Merge branch 'main' into doc_str_details

Author: john-science

.github/workflows/docs.yaml

@@ -55,6 +55,7 @@ jobs:
           cd doc
           git submodule init
           git submodule update
+          git fetch
           echo "make html:"
           make html
           echo "make latex:"

.gitignore

@@ -73,16 +73,20 @@ tags
 temp-*
 venv*/
 
-# Ignore common data files
+# Ignore certain data files
 *.avi
 *.diff
+*.flux_bg
+*.flux_ufg
 *.h5
 *.html
 *.mp4
+*.nucdata
+*.out
 *.ppm
+*.sum
 *.txt
-
-# vis files
 *.vtd
 *.vtu
 *.xdmf
+*dlayxs*

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contribution License Agreement
 
-For information on how to contribute to ARMI, see [our official documenation](https://terrapower.github.io/armi/developer/first_time_contributors.html).
+For information on how to contribute to ARMI, see [our official documentation](https://terrapower.github.io/armi/developer/first_time_contributors.html).
 
 This Contribution License Agreement (**"Agreement"**) is agreed to by the party signing below (**"You"**), and conveys certain license rights to TerraPower, LLC and its affiliates (**"TerraPower"**) for Your contributions to TerraPower open source projects. This Agreement is effective as of the latest signature date below.
 

README.rst

@@ -420,7 +420,7 @@ The ARMI system is licensed as follows:
 	limitations under the License.
 
 Be careful when including any dependency in ARMI (say in the ``pyproject.toml`` file) not
-to include anything with a license that superceeds our Apache license. For instance,
+to include anything with a license that supersedes our Apache license. For instance,
 any third-party Python library included in ARMI with a GPL license will make the whole
 project fall under the GPL license. But a lot of potential users of ARMI will want to
 keep some of their work private, so we can't allow any GPL dependencies.

armi/__init__.py

@@ -134,7 +134,7 @@ def init(choice=None, fName=None, cs=None, skipInspection=False):
         The path to a settings file to load: my_case.yaml
 
     cs : Settings, optional
-        If supplied, this CS object will supercede the other case input methods and use
+        If supplied, this CS object will supersede the other case input methods and use
         the object directly.
 
     skipInspection : bool, optional

armi/bookkeeping/db/database.py

@@ -103,10 +103,9 @@ def initDB(self, fName: Optional[os.PathLike] = None):
 
         Notes
         -----
-        Main Interface calls this so that the database is available as early as
-        possible in the run. The database interface interacts near the end of the
-        interface stack (so that all the parameters have been updated) while the Main
-        Interface interacts first.
+        Main Interface calls this so that the database is available as early as possible in the run.
+        The database interface interacts near the end of the interface stack (so that all the
+        parameters have been updated) while the Main Interface interacts first.
         """
         if fName is None:
             self._dbPath = pathlib.Path(self.cs.caseTitle + ".h5")
@@ -120,18 +119,7 @@ def initDB(self, fName: Optional[os.PathLike] = None):
             )
         self._db = Database(self._dbPath, "w")
         self._db.open()
-
-        # Grab geomString here because the DB-level has no access to the reactor or
-        # blueprints or anything.
-        # There's not always a geomFile; we are moving towards the core grid definition
-        # living in the blueprints themselves. In this case, the db doesnt need to store
-        # a geomFile at all.
-        if self.cs["geomFile"]:
-            with open(os.path.join(self.cs.inputDirectory, self.cs["geomFile"])) as f:
-                geomString = f.read()
-        else:
-            geomString = ""
-        self._db.writeInputsToDB(self.cs, geomString=geomString)
+        self._db.writeInputsToDB(self.cs)
 
     def interactEveryNode(self, cycle, node):
         """
@@ -141,8 +129,8 @@ def interactEveryNode(self, cycle, node):
 
