fix(internal): Flopy fixed to correctly reads in internal keyword whe…

…n no multiplier supplied. Also, header line added to package files. (#962) * fix(internal): Flopy fixed to correctly reads in internal keyword in the case where there is no multiplier supplied. * feat(header): Flopy feature added that by default adds a header line to each package file indicating that it was generated by flopy. Option called "write_headers" added to simulations that allows users to turn on and off headers. * fix(package/simulation): reformatted with "black --line-length 79"
modflowpy · Aug 13, 2020 · af28ed8 · af28ed8
1 parent 573da13
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diff --git a/autotest/t504_test.py b/autotest/t504_test.py
@@ -49,7 +49,8 @@ def test001a_tharmonic():
 
     # load simulation
     sim = MFSimulation.load(model_name, 'mf6', exe_name, pth,
-                            verbosity_level=0, verify_data=True)
+                            verbosity_level=0, verify_data=True,
+                            write_headers=False)
     sim.simulation_data.mfpath.set_sim_path(run_folder)
 
     # write simulation to new location

diff --git a/autotest/t505_test.py b/autotest/t505_test.py
@@ -98,7 +98,7 @@ def np001():
 
     # create simulation
     sim = MFSimulation(sim_name=test_ex_name, version='mf6', exe_name=exe_name,
-                       sim_ws=pth)
+                       sim_ws=pth, write_headers=False)
     tdis_rc = [(6.0, 2, 1.0), (6.0, 3, 1.0)]
     tdis_package = ModflowTdis(sim, time_units='DAYS', nper=1,
                                perioddata=[(2.0, 1, 1.0)])

diff --git a/examples/data/mf6/test036_twrihfb/twrihfb2015.rch b/examples/data/mf6/test036_twrihfb/twrihfb2015.rch
@@ -7,5 +7,20 @@ END Options
 
 BEGIN PERIOD 1
   RECHARGE
-    CONSTANT   0.30000000E-07
+    INTERNAL
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
+	  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08  3.00000000E-08
 END PERIOD
diff --git a/flopy/mf6/data/mfdatastorage.py b/flopy/mf6/data/mfdatastorage.py
@@ -1686,28 +1686,6 @@ def process_internal_line(self, arr_line):
         multiplier = self.get_default_mult()
         print_format = None
         if isinstance(arr_line, list):
-            if len(arr_line) < 2:
-                message = (
-                    'Data array "{}" contains an INTERNAL '
-                    "that is not followed by a multiplier in line "
-                    '"{}".'.format(
-                        self.data_dimensions.structure.name, " ".join(arr_line)
-                    )
-                )
-                type_, value_, traceback_ = sys.exc_info()
-                raise MFDataException(
-                    self.data_dimensions.structure.get_model(),
-                    self.data_dimensions.structure.get_package(),
-                    self.data_dimensions.structure.path,
-                    "processing internal data header",
-                    self.data_dimensions.structure.name,
-                    inspect.stack()[0][3],
-                    type_,
-                    value_,
-                    traceback_,
-                    message,
-                    self._simulation_data.debug,
-                )
             index = 1
             while index < len(arr_line):
                 if isinstance(arr_line[index], str):
@@ -1851,7 +1829,7 @@ def process_open_close_line(self, arr_line, layer, store=True):
                     except Exception as ex:
                         message = (
                             "Data array {} contains an OPEN/CLOSE "
-                            "with an invalid multiplier following the "
+                            "with an invalid factor following the "
                             '"factor" keyword.'
                             ".".format(data_dim.structure.name)
                         )

diff --git a/flopy/mf6/data/mffileaccess.py b/flopy/mf6/data/mffileaccess.py
@@ -787,27 +787,6 @@ def _load_layer(
                 )
         # if internal
         elif arr_line[0].upper() == "INTERNAL":
-            if len(arr_line) < 2:
-                message = (
-                    'Data array "{}" contains a INTERNAL that is not '
-                    "followed by a multiplier"
-                    ".".format(self.structure.name)
-                )
-                type_, value_, traceback_ = sys.exc_info()
-                raise MFDataException(
-                    self.structure.get_model(),
-                    self.structure.get_package(),
-                    self._path,
-                    "loading data layer from file",
-                    self.structure.name,
-                    inspect.stack()[0][3],
-                    type_,
-                    value_,
-                    traceback_,
-                    message,
-                    self._simulation_data.debug,
-                )
-
             try:
                 multiplier, print_format = storage.process_internal_line(
                     arr_line

diff --git a/flopy/mf6/mfpackage.py b/flopy/mf6/mfpackage.py
@@ -2,6 +2,7 @@
 import sys
 import errno
 import inspect
+import datetime
 import numpy as np
 from collections import OrderedDict
 
