Drop nose

It's deprecated and unmaintained, and is broken under Python 3.10 .

doc/source/dev/run_tests_help.txt

@@ -3,6 +3,8 @@
 'run_tests.sh -list'                    for listing all the tool ids
 'run_tests.sh -api (test_path)'         for running all the test scripts in the ./lib/galaxy_test/api directory, test_path
                                     can be pytest selector
+'run_tests.sh -cwl (test_path)'         for running all the test scripts in the ./lib/galaxy_test/api/cwl directory, test_path
+                                    can be pytest selector
 'run_tests.sh -integration (test_path)' for running all integration test scripts in the ./test/integration directory, test_path
                                     can be pytest selector
 'run_tests.sh -toolshed (test_path)'    for running all the test scripts in the ./lib/tool_shed/test directory
@@ -51,7 +53,7 @@ as test_path.  A few examples are shown below.
 Run all API tests:
     ./run_tests.sh -api
 
-The same test as above can be run using nosetests directly as follows:
+The same test as above can be run using pytest directly as follows:
     pytest lib/galaxy_test/api
 
 However when using pytest directly output options defined in this
@@ -141,6 +143,10 @@ Extra options:
  --verbose_errors      Force some tests produce more verbose error reporting.
  --no_cleanup          Do not delete temp files for Python functional tests
                        (-toolshed, -framework, etc...)
+ --coverage            Generate a test coverage report. This option currently
+                       should work with every test that uses pytest, but the
+                       results may not be reliable with selenium or other
+                       frameworks that primarily test the client.
  --debug               On python test error or failure invoke a pdb shell for
                        interactive debugging of the test
  --report_file         Path of HTML report to produce (for Python Galaxy
@@ -150,10 +156,6 @@ Extra options:
                        functional tests).
  --skip-venv           Do not create .venv (passes this flag to
                        common_startup.sh)
- --dockerize           Run tests in a pre-configured Docker container (must be
-                       first argument if present).
- --db <type>           For use with --dockerize, run tests using partially
-                       migrated 'postgres', 'mysql', or 'sqlite' databases.
  --external_url        External URL to use for Galaxy testing (only certain
                        tests).
  --external_master_key Master API key used to configure external tests.
@@ -238,6 +240,7 @@ TOOL_SHED_TEST_TMP_DIR          Defaults to random /tmp directory - place for
                                 tool shed test server files to be placed.
 TOOL_SHED_TEST_OMIT_GALAXY      Do not launch a Galaxy server for tool shed
                                 testing.
+GALAXY_TEST_DISABLE_ACCESS_LOG  Do not log access messages
 
 Unit Test Environment Variables
 

doc/source/lib/galaxy_test.base.rst

@@ -65,14 +65,6 @@ galaxy\_test.base.interactor module
    :undoc-members:
    :show-inheritance:
 
-galaxy\_test.base.nose\_util module
------------------------------------
-
-.. automodule:: galaxy_test.base.nose_util
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 galaxy\_test.base.populators module
 -----------------------------------
 

lib/galaxy/dependencies/dev-requirements.txt

@@ -109,8 +109,6 @@ msgpack==1.0.3; python_version >= "3.7" and python_version < "4"
 mypy-extensions==0.4.3; python_version >= "3.7" and python_version < "4" and python_full_version >= "3.6.2"
 networkx==2.5; python_version >= "3.6" and python_version < "4"
 nodeenv==1.6.0
-nose==1.3.7
-nosehtml==0.4.6
 numpy==1.21.6; python_version >= "3.7" and python_version < "3.11"
 oauthlib==3.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 outcome==1.1.0; python_version >= "3.7" and python_version < "4.0"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -86,7 +86,6 @@ msgpack==1.0.3; python_version >= "3.7" and python_version < "4"
 mypy-extensions==0.4.3; python_version >= "3.6" and python_version < "4"
 networkx==2.5; python_version >= "3.6" and python_version < "4"
 nodeenv==1.6.0
-nose==1.3.7
 numpy==1.21.6; python_version >= "3.7" and python_version < "3.11"
 oauthlib==3.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 oyaml==1.0

lib/galaxy/tool_util/lint.py

@@ -169,7 +169,7 @@ def found_warns(self) -> bool:
         return len(self.warn_messages) > 0
 
     def lint(self, name: str, lint_func: Callable[[LintTargetType, "LintContext"], None], lint_target: LintTargetType):
-        name = name.replace("tsts", "tests")[len("lint_") :]
+        name = name[len("lint_") :]
         if name in self.skip_types:
             return
 

lib/galaxy/tool_util/linters/tests.py

@@ -9,8 +9,7 @@
 from ..verify import asserts
 
 
-# Misspelled so as not be picked up by nosetests.
-def lint_tsts(tool_xml, lint_ctx):
+def lint_tests(tool_xml, lint_ctx):
     # determine node to report for general problems with tests
     tests = tool_xml.findall("./tests/test")
     general_node = tool_xml.find("./tests")

lib/galaxy/tool_util/verify/interactor.py

@@ -18,14 +18,6 @@
 from packaging.version import Version
 from requests.cookies import RequestsCookieJar
 
