Merge branch 'main' into code_cov_20220916

.coveragerc

@@ -6,6 +6,9 @@ omit =
     armi/utils/tests/test_gridGui.py
     venv/
 source = armi
+# change default .coverage file to something that doesn't have a dot
+# because the Windows file server can't handle dots.
+data_file = coverage_results.cov
 
 [coverage:run]
 parallel = true

.github/workflows/black.yaml

@@ -5,7 +5,7 @@ on: [push, pull_request]
 # use workaround due to: https://github.com/psf/black/issues/2079#issuecomment-812359146
 jobs:
     check-formatting:
-        runs-on: ubuntu-20.04
+        runs-on: ubuntu-22.04
         steps:
             - uses: actions/checkout@v2
             - name: Set up Python 3.10

.github/workflows/coverage.yaml

@@ -1,14 +1,19 @@
 name: Coverage
 
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
 
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     env:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
@@ -25,5 +30,18 @@ jobs:
       - name: Run Coverage Part 1
         run: tox -e cov1 || true
       - name: Run Coverage Part 2
-        run: tox -e cov2,report
+        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/github-action@v1.1.2
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          path-to-lcov: lcov.txt
 

.github/workflows/docs.yaml

@@ -8,14 +8,14 @@ on:
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
       - uses: actions/checkout@v2
       - name: Setup Python
         uses: actions/setup-python@v2
         with:
-          python-version: 3.8
+          python-version: 3.9
       - name: Update package index
         run: sudo apt-get update
       - name: Install mpi libs

.github/workflows/licensechecker.yaml

@@ -2,7 +2,7 @@ name: Check License Lines
 on: [push, pull_request]
 jobs:
   check-license-lines:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@master
     - name: Check License Lines

.github/workflows/unittests.yaml

@@ -5,7 +5,7 @@ on: [push, pull_request]
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python: [3.7, 3.8, 3.9, '3.10']

.github/workflows/validatemanifest.yaml

@@ -5,7 +5,7 @@ on: [push, pull_request]
 jobs:
   build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
       - uses: actions/checkout@v2

.gitignore

@@ -48,6 +48,7 @@ tags
 .pytest_cache/
 pytestdebug.log
 dump-temp-*
+dump-tests*
 .vim-bookmarks
 venv*/
 .mypy_cache/

MANIFEST.in

@@ -27,9 +27,7 @@ include armi/nuclearDataIO/tests/library-file-generation/mc2v2-dlayxs.inp
 include armi/nuclearDataIO/tests/library-file-generation/mc2v3-AA.inp
 include armi/nuclearDataIO/tests/library-file-generation/mc2v3-AB.inp
 include armi/nuclearDataIO/tests/library-file-generation/mc2v3-dlayxs.inp
-include armi/nuclearDataIO/tests/longLivedRipleData.dat
 include armi/nuclearDataIO/tests/simple_hexz.inp
-include armi/nuclearDataIO/tests/z036.dat
 include armi/tests/1DslabXSByCompTest.yaml
 include armi/tests/COMPXS.ascii
 include armi/tests/ISOAA

README.rst

@@ -434,6 +434,6 @@ only use third-party Python libraries that have MIT or BSD licenses.
 .. |Build Status| image:: https://github.com/terrapower/armi/actions/workflows/unittests.yaml/badge.svg?branch=main
     :target: https://github.com/terrapower/armi/actions/workflows/unittests.yaml
 
-.. |Code Coverage| image:: https://coveralls.io/repos/github/terrapower/armi/badge.svg?branch=main&kill_cache=7
+.. |Code Coverage| image:: https://coveralls.io/repos/github/terrapower/armi/badge.svg?branch=main&kill_cache=2
     :target: https://coveralls.io/github/terrapower/armi?branch=main
 

armi/_bootstrap.py

@@ -57,8 +57,6 @@ def _addCustomTabulateTables():
 _addCustomTabulateTables()
 
 
-from armi import runLog
-
 from armi.nucDirectory import nuclideBases
 
 # Nuclide bases get built explicitly here to have better determinism

armi/bookkeeping/__init__.py

@@ -22,7 +22,7 @@ class BookkeepingPlugin(plugins.ArmiPlugin):
     @staticmethod
     @plugins.HOOKIMPL
     def exposeInterfaces(cs):
-        from armi.bookkeeping.db import database3
+        from armi.bookkeeping.db import databaseInterface
         from armi.bookkeeping import historyTracker
         from armi.bookkeeping import memoryProfiler
         from armi.bookkeeping import mainInterface
@@ -31,7 +31,7 @@ def exposeInterfaces(cs):
 
         interfaceInfo = []
         interfaceInfo += plugins.collectInterfaceDescriptions(mainInterface, cs)
-        interfaceInfo += plugins.collectInterfaceDescriptions(database3, cs)
+        interfaceInfo += plugins.collectInterfaceDescriptions(databaseInterface, cs)
         interfaceInfo += plugins.collectInterfaceDescriptions(historyTracker, cs)
         interfaceInfo += plugins.collectInterfaceDescriptions(memoryProfiler, cs)
         interfaceInfo += plugins.collectInterfaceDescriptions(reportInterface, cs)

armi/bookkeeping/db/__init__.py

@@ -18,39 +18,47 @@
 As an ARMI run progresses, this is periodically updated as the primary output file.
 It can also be an input file for follow-on analysis or restart runs.
 
-The database can be visualized through various tools such as XTVIEW.
-
 This module contains factories for selecting and building DB-related objects.
 
