Merge pull request #227 from JensTimmerman/cleanup

fix tests and bugs for new vsc-install

bin/logdaemon.py

@@ -5,7 +5,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/__init__.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/__init__.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/affinity.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/dateandtime.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/docs.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/exceptions.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/fancylogger.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #
@@ -187,7 +187,11 @@ class FancyLogger(logging.getLoggerClass()):
 
     # default class for raiseException method, that can be redefined by deriving loggers
     RAISE_EXCEPTION_CLASS = Exception
-    RAISE_EXCEPTION_LOG_METHOD = lambda c, msg: c.warning(msg)
+
+    def log_method(self, msg):
+        self.warning(msg)
+
+    RAISE_EXCEPTION_LOG_METHOD = log_method
 
     # method definition as it is in logging, can't change this
     def makeRecord(self, name, level, pathname, lineno, msg, args, excinfo, func=None, extra=None):

lib/vsc/utils/generaloption.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/mail.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/missing.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/patterns.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/rest.py

@@ -104,7 +104,7 @@ def __init__(self, url, username=None, password=None, token=None, token_type='To
         elif token is not None:
             self.auth_header = '%s %s' % (token_type, token)
 
-    def get(self, url, headers={}, **params):
+    def get(self, url, headers=None, **params):
         """
         Do a http get request on the given url with given headers and parameters
         Parameters is a dictionary that will will be urlencoded
@@ -114,7 +114,7 @@ def get(self, url, headers={}, **params):
         url += self.urlencode(params)
         return self.request(self.GET, url, None, headers)
 
-    def head(self, url, headers={}, **params):
+    def head(self, url, headers=None, **params):
         """
         Do a http head request on the given url with given headers and parameters
         Parameters is a dictionary that will will be urlencoded
@@ -124,7 +124,7 @@ def head(self, url, headers={}, **params):
         url += self.urlencode(params)
         return self.request(self.HEAD, url, None, headers)
 
-    def delete(self, url, headers={}, **params):
+    def delete(self, url, headers=None, **params):
         """
         Do a http delete request on the given url with given headers and parameters
         Parameters is a dictionary that will will be urlencoded
@@ -134,7 +134,7 @@ def delete(self, url, headers={}, **params):
         url += self.urlencode(params)
         return self.request(self.DELETE, url, None, headers)
 
-    def post(self, url, body=None, headers={}, **params):
+    def post(self, url, body=None, headers=None, **params):
         """
         Do a http post request on the given url with given body, headers and parameters
         Parameters is a dictionary that will will be urlencoded
@@ -145,7 +145,7 @@ def post(self, url, body=None, headers={}, **params):
         headers['Content-Type'] = 'application/json'
         return self.request(self.POST, url, json.dumps(body), headers)
 
-    def put(self, url, body=None, headers={}, **params):
+    def put(self, url, body=None, headers=None, **params):
         """
         Do a http put request on the given url with given body, headers and parameters
         Parameters is a dictionary that will will be urlencoded
@@ -156,7 +156,7 @@ def put(self, url, body=None, headers={}, **params):
         headers['Content-Type'] = 'application/json'
         return self.request(self.PUT, url, json.dumps(body), headers)
 
-    def patch(self, url, body=None, headers={}, **params):
+    def patch(self, url, body=None, headers=None, **params):
         """
         Do a http patch request on the given url with given body, headers and parameters
         Parameters is a dictionary that will will be urlencoded
@@ -168,6 +168,9 @@ def patch(self, url, body=None, headers={}, **params):
         return self.request(self.PATCH, url, json.dumps(body), headers)
 
     def request(self, method, url, body, headers):
+        """Low-level networking. All HTTP-method methods call this"""
+        if headers is None:
+            headers = {}
         if self.auth_header is not None:
             headers['Authorization'] = self.auth_header
         headers['User-Agent'] = self.user_agent

lib/vsc/utils/run.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

lib/vsc/utils/testing.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

setup.py

@@ -36,10 +36,10 @@
 import vsc.install.shared_setup as shared_setup
 from vsc.install.shared_setup import ag, kh, jt, sdw
 
-VSC_INSTALL_REQ_VERSION = '0.9.19'
+VSC_INSTALL_REQ_VERSION = '0.10.1'
 
 PACKAGE = {
-    'version': '2.4.18',
+    'version': '2.5.0',
     'author': [sdw, jt, ag, kh],
     'maintainer': [sdw, jt, ag, kh],
     # as long as 1.0.0 is not out, vsc-base should still provide vsc.fancylogger

test/00-import.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #
@@ -23,4 +23,5 @@
 # You should have received a copy of the GNU Library General Public License
 # along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
 #
+#
 from vsc.install.commontest import CommonTest

test/__init__.py

@@ -1 +1,26 @@
+#
+# Copyright 2016-2016 Ghent University
+#
+# This file is part of vsc-base,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/hpcugent/vsc-base
+#
+# vsc-base is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Library General Public License as
+# published by the Free Software Foundation, either version 2 of
+# the License, or (at your option) any later version.
+#
+# vsc-base is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Library General Public License for more details.
+#
+# You should have received a copy of the GNU Library General Public License
+# along with vsc-base. If not, see <http://www.gnu.org/licenses/>.
+#
 

test/asyncprocess.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/dateandtime.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/docs.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/exceptions.py

@@ -5,7 +5,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/fancylogger.py

@@ -5,7 +5,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/generaloption.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #
@@ -41,7 +41,7 @@
 from vsc.utils.missing import shell_quote, shell_unquote
 from vsc.utils.optcomplete import gen_cmdline
 from vsc.utils.run import run_simple
-from vsc.install.shared_setup import REPO_BASE_DIR
+from vsc.install.shared_setup import vsc_setup
 from vsc.install.testing import TestCase
 
 
@@ -117,6 +117,10 @@ def ext_options(self):
 class GeneralOptionTest(TestCase):
     """Tests for general option"""
 
+    def setUp(self):
+        super(GeneralOptionTest, self).setUp()
+        self.setup = vsc_setup()
+
     def test_help_short(self):
         """Generate short help message"""
         topt = TestOption1(go_args=['-h'],
@@ -685,7 +689,7 @@ def test_optcomplete(self):
         partial = '-'
         cmd_list = [script, partial]
 
-        pythonpath = 'PYTHONPATH=%s' % os.pathsep.join([p for p in sys.path if p.startswith(REPO_BASE_DIR)])
+        pythonpath = 'PYTHONPATH=%s' % os.pathsep.join([p for p in sys.path if p.startswith(self.setup.REPO_BASE_DIR)])
         ec, out = run_simple('%s %s; test $? == 1' % (pythonpath, gen_cmdline(cmd_list, partial, shebang=False)))
         # tabcompletion ends with exit 1!; test returns this to 0
         # avoids run.log.error message

test/missing.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/optcomplete.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/rest.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/run.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/runtests/qa.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #

test/runtests/simple.py

@@ -4,7 +4,7 @@
 # This file is part of vsc-base,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
 # with support of Ghent University (http://ugent.be/hpc),
-# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
 # the Flemish Research Foundation (FWO) (http://www.fwo.be/en)
 # and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
 #