Merge pull request #85 from sbesson/pytest_logging

Integration tests: call pytest directly

setup.py

@@ -18,70 +18,8 @@
 #
 #
 import os
-import sys
 
 from setuptools import setup
-from setuptools.command.test import test as test_command
-
-
-class PyTest(test_command):
-    user_options = [
-        ('test-path=', 't', "base dir for test collection"),
-        ('test-ice-config=', 'i',
-         "use specified 'ice config' file instead of default"),
-        ('test-pythonpath=', 'p', "prepend 'pythonpath' to PYTHONPATH"),
-        ('test-string=', 'k', "only run tests matching 'string'"),
-        ('test-marker=', 'm', "only run tests including 'marker'"),
-        ('test-no-capture', 's', "don't suppress test output"),
-        ('test-failfast', 'x', "Exit on first error"),
-        ('test-verbose', 'v', "more verbose output"),
-        ('test-quiet', 'q', "less verbose output"),
-        ('junitxml=', None, "create junit-xml style report file at 'path'"),
-        ('pdb', None, "fallback to pdb on error"),
-        ]
-
-    def initialize_options(self):
-        test_command.initialize_options(self)
-        self.test_pythonpath = None
-        self.test_string = None
-        self.test_marker = None
-        self.test_path = 'test'
-        self.test_failfast = False
-        self.test_quiet = False
-        self.test_verbose = False
-        self.test_no_capture = False
-        self.junitxml = None
-        self.pdb = False
-        self.test_ice_config = None
-
-    def finalize_options(self):
-        test_command.finalize_options(self)
-        self.test_args = [self.test_path]
-        if self.test_string is not None:
-            self.test_args.extend(['-k', self.test_string])
-        if self.test_marker is not None:
-            self.test_args.extend(['-m', self.test_marker])
-        if self.test_failfast:
-            self.test_args.extend(['-x'])
-        if self.test_verbose:
-            self.test_args.extend(['-v'])
-        if self.test_quiet:
-            self.test_args.extend(['-q'])
-        if self.junitxml is not None:
-            self.test_args.extend(['--junitxml', self.junitxml])
-        if self.pdb:
-            self.test_args.extend(['--pdb'])
-        self.test_suite = True
-        if 'ICE_CONFIG' not in os.environ:
-            os.environ['ICE_CONFIG'] = self.test_ice_config
-
-    def run_tests(self):
-        if self.test_pythonpath is not None:
-            sys.path.insert(0, self.test_pythonpath)
-        # import here, cause outside the eggs aren't loaded
-        import pytest
-        errno = pytest.main(self.test_args)
-        sys.exit(errno)
 
 
 def read(fname):
@@ -122,9 +60,7 @@ def read(fname):
     zip_safe=True,
     download_url='%s/v%s.tar.gz' % (url, version),
     keywords=['OMERO.CLI', 'plugin'],
-    cmdclass={'test': PyTest},
     install_requires=[
-        'future',
         'omero-py>=5.6.0',
         'PyYAML',
         'jinja2',

src/omero_metadata/cli.py

@@ -7,13 +7,8 @@
    Use is subject to license terms supplied in LICENSE.txt
 
 """
-from __future__ import division
 
 import omero_ext.argparse as argparse
-from builtins import str
-from builtins import range
-from builtins import object
-from future.utils import native_str
 import logging
 import mimetypes
 import os
@@ -734,5 +729,5 @@ def pixelsize(self, args):
                 pixel.setPhysicalSizeZ(omero.model.LengthI(args.z, unit))
 
         group_id = pixels[0].getDetails().getGroup().getId().getValue()
-        ctx = {'omero.group': native_str(group_id)}
+        ctx = {'omero.group': str(group_id)}
         conn.getUpdateService().saveArray(pixels, ctx)

src/omero_metadata/populate.py

@@ -3,7 +3,6 @@
 """
 Populate bulk metadata tables from delimited text files.
 """
-from __future__ import print_function
 
