Merge remote-tracking branch 'terrapower/main' into drewj-usnctech/gr…

…id-refactor-pre-1278

* terrapower/main:
  Move max assembly number out of global scope (terrapower#1383)
  Ensuring we throw an error on bad YAML files (terrapower#1358)
  Removing unused settings (terrapower#1393)
  Fixing some miscellaneous TODOs (terrapower#1392)
  Removing global plugin flags (terrapower#1388)
  Update reactivity coefficient parameters (terrapower#1355)
  Fixing ruff formatting of doc gallery examples (terrapower#1389)
  Fixing broken link (terrapower#1390)
  Removing unreachable code block (terrapower#1391)
  Removing unnecessary f-strings (terrapower#1387)
  Updating documentation dependencies for Python 3.11 (terrapower#1378)
  Adding a little code coverage to the CLIs (terrapower#1371)
  Remove coveragepy-lcov dependency during CI. (terrapower#1382)
  Reconnect logger after disconnecting in test. (terrapower#1381)
  Add Python 3.11 to GH Actions (terrapower#1341)
  Removing global variable from runLog.py (terrapower#1370)
  Moving the First-Time Contributors guide to the docs (terrapower#1368)

.github/workflows/black.yaml

@@ -8,10 +8,10 @@ jobs:
         runs-on: ubuntu-22.04
         steps:
             - uses: actions/checkout@v2
-            - name: Set up Python 3.10
+            - name: Set up Python 3.11
               uses: actions/setup-python@v2
               with:
-                python-version: '3.10'
+                python-version: '3.11'
             - name: Install Black
               run: pip install 'black==20.8b1' 'click==8.0.1'
             - name: Run black --check .

.github/workflows/coverage.yaml

@@ -8,19 +8,16 @@ on:
 
 jobs:
   build:
-
     runs-on: ubuntu-22.04
-
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-
     steps:
       - uses: actions/checkout@v2
       - name: Setup Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Update package index
         run: sudo apt-get update
       - name: Install mpi libs
@@ -31,17 +28,8 @@ jobs:
         run: tox -e cov1 || true
       - name: Run Coverage Part 2
         run: tox -e cov2
-      - name: Convert Coverage Results
-        env:
-          COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
-        run: |
-          pip install click==8.1.3
-          pip install coverage==6.5.0
-          pip install coveragepy-lcov==0.1.2
-          coveragepy-lcov --data_file_path coverage_results.cov --output_file_path lcov.txt
       - name: Publish to coveralls.io
         uses: coverallsapp/[email protected]
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: lcov.txt
-
+          path-to-lcov: coverage.lcov

.github/workflows/unittests.yaml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       matrix:
-        python: [3.7, 3.8, 3.9, '3.10']
+        python: [3.7, 3.8, 3.9, '3.10', '3.11']
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/validatemanifest.yaml

@@ -12,7 +12,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Install Tox and any other packages
         run: pip install tox
       - name: Run Tox

.github/workflows/wintests.yaml

@@ -12,7 +12,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: Upgrade PIP
         run: python -m pip install --upgrade pip
       - name: Install deps

.gitignore

@@ -24,6 +24,7 @@ doc/gallery
 doc/gallery-src/framework/*.yaml
 .coverage
 coverage.xml
+coverage.lcov
 coverage_results.*
 htmlcov/
 monkeytype.*