-try:
-    from nose.tools import nottest
-except ImportError:
-
-    def nottest(x):
-        return x
-
-
 from galaxy import util
 from galaxy.tool_util.parser.interface import (
     TestCollectionDef,
@@ -351,13 +343,11 @@ def publish_history(self, history_id):
         response = self._put(f"histories/{history_id}", json.dumps({"published": True}))
         response.raise_for_status()
 
-    @nottest
     def test_data_path(self, tool_id, filename, tool_version=None):
         version_fragment = f"&tool_version={tool_version}" if tool_version else ""
         response = self._get(f"tools/{tool_id}/test_data_path?filename={filename}{version_fragment}", admin=True)
         return response.json()
 
-    @nottest
     def test_data_download(self, tool_id, filename, mode="file", is_output=True, tool_version=None):
         result = None
         local_path = None
@@ -1543,7 +1533,6 @@ def to_dict(self):
         }
 
 
-@nottest
 def test_data_iter(required_files):
     for fname, extra in required_files:
         data_dict = dict(

lib/galaxy/tools/test.py

@@ -15,18 +15,9 @@
     unicodify,
 )
 
-try:
-    from nose.tools import nottest
-except ImportError:
-
-    def nottest(x):
-        return x
-
-
 log = logging.getLogger(__name__)
 
 
-@nottest
 def parse_tests(tool, tests_source):
     """
     Build ToolTestDescription objects for each "<test>" elements and

lib/galaxy_test/api/test_jobs.py

@@ -4,6 +4,7 @@
 import time
 import urllib.parse
 from operator import itemgetter
+from unittest import SkipTest
 
 import requests
 from dateutil.parser import isoparse
@@ -496,8 +497,6 @@ def test_purging_output_cleaned_after_ok_run(self, history_id):
             assert not os.path.exists(output_dataset_paths[0])
 
     def _hack_to_skip_test_if_state_ok(self, job_state):
-        from nose.plugins.skip import SkipTest
-
         if job_state().json()["state"] == "ok":
             message = "Job state switch from running to ok too quickly - the rest of the test requires the job to be in a running state. Skipping test."
             raise SkipTest(message)

lib/galaxy_test/base/populators.py

@@ -43,7 +43,6 @@
 import random
 import string
 import time
-import unittest
 import urllib.parse
 from abc import (
     ABCMeta,
@@ -62,6 +61,7 @@
     Set,
     Tuple,
 )
+from unittest import SkipTest
 
 import cwltest
 import requests
@@ -109,11 +109,11 @@ def flakey(method):
     def wrapped_method(test_case, *args, **kwargs):
         try:
             method(test_case, *args, **kwargs)
-        except unittest.SkipTest:
+        except SkipTest:
             raise
         except Exception:
             if SKIP_FLAKEY_TESTS_ON_ERROR:
-                raise unittest.SkipTest("Error encountered during test marked as @flakey.")
+                raise SkipTest("Error encountered during test marked as @flakey.")
             else:
                 raise
 
@@ -220,8 +220,6 @@ def wrapped_method(api_test_case, *args, **kwds):
 
 def _raise_skip_if(check, *args):
     if check:
-        from nose.plugins.skip import SkipTest
-
         raise SkipTest(*args)
 
 

lib/galaxy_test/driver/driver_util.py

@@ -51,7 +51,6 @@
     target_url_parts,
 )
 from galaxy_test.base.instrument import StructuredTestDataPlugin
-from galaxy_test.base.nose_util import run
 from tool_shed.webapp.app import UniverseApplication as ToolshedUniverseApplication
 from tool_shed.webapp.fast_app import initialize_fast_app as init_tool_shed_fast_app
 from .test_logging import logging_config_file
@@ -80,6 +79,22 @@
 install_context = None
 
 
+def run(test_config):
+    loader = nose.loader.TestLoader(config=test_config)
+    plug_loader = test_config.plugins.prepareTestLoader(loader)
+    if plug_loader is not None:
+        loader = plug_loader
+    tests = loader.loadTestsFromNames(test_config.testNames)
+    test_runner = nose.core.TextTestRunner(
+        stream=test_config.stream, verbosity=test_config.verbosity, config=test_config
+    )
+    plug_runner = test_config.plugins.prepareTestRunner(test_runner)
+    if plug_runner is not None:
+        test_runner = plug_runner
+    result = test_runner.run(tests)
+    return result
+
+
 def setup_tool_shed_tmp_dir():
     tool_shed_test_tmp_dir = os.environ.get("TOOL_SHED_TEST_TMP_DIR", None)
     if tool_shed_test_tmp_dir is None:
@@ -333,34 +348,23 @@ def _tool_data_table_config_path(default_tool_data_table_config_path=None):
     return tool_data_table_config_path
 
 
-def nose_config_and_run(argv=None, env=None, ignore_files=None, plugins=None):
+def nose_config_and_run():
     """Setup a nose context and run tests.
 
