initial pass on adding integration test capability to snapblue

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "tests/data/snapred-data"]
+	path = tests/data/snapred-data
+	url = https://code.ornl.gov/sns-hfir-scse/infrastructure/test-data/snapred-data.git
+	branch = main

environment.yml

@@ -8,7 +8,9 @@ channels:
 dependencies:
   - snapred==1.2.0rc2
   # SNAPBlue specific dependencies
+  - snapred==1.1.0rc5
   - scikit-image
+  - git-lfs
   # -- Runtime dependencies
   # base: list all base dependencies here
   - python>=3.8  # please specify the minimum version of python here

pyproject.toml

@@ -74,15 +74,18 @@ packagename-cli = "packagenamepy.packagename:main"
 packagenamepy = "packagenamepy.packagename:gui"
 
 [tool.pytest.ini_options]
-addopts = "-v --cov=packagenamepy --cov-report=term-missing"
+addopts = "-m 'not (integration or datarepo)' -v --cov=packagenamepy --cov-report=term-missing"
 pythonpath = [
   ".", "src", "scripts"
 ]
 testpaths = ["tests"]
 python_files = ["test*.py"]
 norecursedirs = [".git", "tmp*", "_tmp*", "__pycache__", "*dataset*", "*data_set*"]
 markers = [
-    "mymarker: example markers goes here"
+    "integration: mark a test as an integration test",
+    "mount_snap: mark a test as using /SNS/SNAP/ data mount",
+    "golden_data(*, path=None, short_name=None, date=None): mark golden data to use with a test",
+    "datarepo: mark a test as using snapred-data repo"
 ]
 
 [tool.ruff]

src/snapblue/meta/Config.py

@@ -0,0 +1,86 @@
+import importlib.resources as resources
+
+import os
+import sys
+
+from pathlib import Path
+
+from snapred.meta.Config import Resource as RedResource, Config
+
+def _find_root_dir():
+    try:
+        MODULE_ROOT = Path(sys.modules["snapblue"].__file__).parent
+
+        # Using `"test" in env` here allows different versions of "[category]_test.yml" to be used for different
+        #  test categories: e.g. unit tests use "test.yml" but integration tests use "integration_test.yml".
+        env = os.environ.get("snapblue_env")
+        if env and "test" in env and "conftest" in sys.modules:
+            # WARNING: there are now multiple "conftest.py" at various levels in the test hierarchy.
+            MODULE_ROOT = MODULE_ROOT.parent.parent / "tests"
+    except Exception as e:
+        raise RuntimeError("Unable to determine SNAPBlue module-root directory") from e
+
+    return str(MODULE_ROOT)
+
+class _Resource:
+    _packageMode: bool
+    _resourcesPath: str
+
+    def __init__(self):
+        # where the location of resources are depends on whether or not this is in package mode
+        self._packageMode = not self._existsInPackage("application.yml")
+        if self._packageMode:
+            self._resourcesPath = "/resources/"
+        else:
+            self._resourcesPath = os.path.join(_find_root_dir(), "resources/")
+
+    def _existsInPackage(self, subPath) -> bool:
+        with resources.path("snapblue.resources", subPath) as path:
+            return os.path.exists(path)
+
+    def exists(self, subPath) -> bool:
+        if self._packageMode:
+            return self._existsInPackage(subPath)
+        else:
+            return os.path.exists(self.getPath(subPath))
+
+    def getPath(self, subPath):
+        if subPath.startswith("/"):
+            return os.path.join(self._resourcesPath, subPath[1:])
+        else:
+            return os.path.join(self._resourcesPath, subPath)
+
+    def read(self, subPath):
+        with self.open(subPath, "r") as file:
+            return file.read()
+
+    def open(self, subPath, mode):  # noqa: A003
+        if self._packageMode:
+            with resources.path("snapblue.resources", subPath) as path:
+                return open(path, mode)
+        else:
+            return open(self.getPath(subPath), mode)
+
+
+Resource = _Resource()
+RedResource._resourcesPath = Resource._resourcesPath
+RedResource._packageMode = Resource._packageMode
+# use refresh to do initial load, clearing shouldn't matter
+Config.refresh("application.yml")
+
+# ---------- SNAPRed-internal values: --------------------------
+# allow "resources" relative paths to be entered into the "yml"
+#   using "${module.root}"
+Config._config["module"] = {}
+Config._config["module"]["root"] = _find_root_dir()
+
+Config._config["version"] = Config._config.get("version", {})
+Config._config["version"]["default"] = -1
+# ---------- end: internal values: -----------------------------
+
+# see if user used environment injection to modify what is needed
+# this will get from the os environment or from the currently loaded one
+# first case wins
+env = os.environ.get("snapblue_env", Config._config.get("environment", None))
+if env is not None:
+    Config.refresh(env)