CONTRIBUTING.md

@@ -1,77 +1,3 @@
-# How to contribute
+# How to Contribute
 
-The ARMI framework project strongly encourages developers to help contribute to the codebase.
-
-The ARMI framework code is open source, and your contributions will become open source.
-Although fewer laws apply to open source materials because they are publicly-available, you still
-must comply with all applicable laws and regulations.
-
-## Help Wanted
-
-There are a lot of things we need help with right off the bat, to get your feet wet:
-
-* Many more type annotations are desired. Type issues cause lots of bugs.
-* Fewer Pylint warnings
-* Better documentation
-* Better test coverage
-* Targeted speedups (e.g. informed by a profiler)
-* Additional relevance to thermal reactors
-
-Naturally, we encourage other kinds of contributions as well.
-
-## Testing
-
-Any contribution must pass all included unit tests. The tests are built and run with the
-`pytest` system. Please add new tests if you add new functionality. You can generally just run
-`tox` to build the testing environment and execute all the tests and ruff checks.
-
-## Submitting changes
-
-Please send a [GitHub Pull Request to the ARMI main branch](https://github.com/terrapower/armi/pull/new/main) with a clear
-list of what you've done (read more about [pull requests](http://help.github.com/pull-requests/)).  Please follow our
-coding conventions (below) and make sure all of your commits are atomic (one feature per commit).
-
-Please write a clear log messages for your commits. One-liners are OK for small changes, but bigger changes should include more:
-
-    $ git commit -m "A brief summary of the commit
-    >
-    > A paragraph describing what changed and its impact."
-
-Note that a bot will require that you sign [our Contributor License
-Agreement](https://gist.github.com/youngmit/8654abcf93f309771ae9296abebe9d4a)
-before we can accept a pull request from you.
-
-## Coding conventions
-
-We use the [Black](https://black.readthedocs.io/en/stable/) code formatter so we don't have to argue or worry about trivial
-whitespacing conventions during code review. You should always run `black` before submitting a pull request.
-
-We really like Robert C Martin's [Clean Code](https://www.amazon.com/Clean-Code-Handbook-Software-Craftsmanship/dp/0132350882) book
-and at least nominally try to follow some of the advice in there.
-
-  * Consider contacting some ARMI developers before embarking on a major new feature or development on the framework.
-    We may prefer to keep various physics or design-specific developments in modular plugins (which can also be
-    open source, of course!). The framework should be focused on frameworky stuff (broad, sharable stuff).
-    As the Framework matures, we hope it will stabilize, though we recognize we need work before then.
-  * We believe that comments can increase maintenance burdens and should only be used when one fails to explain
-    the entire situation with the code itself. In practice, we fail to do this all the time, and need comments
-    to help guide future readers of the code.
-  * Names //really// matter.
-  * Your PR will be reviewed and probably need some iteration. We aren't trying to be a pain or discourage you,
-    we just want to make sure the code is optimal.
-
-## Licensing of Tools
-
-Be careful when including any dependency in ARMI (say in a requirements.txt file) not
-to include anything with a license that superceeds 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 tools.
-
-For that reason, it is generally considered best-practice in the ARMI ecosystem to
-only use third-party Python libraries that have MIT or BSD licenses.
-
-## Documentation
-
-We use Sphinx for our documentation, and numpydoc to parse docstrings into the API docs section of our documentation.
-Thus, all docstrings are officially part of the technical documentation and should be written as such.
+For information on how to contribute to ARMI, see [our official documenation](https://terrapower.github.io/armi/developer/first_time_contributors.html).

MANIFEST.in

@@ -1,4 +1,4 @@
-include armi/bookkeeping/tests/armiRun-A0039-aHist-ref.txt
+include armi/bookkeeping/tests/armiRun-A0032-aHist-ref.txt
 include armi/nuclearDataIO/cccc/tests/fixtures/labels.ascii
 include armi/nuclearDataIO/cccc/tests/fixtures/labels.binary
 include armi/nuclearDataIO/cccc/tests/fixtures/mc2v3.dlayxs

README.rst

@@ -49,6 +49,8 @@ found in [#touranarmi]_.
      - https://github.com/terrapower/armi
    * - Documentation
      - https://terrapower.github.io/armi
+   * - First time contributor's guide
+     - https://terrapower.github.io/armi/developer/first_time_contributors.html
    * - Bug tracker
      - https://github.com/terrapower/armi/issues
    * - Plugin directory
@@ -58,7 +60,7 @@ found in [#touranarmi]_.
 
 Quick start
 -----------
-Before starting, you need to have `Python <https://www.python.org/downloads/>`_ 3.7+ on
+Before starting, you need to have `Python <https://www.python.org/downloads/>`_ 3.9+ on
 Windows or Linux.
 