-Some notes on versions
-----------------------
-Persistent storage of ARMI models has seen many changes throughout the years.
-Calculation results were originally stored on a SQL database (version 1), which has been
-fully deprecated at this point.
-
-Version 2 was the first to use HDF5 as the primary storage format. This was beneficial,
-as it did not rely on any external infrastructure to operate, and benefited from the
-suite of tools that help interact with HDF5 files. It was eventually replaced because
-it did not store a complete model of the reactor, but rather a ghost of assembly, block,
-and reactor parameters that could be applied to an existing reactor model (so long as
-the dimensions were consistent!). This led to loading reactors being inconvenient and
-error-prone, and also posed a limitation for representing more complex systems that have
-non-core components.
-
-Version 3 was created to make the schema more flexible and to permit storing the entire
-reactor model within the HDF5 file. All objects in the ARMI Composite Model are written
-to the database, and the model can be recovered in its entirety just from the HDF5 file.
-Since it's inception, it has seen a number of tweaks to improve its functionality and
-fix bugs.
-
-Being a serialization format, the code associated with reading and writing database
-files may not benefit from Don't Repeat Yourself (DRY) practices in the same way as
-other code. Therefore, we do not share much, if any, code between different major
-versions of the databases. As such, new major-versioned database implementations should
-exist in their own modules. Minor revisions (e.g. M.(N+1)) to the database structure
-should be simple enough that specialized logic can be used to support all minor versions
-without posing a maintenance burden. A detailed change log should be maintained of each
-minor revision.
+When updating a db version
+--------------------------
+The code associated with reading and writing database files may not benefit from Don't
+Repeat Yourself (DRY) practices in the same way as other code. Therefore, do not share
+code between different major versions of the databases. Create a new module if you are
+creating a new major database version.
+
+
+Database revision changelog
+---------------------------
+ - 1: Originally, calculation results were stored in a SQL database.
+
+ - 2: The storage format was changed to HDF5. This required less external
+   infrastructure than SQL. However, the implementation did not store a complete
+   model of a reactor, but a ghost of assembly, block, and reactor parameters that
+   could be applied to an existing reactor model (so long as the dimensions were
+   consistent). This was inconvenient and error prone.
+
+ - 3: The HDF5 format was kept, but the schema was made more flexible to permit
+   storing the entire reactor model. All objects in the ARMI Composite Model are
+   written to the database, and the model can be completely recovered from just the
+   HDF5 file.
+
+     - 3.1: Improved the handling of reading/writing grids.
+
+     - 3.2: Changed the strategy for storing large attributes to using a special
+       string starting with an "@" symbol (e.g., "@/c00n00/attrs/5_linkedDims"). This
+       was done to support copying time node datasets from one file to another without
+       invalidating the references. Support was maintained for reading previous
+       versions, by performing a ``mergeHistory()`` and converting to the new naming
+       strategy, but the old version cannot be written.
+
+     - 3.3: Compressed the way locations are stored in the database and allow
+       MultiIndex locations to be read and written.
+
+     - 3.4: Modified the way locations are stored in the database to include complete
+       indices for indices that can be composed from multiple grids. Having complete
+       indices allows for more efficient means of extracting information based on
+       location, without having to compose the full model.
 """
 import os
 from typing import Optional, List, Tuple
@@ -62,7 +70,8 @@
 
 # re-export package components for easier import
 from .permissions import Permissions
-from .database3 import Database3, DatabaseInterface, updateGlobalAssemblyNum
+from .database3 import Database3, updateGlobalAssemblyNum
+from .databaseInterface import DatabaseInterface
 from .compareDB3 import compareDatabases
 from .factory import databaseFactory
 
@@ -145,11 +154,13 @@ def loadOperator(pathToDb, loadCycle, loadNode, allowMissing=False):
     updateGlobalAssemblyNum(r)
 
     o = thisCase.initializeOperator(r=r)
-    runLog.warning(
-        "The operator provided is not in the same state as the operator was.\n"
-        "When the reactor was at the prescribed cycle and node, it should have\n"
-        "access to the same interface stack, but the interfaces will also not be in the "
-        "same state.\n"
+    runLog.important(
+        "The operator will not be in the same state that it was at that cycle and "
+        "node, only the reactor.\n"
+        "The operator should have access to the same interface stack, but the "
+        "interfaces will not be in the same state (they will be fresh instances "
+        "of each interface as if __init__ was just called rather than the state "
+        "during the run at this time node.)\n"
         "ARMI does not support loading operator states, as they are not stored."
     )
     return o

armi/bookkeeping/db/compareDB3.py

@@ -289,17 +289,14 @@ def _compareSets(
     src: set, ref: set, out: OutputWriter, name: Optional[str] = None
 ) -> int:
     nDiffs = 0
+    printName = "" if name is None else name + " "
     if ref - src:
         nDiffs += len(ref - src)
-        out.writeln(
-            "ref has {}not in src: {}".format(name + " " or "", list(ref - src))
-        )
+        out.writeln("ref has {}not in src: {}".format(printName, list(ref - src)))
 
     if src - ref:
-        nDiffs += len(ref - src)
-        out.writeln(
-            "src has {}not in ref: {}".format(name + " " or "", list(src - ref))
-        )
+        nDiffs += len(src - ref)
+        out.writeln("src has {}not in ref: {}".format(printName, list(src - ref)))
 
     return nDiffs
 
@@ -493,8 +490,10 @@ def _compareComponentData(
 
         if srcSpecial ^ refSpecial:
             out.writeln(
-                "Could not compare data because one uses special formatting, "
-                "and the other does not. Ref: {} Src: {}".format(refSpecial, srcSpecial)
+                "Could not compare data for parameter {} because one uses special "
+                "formatting, and the other does not. Ref: {} Src: {}".format(
+                    paramName, refSpecial, srcSpecial
+                )
             )
             diffResults.addDiff(
                 refGroup.name, paramName, numpy.inf, numpy.inf, numpy.inf