@@ -22,6 +23,7 @@
 from ..pakbase import PackageInterface
 from .data.mfdatautil import MFComment
 from ..utils.check import mf6check
+from ..version import __version__
 
 
 class MFBlockHeader(object):
@@ -249,7 +251,8 @@ class MFBlock(object):
     Attributes
     ----------
     block_headers : MFBlockHeaderIO
-        block header text (BEGIN/END), header variables, comments in the header
+        block header text (BEGIN/END), header variables, comments in the
+        header
     structure : MFBlockStructure
         structure describing block
     path : tuple
@@ -1007,7 +1010,8 @@ def _find_data_by_keyword(self, line, fd, initial_comment):
                 line, fd, self.block_headers[-1], initial_comment
             )
 
-            # see if first item's name indicates a reference to another package
+            # see if first item's name indicates a reference to another
+            # package
             package_info_list = self._get_package_info(dataset)
             if package_info_list is not None:
                 for package_info in package_info_list:
@@ -2108,6 +2112,19 @@ def write(self, ext_file_action=ExtFileAction.copy_relative_paths):
         # open file
         fd = open(package_file_path, "w")
 
+        # write flopy header
+        if self.simulation_data.write_headers:
+            dt = datetime.datetime.now()
+            header = (
+                "# File generated by Flopy version {} on {} at {}."
+                "\n".format(
+                    __version__,
+                    dt.strftime("%m/%d/%Y"),
+                    dt.strftime("%H:%M:%S"),
+                )
+            )
+            fd.write(header)
+
         # write blocks
         self._write_blocks(fd, ext_file_action)
 
@@ -2207,7 +2224,9 @@ def _write_blocks(self, fd, ext_file_action):
                 self.simulation_data.verbosity_level.value
                 >= VerbosityLevel.verbose.value
             ):
-                print("      writing block {}...".format(block.structure.name))
+                print(
+                    "      writing block {}.." ".".format(block.structure.name)
+                )
             # write block
             block.write(fd, ext_file_action=ext_file_action)
             block_num += 1
@@ -2257,12 +2276,12 @@ def plot(self, **kwargs):
 
         **kwargs : dict
             filename_base : str
-                Base file name that will be used to automatically generate file
-                names for output image files. Plots will be exported as image
-                files if file_name_base is not None. (default is None)
+                Base file name that will be used to automatically generate
+                file names for output image files. Plots will be exported as
+                image files if file_name_base is not None. (default is None)
             file_extension : str
-                Valid matplotlib.pyplot file extension for savefig(). Only used
-                if filename_base is not None. (default is 'png')
+                Valid matplotlib.pyplot file extension for savefig(). Only
+                used if filename_base is not None. (default is 'png')
             mflay : int
                 MODFLOW zero-based layer number to return.  If None, then all
                 all layers will be included. (default is None)

diff --git a/flopy/mf6/modflow/mfsimulation.py b/flopy/mf6/modflow/mfsimulation.py
@@ -128,8 +128,8 @@ def find_in_path(self, key_path, key_leaf):
                     data_item_structures = item.structure.data_item_structures
                     for data_item_struct in data_item_structures:
                         if data_item_struct.name == key_leaf:
-                            # found key_leaf as a data item name in the data in
-                            # the dictionary
+                            # found key_leaf as a data item name in the data
+                            # in the dictionary
                             return item, data_item_index
                         if data_item_struct.type != DatumType.keyword:
                             data_item_index += 1
@@ -221,6 +221,9 @@ class MFSimulationData(object):
         number of decimal points to write for a floating point number
     float_characters : int
         number of characters a floating point number takes up
+    write_headers: bool
+        when true flopy writes a header to each package file indicating that
+        it was created by flopy
     sci_note_upper_thres : float
         numbers greater than this threshold are written in scientific notation
     sci_note_lower_thres : float
@@ -242,6 +245,7 @@ def __init__(self, path):
         self.wrap_multidim_arrays = True
         self.float_precision = 8
         self.float_characters = 15
+        self.write_headers = True
         self._sci_note_upper_thres = 100000
         self._sci_note_lower_thres = 0.001
         self.fast_write = True
@@ -345,6 +349,9 @@ class MFSimulation(PackageContainer):
          the total memory for each simulation component. ALL means print
          information for each variable stored in the memory manager. NONE is
          default if memory_print_option is not specified.
+    write_headers: bool
+        when true flopy writes a header to each package file indicating that
+        it was created by flopy
 
