fix(#831,#858): Data length check and case-insensitive lookup (#864)

* fix(#831,#858): Flopy now verifies data line length meets minimum length criteria. Flopy now retrieves models by case-insensitive name when case-sensitive lookup fails.

* feat(#862): Include message about zero based index variables in the docs.

autotest/t505_test.py

@@ -129,6 +129,9 @@ def np001():
 
     model = ModflowGwf(sim, modelname=model_name,
                        model_nam_file='{}.nam'.format(model_name))
+    # test case insensitive lookup
+    assert(sim.get_model(model_name.upper()) is not None)
+
     # test getting model using attribute
     model = sim.np001_mod
     assert(model is not None and model.name == 'np001_mod')
@@ -299,7 +302,7 @@ def np001():
                                 timeseries=[(0.0, 60.0), (100000.0, 60.0)],
                                 stress_period_data=[((100, 0, 0), np.nan,
                                                      'drn_1'), ((0, 0, 0),
-                                                    10.0)])
+                                                    10.0, 'drn_2')])
     npf_package = ModflowGwfnpf(model, save_flows=True,
                                 alternative_cell_averaging='logarithmic',
                                 icelltype=1, k=100001.0, k33=1e-12)
@@ -310,6 +313,16 @@ def np001():
            'checker threshold of 1e-11' in summary
     assert 'npf package: horizontal hydraulic conductivity values above ' \
            'checker threshold of 100000.0' in summary
+    data_invalid = False
+    try:
+        drn_package = ModflowGwfdrn(model, print_input=True, print_flows=True,
+                                    save_flows=True, maxbound=1,
+                                    timeseries=[(0.0, 60.0), (100000.0, 60.0)],
+                                    stress_period_data=[((0, 0, 0), 10.0)])
+    except MFDataException:
+        data_invalid = True
+    assert data_invalid
+
     return
 
 

flopy/mf6/data/mfdatalist.py

@@ -12,7 +12,7 @@
 from ...datbase import DataListInterface, DataType
 from .mffileaccess import MFFileAccessList
 from .mfdatastorage import DataStorage, DataStorageType, DataStructureType
-from .mfdatautil import to_string
+from .mfdatautil import to_string, iterable
 
 
 class MFList(mfdata.MFMultiDimVar, DataListInterface):
@@ -271,6 +271,26 @@ def get_data(self, apply_mult=False, **kwargs):
         return self._get_data(apply_mult, **kwargs)
 
     def _set_data(self, data, autofill=False):
+        if isinstance(data, dict):
+            if 'data' in data:
+                data_check = data['data']
+            else:
+                data_check = None
+        else:
+            data_check = data
+        if iterable(data_check):
+            # verify data length
+            min_line_size = self.structure.get_min_record_entries()
+            if isinstance(data_check[0], np.record) or \
+                    (iterable(data_check[0]) and not
+                     isinstance(data_check[0], str)):
+                # data contains multiple records
+                for data_line in data_check:
+                    self._check_line_size(data_line, min_line_size)
+            else:
+                # data is a single record
+                self._check_line_size(data_check, min_line_size)
+        # set data
         self._resync()
         try:
             if self._get_storage_obj() is None:
@@ -286,6 +306,24 @@ def _set_data(self, data, autofill=False):
                                   traceback_, None,
                                   self._simulation_data.debug, ex)
 
+    def _check_line_size(self, data_line, min_line_size):
+        if 0 < len(data_line) < min_line_size:
+            min_line_size = self.structure.get_min_record_entries()
+            message = 'Data line {} only has {} entries, ' \
+                      'minimum number of entries is ' \
+                      '{}.'.format(data_line, len(data_line),
+                                   min_line_size)
+            type_, value_, traceback_ = sys.exc_info()
+            raise MFDataException(
+                self.structure.get_model(),
+                self.structure.get_package(),
+                self.structure.path,
+                'storing data',
+                self.structure.name,
+                inspect.stack()[0][3],
+                type_, value_, traceback_, message,
+                self._simulation_data.debug)
+
     def set_data(self, data, autofill=False):
         self._set_data(data, autofill)
 

flopy/mf6/data/mfdatautil.py

@@ -1,12 +1,17 @@
 import sys, inspect
 import numpy as np
 from copy import deepcopy
+from collections import Iterable
 from ..mfbase import MFDataException, FlopyException
 from .mfstructure import DatumType
 from ...utils.datautil import PyListUtil, DatumUtil
 import struct
 
