flopy 3.0.1__zip → 3.0.2__zip

flopy-3.0.2/PKG-INFO

@@ -0,0 +1,148 @@
+Metadata-Version: 1.0
+Name: flopy
+Version: 3.0.2
+Summary: FloPy is a Python package to create, run, and post-process MODFLOW-based models.
+Home-page: https://github.com/modflowpy/flopy/
+Author: Mark Bakker, Vincent Post, Chris Langevin, Joe Hughes, Jeremy White, Jeff Starn, Mike Fienen, and Alain Frances
+Author-email: mark.bakker@tudelft.nl, vincent.post@flinders.edu.au, langevin@usgs.gov, jdhughes@usgs.gov, jwhite@usgs.gov, jjstarn@usgs.gov, mnfienen@usgs.gov, frances.alain@gmail.com
+License: New BSD
+Description: Introduction
+        ------------
+        
+        *FloPy3* includes support for MODFLOW-2000, MODFLOW-2005, and
+        MODFLOW-NWT. Other supported MODFLOW-based models include MODPATH
+        (version 6), MT3D and SEAWAT.
+        
+        FloPy3 Changes
+        --------------
+        
+        *FloPy3* is significantly different from *FloPy2* (hosted on
+        `googlecode <https://code.google.com/p/flopy/>`__). The main changes
+        are:
+        
+        -  *FloPy3* is fully zero-based. This means that layers, rows and
+           columns start counting at *zero*. The reason for this is consistency.
+           Arrays are zero-based by default in Python, so it was confusing to
+           have a mix.
+        -  Input for packages that take *layer, row, column, data* input (like
+           the wel or ghb package) has changed and is much more flexible now.
+           See the notebook
+           `flopy3boundaries <http://nbviewer.ipython.org/github/modflowpy/flopy/blob/master/examples/basic/flopy3boundaries.ipynb>`__
+        -  Support for use of EXTERNAL and OPEN/CLOSE array specifiers has been
+           improved.
+        -  *load()* methods have been developed for all of the standard MODFLOW
+           packages and a few less used packages (*e.g.* SWI2).
+        -  MODFLOW parameter support has been added to the *load()* methods.
+           MULT, PVAL, and ZONE packages are now supported and parameter data
+           are converted to arrays in the *load()* methods. MODFLOW parameters
+           are not supported in *write()* methods. MULT package FUNCTION and
+           EXPRESSION functionality are not currently supported.
+        
+        Installation
+        ------------
+        
+        To install *FloPy3* type:
+        
+        ::
+        
+            pip install flopy
+        
+        To update *FloPy3* type:
+        
+        ::
+        
+            pip install flopy --upgrade
+        
+        To uninstall *FloPy3* type:
+        
+        ::
+        
+            pip uninstall flopy
+        
+        To install the bleeding edge version of *FloPy3* from the git repository
+        type:
+        
+        ::
+        
+            pip install git+https://github.com/modflowpy/flopy.git
+        
+        To update your version of *FloPy3* with the bleeding edge code from the
+        git repository type:
+        
+        ::
+        
+            pip install git+https://github.com/modflowpy/flopy.git --upgrade
+        
+        Documentation
+        -------------
+        
+        Documentation for *FloPy3* is a work in progress. *FloPy3* code
+        documentation is available at:
+        
+        -  http://modflowpy.github.io/flopydoc/
+        
+        Examples
+        --------
+        
+        IPython Notebook Examples
+        ~~~~~~~~~~~~~~~~~~~~~~~~~
+        
+        The following IPython Notebooks contain example FloPy scripts for a
+        variety of models and FloPy features
+        
+        Basic examples
+        ^^^^^^^^^^^^^^
+        
+        -  The `lake
+           example <http://nbviewer.ipython.org/github/modflowpy/flopy/blob/master/examples/basic/lake_example.ipynb>`__,
+           a very simple *FloPy3* example of steady flow in a square model with
+           a fixed head cell in the middle (representing a lake) in a 10-layer
+           model.
+        -  An overview of the options to enter *layer,row,column,data* values
+           for packages such as the wel and ghb packages is given in the
+           `flopy3boundaries <http://nbviewer.ipython.org/github/modflowpy/flopy/blob/master/examples/basic/flopy3boundaries.ipynb>`__
+           Notebook
+        -  The `Henry
+           Problem <http://nbviewer.ipython.org/github/modflowpy/flopy/blob/master/examples/henry/henry.ipynb>`__,
+           a simple saltwater intrusion model developed with Flopy and run using
+           SEAWAT.
