Post 6.7.1 fixes

.github/workflows/makefile.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.12", "3.x"]
+        python-version: ["3.8", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -22,7 +22,7 @@ jobs:
       run: python -m pip install --upgrade pip setuptools wheel numpy h5py matplotlib
 
     - name: Build
-      run: make PYTHON=python
+      run: make PYTHON=python CC=gcc
 
     - name: Run check
       run:  |

.github/workflows/python-app.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.12", "3.x"]
+        python-version: ["3.8", "3.12", "3.13"]
 
     steps:
       - name: Set up Python ${{ matrix.python-version }}
@@ -24,5 +24,10 @@ jobs:
         run: python -m pip install --upgrade pip setuptools wheel numpy h5py
 
       - name: Install FUDGE
-        run: python -m pip install git+https://github.com/LLNL/fudge.git@ci_dev
+        run:  |
+              if [ "$RUNNER_OS" == "Windows" ]; then
+                  export CC=gcc
+              fi
+              python -m pip install git+https://github.com/LLNL/fudge.git
+        shell: bash
 

Merced/Makefile

@@ -5,7 +5,7 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # <<END-copyright>>
 
-subDirs = Doc Src TestSuite bin
+subDirs = Doc MonteCarlo Src TestSuite bin
 
 .PHONY: default bin clean realclean check doc doSubDirs prefixDeploy
 

README.md

@@ -44,22 +44,26 @@ Optional packages matplotlib and PyQT5 are also recommended to support plotting.
 
     - Install FUDGE:
 
-          pip install git+https://github.com/LLNL/fudge.git@6.7.1
+          # Install latest available version:
+          pip install git+https://github.com/LLNL/fudge.git
+
+      Or,
+
+          # Install a tagged release:
+          pip install git+https://github.com/LLNL/fudge.git@fudge6.8.0
 
 
 - Installation by cloning the git repository and building with the unix `make` command: 
   This is the typical mode for active FUDGE maintenance and development.
   The following steps are recommended:
 
-    - Ensure that NumPy (version 1.15 or later) is installed
+    - Ensure that NumPy (version 1.15 or greater) is installed
 
     - Clone FUDGE in the current directory: 
 
-        ```
         git clone https://github.com/LLNL/fudge.git
-        # or using SSH (requires creating a github account and registering an ssh key):
-        git clone git@github.com:LLNL/fudge.git
-        ```
+            # or using SSH (requires creating a github account and registering an ssh key):
+            git clone git@github.com:LLNL/fudge.git
 
     - Build FUDGE:
 
@@ -82,6 +86,18 @@ Optional packages matplotlib and PyQT5 are also recommended to support plotting.
       - on Windows, the environment variable should be added to the registry (see for 
           example <http://www.support.tabs3.com/main/R10463.htm>)
 
+### Notes for Windows users:
+
+FUDGE installations are now regularly tested on Github CI using Windows with the MinGW environment.
+Compiling C extensions on Windows may require an extra step: if command 'cc.exe' is not available,
+locate a C compiler and set environment variable CC to that compiler.  For example,
+```
+set CC=gcc
+pip install git+https://github.com/LLNL/fudge.git
+```
+
+Please let us know if you run into trouble installing or using FUDGE on Windows!
+
 ### Differences between FUDGE installed via `pip install` vs. via `make`:
 
 When FUDGE is installed via `pip install`, several executable scripts are installed into 

bin/Makefile

@@ -14,7 +14,7 @@ merced:
 	mv ../Merced/bin/merced .
 
 upscatter: 
-	cd ../fudge/processing/deterministic/upscatter; $(MAKE) CC=gcc
+	cd ../fudge/processing/deterministic/upscatter; $(MAKE)
 	mv ../fudge/processing/deterministic/upscatter/bin/calcUpscatterKernel .
 
