faster translation

Author: dodu94

libmanager.py

@@ -116,8 +116,8 @@ def check4zaid(self, zaid):
 
         """
         libraries = []
-        for table in self.XS.find_table(zaid):
-            libraries.append(table.name.split('.')[-1])
+        for libname in self.XS.find_table(zaid, mode='default-fast'):
+            libraries.append(libname)
 
         return libraries
 

matreader.py

@@ -993,7 +993,7 @@ def from_input(cls, inputfile):
         ----------
         cls : TYPE
             DESCRIPTION.
-        inputfile : inputfile.InputFile
+        inputfile : os.PathLike
             MCNP input file containing the material section.
 
         Returns

tests/.coverage

@@ -102,7 +102,6 @@ def test_change_density(self):
         newinp = deepcopy(self.testInput)
         density = 1
         newinp.change_density(density, cellidx=2)
-        cellcard = newinp.get_card_byID('cells', '2')
         modline = '2    13  {}  -128 129 1   -2         \n'.format(str(density))
         assert newinp.cards['cells'][2].lines == modline
 
@@ -273,14 +272,15 @@ def test_add_track_contribution(self):
         card = newinp.get_card_byID('settings', 'FU124')
         assert card.lines[0] == 'FU124 0 1001 1002\n'
 
+
 class TestD1S5_Input:
     inp = D1S5_InputFile.from_text(DIS_INP_PATH)
     irrad = IrradiationFile.from_text(IRRAD_PATH)
     react = ReactionFile.from_text(REACT_PATH)
 
     lm = LibManager(XSDIR_FILE, activationfile=ACTIVATION_FILE,
                     isotopes_file=ISOTOPES_FILE)
-    
+
     def test_add_stopCard(self):
         precision = 'F5-0.001'
         ctme = 500
@@ -298,5 +298,3 @@ def test_add_stopCard(self):
             assert False
         except ValueError:
             assert True
-
-

tests/inputfile_test.py

@@ -37,13 +37,15 @@
 XSDIR_FILE = os.path.join(cp, 'TestFiles', 'libmanager', 'xsdir')
 ISOTOPES_FILE = os.path.join(modules_path, 'Isotopes.txt')
 
+
 class SessionMockup:
-    
+
     def __init__(self):
         self.lib_manager = LibManager(XSDIR_FILE,
                                       activationfile=ACTIVATION_FILE,
                                       isotopes_file=ISOTOPES_FILE)
 
+
 class TestUtilities:
     session = SessionMockup()
     inputfile = os.path.join(cp, 'TestFiles', 'utilitiesgui', 'test.i')
@@ -58,7 +60,7 @@ def test_translate_input(self):
                                   outpath=self.outpath)
         shutil.rmtree(self.outpath)
         assert ans
-    
+
     def test_print_libraries(self):
         """
         This is properly tested in libmanager_test
@@ -101,7 +103,7 @@ def test_generate_material(self):
         txt_equal(fileA, fileB)
 
         shutil.rmtree(outpath)
-    
+
     def test_switch_fractions(self):
 
         # Switches are properly tested in matreader
@@ -111,7 +113,7 @@ def test_switch_fractions(self):
                              outpath=self.outpath)
         shutil.rmtree(self.outpath)
         assert True
-    
+
     def test_change_ACElib_suffix(self, monkeypatch):
         acefolder = os.path.join(cp, 'TestFiles', 'utilitiesgui', 'ACEchange',
                                  '99c')
@@ -133,7 +135,7 @@ def test_change_ACElib_suffix(self, monkeypatch):
                         assert False
                     break
         shutil.rmtree(newfolder)
-    
+
     def test_get_reaction_file(self, monkeypatch):
         # The correctness of the file is already tested in parserD1S
         filepath = os.path.join(cp, 'TestFiles', 'utilitiesgui', 'd1stest.i')
@@ -143,13 +145,22 @@ def test_get_reaction_file(self, monkeypatch):
         shutil.rmtree(self.outpath)
         assert True
 
+    def test_input_with_option(self, monkeypatch):
+        msg = ''
+        options = ['option1', 'option2']
+        inputs = iter(['wrongoption', 'option1'])
+        monkeypatch.setattr('builtins.input', lambda msg: next(inputs))
+        valid_input = uty.input_with_options(msg, options)
+        assert valid_input == 'option1'
+
 
 def excel_equal(fileA, fileB, n_sheets):
     for i in range(n_sheets):
         sheetA = pd.read_excel(fileA, sheet_name=i)
         sheetB = pd.read_excel(fileB, sheet_name=i)
         assert sheetA.equals(sheetB)
 