+        
+        SWI2 examples
+        ^^^^^^^^^^^^^
+        
+        -  `Example
+           1 <http://nbviewer.ipython.org/github/modflowpy/flopy/blob/master/examples/swi_examples/swiex1.ipynb>`__
+           of the SWI2 manual, simulating a rotating interface.
+        
+        SWI2 Test Problems for *FloPy3*
+        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+        
+        A zip file containing *FloPy3* scripts for running and post-processing
+        the SWI2 Examples (examples 1 to 5) that are described in `Bakker et al.
+        (2013) <http://pubs.usgs.gov/tm/6a46/>`__ is available at:
+        
+        -  http://flopy.googlecode.com/svn/examples/SWI2ExampleProblems_flopy.zip
+        
+        Note that examples 2 and 5 also include *FloPy3* scripts for running and
+        post-processing SEAWAT models.
+        
+        Tutorials
+        ~~~~~~~~~
+        
+        A few simple *FloPy3* tutorials are available at:
+        
+        -  http://modflowpy.github.io/flopydoc/tutorials.html
+        
+        MODFLOW Resources
+        ~~~~~~~~~~~~~~~~~
+        
+        -  `MODFLOW and Related Programs <http://water.usgs.gov/ogw/modflow/>`__
+        -  `Online guide for
+           MODFLOW-2000 <http://water.usgs.gov/nrp/gwsoftware/modflow2000/Guide/index.html>`__
+        -  `Online guide for
+           MODFLOW-2005 <http://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/>`__
+        -  `Online guide for
+           MODFLOW-NWT <http://water.usgs.gov/ogw/modflow-nwt/MODFLOW-NWT-Guide/>`__
+        
+Platform: Windows
+Platform: Mac OS-X

{flopy-3.0.1 → flopy-3.0.2}/flopy/__init__.py

@@ -21,7 +21,7 @@ contribute.
 """
 
 __name__ = 'flopy'
-__author__ = 'Mark Bakker, Vincent Post, Chris Langevin, Joe Hughes, Jeremy White, Alain Frances, and Jeffrey Starn'
+__author__ = 'Mark Bakker, Vincent Post, Chris Langevin, Joe Hughes, Jeremy White, Jeff Starn, Mike Fienen, and Alain Frances'
 from version import __version__, __build__
 
 #imports

{flopy-3.0.1 → flopy-3.0.2}/flopy/mbase.py

@@ -89,13 +89,13 @@ class BaseModel(object):
         p : Package object
 
         """
-        for pp in (self.packagelist):
+        for i, pp in enumerate(self.packagelist):
             if pp.allowDuplicates:
                 continue
             elif (isinstance(p, type(pp))):
                 print '****Warning -- two packages of the same type: ',type(p),type(pp)                 
-                print 'replacing existing Package...'                
-                pp = p
+                print 'replacing existing Package...'
+                self.packagelist[i] = p
                 return        
         if self.verbose:
             print 'adding Package: ', p.name[0]

{flopy-3.0.1 → flopy-3.0.2}/flopy/utils/binaryfile.py

@@ -216,10 +216,6 @@ class BinaryLayerFile(object):
         
         #read through the file and build the pointer index
         self._build_index()
-        
-        #allocate the value array
-        self.value = np.empty((self.nlay, self.nrow, self.ncol),
-                              dtype=self.realtype)
         return
    
 
@@ -280,10 +276,10 @@ class BinaryLayerFile(object):
         for header in self.recordarray:
             print header
         return
-
-    def _fill_value_array(self, kstp=0, kper=0, totim=0):
+    
+    def _get_data_array(self, kstp=0, kper=0, totim=0):
         """
-        Fill the three dimensional value array, self.value, for the
+        Get the three dimensional data array for the
         specified kstp and kper value or totim value.
 
         """
@@ -298,17 +294,19 @@ class BinaryLayerFile(object):
             raise Exception('Data not found...')
 
         #initialize head with nan and then fill it
-        self.value[:, :, :] = np.nan
+        data = np.empty((self.nlay, self.nrow, self.ncol),
+                         dtype=self.realtype)
+        data[:, :, :] = np.nan
         for idx in keyindices:
             ipos = self.iposarray[idx]
             ilay = self.recordarray['ilay'][idx]
             if self.verbose:
                 print 'Byte position in file: {0}'.format(ipos)
             self.file.seek(ipos, 0)
-            self.value[ilay - 1, :, :] = binaryread(self.file, self.realtype, 
-                                                shape=(self.nrow, self.ncol))
-        return
-    
+            data[ilay - 1, :, :] = binaryread(self.file, self.realtype,
+                                              shape=(self.nrow, self.ncol))
+        return data
+
     def get_times(self):
         """
         Get a list of unique times in the file
@@ -329,11 +327,13 @@ class BinaryLayerFile(object):
         ----------
         out : list of (kstp, kper) tuples
             List of unique kstp, kper combinations in binary file.  kstp and
-            kper values are presently one-based.  This may change in the
-            future.