         Notes
         -----
-        - if tight coupling is enabled, the DB will be written in operator.py::Operator::_timeNodeLoop
-          via writeDBEveryNode
+        - If tight coupling is enabled, the DB will be written in ``Operator::_timeNodeLoop`` via
+          writeDBEveryNode.
         """
         if self.o.cs["tightCoupling"]:
             # h5 cant handle overwriting so we skip here and write once the tight coupling loop has completed

armi/bookkeeping/db/databaseInterface.py

@@ -30,7 +30,7 @@ def databaseFactory(dbName: str, permission: str, version: Optional[str] = None)
     dbName: str
         Path to db file, e.g. `baseCase.h5`
     permission: str
-        String defining permission, `r` for read only. See armi.bookeeping.db.permissions
+        String defining permission, `r` for read only. See armi.bookkeeping.db.permissions
     version: str, optional
         Version of database you want to read or write. In most cases ARMI will
         auto-detect. For advanced users.

armi/bookkeeping/db/factory.py

@@ -114,9 +114,7 @@ def test_compareDatabaseDuplicate(self):
             # validate the file exists, and force it to be readable again
             b = h5py.File(db._fullPath, "r")
             self.assertEqual(list(b.keys()), ["inputs"])
-            self.assertEqual(
-                sorted(b["inputs"].keys()), ["blueprints", "geomFile", "settings"]
-            )
+            self.assertEqual(sorted(b["inputs"].keys()), ["blueprints", "settings"])
             b.close()
 
             # append to lists
@@ -168,9 +166,7 @@ def test_compareDatabaseSim(self):
             self.assertEqual(len(dbKeys), 3)
             self.assertIn("inputs", dbKeys)
             self.assertIn("c00n00", dbKeys)
-            self.assertEqual(
-                sorted(b["inputs"].keys()), ["blueprints", "geomFile", "settings"]
-            )
+            self.assertEqual(sorted(b["inputs"].keys()), ["blueprints", "settings"])
             b.close()
 
             # append to lists

armi/bookkeeping/db/tests/test_comparedb3.py

@@ -555,17 +555,15 @@ def test_readInputsFromDB(self):
             :tests: R_ARMI_DB_BP
         """
         inputs = self.db.readInputsFromDB()
-        self.assertEqual(len(inputs), 3)
+        self.assertEqual(len(inputs), 2)
 
         # settings
         self.assertGreater(len(inputs[0]), 100)
         self.assertIn("settings:", inputs[0])
 
-        self.assertEqual(len(inputs[1]), 0)
-
         # blueprints
-        self.assertGreater(len(inputs[2]), 100)
-        self.assertIn("blocks:", inputs[2])
+        self.assertGreater(len(inputs[1]), 2400)
+        self.assertIn("blocks:", inputs[1])
 
     def test_deleting(self):
         self.assertTrue(isinstance(self.db, database.Database))

armi/bookkeeping/db/tests/test_database3.py

@@ -44,11 +44,10 @@ def getSimpleDBOperator(cs):
     It's used to make the db unit tests run very quickly.
     """
     newSettings = {}
-    newSettings[CONF_LOADING_FILE] = "smallestTestReactor/refOneBlockReactor.yaml"
+    newSettings[CONF_LOADING_FILE] = "smallestTestReactor/refSmallestReactor.yaml"
     newSettings["verbosity"] = "important"
     newSettings["db"] = True
     newSettings["runType"] = "Standard"
-    newSettings["geomFile"] = "geom1Assem.xml"
     newSettings["nCycles"] = 1
     cs = cs.modified(newSettings=newSettings)
     genDBCase = case.Case(cs)
@@ -301,7 +300,6 @@ def goodMethod(cycle, node):
             self.assertEqual(h5.attrs["version"], version)
 
             self.assertIn("caseTitle", h5.attrs)
-            self.assertIn("geomFile", h5["inputs"])
             self.assertIn("settings", h5["inputs"])
             self.assertIn("blueprints", h5["inputs"])
 