src/snapblue/resources/application.yml

@@ -0,0 +1,4 @@
+# put snapred application.yml overrides here
+IPTS:
+  default: /SNS
+  root: /SNS

tests/conftest.py

@@ -0,0 +1,143 @@
+import os
+
+import pytest
+import unittest.mock as mock
+
+from snapred.meta.decorators import Resettable
+from snapred.meta.decorators.Singleton import reset_Singletons
+
+# import sys
+# sys.path.append('.')
+# os.environ['PYTHONPATH'] = './src'
+
+# Allow override: e.g. `env=dev pytest ...`
+# if not os.environ.get("env"):
+#     os.environ["env"] = "test"
+
+from mantid.kernel import ConfigService  # noqa: E402
+from snapblue.meta.Config import (  # noqa: E402
+    Config,  # noqa: E402
+    Resource,  # noqa: E402
+)
+
+
+# PATCH the `unittest.mock.Mock` class: BANNED FUNCTIONS
+def banned_function(function_name: str):
+  _error_message: str = f"`Mock.{function_name}` is a mock, it always evaluates to True. Use `Mock.assert_{function_name}` instead."
+
+  def _banned_function(self, *args, **kwargs):
+      nonlocal _error_message # this line should not be necessary!
+
+      # Ensure that the complete message is in the pytest-captured output stream:
+      print(_error_message)
+
+      raise RuntimeError(_error_message)
+
+  return _banned_function
+
+# `mock.Mock.called` is OK: it exists as a boolean attribute
+mock.Mock.called_once = banned_function("called_once")
+mock.Mock.called_once_with = banned_function("called_once_with")
+mock.Mock.called_with = banned_function("called_with")
+mock.Mock.not_called = banned_function("not_called")
+
+
+def mock_decorator(orig_cls):
+    return orig_cls
+
+###### PATCH THE DECORATORS HERE ######
+
+mockResettable = mock.Mock()
+mockResettable.Resettable = mock_decorator
+mock.patch.dict("sys.modules", {"snapred.meta.decorators.Resettable": mockResettable}).start()
+mock.patch.dict("sys.modules", {"snapred.meta.decorators._Resettable": Resettable}).start()
+
+mantidConfig = config = ConfigService.Instance()
+mantidConfig["CheckMantidVersion.OnStartup"] = "0"
+mantidConfig["UpdateInstrumentDefinitions.OnStartup"] = "0"
+mantidConfig["usagereports.enabled"] = "0"
+
+#######################################
+
+# this at teardown removes the loggers, eliminating logger-related error printouts
+#   see https://github.com/pytest-dev/pytest/issues/5502#issuecomment-647157873
+@pytest.fixture(autouse=True, scope="session")
+def clear_loggers():  # noqa: PT004
+    """Remove handlers from all loggers"""
+    import logging
+
+    yield  # ... teardown follows:
+    loggers = [logging.getLogger()] + list(logging.Logger.manager.loggerDict.values())
+    for logger in loggers:
+        handlers = getattr(logger, "handlers", [])
+        for handler in handlers:
+            logger.removeHandler(handler)
+
+########################################################################################################################
+# In combination, the following autouse fixtures allow unit tests and integration tests
+#   to be run successfully without mocking out the `@Singleton` decorator.
+#
+#   * The main objective is to allow the `@Singleton` classes to function as singletons, for the
+#     duration of the single-test scope.  This functionality is necessary, for example, in order for
+#     the `Indexer` class to function correctly during the state-initialization sequence.
+#
+#   * There are some fine points involved with using `@Singleton` classes during testing at class and module scope.