+            kper values are presently one-based.
 
         """
-        return self.kstpkper
+        kstpkper = []
+        for kstp, kper in self.kstpkper:
+            kstpkper.append((kstp - 1, kper - 1))
+        return kstpkper
 
     def get_data(self, kstpkper=(0, 0), idx=None, totim=0, mflay=None):
         """
@@ -344,7 +344,8 @@ class BinaryLayerFile(object):
         idx : int
             The zero-based record number.  The first record is record 0.
         kstpkper : tuple of ints
-            A tuple containing the time step and stress period (kstp, kper)
+            A tuple containing the time step and stress period (kstp, kper).
+            These are zero-based kstp and kper values.
         totim : float
             The simulation time.
         mflay : integer
@@ -367,13 +368,16 @@ class BinaryLayerFile(object):
         --------
 
         """
+        # One-based kstp and kper for pulling out of recarray
+        kstp1 = kstpkper[0] + 1
+        kper1 = kstpkper[1] + 1
         if idx is not None:
             totim = self.recordarray['totim'][idx]
-        self._fill_value_array(kstpkper[0], kstpkper[1], totim)
+        data = self._get_data_array(kstp1, kper1, totim)
         if mflay is None:
-            return self.value
+            return data
         else:
-            return self.value[mflay, :, :]
+            return data[mflay, :, :]
         return
 
     def get_alldata(self, mflay=None, nodata=-9999):
@@ -406,16 +410,12 @@ class BinaryLayerFile(object):
         --------
 
         """
-        if mflay is None:
-            h = np.zeros((self.nlay,self.nrow,self.ncol),dtype=np.float)
-        else:
-            h = np.zeros((self.nrow,self.ncol),dtype=np.float)
         rv = []
         for totim in self.times:
-            h[:] = self.get_data(totim=totim, mflay=mflay)
+            h = self.get_data(totim=totim, mflay=mflay)
             rv.append(h)
         rv = np.array(rv)
-        rv[ rv == nodata ] = np.nan
+        rv[rv == nodata] = np.nan
         return rv
 
     def get_ts(self, idx):
@@ -648,7 +648,7 @@ class CellBudgetFile(object):
     >>> import flopy.utils.binaryfile as bf
     >>> cbb = bf.CellBudgetFile('mymodel.cbb')
     >>> cbb.list_records()
-    >>> rec = cbb.get_data(kstpkper=(1,1), text='RIVER LEAKAGE')
+    >>> rec = cbb.get_data(kstpkper=(0,0), text='RIVER LEAKAGE')
 
     """
 
@@ -822,11 +822,14 @@ class CellBudgetFile(object):
         ----------
         out : list of (kstp, kper) tuples
             List of unique kstp, kper combinations in binary file.  kstp and
-            kper values are presently one-based.  This may change in the
+            kper values are zero-based.  This may change in the
             future.
 
         """
-        return self.kstpkper
+        kstpkper = []
+        for kstp, kper in self.kstpkper:
+            kstpkper.append(kstp - 1, kper - 1)
+        return kstpkper
 
     def get_data(self, idx=None, kstpkper=None, totim=None, text=None,
                  verbose=False, full3D=False):
@@ -838,7 +841,8 @@ class CellBudgetFile(object):
         idx : int
             The zero-based record number.  The first record is record 0.
         kstpkper : tuple of ints
-            A tuple containing the time step and stress period (kstp, kper)
+            A tuple containing the time step and stress period (kstp, kper).
+            The kstp and kper values are zero based.
         totim : float
             The simulation time.