 Get the ARMI code, install the prerequisites, and fire up the launcher with the following
@@ -83,6 +85,11 @@ and then run::
 This runs the unit tests in parallel on 6 processes. Omit the ``-n 6`` argument
 to run on a single process.
 
+The tests can also be run directly, using ``pytest``::
+
+    $ pip3 install -r requirements-testing.txt
+    $ pytest -n 4 armi
+
 From here, we recommend going through a few of our `gallery examples
 <https://terrapower.github.io/armi/gallery/index.html>`_ and
 `tutorials <https://terrapower.github.io/armi/tutorials/index.html>`_ to

armi/__init__.py

@@ -307,7 +307,7 @@ def configure(app: Optional[apps.App] = None, permissive=False):
     pm = app.pluginManager
     parameters.collectPluginParameters(pm)
     parameters.applyAllParameters()
-    flags.registerPluginFlags(pm)
+    _app.registerPluginFlags()
 
 
 def applyAsyncioWindowsWorkaround() -> None:

armi/apps.py

@@ -75,6 +75,7 @@ def __init__(self):
         For a description of the things that an ARMI plugin can do, see the
         :py:mod:`armi.plugins` module.
         """
+        self._pluginFlagsRegistered: bool = False
         self._pm: Optional[pluginManager.ArmiPluginManager] = None
         self._paramRenames: Optional[Tuple[Dict[str, str], int]] = None
         self.__initNewPlugins()
@@ -228,6 +229,24 @@ def getParamRenames(self) -> Dict[str, str]:
             self._paramRenames = renames, self._pm.counter
         return renames
 
+    def registerPluginFlags(self):
+        """
+        Apply flags specified in the passed ``PluginManager`` to the ``Flags`` class.
+
+        See Also
+        --------
+        armi.plugins.ArmiPlugin.defineFlags
+        """
+        if self._pluginFlagsRegistered:
+            raise RuntimeError(
+                "Plugin flags have already been registered. Cannot do it twice!"
+            )
+
+        for pluginFlags in self._pm.hook.defineFlags():
+            Flags.extend(pluginFlags)
+
+        self._pluginFlagsRegistered = True
+
     def registerUserPlugins(self, pluginPaths):
         r"""
         Register additional plugins passed in by importable paths.

armi/bookkeeping/db/__init__.py

@@ -67,7 +67,7 @@
 
 # re-export package components for easier import
 from .permissions import Permissions
-from .database3 import Database3, updateGlobalAssemblyNum
+from .database3 import Database3
 from .databaseInterface import DatabaseInterface
 from .compareDB3 import compareDatabases
 from .factory import databaseFactory
@@ -144,12 +144,6 @@ def loadOperator(pathToDb, loadCycle, loadNode, allowMissing=False):
 
     settings.setMasterCs(cs)
 
-    # Update the global assembly number because, if the user is loading a reactor from
-    # blueprints and does not have access to an operator, it is unlikely that there is
-    # another reactor that has alter the global assem num. Fresh cases typically want
-    # this updated.
-    updateGlobalAssemblyNum(r)
-
     o = thisCase.initializeOperator(r=r)
     runLog.important(
         "The operator will not be in the same state that it was at that cycle and "

armi/bookkeeping/db/database3.py

@@ -70,7 +70,6 @@
 from armi.bookkeeping.db.typedefs import History, Histories
 from armi.nucDirectory import nuclideBases
 from armi.physics.neutronics.settings import CONF_LOADING_FILE
-from armi.reactor import assemblies
 from armi.reactor import grids
 from armi.reactor import parameters
 from armi.reactor import systemLayoutInput
@@ -101,18 +100,6 @@ def getH5GroupName(cycle: int, timeNode: int, statePointName: str = None) -> str
     return "c{:0>2}n{:0>2}{}".format(cycle, timeNode, statePointName or "")
 
