Make tests more independent

MANIFEST.in

@@ -1 +1,10 @@
 include requirements*.txt
+include src/toil/server/api_spec/workflow_execution_service.swagger.yaml
+include src/toil/test/cwl/colon_test_output_job.yaml
+include src/toil/test/cwl/conditional_wf.yaml
+include src/toil/test/cwl/mock_mpi/fake_mpi.yml
+include src/toil/test/docs/scripts/*
+include src/toil/test/utils/ABCWorkflowDebug/sleep.yaml
+include src/toil/test/utils/ABCWorkflowDebug/*
+recursive-include src/toil/test/ *.cwl
+recursive-include src/toil/test/ *.txt

Makefile

@@ -118,6 +118,7 @@ endif
 endif
 
 develop: check_venv
+	python3 setup.py check
 	pip install -e .$(extras) $(packages)
 
 clean_develop: check_venv

pyproject.toml

@@ -0,0 +1,3 @@
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"

setup.py

@@ -111,9 +111,7 @@ def run_setup():
         extras_require=extras_require,
         package_dir={"": "src"},
         packages=find_packages(where="src"),
-        package_data={
-            "": ["*.yml", "*.yaml", "cloud-config", "*.cwl"],
-        },
+        include_package_data=True,
         # Unfortunately, the names of the entry points are hard-coded elsewhere in the code base so
         # you can't just change them here. Luckily, most of them are pretty unique strings, and thus
         # easy to search for.

src/toil/test/__init__.py

@@ -13,6 +13,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+import atexit
 import datetime
 import logging
 import os
@@ -28,8 +29,10 @@
 import zoneinfo
 from abc import ABCMeta, abstractmethod
 from collections.abc import Generator
-from contextlib import contextmanager
+from contextlib import ExitStack, contextmanager
+from importlib.resources import as_file, files
 from inspect import getsource
+from pathlib import Path
 from shutil import which
 from tempfile import mkstemp
 from textwrap import dedent
@@ -52,6 +55,24 @@
 logger = logging.getLogger(__name__)
 
 
+def get_data(filename: str) -> str:
+    """Returns an absolute path for a file from this package."""
+    # normalizing path depending on OS or else it will cause problem when joining path
+    filename = os.path.normpath(filename)
+    filepath = None
+    # import ipdb; ipdb.set_trace()
+    try:
+        file_manager = ExitStack()
+        atexit.register(file_manager.close)
+        traversable = files("toil") / filename
+        filepath = file_manager.enter_context(as_file(traversable))
+    except ModuleNotFoundError:
+        pass
+    if not filepath or not os.path.isfile(filepath):
+        filepath = Path(os.path.dirname(__file__)) / ".." / ".." / ".." / filename
+    return str(filepath.resolve())
+
+
 class ToilTest(unittest.TestCase):
     """
     A common base class for Toil tests.