 
+def iterable(obj):
+    return isinstance(obj, Iterable)
+
+
 def get_first_val(arr):
     while isinstance(arr, list) or isinstance(arr, np.ndarray):
         arr = arr[0]

flopy/mf6/data/mfstructure.py

@@ -14,6 +14,13 @@
 from ..mfbase import PackageContainer, StructException
 
 
+numeric_index_text = 'This argument is an index variable, which means that ' \
+                     'it should be treated as zero-based when working with ' \
+                     'FloPy and Python. Flopy will automatically subtract ' \
+                     'one when loading index variables and add one when ' \
+                     'writing index variables.'
+
+
 class DfnType(Enum):
     common = 1
     sim_name_file = 2
@@ -933,6 +940,10 @@ def get_type_string(self):
     def get_description(self, line_size, initial_indent, level_indent):
         item_desc = '* {} ({}) {}'.format(self.name, self.type_string,
                                           self.description)
+        if self.numeric_index or self.is_cellid:
+            # append zero-based index text
+            item_desc = '{} {}'.format(item_desc,
+                                       numeric_index_text)
         twr = TextWrapper(width=line_size, initial_indent=initial_indent,
                           drop_whitespace = True,
                           subsequent_indent='  {}'.format(initial_indent))
@@ -952,7 +963,6 @@ def get_doc_string(self, line_size, initial_indent, level_indent):
         param_doc_string = '{}\n{}'.format(param_doc_string, description)
         return param_doc_string
 
-
     def get_keystring_desc(self, line_size, initial_indent, level_indent):
         if self.type != DatumType.keystring:
             raise StructException('Can not get keystring description for "{}" '
@@ -1169,6 +1179,9 @@ class MFDataStructure(object):
         (<model>,<package>,<block>,<data>)
     get_datatype : () : DataType
         returns the DataType of this data (array, list, scalar, ...)
+    get_min_record_entries : () : int
+        gets the minimum number of entries, as entered in a package file,
+        for a single record. excludes optional data items
     get_record_size : () : int
         gets the number of data items, excluding keyword data items, in this
         MFDataStructure
@@ -1431,6 +1444,18 @@ def is_mult_or_trans(self):
             return True
         return False
 
+    def get_min_record_entries(self):
+        count = 0
+        for data_item_structure in self.data_item_structures:
+            if not data_item_structure.optional:
+                if data_item_structure.type == DatumType.record:
+                    count += data_item_structure.get_record_size()[0]
+                else:
+                    if data_item_structure.type != DatumType.keyword or \
+                            count > 0:
+                        count += 1
+        return count
+
     def get_record_size(self):
         count = 0
         repeating = False
@@ -1503,8 +1528,14 @@ def get_description(self, line_size=79, initial_indent='        ',
             elif datastr.display_item(index):
                 if len(description.strip()) > 0:
                     description = '{}\n'.format(description)
+                item_desc = item.description
+                if item.numeric_index or item.is_cellid:
+                    # append zero-based index text
+                    item_desc = '{} {}'.format(item_desc,
+                                               numeric_index_text)
+
                 item_desc = '* {} ({}) {}'.format(item.name, itype,
-                                                  item.description)
+                                                  item_desc)
                 twr = TextWrapper(width=line_size,
                                   initial_indent=initial_indent,
                                   subsequent_indent='  {}'.format(
@@ -1553,6 +1584,7 @@ def get_doc_string(self, line_size=79, initial_indent='    ',
                                                level_indent)
             var_name = self.python_name
             type_name = self.get_type_string()
+
         param_doc_string = '{} : {}'.format(var_name, type_name)
         twr = TextWrapper(width=line_size, initial_indent=initial_indent,
                           subsequent_indent='  {}'.format(initial_indent))

flopy/mf6/mfbase.py

@@ -610,7 +610,7 @@ def get_package(self, name=None):
         if name.lower() in self.package_key_dict:
             return self.package_key_dict[name.lower()]
 
-        # search for partial package name
+        # search for partial and case-insensitive package name
         for pp in self._packagelist:
             if pp.package_name is not None:
                 # get first package of the type requested