From 6e65b3e9b7220c7e4f86f70b90e07cd2e07f9614 Mon Sep 17 00:00:00 2001
From: ehinrichs <54997013+ehinrichs@users.noreply.github.com>
Date: Fri, 24 May 2024 08:26:11 -0600
Subject: [PATCH 1/4] Update to fehmpytests

Update to fehmpytests
---
 fehmpytests/fehmpytests.py | 44 +++++++++++++++++++++++++++-----------
 1 file changed, 32 insertions(+), 12 deletions(-)

diff --git a/fehmpytests/fehmpytests.py b/fehmpytests/fehmpytests.py
index f66052cf..c3efaeeb 100755
--- a/fehmpytests/fehmpytests.py
+++ b/fehmpytests/fehmpytests.py
@@ -618,14 +618,25 @@ def test_case(self, name, parameters={}):
         filenames = glob.glob(os.path.join('input','control','*.files'))
         subcases  = []
         for filename in filenames:
-            subcase = re.sub(os.path.join('input','control',''), '', filename)
-            subcase = re.sub('.files', '', subcase)
+            print('\nfilename: ', filename)
+
+            path = os.path.join('input', 'control', ' ')
+            if os.name == 'nt':  # For Windows
+                subcase = re.sub(r'input[\\/]', '', filename)
+                subcase = re.sub(r'control[\\/]', '', subcase)
+                subcase = re.sub(r'\.files$', '', subcase)
+            else:  # For Unix-based systems
+                subcase = re.sub(os.path.join('input','control',''), '', filename)
+                subcase = re.sub('.files', '', subcase)
+            #print('subcase: ', subcase)
             
             #File named 'fehmn.files' to be used for tests with single case.
             if subcase != 'fehmn':
                 subcases.append(subcase)
+                #print('append subases')
             else:
                 subcases = ['']
+                #print('broken subases')
                 break
                 
         try:
@@ -639,25 +650,34 @@ def test_case(self, name, parameters={}):
                 os.chdir( output_dir )
                 filetypes = ['*.avs','*.csv','*.his','*.out','*.trc','*.ptrk']
                 test_flag = False
+                
                 for filetype in filetypes:
                     parameters['filetype'] = filetype
-                    #Check to make sure there are files of this type.
-                    if len(glob.glob(os.path.join('..','compare','')+'*'+subcase+filetype)) > 0: 
-                        test_method = \
-                          self._test_template(filetype, subcase, parameters)
+                    compare_pattern = (os.path.join('..', 'compare', '*' )+ subcase + filetype)
+                    found_files = glob.glob(compare_pattern)
+                    print('\nsubcase: ', subcase)
+
+                    print('Checking for files with pattern: ', compare_pattern)
+                    print('Found files: ', found_files)
+                    print('Number of found files: ', len(found_files))
+
+                    if len(found_files) > 0:
+                        test_method = self._test_template(filetype, subcase, parameters)
                         test_method()
+                        print('Test method executed for filetype: ', filetype)
                         test_flag = True
-                os.chdir( '..' )
+                    else:
+                        print('Test method NOT executed for filetype: ', filetype)
+
+                os.chdir('..')
                 if not test_flag:
-                    #Write to fail log if switch is on.
                     if self.log:
-                        line = '\nFailed at subcase:'+subcase
-                        line = line+' filetype:'+filetype
+                        line = f'\nFailed at subcase: {subcase} filetype: {filetype}'
                         self.fail_log.write(line)
                     self.fail("Missing any valid comparison files, no test performed")
-                                        
+
         finally:
-            #Allows other tests to be performed after exception.
+            # Allows other tests to be performed after exception.
             os.chdir(self.maindir)
             
     def _test_template(self, filetype, subcase, parameters={}):

From 0929a3982fadf620e7939474496e633af83dd33b Mon Sep 17 00:00:00 2001
From: ehinrichs <54997013+ehinrichs@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:03:55 -0600
Subject: [PATCH 2/4] Updated Fehmpytests

Updated Fehmpytests
---
 fehmpytests/fehmpytests.py | 28 ++++++++------
 fehmpytests/fpost.py       | 75 +++++++++++++++++++++++++++++---------
 2 files changed, 75 insertions(+), 28 deletions(-)

diff --git a/fehmpytests/fehmpytests.py b/fehmpytests/fehmpytests.py
index c3efaeeb..5eba7940 100755
--- a/fehmpytests/fehmpytests.py
+++ b/fehmpytests/fehmpytests.py
@@ -616,9 +616,10 @@ def test_case(self, name, parameters={}):
         