 check:

bin/buildMapFile.py

@@ -201,7 +201,7 @@ def sortFiles(files):
     try :
         name, data = GNDS_fileModule.type(file)
     except :
-        if args.verbose > 2: print('    WARNING: Invalid file "%s".' % file)
+        print('    WARNING: Invalid file "%s".' % file)
         continue
     if( name == reactionSuiteModule.ReactionSuite.moniker ) :
         if data['interaction'] is None:

bin/crossSections.py

@@ -22,6 +22,7 @@
 from fudge.reactionData import crossSection as crossSectionModule
 from fudge.reactionData.doubleDifferentialCrossSection.photonScattering import coherent as coherentModule
 from fudge.reactionData.doubleDifferentialCrossSection.photonScattering import incoherent as incoherentModule
+from fudge.reactionData.doubleDifferentialCrossSection.photonScattering import incoherentDoppler as incoherentDopplerModule
 
 summaryDocString__FUDGE = '''Outputs the evaluated cross section for each reaction and total for a GNDS reactionSuite.  The processed data are written to files if the "-o" and "--processed" options are used.'''
 
@@ -171,7 +172,7 @@ def outputLabel(crossSection, MT, reactionStr, reactionIndex):
 
 crossSections = []
 if args.verbose > 0: print(protare.sourcePath)
-total = crossSectionModule.XYs1d(axes=protare.reactions[0].crossSection[-1].axes)
+total = crossSectionModule.XYs1d(axes=crossSectionModule.defaultAxes(energyUnit=protare.domainUnit))
 for reactionCounter, reaction in enumerate(protare.reactions):
     if args.verbose > 1: print('    %s' % reaction)
     crossSection = reaction.crossSection.toPointwise_withLinearXYs(lowerEps=1e-6, upperEps=1e-6)
@@ -192,7 +193,8 @@ def outputLabel(crossSection, MT, reactionStr, reactionIndex):
 reactionCounterOffset = reactionCounter + 1
 
 if len(protare.sums.crossSectionSums) > 0:
-    outputLog.write('\nData in crossSectionSums:\n')
+    if outputDir is not None:
+        outputLog.write('\nData in crossSectionSums:\n')
 
 for reactionCounter2, reaction in enumerate(protare.sums.crossSectionSums):
     reactionCounter = reactionCounterOffset + reactionCounter2
@@ -224,6 +226,10 @@ def outputLabel(crossSection, MT, reactionStr, reactionIndex):
                 prefix = 'incoherentScatteringFactor'
                 formClass = incoherentModule.Form
                 dataName = 'scatteringFactor'
+            elif reaction.ENDF_MT >= 1534 and reaction.ENDF_MT <= 1572:
+                prefix = 'incoherentDoppler'
+                formClass = incoherentDopplerModule.Form
+                dataName = 'ComptonProfile'
             else:
                 continue
             for form in reaction.doubleDifferentialCrossSection:

bin/cullProcessedData.py

@@ -15,23 +15,23 @@
 
 summaryDocString__FUDGE = """This script removed all processed data (except resonance reconstructed data) for the specified GNDS protare file."""
 
-description = summaryDocString__FUDGE
+description = summaryDocString__FUDGE + """ If option "--outputDir" is present, the directory is striped from the output path and replaced 
+with the specified path."""
 
 parser = argparse.ArgumentParser(description=description, allow_abbrev=False)
 singleProtareArguments = argumentsForScriptsModule.SingleProtareArguments(parser)
-parser.add_argument('output', nargs='?', default=None,                  help='Output file name.')
+parser.add_argument('outputPath', default=None, type=pathlib.Path,             help='Output file name.')
+parser.add_argument('--outputDir', action='store', default=None, type=pathlib.Path,     help='The output directory to write the output file to.')
 
 args = parser.parse_args()
 
 protare = singleProtareArguments.protare(args)
+protare.cullProcessedData()
 
-stylesToRemove = []
-preProcessingStyles = protare.styles.preProcessingStyles()
-for style in protare.styles :
-    if not isinstance(style, preProcessingStyles):
-        stylesToRemove.append(style.label)
-protare.removeStyles(stylesToRemove)
+outputPath = args.outputPath
+if outputPath is None:
+    outputPath = pathlib.Path(protare.sourcePath).with_suffix('.culled.xml')
+if args.outputDir is not None:
+    outputPath = args.outputDir / outputPath.name
 