@@ -344,7 +342,7 @@ def test_getHistory(self):
         expectedFluxes7 = {}
 
         def setFluxAwesome(cycle, node):
-            for bi, b in enumerate(self.r.core.getBlocks()):
+            for bi, b in enumerate(self.r.core.iterBlocks()):
                 b.p.flux = 1e6 * bi + 1e3 * cycle + node
                 if bi == 0:
                     expectedFluxes0[cycle, node] = b.p.flux
@@ -358,8 +356,7 @@ def getFluxAwesome(cycle, node):
             if cycle != 0 or node != 2:
                 return
 
-            blocks = self.r.core.getBlocks()
-            b0 = blocks[0]
+            b0 = next(self.r.core.iterBlocks())
 
             db = self.o.getInterface("database")._db
 
@@ -378,15 +375,14 @@ def getFluxAwesome(cycle, node):
 
     def test_getHistoryByLocation(self):
         def setFluxAwesome(cycle, node):
-            for bi, b in enumerate(self.r.core.getBlocks()):
+            for bi, b in enumerate(self.r.core.iterBlocks()):
                 b.p.flux = 1e6 * bi + 1e3 * cycle + node
 
         def getFluxAwesome(cycle, node):
             if cycle != 1 or node != 2:
                 return
 
-            blocks = self.r.core.getBlocks()
-            b = blocks[0]
+            b = next(self.r.core.iterBlocks())
 
             db = self.o.getInterface("database").database
 
@@ -426,7 +422,7 @@ def setUpClass(cls):
 
         # update a few parameters
         def writeFlux(cycle, node):
-            for bi, b in enumerate(o.r.core.getBlocks()):
+            for bi, b in enumerate(o.r.core.iterBlocks()):
                 b.p.flux = 1e6 * bi + cycle * 100 + node
                 b.p.mgFlux = np.repeat(b.p.flux / 33, 33)
 
@@ -555,11 +551,11 @@ def test_readWithoutInputs(self):
         with Database(self.dbName, "r") as db:
             r2 = db.load(0, 0)
 
-        for b1, b2 in zip(self.r.core.getBlocks(), r2.core.getBlocks()):
+        for b1, b2 in zip(self.r.core.iterBlocks(), r2.core.iterBlocks()):
             for c1, c2 in zip(sorted(b1), sorted(b2)):
                 self.assertEqual(c1.name, c2.name)
 
-        for bi, b in enumerate(r2.core.getBlocks()):
+        for bi, b in enumerate(r2.core.iterBlocks()):
             assert_allclose(b.p.flux, 1e6 * bi)
 
     def test_variousTypesWork(self):

armi/bookkeeping/db/tests/test_databaseInterface.py

@@ -36,13 +36,19 @@ def setUp(self):
         """
         self.app = getApp()
         self._backupApp = deepcopy(self.app)
+        self._cacheBPSections = PassiveDBLoadPlugin.SKIP_BP_SECTIONS
+        self._cacheUnkownParams = PassiveDBLoadPlugin.UNKNOWN_PARAMS
+        PassiveDBLoadPlugin.SKIP_BP_SECTIONS = []
+        PassiveDBLoadPlugin.UNKNOWN_PARAMS = {}
 
     def tearDown(self):
         """Restore the App to its original state."""
         import armi
 
         armi._app = self._backupApp
         context.APP_NAME = "armi"
+        PassiveDBLoadPlugin.SKIP_BP_SECTIONS = self._cacheBPSections
+        PassiveDBLoadPlugin.UNKNOWN_PARAMS = self._cacheUnkownParams
 
     def test_passiveDBLoadPlugin(self):
         plug = PassiveDBLoadPlugin()

armi/bookkeeping/db/tests/test_passiveDBLoadPlugin.py

@@ -41,7 +41,7 @@ def describeInterfaces(_cs):
 
 class MainInterface(interfaces.Interface):
     """
-    Do some basic manipulations, calls, Instantiates the databse.
+    Do some basic manipulations, calls, Instantiates the database.
 