     Attributes
     ----------
@@ -377,8 +384,8 @@ class MFSimulation(PackageContainer):
         file paths
     get_model : (model_name : string)
               : [MFModel]
-        returns the models in the simulation with a given model name, name file
-        name, or model type
+        returns the models in the simulation with a given model name, name
+        file name, or model type
     add_model : (model : MFModel, sln_group : integer)
         add model to the simulation
     remove_model : (model_name : string)
@@ -412,11 +419,13 @@ def __init__(
         continue_=None,
         nocheck=None,
         memory_print_option=None,
+        write_headers=True,
     ):
         super(MFSimulation, self).__init__(MFSimulationData(sim_ws), sim_name)
         self.simulation_data.verbosity_level = self._resolve_verbosity_level(
             verbosity_level
         )
+        self.simulation_data.write_headers = write_headers
         # verify metadata
         fpdata = mfstructure.MFStructure()
         if not fpdata.valid:
@@ -543,8 +552,10 @@ def __str__(self):
 
     def _get_data_str(self, formal):
         file_mgt = self.simulation_data.mfpath
-        data_str = "sim_name = {}\nsim_path = {}\nexe_name = " "{}\n\n".format(
-            self.name, file_mgt.get_sim_path(), self.exe_name
+        data_str = (
+            "sim_name = {}\nsim_path = {}\nexe_name = "
+            "{}\n"
+            "\n".format(self.name, file_mgt.get_sim_path(), self.exe_name)
         )
 
         for package in self._packagelist:
@@ -604,6 +615,7 @@ def load(
         verbosity_level=1,
         load_only=None,
         verify_data=False,
+        write_headers=True,
     ):
         """Load an existing model.
 
@@ -636,6 +648,9 @@ def load(
             example list: ['ic', 'maw', 'npf', 'oc', 'ims', 'gwf6-gwf6']
         verify_data : bool
             verify data when it is loaded. this can slow down loading
+        write_headers: bool
+            when true flopy writes a header to each package file indicating
+            that it was created by flopy
 
         Returns
         -------
@@ -647,7 +662,14 @@ def load(
 
         """
         # initialize
-        instance = cls(sim_name, version, exe_name, sim_ws, verbosity_level)
+        instance = cls(
+            sim_name,
+            version,
+            exe_name,
+            sim_ws,
+            verbosity_level,
+            write_headers=write_headers,
+        )
         verbosity_level = instance.simulation_data.verbosity_level
         instance.simulation_data.verify_data = verify_data
 
@@ -1099,7 +1121,8 @@ def register_ims_package(self, ims_file, model_list):
             # add ims package to simulation
             self._ims_files[ims_file.filename] = ims_file
 
-        # If ims file is being replaced, replace ims filename in solution group
+        # If ims file is being replaced, replace ims filename in
+        # solution group
         if pkg_with_same_name is not None and self._is_in_solution_group(
             pkg_with_same_name.filename, 1
         ):
@@ -1208,10 +1231,10 @@ def write_simulation(
 
         Parameters
             ext_file_action : ExtFileAction
-                defines what to do with external files when the simulation path
-                has changed.  defaults to copy_relative_paths which copies only
-                files with relative paths, leaving files defined by absolute
-                paths fixed.
+                defines what to do with external files when the simulation
+                path has changed.  defaults to copy_relative_paths which
+                copies only files with relative paths, leaving files defined
+                by absolute paths fixed.
             silent : bool
                 writes out the simulation in silent mode (verbosity_level = 0)
 
@@ -1244,7 +1267,8 @@ def write_simulation(
                 >= VerbosityLevel.normal.value
             ):
                 print(
-                    "  writing ims package {}...".format(ims_file._get_pname())
+                    "  writing ims package {}.."
+                    ".".format(ims_file._get_pname())
                 )
             ims_file.write(ext_file_action=ext_file_action)
 
@@ -2136,14 +2160,15 @@ def plot(self, model_list=None, SelPackList=None, **kwargs):
                 all packages will be plotted
             kwargs:
                 filename_base : str
-                    Base file name that will be used to automatically generate file
-                    names for output image files. Plots will be exported as image
-                    files if file_name_base is not None. (default is None)
+                    Base file name that will be used to automatically
+                    generate file names for output image files. Plots will be
+                    exported as image files if file_name_base is not None.
+                    (default is None)
                 file_extension : str
-                    Valid matplotlib.pyplot file extension for savefig(). Only used
-                    if filename_base is not None. (default is 'png')
+                    Valid matplotlib.pyplot file extension for savefig().
+                    Only used if filename_base is not None. (default is 'png')
                 mflay : int
-                    MODFLOW zero-based layer number to return.  If None, then all
+                    MODFLOW zero-based layer number to return.  If None, then
                     all layers will be included. (default is None)
                 kper : int
                     MODFLOW zero-based stress period number to return.