Merge branch 'master' into cwlprov-add_output

Author: FarahZKhan

release-test.sh

@@ -9,7 +9,17 @@ package=cwltool
 module=cwltool
 slug=${TRAVIS_PULL_REQUEST_SLUG:=common-workflow-language/cwltool}
 repo=https://github.com/${slug}.git
-run_tests="bin/py.test --ignore ${module}/schemas/ --pyarg -x cwltool -n$(nproc) --dist=loadfile"
+parallel=""
+if [[ "${OSTYPE}" == linux* ]]
+then
+	parallel=-n$(( $(nproc) / 2 ))
+fi
+if [[ "${OSTYPE}" == darwin* ]]
+then
+	parallel=-n$(( $(sysctl -n hw.physicalcpu) / 2 ))
+fi
+
+run_tests="bin/py.test --ignore ${module}/schemas/ --pyarg -x cwltool ${parallel} --dist=loadfile"
 pipver=7.0.2 # minimum required version of pip
 setuptoolsver=24.2.0 # required to generate correct metadata for
                      # python_requires

tests/test_examples.py

@@ -376,25 +376,27 @@ def test_typecomparestrict(self):
 
     def test_recordcompare(self):
         src = {
-            'fields': [{
-                'type': {'items': 'string', 'type': 'array'},
-                'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/description'
-            },
-                {
-                    'type': {'items': 'File', 'type': 'array'},
-                    'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file'
+            'fields': [
+                {'type': {'items': 'string', 'type': 'array'},
+                 'name': u'file:///home/chapmanb/drive/work/cwl/'
+                         'test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/description'
+                },
+                {'type': {'items': 'File', 'type': 'array'},
+                 'name': u'file:///home/chapmanb/drive/work/cwl/'
+                         'test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec/vrn_file'
                 }],
             'type': 'record',
             'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/wf-variantcall.cwl#vc_rec/vc_rec'
         }
         sink = {
-            'fields': [{
-                'type': {'items': 'string', 'type': 'array'},
-                'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/description'
-            },
-                {
-                    'type': {'items': 'File', 'type': 'array'},
-                    'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/vrn_file'
+            'fields': [
+                {'type': {'items': 'string', 'type': 'array'},
+                 'name': u'file:///home/chapmanb/drive/work/cwl/'
+                         'test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/description'
+                },
+                {'type': {'items': 'File', 'type': 'array'},
+                 'name': u'file:///home/chapmanb/drive/work/cwl/'
+                         'test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec/vrn_file'
                 }],
             'type': 'record',
             'name': u'file:///home/chapmanb/drive/work/cwl/test_bcbio_cwl/run_info-cwl-workflow/steps/vc_output_record.cwl#vc_rec/vc_rec'}
@@ -618,7 +620,7 @@ def get_main_output(self, new_args):
             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
 
         stdout, stderr = process.communicate()
-        return process.returncode, stdout.decode(), stderr.decode()
+        return process.returncode, stdout.decode('utf-8'), stderr.decode('utf-8')
 
 
 class TestJsConsole(TestCmdLine):