-output = args.output
-if output is None: output = pathlib.Path(protare.sourcePath).with_suffix('.culled.xml')
-protare.saveToFile(output)
+protare.saveToFile(outputPath)

bin/energyBalance.py

@@ -131,6 +131,8 @@ def output(reactionOutputDir, fileName, curve, crossSection=None):
                 priorEnergy = energy
             if priorEnergy is not None:                     # Add a point at the last zero cross section point.
                 curve.setValue(priorEnergy, curve.evaluate(priorEnergy))
+        elif fileName == 'Q.dat':
+            curve = curve * crossSection.domainSlice(domainMin=curve.domainMin)
 
         weighted = []
         for index, (xValue, yValue) in enumerate(curve):
@@ -216,14 +218,17 @@ def process(reaction, isReaction):
     crossSection = reaction.crossSection.toPointwise_withLinearXYs(lowerEps=1e-6)
     output(reactionOutputDir, 'crossSection.dat', crossSection)
 
+    outputChannel = reaction.outputChannel
     if isReaction:
+        Q = outputChannel.Q[0].toPointwise_withLinearXYs(accuracy=1e-5, lowerEps=1e-6)
+        output(reactionOutputDir, 'Q.dat', Q, crossSection)
         availableEnergy = reaction.availableEnergy[apdLabel]
         output(reactionOutputDir, 'availableEnergy.dat', availableEnergy, crossSection)
 
-        checkTwoBody(reactionOutputDir, crossSection, reaction.outputChannel)
+        checkTwoBody(reactionOutputDir, crossSection, outputChannel)
 
     productSums = {}
-    outputProductData(reactionOutputDir, crossSection, reaction.outputChannel, productSums, 0)
+    outputProductData(reactionOutputDir, crossSection, outputChannel, productSums, 0)
 
     totalProductEnergy = XYs1dModule.XYs1d(axes=averageProductEnergyAxes)
     for pid in productSums:

bin/peek.py

@@ -18,6 +18,7 @@
 from fudge import outputChannel as outputChannelModule
 from fudge import product as productModule
 from fudge import sums as sumsModule
+from fudge import institution as institutionModule
 from fudge.reactionData import crossSection as crossSectionModule
 from fudge.productData import multiplicity as multiplicityModule
 from fudge.productData.distributions import unspecified as unspecifiedModule
@@ -45,6 +46,7 @@
 parser.add_argument('--doNotShowProducts', action='store_true',             help='If present, no product data are displayed.')
 parser.add_argument('--skipProductions', action='store_true',               help='If present, skips the "productions" node.')
 parser.add_argument('--skipIncompleteReactions', action='store_true',       help='If present, skips the "incompleteReactions" node.')
+parser.add_argument('--skipPhotoAtomicIncoherentDoppler', action='store_true',      help='If present, skips the photo-atomic incoherent Doppler reactions.')
 parser.add_argument('--products', action='append', default=[],              help='Only show reactions with these products in their list. If empty, all reactions are shown.')
 parser.add_argument('--MT', action='append', type=int, default=[],          help='Only show reactions with these MTs. If empty, all reactions are shown.')
 parser.add_argument('--crossSectionSums', action='store_true',              help='If present, also show crossSectionSum information.')
@@ -176,8 +178,8 @@ def reactionPeek(self, prefix, index, indent, reactionIndex):
         QStr = 'Q_threshold = %11s' % self.outputChannel.Q[0].evaluate(self.domainMin)
     except:
         QStr = '"Q_threshold issue, please report to FUDGE developers"'
-    print('%s%-36s (%4d): %s domainMin = %11s domainMax = %10s %s%s' %
-            (indent, prefix % str(self), index, QStr, self.domainMin, self.domainMax, self.domainUnit, crossSectionStr))
+    print('%s%-36s (%4d): %s domainMin = %11.6g domainMax = %10.6g %s MT = %s%s' %
+            (indent, prefix % str(self), index, QStr, self.domainMin, self.domainMax, self.domainUnit, self.ENDF_MT, crossSectionStr))
     productPath = [str(index)]
     if not args.doNotShowProducts:
         self.outputChannel.__peek(indent + indentIncrement, [str(reactionIndex)])
@@ -202,12 +204,14 @@ def crossSectionSum(self, index, indent):
     print('%s%-32s (%4d): domainMin = %s, domainMax = %s %s%s' % (indent, str(self), index, crossSection.domainMin, 
             crossSection.domainMax, crossSection.domainUnit, crossSectionStr))
 