         text : str
@@ -894,16 +898,16 @@ class CellBudgetFile(object):
                 raise Exception(errmsg)
 
         if kstpkper is not None:
-            kstp = kstpkper[0]
-            kper = kstpkper[1]
+            kstp1 = kstpkper[0] + 1
+            kper1 = kstpkper[1] + 1
             if text is None:
                 select_indices = np.where(
-                    (self.recordarray['kstp'] == kstp) &
-                    (self.recordarray['kper'] == kper))
+                    (self.recordarray['kstp'] == kstp1) &
+                    (self.recordarray['kper'] == kper1))
             else:
                 select_indices = np.where(
-                    (self.recordarray['kstp'] == kstp) &
-                    (self.recordarray['kper'] == kper) &
+                    (self.recordarray['kstp'] == kstp1) &
+                    (self.recordarray['kper'] == kper1) &
                     (self.recordarray['text'] == text16))
 
         elif totim is not None:

flopy-3.0.2/flopy/version.py

@@ -0,0 +1,4 @@
+#flopy version file automatically created using...updateversion.pyc
+#            created on......February 15, 2015 14:04:58
+__version__='3.0.2'
+__build__='3.0.2.400'

flopy-3.0.2/setup.py

@@ -0,0 +1,30 @@
+import os
+import sys
+from distutils.core import setup
+
+# To use:
+#	   python setup.py bdist --format=wininst
+
+from flopy import __version__, __name__, __author__
+
+long_description = ''
+ 
+try:
+   import pypandoc
+   long_description = pypandoc.convert('README.md', 'rst')
+except:
+   pass  
+       
+setup(name=__name__,
+      description='FloPy is a Python package to create, run, and post-process MODFLOW-based models.',
+      long_description=long_description,  
+      author=__author__,
+      author_email='mark.bakker@tudelft.nl, vincent.post@flinders.edu.au, langevin@usgs.gov, jdhughes@usgs.gov, jwhite@usgs.gov, jjstarn@usgs.gov, mnfienen@usgs.gov, frances.alain@gmail.com',
+      url='https://github.com/modflowpy/flopy/',
+      license='New BSD',
+      platforms='Windows, Mac OS-X',
+      setup_requires=['numpy>=1.9'],
+      install_requires=['numpy>=1.9'],
+      packages=['flopy','flopy.modflow','flopy.modpath','flopy.mt3d','flopy.seawat','flopy.utils'],
+      # use this version ID if .svn data cannot be found
+      version=__version__ )

flopy-3.0.1/PKG-INFO

@@ -1,82 +0,0 @@
-Metadata-Version: 1.0
-Name: flopy
-Version: 3.0.1
-Summary: FloPy is a Python package to create, run, and post-process MODFLOW-based models.
-Home-page: https://code.google.com/p/flopy/
-Author: Mark Bakker, Vincent Post, Chris Langevin, Joe Hughes, Jeremy White, Alain Frances, and Jeffrey Starn
-Author-email: mark.bakker@tudelft.nl, vincent.post@flinders.edu.au, langevin@usgs.gov, jdhughes@usgs.gov, jwhite@usgs.gov, frances.alain@gmail.com
-License: New BSD
-Description: Introduction
-        -----------------------------------------------
-        
-                *FloPy* includes support for MODFLOW-2000, MODFLOW-2005, and MODFLOW-NWT. Other supported MODFLOW-based models include MODPATH (version 6), MT3D and SEAWAT.
-        
-        
-        Installation
-        -----------------------------------------------
-        
-                To install *FloPy* type:
-        
-                        ``pip install flopy``
-        
-                To update *FloPy* type:
-        
-                        ``pip install flopy --update``
-        
-                To uninstall *FloPy* type:
-        
-                        ``pip uninstall flopy``
-        
-        
-        Documentation
-        -----------------------------------------------
-        
-                Documentation for *FloPy* is a work in progress. *FloPy* code documentation is available at: 
-        
-                        `<https://flopy.googlecode.com/svn/sphinx/_build/html/index.html>`_
-        
-        
-        Examples
-        -----------------------------------------------
-        
-        
-        MODFLOW Example
-        ++++++++++++++++++++++++++++++++++
-        
-                A *FloPy* script to create a simple MODFLOW example (**Lake Example**) with a square domain and constant heads in the center of the domain, which represent a lake, is available at:
-        
-                        `<https://code.google.com/p/flopy/source/browse/examples/lake_example.html>`_
-        
-                A iPython Notebook for the **Lake Example** problem is also available at:
-        
-                                `<http://nbviewer.ipython.org/url/flopy.googlecode.com/svn/example_notebooks/lake_example.ipynb>`_
-        
-        
-        SWI2 Test Problems
-        ++++++++++++++++++++++++++++++++++
-        
-                A zip file containing *FloPy* scripts for running and post-processing the SWI2 Examples (examples 1 to 5) that are described in `Bakker et al. (2013) <http://pubs.usgs.gov/tm/6a46/>`_ is available at:
-        
-                        `<http://flopy.googlecode.com/svn/examples/SWI2ExampleProblems_flopy.zip>`_
-        
-                Note that examples 2 and 5 also include *FloPy* scripts for running and post-processing SEAWAT models.