-    Tests are specified by argv (defaulting to sys.argv).
+    Tests are specified by sys.argv .
     """
-    if env is None:
-        env = os.environ
-    if ignore_files is None:
-        ignore_files = []
-    if plugins is None:
-        plugins = nose.plugins.manager.DefaultPluginManager()
-    if argv is None:
-        argv = sys.argv
-
     test_config = nose.config.Config(
         env=os.environ,
-        ignoreFiles=ignore_files,
-        plugins=plugins,
+        ignoreFiles=[],
+        plugins=nose.plugins.manager.DefaultPluginManager(),
     )
 
     # Add custom plugin to produce JSON data used by planemo.
     test_config.plugins.addPlugin(StructuredTestDataPlugin())
-    test_config.configure(argv)
+    test_config.configure(sys.argv)
 
     result = run(test_config)
-
-    success = result.wasSuccessful()
-    return success
+    return result.wasSuccessful()
 
 
 def copy_database_template(source, db_path):
@@ -1096,7 +1100,6 @@ def drive_test(test_driver_class):
     "FRAMEWORK_DATATYPES_CONF",
     "database_conf",
     "get_webapp_global_conf",
-    "nose_config_and_run",
     "setup_galaxy_config",
     "TestDriver",
     "wait_for_http_server",

lib/galaxy_test/selenium/framework.py

@@ -96,13 +96,6 @@
 window.localStorage && window.localStorage.setItem("galaxy:debug:flatten", true);
 """
 
-try:
-    from nose.tools import nottest
-except ImportError:
-
-    def nottest(x):
-        return x
-
 
 def managed_history(f):
     """Ensure a Selenium test has a distinct, named history.
@@ -167,7 +160,6 @@ def write_file(name, content, raw=False):
                 continue
 
 
-@nottest
 def selenium_test(f):
     test_name = f.__name__
 
@@ -238,7 +230,7 @@ def workflow_populator(self) -> populators.BaseWorkflowPopulator:
 
 
 class TestWithSeleniumMixin(GalaxyTestSeleniumContext, UsesApiTestCaseMixin):
-    # If run one-off via nosetests, the next line ensures test
+    # If run one-off via pytest, the next line ensures test
     # tools and datatypes are used instead of configured tools.
     framework_tool_and_types = True
 

pyproject.toml

@@ -69,7 +69,6 @@ MarkupSafe = "*"
 Mercurial = "*"
 mrcfile = "*"
 nodeenv = "*"
-nose = "*"
 numpy = "*"
 paramiko = "!=2.9.0, !=2.9.1"  # https://github.com/paramiko/paramiko/issues/1961
 Parsley = "*"
@@ -119,7 +118,6 @@ httpx = "*"
 isort = "^5.10.1"
 lxml = "!=4.2.2"
 markdown-it-reporter = "*"
-NoseHTML = "*"
 PyGithub = "*"
 pytest = "*"
 pytest-asyncio = "*"

run_tests.sh

@@ -269,6 +269,7 @@ exists() {
     type "$1" >/dev/null 2>/dev/null
 }
 
+debug=""
 test_script="./scripts/functional_tests.py"
 report_file="run_functional_tests.html"
 coverage_arg=""
@@ -495,9 +496,7 @@ do
           shift
           ;;
       --debug)
-          #TODO ipdb would be nicer.
-          NOSE_PDB=True
-          export NOSE_PDB
+          debug="--pdb"
           shift
           ;;
       -u|-unit|--unit)
@@ -651,10 +650,10 @@ if [ "$test_script" = 'pytest' ]; then
     else
         marker_args=()
     fi
-    args=(-v $structured_data_args --html "$report_file" --self-contained-html $coverage_arg $xunit_args $extra_args "${marker_args[@]}" "$@")
+    args=(-v $debug $structured_data_args --html "$report_file" --self-contained-html $coverage_arg $xunit_args $extra_args "${marker_args[@]}" "$@")
     "$test_script" "${args[@]}"
 else
-    python "$test_script" $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args "$@"
+    python "$test_script" $coverage_arg -v --html-report-file $report_file $xunit_args $structured_data_args $extra_args "$@"
 fi
 exit_status=$?
 echo "Testing complete. HTML report is in \"$report_file\"." 1>&2