Merge remote-tracking branch 'origin/main' into drewj/block-rotate/1939

* origin/main:
  Updating cluster settings (#1958)
  Reducing warnings while building the docs (#1959)
  Moving anl-afci-177 test files to their own directory (#1957)

.gitignore

@@ -18,6 +18,7 @@ coverage_results.*
 dist-*/
 dist/
 doc/_build
+doc/anl-afci-177
 doc/gallery
 doc/gallery-src/framework/*.yaml
 doc/tutorials/anl-afci-177*

armi/bookkeeping/db/tests/test_database3.py

@@ -535,7 +535,7 @@ def test_open(self):
 
     def test_loadCS(self):
         cs = self.db.loadCS()
-        self.assertEqual(cs["numProcessors"], 1)
+        self.assertEqual(cs["nTasks"], 1)
         self.assertEqual(cs["nCycles"], 2)
 
     def test_loadBlueprints(self):

armi/bookkeeping/report/newReportUtils.py

@@ -426,7 +426,7 @@ def insertSettingsData(cs, report):
         "burnSteps",
         "skipCycles",
         "cycleLength",
-        "numProcessors",
+        "nTasks",
     ]:
         report[COMPREHENSIVE_REPORT][CASE_PARAMETERS].addRow([key, cs[key]])
 

armi/bookkeeping/tests/_constants.py

@@ -18,13 +18,17 @@
 also re-exported by `__init__.py`, so that other things (like the documentation system)
 can use it without having to import the rest of ARMI.
 """
+import os
+
+from armi.tests import TEST_ROOT
+
 
 # These files are needed to run the data_model ipython notebook, which is done in
 # test_historyTracker, and when building the docs.
 TUTORIAL_FILES = [
-    "anl-afci-177-blueprints.yaml",
-    "anl-afci-177-coreMap.yaml",
-    "anl-afci-177-fuelManagement.py",
-    "anl-afci-177.yaml",
-    "data_model.ipynb",
+    os.path.join(TEST_ROOT, "anl-afci-177", "anl-afci-177-blueprints.yaml"),
+    os.path.join(TEST_ROOT, "anl-afci-177", "anl-afci-177-coreMap.yaml"),
+    os.path.join(TEST_ROOT, "anl-afci-177", "anl-afci-177-fuelManagement.py"),
+    os.path.join(TEST_ROOT, "anl-afci-177", "anl-afci-177.yaml"),
+    os.path.join(TEST_ROOT, "tutorials", "data_model.ipynb"),
 ]

armi/bookkeeping/tests/test_historyTracker.py

@@ -56,20 +56,29 @@ class TestHistoryTracker(ArmiTestHelper):
 
     @classmethod
     def setUpClass(cls):
-        # We need to be in the TUTORIAL_DIR so that for `filesToMove` to work right.
-        os.chdir(TUTORIAL_DIR)
-
         # Do this work in a temp dir, to avoid race conditions.
-        cls.dirChanger = TemporaryDirectoryChanger(filesToMove=TUTORIAL_FILES)
+        cls.dirChanger = TemporaryDirectoryChanger()
         cls.dirChanger.__enter__()
+
+        os.mkdir("tutorials")
+        os.mkdir(CASE_TITLE)
+
+        for filePath in TUTORIAL_FILES:
+            dirName = CASE_TITLE if CASE_TITLE in filePath else "tutorials"
+            outFile = os.path.join(
+                cls.dirChanger.destination, dirName, os.path.basename(filePath)
+            )
+            shutil.copyfile(filePath, outFile)
+
+        os.chdir(os.path.join(cls.dirChanger.destination, "tutorials"))
         runTutorialNotebook()
 
     @classmethod
     def tearDownClass(cls):
         cls.dirChanger.__exit__(None, None, None)
 
     def setUp(self):
-        cs = settings.Settings(f"{CASE_TITLE}.yaml")
+        cs = settings.Settings(f"../{CASE_TITLE}/{CASE_TITLE}.yaml")
         newSettings = {}
         newSettings["db"] = True
         newSettings["nCycles"] = 2

armi/cases/tests/test_suiteBuilder.py

@@ -33,7 +33,7 @@
         "..",
         "..",
         "tests",
-        "tutorials",
+        "anl-afci-177",
         "anl-afci-177.yaml",
     )
 )

armi/cli/modify.py

@@ -30,7 +30,7 @@ class ModifyCaseSettingsCommand(EntryPoint):
 