-def showChildren(node, skip):
+def showChildren(node, skip, label=None):
 
     if skip:
         return
     if len(node) > 0:
-        print('%s%s:' % (indent, node.moniker))
+        if label is None:
+            label = node.moniker
+        print('%s%s:' % (indent, label))
         for reactionIndex, reaction in enumerate(node):
             reaction.__peek('%s', reactionIndex, 2 * indentIncrement, reactionIndex)
 
@@ -236,3 +240,10 @@ def showChildren(node, skip):
         print('%sCross section sums:' % indent)
         for crossSectionSumIndex, crossSectionSum in enumerate(protare.sums.crossSectionSums):
             crossSectionSum.__peek(crossSectionSumIndex, 2 * indentIncrement)
+
+    try:
+        photoAtomicIncoherentDoppler = protare.applicationData[institutionModule.photoAtomicIncoherentDoppler]
+        showChildren(photoAtomicIncoherentDoppler.data[0], args.skipPhotoAtomicIncoherentDoppler,
+                label='Photo-atomic incoherent doppler reactions')
+    except:
+        pass

bin/processProtare.py

@@ -218,21 +218,7 @@ def listFileProperties(_fileName):
 preProcessedStyles = reactionSuite.styles.preProcessingStyles()
 
 if args.cullProcessedData:
-    stylesToRemove = []
-    for style in reactionSuite.styles:
-        if not isinstance(style, preProcessedStyles):
-            stylesToRemove.append(style.label)
-    reactionSuite.removeStyles(stylesToRemove)
-
-    # applicationData requires special handling:
-    from fudge.processing.deterministic import tokens as deterministicTokensModule
-    from fudge.resonances import probabilityTables as probabilityTablesModule
-    for label in (deterministicTokensModule.multiGroupReactions,
-                  deterministicTokensModule.multiGroupDelayedNeutrons,
-                  deterministicTokensModule.multiGroupIncompleteProducts,
-                  probabilityTablesModule.LLNLProbabilityTablesToken):
-        if label in reactionSuite.applicationData:
-            reactionSuite.applicationData.pop(label)
+    reactionSuite.cullProcessedData()
 
 for style in reactionSuite.styles:                 # Fail on detection of existing processed data.
     if not isinstance(style, preProcessedStyles): 

brownies/BNL/plot_evaluation/__init__.py

@@ -310,12 +310,6 @@ def getEXFORSets(sym, A, metastable, reaction=None, quantity="SIG", nox4evals=Tr
         print('WARNING: x4i not successfully imported (check your PYTHONPATH?), so EXFOR data not plotted')
         return exforData
 