         #Search for fehmn control files and extract subcases.
         filenames = glob.glob(os.path.join('input','control','*.files'))
+        #print('filenames: ', filenames)
         subcases  = []
         for filename in filenames:
-            print('\nfilename: ', filename)
+            #print('\nfilename: ', filename)
 
             path = os.path.join('input', 'control', ' ')
             if os.name == 'nt':  # For Windows
@@ -636,7 +637,7 @@ def test_case(self, name, parameters={}):
                 #print('append subases')
             else:
                 subcases = ['']
-                #print('broken subases')
+                #print('broken subcases')
                 break
                 
         try:
@@ -655,19 +656,19 @@ def test_case(self, name, parameters={}):
                     parameters['filetype'] = filetype
                     compare_pattern = (os.path.join('..', 'compare', '*' )+ subcase + filetype)
                     found_files = glob.glob(compare_pattern)
-                    print('\nsubcase: ', subcase)
 
-                    print('Checking for files with pattern: ', compare_pattern)
-                    print('Found files: ', found_files)
-                    print('Number of found files: ', len(found_files))
+                    #print('Checking for files with pattern: ', compare_pattern)
+                    #print('Found files: ', found_files)
+                    #print('Number of found files: ', len(found_files))
 
                     if len(found_files) > 0:
                         test_method = self._test_template(filetype, subcase, parameters)
                         test_method()
-                        print('Test method executed for filetype: ', filetype)
+                        #print('Test method executed for filetype: ', filetype)
                         test_flag = True
                     else:
-                        print('Test method NOT executed for filetype: ', filetype)
+                        #print('Test method NOT executed for filetype: ', filetype)
+                        pass
 
                 os.chdir('..')
                 if not test_flag:
@@ -718,7 +719,7 @@ def contour_case():
             f_dif = fpost.fdiff(f_new, f_old)
                 
             msg = 'Incorrect %s at time %s.'
-            
+
             #If no pre-specified times, grab them from f_dif.
             if len(values['times']) == 0:
                 times = f_dif.times
@@ -734,6 +735,7 @@ def contour_case():
             #Check the variables at each time for any significant differences.
             test_flag = False
             for t in times: 
+                #print(subcase)
                 #Its possible some times do not have all variables in f_dif.
                 for v in np.intersect1d(variables, list(f_dif[t].keys())):
                     #Measure the difference into a single quantity.
@@ -749,6 +751,7 @@ def contour_case():
                             float(len(f_dif[t][v]))
                     }[test_measure]
                     try:
+                       # print('true? ', difference, '<', mxerr, '=', difference<mxerr)
                         self.assertTrue(difference<mxerr, msg%(v, t))
                         test_flag = True
                     except AssertionError as e:
@@ -765,7 +768,7 @@ def contour_case():
                 self.fail("Missing common nodes in compare and output contour files, no test performed")
         def history_case():
             #Find the difference between the old and new
-            f_old = fpost.fhistory(os.path.join('..','compare','*')+subcase+filetype) 
+            f_old = fpost.fhistory(os.path.join('..','compare','*')+subcase+filetype)
             f_new = fpost.fhistory('*'+subcase+filetype)
             f_dif = fpost.fdiff(f_new, f_old)
 
@@ -991,11 +994,13 @@ def _run_fehm(self, subcase):
         
         #Find the control file for the test-case or for the subcase. 
         if subcase == '':
+            #print('subcase empty assume fehm at: \n',  os.path.join('..','input','control','fehmn.files'))
             filesfile = os.path.join('..','input','control','fehmn.files')
         else:
             filesfile = os.path.join('..','input','control',subcase+'.files')
             
         evalstr = exe+' '+filesfile
+        #print('evalstr: ', evalstr)
         
         with open(os.devnull, "w") as f:
             call(evalstr, shell=True, stdout=f)
@@ -1028,7 +1033,8 @@ def _run_fehm(self, subcase):
             errstr = open( errfile, 'r' ).read()
         else: 
             errstr = ''
-        # Change to maindir in case assertTrue fails    
+        # Change to maindir in case assertTrue fails 
+        #print('CWD: ',  os.getcwd() )   
         curdir = os.getcwd() 
         os.chdir(self.maindir)
         