+#     Such usage should probably be avoided whenever possible.  It's a bit tricky to get this to work correctly
+#     within the test framework.
+#
+#   * TODO: Regardless of these fixtures, at the moment the `@Singleton` decorator must be completely turned ON during
+#     integration tests, without any modification (e.g. or "reset").  There is something going on at "session" scope
+#     with specific singletons not being deleted between tests, which results in multiple singleton instances when the
+#     fixtures are used.  This behavior does not seem to be an issue for the unit tests.
+#     We can track this down by turning on the garbage collector `gc`, but this work has not yet been completed.
+#
+# Implementation notes:
+#
+#   * Right now, there are > 36 `@Singleton` decorated classes.  Probably, there should be far fewer.
+#     Almost none of these classes are compute-intensive to initialize, or retain any cached data.
+#     These would be the normal justifications for the use of this pattern.
+#
+#   * Applying the `@Singleton` decorator changes the behavior of the classes,
+#     so we don't want to mock the decorator out during testing. At present, the key class where this is important
+#     is the `Indexer` class, which is not itself a singleton, but which is owned and cached
+#     by the `LocalDataService` singleton.  `Indexer` instances retain local data about indexing events
+#     that have occurred since their initialization.
+#
+
+@pytest.fixture(autouse=True)
+def _reset_Singletons(request):
+    if not "integration" in request.keywords:
+        reset_Singletons()
+    yield
+
+@pytest.fixture(scope="class", autouse=True)
+def _reset_class_scope_Singletons(request):
+    if not "integration" in request.keywords:
+        reset_Singletons()
+    yield
+
+@pytest.fixture(scope="module", autouse=True)
+def _reset_module_scope_Singletons(request):
+    if not "integration" in request.keywords:
+        reset_Singletons()
+    yield
+
+########################################################################################################################
+
+
+## Import various `pytest.fixture` defined in separate `tests/util` modules:
+#  -------------------------------------------------------------------------
+# *** IMPORTANT WARNING: these must be included _after_ the `Singleton` decorator is patched ! ***
+#   * Otherwise, the modules imported by these will not have the patched decorator applied to them.
+
+# from util.golden_data import goldenData, goldenDataFilePath
+# from util.state_helpers import state_root_fixture
+# from util.IPTS_override import IPTS_override_fixture
+from util.Config_helpers import Config_override_fixture
+from util.pytest_helpers import (
+    calibration_home_from_mirror,
+    cleanup_workspace_at_exit,
+    cleanup_class_workspace_at_exit,
+    get_unique_timestamp,
+    reduction_home_from_mirror
+)

tests/integration/test_filesystem.py

@@ -0,0 +1,16 @@
+
+
+import pytest
+from util.pytest_helpers import calibration_home_from_mirror, handleStateInit, reduction_home_from_mirror  # noqa: F401
+from snapblue.meta.Config import Config
+from pathlib import Path
+
+
+@pytest.mark.integration
+@pytest.mark.datarepo
+def test_calibrationHomeExists(calibration_home_from_mirror):
+    tmpCalibrationHomeDirectory = calibration_home_from_mirror()
+    calibrationHomePath = Path(Config["instrument.calibration.home"])
+    assert calibrationHomePath.exists()
+    iptsHomePath = Path(Config["IPTS.root"])
+    assert iptsHomePath.exists()