     Run the entry point like this::
 
-        $ python -m armi modify --numProcessors=3 *.yaml
+        $ python -m armi modify --nTasks=3 *.yaml
 
     """
 

armi/cli/tests/test_runEntryPoint.py

@@ -369,15 +369,15 @@ def test_modifyCaseSettingsCommandInvoke(self):
             for fileName in ["armiRun.yaml", "refSmallReactor.yaml"]:
                 copyfile(os.path.join(TEST_ROOT, fileName), fileName)
 
-            # pass in --numProcessors=333
-            mcs.parse_args(["--numProcessors=333", "--rootDir", ".", "armiRun.yaml"])
+            # pass in --nTasks=333
+            mcs.parse_args(["--nTasks=333", "--rootDir", ".", "armiRun.yaml"])
 
             # invoke the CLI
             mcs.invoke()
 
-            # validate the change to numProcessors was made
+            # validate the change to nTasks was made
             txt = open("armiRun.yaml", "r").read()
-            self.assertIn("numProcessors: 333", txt)
+            self.assertIn("nTasks: 333", txt)
 
 
 class TestReportsEntryPoint(unittest.TestCase):

armi/settings/fwSettings/globalSettings.py

@@ -80,10 +80,9 @@
 CONF_MATERIAL_NAMESPACE_ORDER = "materialNamespaceOrder"
 CONF_MIN_MESH_SIZE_RATIO = "minMeshSizeRatio"
 CONF_MODULE_VERBOSITY = "moduleVerbosity"
-CONF_MPI_TASKS_PER_NODE = "mpiTasksPerNode"
 CONF_N_CYCLES = "nCycles"
 CONF_NON_UNIFORM_ASSEM_FLAGS = "nonUniformAssemFlags"
-CONF_NUM_PROCESSORS = "numProcessors"
+CONF_N_TASKS = "nTasks"
 CONF_OPERATOR_LOCATION = "operatorLocation"
 CONF_OUTPUT_CACHE_LOCATION = "outputCacheLocation"
 CONF_OUTPUT_FILE_EXTENSION = "outputFileExtension"
@@ -154,11 +153,12 @@ def defineSettings() -> List[setting.Setting]:
     """
     settings = [
         setting.Setting(
-            CONF_NUM_PROCESSORS,
+            CONF_N_TASKS,
             default=1,
-            label="CPUs",
-            description="Number of CPUs to request on the cluster",
+            label="parallel tasks",
+            description="Number of parallel tasks to request on the cluster",
             schema=vol.All(vol.Coerce(int), vol.Range(min=1)),
+            oldNames=[("numProcessors", None)],
         ),
         setting.Setting(
             CONF_INITIALIZE_BURN_CHAIN,
@@ -587,14 +587,6 @@ def defineSettings() -> List[setting.Setting]:
             description="Description needed",
             schema=vol.All(vol.Coerce(float), vol.Range(min=0, max=1)),
         ),
-        setting.Setting(
-            CONF_MPI_TASKS_PER_NODE,
-            default=0,
-            label="MPI Tasks per Node",
-            description="Number of independent processes that are allocated to each "
-            "cluster node. 0 means 1 process per CPU.",
-            schema=vol.All(vol.Coerce(int), vol.Range(min=0)),
-        ),
         setting.Setting(
             CONF_N_CYCLES,
             default=1,

armi/settings/fwSettings/tests/test_fwSettings.py

@@ -26,7 +26,7 @@ class TestSchema(unittest.TestCase):
     def setUp(self):
         self.cs = caseSettings.Settings()
         self.settings = {
-            "numProcessors": {
+            "nTasks": {
                 "valid": 1,
                 "invalid": -1,
                 "error": vol.error.MultipleInvalid,
@@ -91,11 +91,6 @@ def setUp(self):
                 "invalid": 2,
                 "error": vol.error.MultipleInvalid,
             },
-            "mpiTasksPerNode": {
-                "valid": 0,
-                "invalid": -1,
-                "error": vol.error.MultipleInvalid,
-            },
             "nCycles": {"valid": 1, "invalid": -1, "error": vol.error.MultipleInvalid},
             "power": {"valid": 0, "invalid": -1, "error": vol.error.MultipleInvalid},
             "skipCycles": {

