refactor(load methods): avoid ResourceWarning with unclosed files (#673)

* Nam load function already opens each file, so pass the filehandle
  rather than the filename to each load operation
* For each load method, only close the file if it was opened by the method

flopy/modflow/mf.py

@@ -728,14 +728,14 @@ def load(f, version='mf2005', exe_name='mf2005.exe', verbose=False,
         if dis_key is None:
             raise KeyError('discretization entry not found in nam file')
         disnamdata = ext_unit_dict[dis_key]
-        dis = disnamdata.package.load(disnamdata.filename, ml,
+        dis = disnamdata.package.load(disnamdata.filehandle, ml,
                                       ext_unit_dict=ext_unit_dict,
                                       check=False)
         files_successfully_loaded.append(disnamdata.filename)
         if ml.verbose:
             print('   {:4s} package load...success'.format(dis.name[0]))
         assert ml.pop_key_list.pop() == dis_key
-        ext_unit_dict.pop(dis_key)
+        ext_unit_dict.pop(dis_key).filehandle.close()
 
         dis.start_datetime = ml._start_datetime
 
@@ -774,11 +774,11 @@ def load(f, version='mf2005', exe_name='mf2005.exe', verbose=False,
                     if forgive:
                         try:
                             if "check" in package_load_args:
-                                item.package.load(item.filename, ml,
+                                item.package.load(item.filehandle, ml,
                                                   ext_unit_dict=ext_unit_dict,
                                                   check=False)
                             else:
-                                item.package.load(item.filename, ml,
+                                item.package.load(item.filehandle, ml,
                                                   ext_unit_dict=ext_unit_dict)
                             files_successfully_loaded.append(item.filename)
                             if ml.verbose:
@@ -795,11 +795,11 @@ def load(f, version='mf2005', exe_name='mf2005.exe', verbose=False,
                             files_not_loaded.append(item.filename)
                     else:
                         if "check" in package_load_args:
-                            item.package.load(item.filename, ml,
+                            item.package.load(item.filehandle, ml,
                                               ext_unit_dict=ext_unit_dict,
                                               check=False)
                         else:
-                            item.package.load(item.filename, ml,
+                            item.package.load(item.filehandle, ml,
                                               ext_unit_dict=ext_unit_dict)
                         files_successfully_loaded.append(item.filename)
                         if ml.verbose:
@@ -840,7 +840,9 @@ def load(f, version='mf2005', exe_name='mf2005.exe', verbose=False,
         for key in ml.pop_key_list:
             try:
                 ml.remove_external(unit=key)
-                ext_unit_dict.pop(key)
+                item = ext_unit_dict.pop(key)
+                if hasattr(item.filehandle, 'close'):
+                    item.filehandle.close()
             except KeyError:
                 if ml.verbose:
                     msg = 'Warning: external file unit {} '.format(key) + \

flopy/modflow/mfbas.py

@@ -302,9 +302,11 @@ def load(f, model, ext_unit_dict=None, check=True, **kwargs):
             ncol = None
 
         # open the file if not already open
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
+
         # dataset 0 -- header
         while True:
             line = f.readline()
@@ -339,7 +341,8 @@ def load(f, model, ext_unit_dict=None, check=True, **kwargs):
         # dataset 4 -- strt
         strt = Util3d.load(f, model, (nlay, nrow, ncol), np.float32, 'strt',
                            ext_unit_dict)
-        f.close()
+        if openfile:
+            f.close()
 
         # set package unit number
         unitnumber = None

flopy/modflow/mfbcf.py

@@ -269,7 +269,8 @@ def load(f, model, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading bcf package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
 
@@ -406,6 +407,9 @@ def load(f, model, ext_unit_dict=None):
                                 ext_unit_dict)
                 wetdry[k] = t
 
+        if openfile:
+            f.close()
+
         # set package unit number
         unitnumber = None
         filenames = [None, None]

flopy/modflow/mfde4.py

@@ -239,9 +239,11 @@ def load(f, model, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading de4 package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
+
         # read dataset 0 -- header
         while True:
             line = f.readline()
@@ -277,6 +279,9 @@ def load(f, model, ext_unit_dict=None):
             hclose = float(line[30:40].strip())
             iprd4 = int(line[40:50].strip())
 
+        if openfile:
+            f.close()
+
         # set package unit number
         unitnumber = None
         filenames = [None]

flopy/modflow/mfdis.py

@@ -859,9 +859,11 @@ def load(f, model, ext_unit_dict=None, check=True):
         if model.verbose:
             sys.stdout.write('loading dis package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
+
         # dataset 0 -- header
         header = ''
         while True:
@@ -1000,6 +1002,9 @@ def load(f, model, ext_unit_dict=None, check=True):
             tsmult.append(a3)
             steady.append(a4)
 
+        if openfile:
+            f.close()
+
         # set package unit number
         unitnumber = None
         filenames = [None]

flopy/modflow/mfdisu.py

@@ -459,7 +459,8 @@ def load(f, model, ext_unit_dict=None, check=False):
             print(msg)
             model.version = 'mfusg'
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
 