     Notes
     -----

armi/bookkeeping/mainInterface.py

@@ -172,7 +172,7 @@ def reportSFP(sfp):
         runLog.important(title)
         runLog.important("-" * len(title))
         totFis = 0.0
-        for a in sfp.getChildren():
+        for a in sfp:
             runLog.important(
                 "{assembly:15s} discharged at t={dTime:10f} after {residence:10f} yrs. It entered at cycle: {cycle}. "
                 "It has {fiss:10f} kg (x {mult}) fissile and peak BU={bu:.2f} %.".format(
@@ -196,16 +196,16 @@ def reportSFP(sfp):
     @staticmethod
     def countAssembliesSFP(sfp):
         """Report on the count of assemblies in the SFP at each timestep."""
-        if not sfp.getChildren():
+        if not len(sfp):
             return
 
         runLog.important("Count:")
         totCount = 0
         thisTimeCount = 0
-        a = sfp.getChildren()[0]
+        a = sfp[0]
         lastTime = a.getAge() / units.DAYS_PER_YEAR + a.p.chargeTime
 
-        for a in sfp.getChildren():
+        for a in sfp:
             thisTime = a.getAge() / units.DAYS_PER_YEAR + a.p.chargeTime
 
             if thisTime != lastTime:

armi/bookkeeping/report/reportInterface.py

@@ -109,14 +109,10 @@ def _listInputFiles(cs):
             includedBlueprints = []
 
         inputInfo = []
-        inputFiles = (
-            [
-                ("Case Settings", cs.caseTitle + ".yaml"),
-                ("Blueprints", cs[CONF_LOADING_FILE]),
-            ]
-            + [("Included blueprints", inclBp) for inclBp in includedBlueprints]
-            + [("Geometry", cs["geomFile"])]
-        )
+        inputFiles = [
+            ("Case Settings", cs.caseTitle + ".yaml"),
+            ("Blueprints", cs[CONF_LOADING_FILE]),
+        ] + [("Included blueprints", inclBp) for inclBp in includedBlueprints]
 
         activeInterfaces = interfaces.getActiveInterfaceInfo(cs)
         for klass, kwargs in activeInterfaces:
@@ -672,7 +668,7 @@ def summarizePinDesign(core):
     designInfo = collections.defaultdict(list)
 
     try:
-        for b in core.getBlocks(Flags.FUEL):
+        for b in core.iterBlocks(Flags.FUEL):
             fuel = b.getComponent(Flags.FUEL)
             duct = b.getComponent(Flags.DUCT)
             clad = b.getComponent(Flags.CLAD)
@@ -831,9 +827,6 @@ def _setGeneralCoreDesignData(cs, coreDesignTable):
     report.setData(
         "Run Type", "{}".format(cs["runType"]), coreDesignTable, report.DESIGN
     )
-    report.setData(
-        "Geometry File", "{}".format(cs["geomFile"]), coreDesignTable, report.DESIGN
-    )
     report.setData(
         "Loading File",
         "{}".format(cs[CONF_LOADING_FILE]),

armi/bookkeeping/report/reportingUtils.py

@@ -111,7 +111,7 @@ def test_calcMGFluence(self):
         r"""
         This test confirms that mg flux has many groups when loaded with the history tracker.
 
-        armi.bookeeping.db.hdf.hdfDB.readBlocksHistory requires
+        armi.bookkeeping.db.hdf.hdfDB.readBlocksHistory requires
         historical_values\[historical_indices\] to be cast as a list to read more than the
         first energy group. This test shows that this behavior is preserved.
 

armi/bookkeeping/tests/test_historyTracker.py

@@ -68,7 +68,7 @@ def setUpClass(cls):
             inputFileName="smallestTestReactor/armiRunSmallest.yaml"
         )
 
-        cls.hexBlock = cls.r.core.getBlocks()[0]
+        cls.hexBlock = next(cls.r.core.iterBlocks())
 
         cls.cartesianBlock = blocks.CartesianBlock("TestCartesianBlock", caseSetting)
         cartesianComponent = components.HoledSquare(