diff --git a/fehmpytests/fpost.py b/fehmpytests/fpost.py
index 49c5d849..74fdcc3c 100755
--- a/fehmpytests/fpost.py
+++ b/fehmpytests/fpost.py
@@ -1026,13 +1026,38 @@ def read(self,filename):                        # read contents of file
         '''
         from glob import glob
         import re
+        #print('\n*********************************************\nFilename as imported from fehmpytests fhistory: ', filename)
         glob_pattern = re.sub(r'\[','[[]',filename)
         glob_pattern = re.sub(r'(?<!\[)\]','[]]', glob_pattern)
         files=glob(glob_pattern)
         configured=False
         for i,fname in enumerate(files):
+            #print('Names of files: \n', files)
             #if self._verbose:
-            #   print(fname)
+            if '..' in fname:
+                #print('fname is in compare: ', fname)
+                if os.name == 'nt':  # For Windows
+                    tmp=fname.split('\\')[-1]
+                else:
+                    tmp = fname.rsplit('/', 1)[0]
+                #print('tmp: ', tmp)
+                if os.path.exists(tmp):
+                    #print('valid comparison of: ', fname, ' and ', tmp)
+                    pass
+                else:
+                    #print('No valid comparison file. Skipping file: ', fname)
+                    continue
+            elif '..' not in fname:
+                #print('fname is in output: ', fname)
+                path=os.path.join('..', 'compare', '')+fname
+                #print('PATH', path)
+                if os.path.exists(path):
+                    #print('valid comparison of: ', fname, ' and ', path)
+                    pass
+                else:
+                   # print('No valid comparison file. Skipping file: ', fname)
+                    continue
+
             with open(fname, 'r') as self._file:
                 header=self._file.readline()
                 if header.strip()=='': continue             # empty file
@@ -1050,15 +1075,21 @@ def read(self,filename):                        # read contents of file
                 elif self._format=='surf': 
                     self._setup_headers_surf(header)
                 elif self._format=='default': 
+                    #print('headers1', header)
                     header=self._file.readline()
+                    #print('headers2', header)
                     header=self._file.readline()
+                    #print('headers3', header)
                     if header.strip()=='': continue         # empty file
                     i = 0; sum_file = False
-                    while not header.startswith('Time '): 
+                    while 'Time' not in header: 
                         header=self._file.readline()
+                        #print('iteratin through i = ',i , header)
                         i = i+1
                         if i==10: sum_file=True; break
-                    if sum_file: continue
+                    if sum_file: 
+                        #print('final interation' , header)
+                        continue
                     self._setup_headers_default(header)
                 else: print('Unrecognised format');return
                 if not configured:
@@ -1069,7 +1100,13 @@ def read(self,filename):                        # read contents of file
                 elif self._format=='surf':
                     self._read_data_surf(fname.split('_')[-2])
                 elif self._format=='default':
-                    self._read_data_default(fname.split('_')[-1].split('.')[0])
+                    if 'temp' in fname:
+                        #print('fname with temp:', fname.split('_')[1].split('.')[0])
+                        self._read_data_default(fname.split('_')[1].split('.')[0])
+                    else: 
+                        #print('fname without temp:', fname.split('_')[-1].split('.')[0])
+                        self._read_data_default(fname.split('_')[-1].split('.')[0])
+                #self._get_information()
                 #self._file.close()
     def _detect_format(self,header):
         if header.startswith('TITLE'):
@@ -1113,12 +1150,15 @@ def _read_data_surf(self,var_key):
         self._data[hist_var_names[var_key]] = dict([(node,data[:,icol+1]) for icol,node in enumerate(self.nodes)])
     def _read_data_default(self,var_key):
         self._variables.append(hist_var_names[var_key])
+        #print('These are the variables: ', self._variables)
         lns = self._file.readlines()
+        #print('lns: ', lns)
         data = []
         for ln in lns: data.append([float(d) for d in ln.strip().split()])
         data = np.array(data)
         if data[-1,0]<data[-2,0]: data = data[:-1,:]
         self._times = np.array(data[:,0])
+        #print(' TIMES ', self._times)
         self._data[hist_var_names[var_key]] = dict([(node,data[:,icol+1]) for icol,node in enumerate(self.nodes)])
     def _get_variables(self): return self._variables
     variables = property(_get_variables)#: (*lst[str]*) List of variables for which output data are available.
@@ -1133,19 +1173,19 @@ def _get_times(self): return np.sort(self._times)
     times = property(_get_times)    #: (*lst[fl64]*) List of times (in seconds) for which output data are available.
     def _get_nodes(self): return self._nodes
     nodes = property(_get_nodes)    #: (*lst[fl64]*) List of node indices for which output data are available.
-    #def _get_information(self):
-    #    print('FEHM history output - format '+self._format)
-    #    print(' call format: fhistory[variable][node][time_index]')
-    #    prntStr = ' nodes: '
-    #    for nd in self.nodes: prntStr += str(nd)+', '
-    #    print(prntStr)
-    #    prntStr =  '    times ('+str(len(self.times))+'): '
-    #    for time in self.times: prntStr += str(time)+', '
-    #    print(prntStr[:-2]+' days')
-    #    prntStr = ' variables: '
-    #    for var in self.variables: prntStr += str(var)+', '
-    #    print(prntStr)
-    #what = property(_get_information) #:(*str*) Print out information about the fhistory object.
+    def _get_information(self):
+        print('FEHM history output - format '+self._format)
+        print('call format: fhistory[variable][node][time_index]')
+        prntStr = ' nodes: '
+        for nd in self.nodes: prntStr += str(nd)+', '
+        print(prntStr)
+        prntStr =  'times \n('+str(len(self.times))+'): '
+        for time in self.times: prntStr += str(time)+', '
+        print(prntStr[:-2]+' days')
+        prntStr = 'variables: '
+        for var in self.variables: prntStr += str(var)+', '
+        print(prntStr)
+    what = property(_get_information) #:(*str*) Print out information about the fhistory object.
 class fzoneflux(fhistory):                  # Derived class of fhistory, for zoneflux output
     '''Zone flux history output information object.
     '''
@@ -1409,6 +1449,7 @@ def fdiff( in1, in2, format='diff', times=[], variables=[], components=[], nodes
         return
     if isinstance(in1, fcontour) or isinstance(in1, fhistory) or 'foutput' in str(in1.__class__):
         # Find common timesclear
+        #print('from diff', in1.times , in2.times)
         t = np.intersect1d(in1.times,in2.times)
         if len(t) == 0:
             print("ERROR: fpost object times do not have any matching values")