-    def barnsConverter(x):
-        if x == 'barns':
-            return 'b'
-        else:
-            return x
-
     db = exfor_manager.X4DBManagerPlainFS()
     i = 0
     M = ""
@@ -357,30 +351,24 @@ def barnsConverter(x):
             legend = ds[d].legend()
             if verbose:
                 print('       ', d, legend)
-            dat = []
-            unc = []
-            for line in ds[d].data:
-                if len(line) != 4:
-                    continue
-                if line[0] is None or line[1] is None:
-                    continue
-                dx = 0.0
-                dy = 0.0
-                if line[2] is not None:
-                    dx = line[2]
-                if line[3] is not None:
-                    dy = line[3]
-                dat.append([line[0], line[1]])
-                unc.append([dx, dy])
-                if None in unc[-1]:
-                    unc[-1][unc[-1].index(None)] = 0.0
-            if len(dat) > 0:
+            if 'Energy' in ds[d].data and 'Data' in ds[d].data:
+                dat = ds[d].data[['Energy', 'Data']].pint.dequantify().values.tolist()
+                try:
+                    unc = ds[d].data[['d(Energy)', 'd(Data)']].pint.dequantify().values.tolist()
+                except KeyError as err:  # There was a problem getting uncertainties, so skip it
+                    unc = None
+                xUnit = str(ds[d].data['Energy'].pint.units)
+                yUnit = str(ds[d].data['Data'].pint.units)
+                if yUnit == 'b/sr':
+                    yUnit='b'  # newish strange choice in EXFOR management
                 if e.startswith('V') or not suppressEXFORLegend:
                     theLegend = legend + ' (' + str(d[0]) + '.' + str(d[1][-3:]) + ')'
                 else:
                     theLegend = '_noLegend_'
                 exforData.append(
-                    DataSet2d(data=dat, uncertainty=unc, xUnit=ds[d].units[0], yUnit=barnsConverter(ds[d].units[1]),
+                    DataSet2d(data=dat, uncertainty=unc, 
+                              xUnit=xUnit, 
+                              yUnit=yUnit,
                               legend=theLegend, lineStyle=' ', symbol=plotstyles.getPlotSymbol(i),
                               color=plotstyles.getPlotColor(theLegend, False)))
                 i += 1
@@ -1298,8 +1286,8 @@ def makeAngDistMubarPlot(gndsMap={}, xyData={}, xydyData={}, xdxydyData={},
                      xdxydyData=xdxydyData,
                      plotStyle=plotStyle,
                      suggestTitle=getSuggestTitle(target, projectile, reactionName, mt),
-                     suggestXLog=(mt in [1, 2, 18, 102] + range(501, 574)),
-                     suggestYLog=(mt in [1, 2, 18, 102] + range(501, 574)),
+                     suggestXLog=(mt in [1, 2, 18, 102] + list(range(501, 574))),
+                     suggestYLog=(mt in [1, 2, 18, 102] + list(range(501, 574))),
                      suggestFrame=suggestFrame,
                      figsize=figsize,
                      useBokeh=useBokeh)

brownies/BNL/restools/resonance_generator.py

@@ -32,7 +32,7 @@ def getFakeResonanceSet(
     :param L: orbital angular momentum
     :param J: total angular momentum
     :param levelDensity: dictionary containing L/J-specific energy-dependent level densities
-    :param aveWidthFuncs': dictionary containing L/J-specific energy-dependent widths
+    :param aveWidthFuncs: dictionary containing L/J-specific energy-dependent widths
     :param DOFs: Chi-square degrees of freedom for each reaction channel, used for drawing resonance widths.
     :param widthKeys: column headers for resulting Table
     :param domainMin: lower bound for generating resonances, usually equal to lower bound for level densities / widths

brownies/bin/endf2gnds.py

@@ -90,9 +90,9 @@ def process_args( ) :
             if hasattr(topLevel, 'convertUnits') and args.energyUnit != 'eV':
                 topLevel.convertUnits({'eV': args.energyUnit})
             if hasattr(topLevel, 'saveAllToFile'):
-                topLevel.saveAllToFile(outFile)
+                topLevel.saveAllToFile(outFile, formatVersion=args.formatVersion)
             else:
-                topLevel.saveToFile(outFile)
+                topLevel.saveToFile(outFile, formatVersion=args.formatVersion)
             break
 except Exception as err:
     sys.stderr.write('WARNING: ENDF write error: %s\n' % err)

brownies/bin/plot_covariance.py

@@ -88,4 +88,7 @@
         otherMT = args.crossMT
     elif c.columnData is None:
         otherMT = args.MT
+    else:
+        otherMT = args.MT
+
     raise KeyError("(MF0,MT0)x(MF1,MT1) = (%s,%s)x(%s,%s) not found" % (args.MF, args.MT, args.MF, otherMT))