armi/settings/tests/test_inspectors.py

@@ -152,10 +152,10 @@ def test_assignCS(self):
         self.assertIn("nCycles", keys)
 
     def test_createQueryRevertBadPathToDefault(self):
-        query = createQueryRevertBadPathToDefault(self.inspector, "numProcessors")
+        query = createQueryRevertBadPathToDefault(self.inspector, "nTasks")
         self.assertEqual(
             str(query),
-            "<Query: Setting numProcessors points to a nonexistent location:\n1>",
+            "<Query: Setting nTasks points to a nonexistent location:\n1>",
         )
 
     def test_correctCyclesToZeroBurnup(self):

armi/settings/tests/test_settings.py

@@ -324,7 +324,7 @@ def test_getSettingsSetByUser(self):
         # some default settings values
         for sett in ["availabilityFactor", "db"]:
             self.assertIn(sett, settingsList)
-        self.assertNotIn("numProcessors", settingsList)
+        self.assertNotIn("nTasks", settingsList)
 
     def test_setModuleVerbosities(self):
         # init settings and use them to set module-level logging levels

armi/settings/tests/test_settingsIO.py

@@ -63,7 +63,7 @@ def setUp(self):
     def test_basicSettingsReader(self):
         reader = settingsIO.SettingsReader(self.cs)
 
-        self.assertEqual(reader["numProcessors"], 1)
+        self.assertEqual(reader["nTasks"], 1)
         self.assertEqual(reader["nCycles"], 1)
 
         self.assertFalse(getattr(reader, "filelessBP"))
@@ -165,18 +165,18 @@ def test_writeShort(self):
         self.cs.loadFromInputFile(self.filepathYaml)
         txt = open(self.filepathYaml, "r").read()
         self.assertIn("nCycles: 55", txt)
-        self.assertNotIn("numProcessors", txt)
+        self.assertNotIn("nTasks", txt)
 
     def test_writeMedium(self):
         """Setting output as a sparse file that only includes defaults if they are
         user-specified.
         """
         with open(self.filepathYaml, "w") as stream:
             # Specify a setting that is also a default
-            self.cs.writeToYamlStream(stream, "medium", ["numProcessors"])
+            self.cs.writeToYamlStream(stream, "medium", ["nTasks"])
         txt = open(self.filepathYaml, "r").read()
         self.assertIn("nCycles: 55", txt)
-        self.assertIn("numProcessors: 1", txt)
+        self.assertIn("nTasks: 1", txt)
 
     def test_writeFull(self):
         """Setting output as a full, all defaults included file.
@@ -189,7 +189,7 @@ def test_writeFull(self):
         txt = open(self.filepathYaml, "r").read()
         self.assertIn("nCycles: 55", txt)
         # check a default setting
-        self.assertIn("numProcessors: 1", txt)
+        self.assertIn("nTasks: 1", txt)
 
     def test_writeYaml(self):
         self.cs.writeToYamlFile(self.filepathYaml)

armi/tests/test_apps.py

@@ -165,7 +165,7 @@ def test_getSettings(self):
         settings = app.getSettings()
 
         self.assertGreater(len(settings), 100)
-        self.assertEqual(settings["numProcessors"].value, 1)
+        self.assertEqual(settings["nTasks"].value, 1)
         self.assertEqual(settings["nCycles"].value, 1)
 
     def test_splashText(self):

armi/tests/test_notebooks.py

@@ -28,6 +28,7 @@
 from armi.tests import TEST_ROOT
 
 TUTORIALS = os.path.join(TEST_ROOT, "tutorials")
+ANL_ACFI_177 = os.path.join(TEST_ROOT, "anl-afci-177")
 
 
 class NotebookTests(unittest.TestCase):