 #
 #  Copyright (C) 2011-2019 University of Dundee. All rights reserved.
@@ -24,12 +23,6 @@
 #
 
 
-from builtins import chr
-from builtins import str
-from builtins import range
-from future.utils import native_str
-from past.builtins import basestring
-from builtins import object
 import logging
 import gzip
 import sys
@@ -1197,7 +1190,7 @@ def create_table(self):
         group = str(self.value_resolver.target_group)
         sr = sf.sharedResources()
         table = sr.newTable(1, self.table_name,
-                            {'omero.group': native_str(group)})
+                            {'omero.group': str(group)})
         if table is None:
             raise MetadataError(
                 "Unable to create table: %s" % DEFAULT_TABLE_NAME)
@@ -1235,7 +1228,7 @@ def preprocess_data(self, reader):
                     break
                 try:
                     log.debug("Value's class: %s" % value.__class__)
-                    if isinstance(value, basestring):
+                    if isinstance(value, str):
                         column.size = max(
                             column.size, len(value.encode('utf-8')))
                     # The following IDs are needed for
@@ -1339,7 +1332,7 @@ def create_file_annotation(self, table):
         link = self.create_annotation_link()
         link.parent = self.target_object
         link.child = file_annotation
-        update_service.saveObject(link, {'omero.group': native_str(group)})
+        update_service.saveObject(link, {'omero.group': str(group)})
 
     def populate(self, rows):
         nrows = len(rows)
@@ -1602,7 +1595,7 @@ def projection(self, q, ids, nss=None, batch_size=None):
             nids = 1
             single_id = ids
 
-        if isinstance(nss, basestring):
+        if isinstance(nss, str):
             params.addString("ns", nss)
         elif nss:
             params.map['nss'] = rlist(rstring(s) for s in nss)
@@ -1804,7 +1797,7 @@ def _save_annotation_links(self, links):
         group = str(self.target_object.details.group.id)
         update_service = sf.getUpdateService()
         arr = update_service.saveAndReturnArray(
-            links, {'omero.group': native_str(group)})
+            links, {'omero.group': str(group)})
         return arr
 
     def _save_annotation_and_links(self, links, ann, batch_size):
@@ -1829,7 +1822,7 @@ def _save_annotation_and_links(self, links, ann, batch_size):
             for link in batch:
                 link.setChild(annobj)
             update_service.saveArray(
-                batch, {'omero.group': native_str(group)})
+                batch, {'omero.group': str(group)})
             sz += len(batch)
         return sz
 

test/integration/clitest/test_metadata.py

@@ -20,7 +20,6 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 
 import pytest
-from past.builtins import long
 
 import omero
 import omero.gateway
@@ -43,7 +42,7 @@ def setup_method(self, method):
 
         conn = BlitzGateway(client_obj=self.client)
         self.imageid = unwrap(self.image.getId())
-        assert isinstance(self.imageid, long)
+        assert isinstance(self.imageid, int)
         wrapper = conn.getObject("Image", self.imageid)
         self.md = Metadata(wrapper)
 
@@ -245,9 +244,10 @@ def test_deletebulkanns(self, capfd):
         o = self.invoke(capfd)
         assert "FileAnnotation:" in o
 
-        # Should have no FileAnnotation since it's deleted
+        # Should be empty since it's deleted
         o = self.invoke(capfd)
-        assert "FileAnnotation:" not in o
+        assert o == ""
+        assert len(o.strip()) == 0
 
     @pytest.mark.parametrize('report', [False, True])
     def test_measures(self, capfd, report):

test/integration/metadata/test_populate.py

@@ -24,10 +24,6 @@
    and populate_roi.py scripts.
 """
 
-from builtins import str
-from builtins import zip
-from builtins import range
-from builtins import object
 from omero.testlib import ITest
 import string
 import csv

test/integration/tablestest/test_populate_metadata.py

@@ -24,7 +24,6 @@
 
 """
 
-from builtins import range
 from omero.testlib import ITest
 import os