Remove the galaxy-app package for now, and PEP 8 fixes

.ci/flake8_blacklist.txt

@@ -4,3 +4,5 @@ database/
 doc/patch.py
 doc/source/conf.py
 lib/galaxy/util/jstree.py
+build/
+dist/

MANIFEST.in.galaxy

@@ -1,3 +1,4 @@
 recursive-include lib/galaxy/web/framework/templates *.mako
 recursive-include lib/galaxy/web/framework/static *
 recursive-include lib/galaxy/tools/bundled *
+recursive-include lib/galaxy/web/proxy/js *

lib/galaxy/datatypes/registry.py

@@ -107,7 +107,7 @@ class Registry( object ):
                 self.converters_path_attr = registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' )
                 self.converters_path = os.path.join( root_dir, self.converters_path_attr )
                 if self.converters_path_attr == 'lib/galaxy/datatypes/converters' \
-                    and not os.path.isdir( self.converters_path ):
+                        and not os.path.isdir( self.converters_path ):
                     # Deal with the old default of this path being set in
                     # datatypes_conf.xml.sample (this path is not useful in an
                     # "installed Galaxy" world)
@@ -119,7 +119,7 @@ class Registry( object ):
                 self.display_path_attr = registration.get( 'display_path', 'display_applications' )
                 self.display_applications_path = os.path.join( root_dir, self.display_path_attr )
                 if self.display_path_attr == 'display_applications' \
-                    and not os.path.isdir( 'display_applications' ):
+                        and not os.path.isdir( 'display_applications' ):
                     # Ditto as with converters_path
                     self.display_path_attr = os.path.abspath( os.path.join( os.path.dirname( __file__ ), 'display_applications', 'configs' ) )
                     self.display_applications_path = self.display_path_attr

lib/galaxy/web/framework/webapp.py

@@ -904,6 +904,10 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
         return str(template)
 
 
+def default_url_path( path ):
+    return os.path.abspath( os.path.join( os.path.dirname( __file__ ), path ) )
+
+
 def build_url_map( app, global_conf, local_conf ):
     from paste.urlmap import URLMap
     from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
@@ -915,14 +919,13 @@ def build_url_map( app, global_conf, local_conf ):
     cache_time = conf.get( "static_cache_time", None )
     if cache_time is not None:
         cache_time = int( cache_time )
-    _def = lambda x: os.path.abspath( os.path.join( os.path.dirname( __file__ ), x ) )
     # Send to dynamic app by default
     urlmap["/"] = app
     # Define static mappings from config
-    urlmap["/static"] = Static( conf.get( "static_dir", _def("static/") ), cache_time )
-    urlmap["/images"] = Static( conf.get( "static_images_dir", _def("static/images") ), cache_time )
-    urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", _def("static/scripts/") ), cache_time )
-    urlmap["/static/style"] = Static( conf.get( "static_style_dir", _def("./static/style/blue") ), cache_time )
-    urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", _def("./static/favicon.ico") ), cache_time )
-    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", _def("./static/robots.txt") ), cache_time )
+    urlmap["/static"] = Static( conf.get( "static_dir", default_url_path("static/") ), cache_time )
+    urlmap["/images"] = Static( conf.get( "static_images_dir", default_url_path("static/images") ), cache_time )
+    urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", default_url_path("static/scripts/") ), cache_time )
+    urlmap["/static/style"] = Static( conf.get( "static_style_dir", default_url_path("./static/style/blue") ), cache_time )
+    urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", default_url_path("./static/favicon.ico") ), cache_time )
+    urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", default_url_path("./static/robots.txt") ), cache_time )
     return urlmap, cache_time

setup.py

@@ -6,13 +6,9 @@ from setuptools import setup, find_packages
 
 readme = open('README.rst').read()
 
-# Obviously this should not be empty, but for the moment, use:
-# pip install -e git+https://github.com/natefoo/pip@linux-wheels#egg=pip && \
-# pip install -r requirements.txt --index-url https://wheels.galaxyproject.org/simple/
-requirements = [
-]
-
 GALAXY_PACKAGE = os.environ.get("GALAXY_PACKAGE", "galaxy-lib")
+VERSION = None
+
 
 def _find_packages(base):
     r = []
@@ -40,18 +36,30 @@ if GALAXY_PACKAGE == "galaxy-lib":
         'tools/imp_exp/imp_history_from_archive.xml',
         'tools/imp_exp/exp_history_to_archive.xml',
     ]
-elif GALAXY_PACKAGE == "galaxy-app":
+elif GALAXY_PACKAGE == "galaxy":
     requirements = [
         'galaxy-lib',
     ]
     base_packages = [
+        'galaxy.actions',
         'galaxy.auth',
+        'galaxy.dataset_collections',
         'galaxy.dependencies',
         'galaxy.external_services',
+        'galaxy.forms',
         'galaxy.jobs',
+        'galaxy.managers',
         'galaxy.model',
+        'galaxy.openid',
         'galaxy.quota',
+        'galaxy.sample_tracking',
         'galaxy.security',
+        'galaxy.tags',
+        'galaxy.tours',
+        'galaxy.visualization',
+        'galaxy.web',
+        'galaxy.webapps',
+        'galaxy.workflow',
         'galaxy.work',
     ]
     package_data = [
@@ -59,28 +67,7 @@ elif GALAXY_PACKAGE == "galaxy-app":
         'jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh',
         'model/migrate/migrate.cfg',
         'dependencies/*.txt',
-        # FIXME: web/proxy/js/lib doesn't exist
-        #'web/proxy/js/*',
     ]
-elif GALAXY_PACKAGE == "galaxy":
-    requirements = [
-        'galaxy-app',
-    ]
-    base_packages = [
-        'galaxy.actions',
-        'galaxy.dataset_collections',
-        'galaxy.forms',
-        'galaxy.managers',
-        'galaxy.openid',
-        'galaxy.sample_tracking',
-        'galaxy.tags',
-        'galaxy.tours',
-        'galaxy.visualization',
-        'galaxy.web',
-        'galaxy.webapps',
-        'galaxy.workflow',
-    ]
-    package_data = []
 elif GALAXY_PACKAGE == 'tool-shed':
     requirements = [
         'galaxy-app',
@@ -105,7 +92,6 @@ execfile('lib/galaxy/version.py')
 scripts = ["scripts/galaxy"]
 
 setup(
-    #name='galaxy',
     name=GALAXY_PACKAGE,
     version=VERSION,
     description='Galaxy (http://galaxyproject.org/).',
@@ -113,7 +99,6 @@ setup(
     author='Galaxy Project',
     author_email='galaxy-dev@lists.galaxyproject.org',
     url='https://github.com/galaxyproject/galaxy',
-    #packages=find_packages('lib'),
     packages=packages,
     entry_points='''
         [console_scripts]

test/functional/tools/upload.py

@@ -1 +1 @@
-../../../tools/data_source/upload.py
+../../../lib/galaxy/tools/bundled/data_source/upload.py

test/functional/tools/upload.xml

@@ -1 +1 @@
-../../../tools/data_source/upload.xml
+../../../lib/galaxy/tools/bundled/data_source/upload.xml