armi/tests/tutorials/data_model.ipynb

@@ -53,7 +53,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "o=armi.init(fName=\"anl-afci-177.yaml\");\n",
+    "o=armi.init(fName=\"../anl-afci-177/anl-afci-177.yaml\");\n",
     "o.r.core.sortAssemsByRing() # makes innermost assemblies appear first"
    ]
   },
@@ -468,7 +468,7 @@
    "outputs": [],
    "source": [
     "from armi.bookkeeping import db\n",
-    "databaseLocation = \"anl-afci-177.h5\"\n",
+    "databaseLocation = \"../tutorials/anl-afci-177.h5\"\n",
     "cycle, timeNode = 0, 1\n",
     "dbo = db.databaseFactory(databaseLocation, \"r\")\n",
     "with dbo:\n",

armi/tests/tutorials/param_sweep.ipynb

@@ -52,7 +52,7 @@
     "from armi.cases import suiteBuilder\n",
     "from armi.cases.inputModifiers import inputModifiers\n",
     "\n",
-    "cs = settings.Settings('anl-afci-177.yaml')\n",
+    "cs = settings.Settings('../anl-afci-177/anl-afci-177.yaml')\n",
     "case = cases.Case(cs)"
    ]
   },
@@ -268,7 +268,7 @@
    "source": [
     "def loadSuite():\n",
     "    print('Loading suite results...')\n",
-    "    cs = settings.Settings('anl-afci-177.yaml')\n",
+    "    cs = settings.Settings('../anl-afci-177/anl-afci-177.yaml')\n",
     "    suite = cases.CaseSuite(cs)\n",
     "    suite.discover(patterns=[\"anl-afci-177-????.yaml\"])\n",
     "    suite = sorted(suite, key=lambda c: c.cs.inputDirectory)\n",

armi/utils/directoryChangers.py

@@ -53,11 +53,11 @@ class DirectoryChanger:
         Filenames to bring back from the destination to the cwd. Note that if any of these
         files do not exist then the file will be skipped and a warning will be provided.
     dumpOnException : bool, optional
-        Flag to tell system to retrieve the entire directory if an exception
-        is raised within a the context manager.
+        Flag to tell system to retrieve the entire directory if an exception is raised within a the
+        context manager.
     outputPath : str, optional
-        Output path for filesToRetrieve. If None, default is the initial working directory
-        from which the DirectoryChanger is called.
+        Output path for filesToRetrieve. If None, default is the initial working directory from
+        which the DirectoryChanger is called.
     """
 
     def __init__(
@@ -177,10 +177,9 @@ def _transferFiles(initialPath, destinationPath, fileList):
         """
         Transfer files into or out of the directory.
 
-        This is used in ``moveFiles`` and ``retrieveFiles`` to shuffle files about when
-        creating a target directory or when coming back, respectively. Beware that this
-        uses ``shutil.copy()`` under the hood, which doesn't play nicely with
-        directories. Future revisions should improve this.
+        This is used in ``moveFiles`` and ``retrieveFiles`` to shuffle files about when creating a
+        target directory or when coming back, respectively. Beware that this uses ``shutil.copy()``
+        under the hood, which doesn't play nicely with directories.
 
         Parameters
         ----------
@@ -189,20 +188,22 @@ def _transferFiles(initialPath, destinationPath, fileList):
         destinationPath: str
             Path to the folder to move file to.
         fileList : list of str or list of tuple
-            File names to move from initial to destination. If this is a
-            simple list of strings, the files will be transferred. Alternatively
-            tuples of (initialName, finalName) are allowed if you want the file
-            renamed during transit. In the non-tuple option, globs/wildcards
+            File names to move from initial to destination. If this is a simple list of strings, the
+            files will be transferred. Alternatively tuples of (initialName, finalName) are allowed
+            if you want the file renamed during transit. In the non-tuple option, globs/wildcards
             are allowed.
 
-        .. warning:: On Windows the max number of characters in a path is 260.
-            If you exceed this you will see FileNotFound errors here.
-
+        Warning
+        -------
+        On Windows the max number of characters in a path is 260.
+        If you exceed this you will see FileNotFound errors here.
         """
         if not fileList:
             return
+
         if not os.path.exists(destinationPath):
             os.makedirs(destinationPath)
+
         for pattern in fileList:
             if isinstance(pattern, tuple):
                 # allow renames in transit