg',
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'scripts/bootstrap_tool_shed/parse_run_sh_args.sh',
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@@ -117,7 +53,60 @@ setup(
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},
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package_dir={'': 'lib'},
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include_package_data=True,
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install_requires=requirements,
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dependency_links=['https://wheels.galaxyproject.org/packages'],
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setup_requires=['pip>=8.1'],
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# FIXME: read requirements.txt into a list...
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install_requires=[
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'bx-python==0.7.3',
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'MarkupSafe==0.23',
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'PyYAML==3.11',
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'SQLAlchemy==1.0.8',
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'mercurial==3.7.3',
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'numpy==1.9.2',
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'pycrypto==2.6.1',
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'Paste==2.0.2',
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'PasteDeploy==1.5.2',
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'docutils==0.12',
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'wchartype==0.1',
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'repoze.lru==0.6',
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'Routes==2.2',
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'WebOb==1.4.1',
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'WebHelpers==1.3',
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'Mako==1.0.2',
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'pytz==2015.4',
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'Babel==2.0',
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'Beaker==1.7.0',
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'dictobj==0.3.1',
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'nose==1.3.7',
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'Parsley==1.3',
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'six==1.9.0',
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'Whoosh==2.7.4',
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'Cheetah==2.4.4',
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'Markdown==2.6.3',
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'bioblend==0.7.0',
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'boto==2.38.0',
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'requests==2.8.1',
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'requests-toolbelt==0.4.0',
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'kombu==3.0.30',
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'amqp==1.4.8',
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'anyjson==0.3.3',
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'psutil==4.1.0',
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'pulsar-galaxy-lib==0.7.0.dev4',
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'sqlalchemy-migrate==0.10.0',
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'decorator==4.0.2',
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'Tempita==0.5.3dev',
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'sqlparse==0.1.16',
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'pbr==1.8.0',
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'svgwrite==1.1.6',
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'pyparsing==2.1.1',
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'Fabric==1.10.2',
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'paramiko==1.15.2',
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'ecdsa==0.13',
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'pysam==0.8.4+gx1',
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],
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extras_require={
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'postgresql': ['psycopg2==2.6.1'],
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},
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license="Academic Free License 3.0",
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zip_safe=False,
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keywords='galaxy',
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