tests/integration/test_reduction.py

@@ -0,0 +1,10 @@
+
+
+import pytest
+from util.pytest_helpers import calibration_home_from_mirror, handleStateInit, reduction_home_from_mirror  # noqa: F401
+
+
+@pytest.mark.integration
+@pytest.mark.datarepo
+def test_reduction(reduction_home_from_mirror):
+    pass

tests/resources/application.yml

@@ -0,0 +1,4 @@
+# put snapred application.yml overrides here
+IPTS:
+  default: /SNS
+  root: /SNS

tests/resources/integration_test.yml

@@ -0,0 +1,86 @@
+# environment: integration_test
+# At present:
+#   * this "integration_test.yml" overrides "IPTS.root", and "constants.maskedPixelThreshold";
+#   * "module.root" will still be defined as in "test.yml".
+
+IPTS:
+  # Eventually, for SNAPRed's test framework:
+  #   this should be a shared location on "analysis.sns.gov".
+  # For the moment, each developer needs to set this individually to their local path.
+  root: ${module.root}/data/snapred-data/SNS
+
+constants:
+  # For tests with '46680' this seems to be necessary.
+  maskedPixelThreshold: 1.0
+
+  DetectorPeakPredictor:
+    fwhm: 1.17741002252 # used to convert gaussian to fwhm (2 * log_e(2))
+  CropFactors:
+    lowWavelengthCrop: 0.05
+    lowdSpacingCrop: 0.1
+    highdSpacingCrop: 0.15
+  RawVanadiumCorrection:
+    numberOfSlices: 1
+    numberOfAnnuli: 1
+
+instrument:
+  native:
+    pixelResolution: 72
+    definition:
+      file: ${module.root}/resources/ultralite/CRACKLE_Definition.xml
+  lite:
+    pixelResolution: 18
+    definition:
+      file: ${module.root}/resources/ultralite/CRACKLELite_Definition.xml
+    map:
+      file: ${module.root}/resources/ultralite/CRACKLELiteDataMap.xml
+
+  PVLogs:
+    # Swap these when running with ultralite data
+    # rootGroup: "entry/DASlogs"
+    rootGroup: "/mantid_workspace_1/logs"
+
+    # PV-log keys relating to instrument settings:
+    instrumentPVKeys:
+    - "BL3:Chop:Gbl:WavelengthReq"
+    - "BL3:Chop:Skf1:WavelengthUserReq"
+    - "det_arc1"
+    - "det_arc2"
+    - "BL3:Det:TH:BL:Frequency"
+    - "BL3:Mot:OpticsPos:Pos"
+    - "det_lin1"
+    - "det_lin2"
+
+mantid:
+  workspace:
+    nameTemplate:
+      delimiter: "_"
+      template:
+        run: "{unit},{group},{lite},{auxiliary},{runNumber}"
+        diffCal:
+          input: "{unit},{runNumber},raw"
+          table: "diffract_consts,{runNumber},{version}"
+          output: "{unit},{group},{runNumber},{version}"
+          diagnostic: "diagnostic,{group},{runNumber},{version}"
+          mask: "diffract_consts,mask,{runNumber},{version}"
+          metric: "calib_metrics,{metricName},{runNumber},{version}"
+          timedMetric: "calib_metrics,{metricName},{runNumber},{timestamp}"
+        normCal:
+          rawVanadium: "{unit},{group},{runNumber},raw_van_corr,{version}"
+          focusedRawVanadium: "{unit},{group},{runNumber},raw_van_corr,{version}"
+          smoothedFocusedRawVanadium: "{unit},{group},{runNumber},fitted_van_corr,{version}"
+
+calibration:
+  parameters:
+    default:
+      alpha: 0.1
+      # alpha: 1.1
+      beta:
+        - 0.02
+        - 0.05
+      # beta:
+      #   - 1
+      #   - 2
+  fitting:
+    # minSignal2Noise: 0.0
+    minSignal2Noise: 10