Depend on newer style Galaxy library dependencies.

pulsar/managers/queued_external_drmaa.py

@@ -6,7 +6,10 @@ from .base.base_drmaa import BaseDrmaaManager
 from .util.sudo import sudo_popen
 from ..managers import status
 
-from galaxy.tools.deps.commands import which
+try:
+    from galaxy.tools.deps.commands import which
+except ImportError:
+    from galaxy.tool_util.deps.commands import which
 
 from logging import getLogger
 log = getLogger(__name__)

requirements.txt

@@ -3,12 +3,14 @@ psutil
 PasteDeploy
 six
 pyyaml
-galaxy-lib
+galaxy-job-metrics>=19.9.0.dev0
+galaxy-objectstore>=19.9.0.dev0
+galaxy-tool-util>=19.9.0.dev0
 paramiko
 
 # Problematic for Python 3.
-paste
-PasteScript
+paste ; python_version == '2.7'
+PasteScript ; python_version == '2.7'
 
 ## Uncomment if using DRMAA queue manager.
 #drmaa

requirements3.txt

-## Python 3 is not yet working, but when it does it will require
-## different libraries. Hence this file.
-webob
-psutil
-PasteDeploy
-six
-galaxy-lib
-paramiko
-
-chaussette

setup.py

@@ -23,15 +23,16 @@ PULSAR_GALAXY_LIB = os.environ.get("PULSAR_GALAXY_LIB", "%d" % DEFAULT_PULSAR_GA
 readme = open('README.rst').read()
 history = open('HISTORY.rst').read().replace('.. :changelog:', '')
 
-requirements = [
-    'six',
-    'webob',
-    'psutil',
-    'pyyaml',
-]
+if os.path.exists("requirements.txt"):
+    requirements = [r for r in open("requirements.txt").read().split("\n") if ";" not in r]
+    py27_requirements = [r.split(";", 1)[0].strip() for r in open("requirements.txt").read().split("\n") if ";" in r]
+else:
+    # In tox, it will cover them anyway.
+    requirements = []
+    py27_requirements = []
 
-if not PULSAR_GALAXY_LIB:
-    requirements.append("galaxy-lib")
+if PULSAR_GALAXY_LIB:
+    requirements = [r for r in requirements if not r.startswith("galaxy-")]
 
 # TODO: use extra_requires here to be more correct.
 if sys.version_info[0] == 2:
@@ -108,6 +109,9 @@ setup(
     package_dir={'pulsar': 'pulsar'},
     include_package_data=True,
     install_requires=requirements,
+    extras_require={
+        ':python_version=="2.7"': py27_requirements,
+    },
     license="Apache License 2.0",
     zip_safe=False,
     keywords='pulsar',

test/client_staging_test.py

@@ -5,8 +5,8 @@ from .test_utils import TempDirectoryTestCase
 from pulsar.client.test.test_common import write_config
 from pulsar.client import submit_job, ClientJobDescription
 from pulsar.client import ClientOutputs
-from galaxy.tools.deps.dependencies import DependenciesDescription
-from galaxy.tools.deps.requirements import ToolRequirement
+from galaxy.tool_util.deps.dependencies import DependenciesDescription
+from galaxy.tool_util.deps.requirements import ToolRequirement
 
 TEST_REQUIREMENT_1 = ToolRequirement("test1", "1.0")
 TEST_REQUIREMENT_2 = ToolRequirement("test2", "1.0")

test/persistence_test.py

@@ -9,8 +9,8 @@ from .test_utils import (
     temp_directory,
     TestDependencyManager
 )
+from galaxy.job_metrics import NULL_JOB_INSTRUMENTER
 from galaxy.util.bunch import Bunch
-from galaxy.jobs.metrics import NULL_JOB_INSTRUMENTER
 
 TEST_JOB_ID = "4"
 TEST_STAGED_FILE = "cow"

test/test_utils.py

@@ -22,8 +22,8 @@ from webtest.http import StopableWSGIServer
 
 import galaxy.util
 import pulsar.util
+from galaxy.job_metrics import NULL_JOB_INSTRUMENTER
 from galaxy.util.bunch import Bunch
-from galaxy.jobs.metrics import NULL_JOB_INSTRUMENTER
 
 from pulsar.managers.util import drmaa
 from pulsar.tools import ToolBox

tox.ini

@@ -15,14 +15,14 @@ commands = nosetests --exclude '.*integration.*' []
 
 [testenv:py35]
 deps =
-    -rrequirements3.txt
+    -rrequirements.txt
     -rdev-requirements.txt
     drmaa
 
 [testenv:py35-unit]
 commands = nosetests --verbose --exclude '.*integration.*' []
 deps =
-    -rrequirements3.txt
+    -rrequirements.txt
     -rdev-requirements.txt
     drmaa