From ed23623fefb0b9b0ff3bda1a391ec5d2dfd32f6c Mon Sep 17 00:00:00 2001
From: ehinrichs <54997013+ehinrichs@users.noreply.github.com>
Date: Tue, 4 Jun 2024 11:56:28 -0600
Subject: [PATCH 3/4] Update fpost

Update fpost
---
 fehmpytests/fpost.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/fehmpytests/fpost.py b/fehmpytests/fpost.py
index 74fdcc3c..a31ee29c 100755
--- a/fehmpytests/fpost.py
+++ b/fehmpytests/fpost.py
@@ -1045,7 +1045,7 @@ def read(self,filename):                        # read contents of file
                     #print('valid comparison of: ', fname, ' and ', tmp)
                     pass
                 else:
-                    #print('No valid comparison file. Skipping file: ', fname)
+                    print('\n    **WARNING**   The file ', tmp , ' is in compare, but not in output. Skipping file...')
                     continue
             elif '..' not in fname:
                 #print('fname is in output: ', fname)
@@ -1055,7 +1055,7 @@ def read(self,filename):                        # read contents of file
                     #print('valid comparison of: ', fname, ' and ', path)
                     pass
                 else:
-                   # print('No valid comparison file. Skipping file: ', fname)
+                    #print('\n    **WARNING**   The file ', fname , 'is in output, but doesn''t have a valid compare file. Skipping file...')
                     continue
 
             with open(fname, 'r') as self._file:

From 123ccf9077f3dc7c0ba0bbad80724be4a4293666 Mon Sep 17 00:00:00 2001
From: ehinrichs <54997013+ehinrichs@users.noreply.github.com>
Date: Tue, 4 Jun 2024 13:38:49 -0600
Subject: [PATCH 4/4] Update to fpost

Update to fpost
---
 fehmpytests/fpost.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fehmpytests/fpost.py b/fehmpytests/fpost.py
index a31ee29c..f6dfde08 100755
--- a/fehmpytests/fpost.py
+++ b/fehmpytests/fpost.py
@@ -1039,7 +1039,7 @@ def read(self,filename):                        # read contents of file
                 if os.name == 'nt':  # For Windows
                     tmp=fname.split('\\')[-1]
                 else:
-                    tmp = fname.rsplit('/', 1)[0]
+                    tmp = fname.split('/')[-1]
                 #print('tmp: ', tmp)
                 if os.path.exists(tmp):
                     #print('valid comparison of: ', fname, ' and ', tmp)