-        
-        
-        Tutorials
-        -----------------------------------------------
-        
-                A few simple *FloPy* tutorials are available at:
-        
-                        `<https://flopy.googlecode.com/svn/sphinx/_build/html/tutorials.html>`_
-        
-        
-        MODFLOW Resources
-        -----------------------------------------------
-        
-                + `MODFLOW and Related Programs <http://water.usgs.gov/ogw/modflow/>`_
-                + `Online guide for MODFLOW-2000 <http://water.usgs.gov/nrp/gwsoftware/modflow2000/Guide/index.html>`_
-                + `Online guide for MODFLOW-2005 <http://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/>`_
-                + `Online guide for MODFLOW-NWT <http://water.usgs.gov/ogw/modflow-nwt/MODFLOW-NWT-Guide/>`_',
-        
-Platform: Windows
-Platform: Mac OS-X

flopy-3.0.1/flopy/version.py

@@ -1,4 +0,0 @@
-#flopy version file automatically created using...updateversion.py
-#            created on......February 08, 2015
-__version__='3.0.1'
-__build__='3.0.1.376'

flopy-3.0.1/setup.py

@@ -1,93 +0,0 @@
-import sys
-from distutils.core import setup
-
-# To use:
-#	   python setup.py bdist --format=wininst
-
-from flopy import __version__, __name__, __author__
-
-long_description = \
-"""Introduction
------------------------------------------------
-
-        *FloPy* includes support for MODFLOW-2000, MODFLOW-2005, and MODFLOW-NWT. Other supported MODFLOW-based models include MODPATH (version 6), MT3D and SEAWAT.
-
-
-Installation
------------------------------------------------
-
-        To install *FloPy* type:
-
-                ``pip install flopy``
-
-        To update *FloPy* type:
-
-                ``pip install flopy --update``
-
-        To uninstall *FloPy* type:
-
-                ``pip uninstall flopy``
-
-
-Documentation
------------------------------------------------
-
-        Documentation for *FloPy* is a work in progress. *FloPy* code documentation is available at: 
-
-                `<https://flopy.googlecode.com/svn/sphinx/_build/html/index.html>`_
-
-
-Examples
------------------------------------------------
-
-
-MODFLOW Example
-++++++++++++++++++++++++++++++++++
-
-        A *FloPy* script to create a simple MODFLOW example (**Lake Example**) with a square domain and constant heads in the center of the domain, which represent a lake, is available at:
-
-                `<https://code.google.com/p/flopy/source/browse/examples/lake_example.html>`_
-
-        A iPython Notebook for the **Lake Example** problem is also available at:
-
-                        `<http://nbviewer.ipython.org/url/flopy.googlecode.com/svn/example_notebooks/lake_example.ipynb>`_
-
-
-SWI2 Test Problems
-++++++++++++++++++++++++++++++++++
-
-        A zip file containing *FloPy* scripts for running and post-processing the SWI2 Examples (examples 1 to 5) that are described in `Bakker et al. (2013) <http://pubs.usgs.gov/tm/6a46/>`_ is available at:
-
-                `<http://flopy.googlecode.com/svn/examples/SWI2ExampleProblems_flopy.zip>`_
-
-        Note that examples 2 and 5 also include *FloPy* scripts for running and post-processing SEAWAT models.
-
-
-Tutorials
------------------------------------------------
-
-        A few simple *FloPy* tutorials are available at:
-
-                `<https://flopy.googlecode.com/svn/sphinx/_build/html/tutorials.html>`_
-
-
-MODFLOW Resources
------------------------------------------------
-
-        + `MODFLOW and Related Programs <http://water.usgs.gov/ogw/modflow/>`_
-        + `Online guide for MODFLOW-2000 <http://water.usgs.gov/nrp/gwsoftware/modflow2000/Guide/index.html>`_
-        + `Online guide for MODFLOW-2005 <http://water.usgs.gov/ogw/modflow/MODFLOW-2005-Guide/>`_
-        + `Online guide for MODFLOW-NWT <http://water.usgs.gov/ogw/modflow-nwt/MODFLOW-NWT-Guide/>`_',
-""" 
-
-setup(name=__name__,
-      description='FloPy is a Python package to create, run, and post-process MODFLOW-based models.',
-      long_description=long_description,      
-      author=__author__,
-      author_email='mark.bakker@tudelft.nl, vincent.post@flinders.edu.au, langevin@usgs.gov, jdhughes@usgs.gov, jwhite@usgs.gov, frances.alain@gmail.com',
-      url='https://code.google.com/p/flopy/',
-      license='New BSD',
-      platforms='Windows, Mac OS-X',
-      packages=['flopy','flopy.modflow','flopy.modpath','flopy.mt3d','flopy.seawat','flopy.utils'],
-      # use this version ID if .svn data cannot be found
-      version=__version__ )