@@ -656,6 +657,9 @@ def load(f, model, ext_unit_dict=None, check=False):
             print('   TSMULT {}'.format(tsmult))
             print('   STEADY {}'.format(steady))
 
+        if openfile:
+            f.close()
+
         # set package unit number
         unitnumber = None
         filenames = [None]

flopy/modflow/mfevt.py

@@ -226,9 +226,11 @@ def load(f, model, nper=None, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading evt package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
+
         # Dataset 0 -- header
         while True:
             line = f.readline()
@@ -331,6 +333,9 @@ def load(f, model, nper=None, ext_unit_dict=None):
                     current_ievt = t
                 ievt[iper] = current_ievt
 
+        if openfile:
+            f.close()
+
         # create evt object
         args = {}
         if ievt:

flopy/modflow/mffhb.py

@@ -423,7 +423,8 @@ def load(f, model, nper=None, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading fhb package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
 
@@ -668,6 +669,9 @@ def load(f, model, nper=None, ext_unit_dict=None):
                         current[n] = tuple(raw[:len(dtype.names)])
                     ds8.append(current.copy())
 
+        if openfile:
+            f.close()
+
         # determine specified unit number
         unitnumber = None
         filenames = [None, None]

flopy/modflow/mfflwob.py

@@ -389,7 +389,8 @@ def load(f, model, ext_unit_dict=None, check=True):
         if model.verbose:
             sys.stdout.write('loading flwob package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
 
@@ -483,8 +484,8 @@ def load(f, model, ext_unit_dict=None, check=True):
         column = np.array(column) - 1
         factor = np.array(factor)
 
-        # close the file
-        f.close()
+        if openfile:
+            f.close()
 
         # get ext_unit_dict if none passed
         if ext_unit_dict is None:

flopy/modflow/mfgage.py

@@ -294,7 +294,8 @@ def load(f, model, nper=None, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading gage package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             if sys.version_info[0] == 2:
                 f = open(filename, 'r')
@@ -351,6 +352,9 @@ def load(f, model, nper=None, ext_unit_dict=None):
                         files.append(relpth)
                         break
 
+        if openfile:
+            f.close()
+
         # determine specified unit number
         unitnumber = None
         filenames = []

flopy/modflow/mfgmg.py

@@ -319,9 +319,11 @@ def load(f, model, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading gmg package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
+
         # dataset 0 -- header
         while True:
             line = f.readline()
@@ -358,8 +360,8 @@ def load(f, model, ext_unit_dict=None):
         t = line.strip().split()
         relax = float(t[0])
 
-        # close the open file
-        f.close()
+        if openfile:
+            f.close()
 
         # determine specified unit number
         unitnumber = None

flopy/modflow/mfhfb.py

@@ -262,9 +262,11 @@ def load(f, model, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading hfb6 package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
+
         # dataset 0 -- header
         while True:
             line = f.readline()
@@ -360,6 +362,10 @@ def load(f, model, ext_unit_dict=None):
                 else:
                     bnd_output = stack_arrays((bnd_output, par_current),
                                               asrecarray=True, usemask=False)
+
+        if openfile:
+            f.close()
+
         # set package unit number
         unitnumber = None
         filenames = [None]

flopy/modflow/mfhob.py

@@ -319,9 +319,11 @@ def load(f, model, ext_unit_dict=None, check=True):
         if model.verbose:
             sys.stdout.write('loading hob package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
+
         # dataset 0 -- header
         while True:
             line = f.readline()
@@ -417,8 +419,8 @@ def load(f, model, ext_unit_dict=None, check=True):
             if nobs == nh:
                 break
 
-        # close the file
-        f.close()
+        if openfile:
+            f.close()
 
         # set package unit number
         unitnumber = None

flopy/modflow/mfhyd.py

@@ -299,7 +299,8 @@ def load(f, model, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading hydmod package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             f = open(filename, 'r')
 
@@ -327,8 +328,8 @@ def load(f, model, ext_unit_dict=None):
             obs['yl'][idx] = float(t[5])
             obs['hydlbl'][idx] = t[6].strip()
 
-        # close the file
-        f.close()
+        if openfile:
+            f.close()
 
         # set package unit number
         unitnumber = None

flopy/modflow/mflak.py

@@ -611,7 +611,8 @@ def load(f, model, nper=None, ext_unit_dict=None):
         if model.verbose:
             sys.stdout.write('loading lak package file...\n')
 
-        if not hasattr(f, 'read'):
+        openfile = not hasattr(f, 'read')
+        if openfile:
             filename = f
             if sys.version_info[0] == 2:
                 f = open(filename, 'r')
@@ -789,6 +790,9 @@ def load(f, model, nper=None, ext_unit_dict=None):
                     ds9[n] = tds
                 flux_data[iper] = ds9
 
+        if openfile:
+            f.close()
+
         # convert lake data to Transient3d objects
         lake_loc = Transient3d(model, (nlay, nrow, ncol), np.int32,
                                lake_loc, name='lakarr_')