Fix `--coverage option of run_tests.sh`

for pytest-based tests.

Also:
- do not create a giant XML coverage report file
- update other dependencies using `make update-dependencies`.

Introduced in commit 1152a19fd2 .

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -15,6 +15,7 @@ mock = "*"
 NoseHTML = "*"
 pygithub3 = {version = "*", markers = "python_version < '3'"}
 pytest = "*"
+pytest-cov = "*"
 pytest-html = "*"
 pytest-pythonpath = "*"
 pytest-postgresql = "*"

lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt

@@ -10,13 +10,14 @@ chardet==3.0.4
 commonmark==0.9.0
 configparser==3.7.4 ; python_version < '3.2'
 contextlib2==0.5.5 ; python_version < '3.5'
+coverage==4.5.3
 docutils==0.14
 funcsigs==1.0.2 ; python_version < '3.3'
 future==0.17.1
 gunicorn==19.9.0
 idna==2.8
 imagesize==1.1.0
-importlib-metadata==0.17
+importlib-metadata==0.18
 jinja2==2.10.1
 lxml==4.3.4
 markdown==2.6.11
@@ -31,16 +32,17 @@ pathlib2==2.3.2 ; python_version < '3'
 pathtools==0.1.2
 pluggy==0.12.0
 port-for==0.4
-psutil==5.6.2
+psutil==5.6.3
 py==1.8.0
 pygithub3==0.5.1 ; python_version < '3'
 pygments==2.4.2
 pyparsing==2.4.0
+pytest-cov==2.7.1
 pytest-html==1.20.0
 pytest-metadata==1.8.0
 pytest-postgresql==1.4.1
 pytest-pythonpath==0.7.3
-pytest==4.6.2
+pytest==4.6.3
 pytz==2019.1
 pyyaml==5.1.1
 recommonmark==0.5.0

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

@@ -29,7 +29,7 @@ bleach==3.1.0
 boltons==19.1.0
 boto3==1.9.114
 boto==2.49.0
-botocore==1.12.165
+botocore==1.12.167
 bx-python==0.8.2
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
@@ -118,7 +118,7 @@ pathlib2==2.3.2 ; python_version < '3'
 pbr==5.2.1
 prettytable==0.7.2
 prov==1.5.1
-psutil==5.6.2
+psutil==5.6.3
 pulsar-galaxy-lib==0.12.1
 pyasn1-modules==0.2.5
 pyasn1==0.4.5

run_tests.sh

@@ -374,7 +374,6 @@ do
               api_script="./test/api"
               shift 1
           fi
-          coverage_file="api_coverage.xml"
           ;;
       -selenium|--selenium)
           GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
@@ -428,7 +427,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_framework_tests.html"
-          coverage_file="framework_coverage.xml"
           framework_test=1;
           shift 1
           ;;
@@ -437,7 +435,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_framework_tests.html"
-          coverage_file="main_tools_coverage.xml"
           framework_test=1;
           shift 1
           ;;
@@ -445,7 +442,6 @@ do
           marker="-m data_manager"
           test_script="pytest"
           report_file="run_data_managers_tests.html"
-          coverage_file="data_managers_coverage.xml"
           data_managers_test=1;
           shift 1
           ;;
@@ -454,7 +450,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_migrated_tests.html"
-          coverage_file="migrated_coverage.xml"
           migrated_test=1;
           shift
           ;;
@@ -463,7 +458,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_installed_tests.html"
-          coverage_file="installed_coverage.xml"
           installed_test=1;
           shift
           ;;
@@ -503,7 +497,6 @@ do
           # Must have coverage installed (try `which coverage`) - only valid with --unit
           # for now. Would be great to get this to work with functional tests though.
           coverage_arg="--with-coverage"
-          NOSE_WITH_COVERAGE=true
           shift
           ;;
       --debug)
@@ -523,7 +516,6 @@ do
               unit_extra="$unit_extra lib test/unit"
               shift 1
           fi
-          coverage_file="unit_coverage.xml"
           ;;
       -i|-integration|--integration)
           GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
@@ -535,7 +527,6 @@ do
           else
               integration_extra="./test/integration"
               shift 1
-          coverage_file="integration_coverage.xml"
           fi
           ;;
       --no_cleanup)
@@ -645,8 +636,8 @@ else
 fi
 export GALAXY_TEST_TOOL_CONF
 if [ "$test_script" = 'pytest' ]; then
-    if [ "$coverage_arg" = "--with_coverage" ]; then
-        coverage_arg="--cov-report term --cov-report xml:cov-unit.xml --cov=lib"
+    if [ "$coverage_arg" = '--with-coverage' ]; then
+        coverage_arg="--cov-report term --cov=lib"
     fi
     "$test_script" -v --html "$report_file" $coverage_arg  $xunit_args $extra_args "$@"
 else