+
 def txt_equal(fileA, fileB):
     with open(fileA, 'r') as infileA, open(fileB, 'r') as infileB:
         for lineA, lineB in zip(infileA, infileB):

tests/utilitiesgui_test.py

@@ -0,0 +1,61 @@
+"""
+@author: Davide Laghi
+
+Copyright 2021, the JADE Development Team. All rights reserved.
+
+This file is part of JADE.
+
+JADE is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+JADE is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with JADE.  If not, see <http://www.gnu.org/licenses/>.
+"""
+
+from xsdirpyne import Xsdir
+
+import sys
+import os
+
+cp = os.path.dirname(os.path.abspath(__file__))
+modules_path = os.path.dirname(cp)
+sys.path.insert(1, modules_path)
+
+XSDIR_FILE = os.path.join(cp, 'TestFiles', 'libmanager', 'xsdir')
+
+
+class TestXsdir:
+    """No need to test the entire class since it is from Pyne distro.
+    New functionalities or modifications will be tested instead
+    """
+
+    xsdir = Xsdir(XSDIR_FILE)
+
+    def test_find_table(self):
+        names = ['1001.31c', '20000.21c', '8016.00c']
+        for zaidname in names:
+            ans = self.xsdir.find_table(zaidname, mode='exact')
+            assert ans
+
+        zaidname = '1001'
+        tables = self.xsdir.find_table(zaidname, mode='default')
+        assert len(tables) == 43
+        assert tables[0].name == '1001.03c'
+
+        zaidname = '1001'
+        libs = self.xsdir.find_table(zaidname, mode='default-fast')
+        assert len(libs) == 43
+        assert libs[0] == '03c'
+
+    def test_find_zaids(self):
+        lib = '21c'
+        zaids = self.xsdir.find_zaids(lib)
+        print(zaids)
+        assert len(zaids) == 80

tests/xsdirpyne_test.py

@@ -31,6 +31,7 @@
 or implied, of the stakeholders of the PyNE project or the employers of PyNE developers.
 """
 import os
+from typing import List, Tuple
 
 
 class Xsdir(object):
@@ -72,6 +73,16 @@ def __init__(self, filename):
 
         self.read()
 
+        # It is useful to have a list of the available tables names to be
+        # computed only once at initializations
+        tablenames = []
+        for table in self:
+            name = table.name
+            zaidname = name[:-4]
+            libname = name[-3:]
+            tablenames.append((zaidname, libname))
+        self.tablenames = tablenames
+
     def read(self):
         """Populate the Xsdir object by reading the file.
         """
@@ -142,9 +153,14 @@ def read(self):
             if len(words) > 10:
                 table.ptable = (words[10] == 'ptable')
 
-
-    def find_table(self, name, mode = 'default'):
+    def find_table(self, name, mode='default'):
         """Find all tables for a given ZIAD.
+        *Modified for JADE, a bug was corrected since table.name do not
+        find natural zaids.
+
+        mode: 'default' default behaviour
+              'exact' check also the library
+              'default-fast' accelerated loop giving only the lib names
 
         Parameters
         ----------
@@ -155,31 +171,43 @@ def find_table(self, name, mode = 'default'):
         -------
         tables : list
             All XsdirTable objects for a given ZIAD.
-            
-        mode: 'default' default behaviour
-              'exact' check also the library
         """
         if mode == 'exact':
-            toreturn = False
-        else:
+            # Faster, checks for the exact name
+            ans = self._exact_loop(name, self.tablenames)
+
+        elif mode == 'default':
+            # Checks all available libraries for the zaid
             tables = []
-            
-        for table in self:
-            #if name in table.name:#BUG! for natural zaids!!!
-            ################# correction ####################
-            tablename = table.name.split('.')[0]
-            if mode == 'default':
-                if name == tablename:
+            for table in self:
+                # tablename = table.name.split('.')[0]
+                if name == table.name[:-4]:
                     tables.append(table)
-            elif mode == 'exact':
-                if name == table.name:
-                    toreturn = True
-                    break
-            ################# end correction ####################
-        if mode == 'exact':
-            return toreturn
-        else:
-            return tables
+
+            ans = tables
+
+        elif mode == 'default-fast':
+            ans = self._all_fast_loop(name, self.tablenames)
+
+        return ans
+
+    @staticmethod
+    def _exact_loop(name: str, tablenames: List[Tuple[str, str]]) -> bool:
+        print(name)
+        for zaidname, libname in tablenames:
+            if name == zaidname+'.'+libname:
+                return True
+
+        return False
+
+    @staticmethod
+    def _all_fast_loop(name: str, tablenames: List[Tuple[str, str]]) -> List[str]:
+        libs = []
+        for zaidname, libname in tablenames:
+            if name == zaidname:
+                libs.append(libname)
+
+        return libs
 
 #################  Added by Davide Laghi ###############################  
     def find_zaids(self, lib):