 
-def updateGlobalAssemblyNum(r) -> None:
-    """
-    Updated the global assembly number counter in ARMI, using the assemblies
-    read from a database.
-    """
-    assemNum = r.core.p.maxAssemNum
-    if assemNum is not None:
-        assemblies.setAssemNumCounter(int(assemNum + 1))
-    else:
-        raise ValueError("Could not load maxAssemNum from the database")
-
-
 class Database3:
     """
     Version 3 of the ARMI Database, handling serialization and loading of Reactor states.
@@ -691,8 +678,7 @@ def load(
             Whether to emit a warning, rather than crash if reading a database
             with undefined parameters. Default False.
         updateGlobalAssemNum : bool, optional
-            Whether to update the global assembly number to the value stored in
-            r.core.p.maxAssemNum. Default True.
+            DeprecationWarning: This is unused.
         updateMasterCs : bool, optional
             Whether to apply the cs (whether provided as an argument or read from
             the database) as the primary for the case. Default True. Can be useful
@@ -741,9 +727,11 @@ def load(
         )
         root = comps[0][0]
 
-        # ensure the max assembly number is correct, unless the user says no
         if updateGlobalAssemNum:
-            updateGlobalAssemblyNum(root)
+            runLog.warning(
+                "The method input `updateGlobalAssemNum` is no longer used.",
+                single=True,
+            )
 
         # return a Reactor object
         if cs[CONF_SORT_REACTOR]:

armi/bookkeeping/db/databaseInterface.py

@@ -281,7 +281,6 @@ def _checkThatCyclesHistoriesAreEquivalentUpToRestartTime(
                 "The cycle history up to the restart cycle/node must be equivalent."
             )
 
-    # TODO: The use of "yield" here is suspect.
     def _getLoadDB(self, fileName):
         """
         Return the database to load from in order of preference.

armi/bookkeeping/db/layout.py

@@ -356,7 +356,7 @@ def _initComps(self, caseTitle, bp):
             elif issubclass(Klass, Core):
                 comp = Klass(name)
             elif issubclass(Klass, Component):
-                # TODO: init all dimensions to 0, they will be loaded and assigned after load
+                # init all dimensions to 0, they will be loaded and assigned after load
                 kwargs = dict.fromkeys(Klass.DIMENSION_NAMES, 0)
                 kwargs["material"] = material
                 kwargs["name"] = name
@@ -851,18 +851,11 @@ def replaceNonsenseWithNones(data: numpy.ndarray, paramName: str) -> numpy.ndarr
             if isNone[i].all():
                 result[i] = None
             elif isNone[i].any():
-                # TODO: This is not symmetric with the replaceNonesWithNonsense impl.
-                # That one assumes that Nones apply only at the highest dimension, and
-                # that the lower dimensions will be filled with the magic None value.
-                # Non-none entries below the top level fail to coerce to a serializable
-                # numpy array and would raise an exception when trying to write. TL;DR:
-                # this is a dead branch until the replaceNonesWithNonsense impl is more
-                # sophisticated.
+                # This is the meat of the logic to replace "nonsense" with None.
                 result[i] = numpy.array(data[i], dtype=numpy.dtype("O"))
                 result[i][isNone[i]] = None
             else:
                 result[i] = data[i]
-
     else:
         result = numpy.ndarray(data.shape, dtype=numpy.dtype("O"))
         result[:] = data

armi/bookkeeping/db/tests/test_comparedb3.py

@@ -125,7 +125,7 @@ def test_compareDatabaseDuplicate(self):
         self.assertEqual(diffs.nDiffs(), 0)
 
     def test_compareDatabaseSim(self):
-        """end-to-end test of compareDatabases() on very simlar databases."""
+        """End-to-end test of compareDatabases() on very simlar databases."""
         # build two super-simple H5 files for testing
         o, r = test_reactors.loadTestReactor(
             TEST_ROOT, customSettings={"reloadDBName": "reloadingDB.h5"}
@@ -177,7 +177,7 @@ def test_compareDatabaseSim(self):
             dbs[1]._fullPath,
             timestepCompare=[(0, 0), (0, 1)],
         )
-        self.assertEqual(len(diffs.diffs), 465)
+        self.assertEqual(len(diffs.diffs), 468)
         # Cycle length is only diff (x3)
         self.assertEqual(diffs.nDiffs(), 3)