Drop nose

doc/source/dev/run_tests_help.txt

@@ -19,7 +19,7 @@
 'run_tests.sh -selenium (test_selector)' for running specified selenium web tests (using pytest selector syntax)
 
 This wrapper script largely serves as a point documentation and convenience for
-running Galaxy's Python tests. Most Python tests shipped with Galaxy can be run with
+running Galaxy's Python tests. All Python tests shipped with Galaxy can be run with
 pytest directly. Galaxy's client unit tests can be run with make client-test
 or yarn directly as documented in detail in client/README.md.
 
@@ -44,7 +44,7 @@ The main test types are as follows:
    framework twill to test ToolShed related functionality. These are
    located in lib/tool_shed/test.
 
-Python testing is mostly done via pytest. Specific tests can be selected
+Python testing is done via pytest. Specific tests can be selected
 using the syntax described at https://docs.pytest.org/en/latest/how-to/usage.html .
 A few examples are shown below.
 
@@ -142,7 +142,7 @@ Extra options:
  --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
+                       works with every python test, 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

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

@@ -61,8 +61,6 @@ mistune==0.8.4 ; python_version >= "3.7" and python_version < "3.11"
 msgpack==1.0.4 ; python_version >= "3.7" and python_version < "3.11"
 multidict==6.0.2 ; python_version >= "3.7" and python_version < "3.11"
 mypy-extensions==0.4.3 ; python_version >= "3.7" and python_version < "3.11"
-nose==1.3.7 ; python_version >= "3.7" and python_version < "3.11"
-nosehtml==0.4.6 ; python_version >= "3.7" and python_version < "3.11"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.11"
 outcome==1.2.0 ; python_version >= "3.7" and python_version < "3.11"
 packaging==21.3 ; python_version >= "3.7" and python_version < "3.11"

lib/galaxy/dependencies/pinned-requirements.txt

@@ -95,7 +95,6 @@ multidict==6.0.2 ; python_version >= "3.7" and python_version < "3.11"
 mypy-extensions==0.4.3 ; python_version >= "3.7" and python_version < "3.11"
 networkx==2.5 ; python_version >= "3.7" and python_version < "3.11"
 nodeenv==1.7.0 ; python_version >= "3.7" and python_version < "3.11"
-nose==1.3.7 ; python_version >= "3.7" and python_version < "3.11"
 numpy==1.21.6 ; python_version >= "3.7" and python_version < "3.11"
 oauthlib==3.2.2 ; python_version >= "3.7" and python_version < "3.11"
 oyaml==1.0 ; python_version >= "3.7" and python_version < "3.11"

lib/galaxy/tool_util/lint.py

@@ -167,7 +167,7 @@ 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

@@ -27,14 +27,6 @@
 from requests.cookies import RequestsCookieJar
 from typing_extensions import Protocol
 
-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,
@@ -374,13 +366,11 @@ 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
@@ -1585,7 +1575,6 @@ 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
@@ -601,8 +602,6 @@ 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/driver/driver_util.py

@@ -20,11 +20,6 @@
 )
 from urllib.parse import urlparse
 
-import nose.config
-import nose.core
-import nose.loader
-import nose.plugins.manager
-
 from galaxy.app import UniverseApplication as GalaxyUniverseApplication
 from galaxy.config import LOGGING_CONFIG_DEFAULT
 from galaxy.model import mapping
@@ -54,8 +49,6 @@
     DEFAULT_WEB_HOST,
     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
@@ -102,19 +95,6 @@ def get_galaxy_test_tmp_dir():
     return galaxy_test_tmp_dir
 
 
-def configure_environment():
-    """Hack up environment for test cases."""
-    # no op remove if unused
-    if "HTTP_ACCEPT_LANGUAGE" not in os.environ:
-        os.environ["HTTP_ACCEPT_LANGUAGE"] = DEFAULT_LOCALES
-
-    # Used by get_filename in tool shed's twilltestcase.
-    if "TOOL_SHED_TEST_FILE_DIR" not in os.environ:
-        os.environ["TOOL_SHED_TEST_FILE_DIR"] = TOOL_SHED_TEST_DATA
-
-    os.environ["GALAXY_TEST_ENVIRONMENT_CONFIGURED"] = "1"
-
-
 def build_logger():
     """Build a logger for test driver script."""
     return log
@@ -340,36 +320,6 @@ 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):
-    """Setup a nose context and run tests.
-
-    Tests are specified by argv (defaulting to 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,
-    )
-
-    # Add custom plugin to produce JSON data used by planemo.
-    test_config.plugins.addPlugin(StructuredTestDataPlugin())
-    test_config.configure(argv)
-
-    result = run(test_config)
-
-    success = result.wasSuccessful()
-    return success
-
-
 def copy_database_template(source, db_path):
     """Copy a 'clean' sqlite template database.
 
@@ -870,7 +820,7 @@ def launch_server(app_factory, webapp_factory, prefix=DEFAULT_CONFIG_PREFIX, gal
 class TestDriver:
     """Responsible for the life-cycle of a Galaxy-style functional test.
 
-    Sets up servers, configures tests, runs nose, and tears things
+    Sets up servers, configures tests, and tears things
     down. This is somewhat like a Python TestCase - but different
     because it is meant to provide a main() endpoint.
     """
@@ -886,7 +836,7 @@ def setup(self):
         """Called before tests are built."""
 
     def build_tests(self):
-        """After environment is setup, setup nose tests."""
+        """After environment is setup, setup tests."""
 
     def tear_down(self):
         """Cleanup resources tracked by this object."""
@@ -914,28 +864,9 @@ def mkdtemp(self):
         self.temp_directories.append(temp_directory)
         return temp_directory
 
-    def run(self):
-        """Driver whole test.
-
-        Setup environment, build tests (if needed), run test,
-        and finally cleanup resources.
-        """
-        configure_environment()
-        self.setup()
-        self.build_tests()
-        try:
-            success = nose_config_and_run()
-            return 0 if success else 1
-        except Exception as e:
-            log.info("Failure running tests")
-            raise e
-        finally:
-            log.info("Shutting down")
-            self.tear_down()
-
 
 class GalaxyTestDriver(TestDriver):
-    """Instantial a Galaxy-style nose TestDriver for testing Galaxy."""
+    """Instantial a Galaxy-style TestDriver for testing Galaxy."""
 
     server_wrappers: List[ServerWrapper]
     testing_shed_tools = False
@@ -1113,7 +1044,6 @@ 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",