Merge e5f1e9a into 31aa16d

.travis.yml

@@ -3,8 +3,10 @@ language: python
 os: linux
 
 env:
-  - TEST_PACKAGE="pyclaw"
-  - TEST_PACKAGE="petclaw"
+  matrix: 
+    - TEST_PACKAGE="pyclaw"
+    - TEST_PACKAGE="petclaw"
+    - TEST_PACKAGE="forestclaw"
 
 python:
   - 2.7
@@ -48,15 +50,20 @@ install:
   - python -c "import scipy; print(scipy.__version__)"
   - python setup.py install
 
+# The test commands below go in the following order:
+#  1. pyclaw doc-tests
+#  2. pyclaw examples and io tests
+#  3. petclaw examples
+#  4. forestclaw tests
 script:
   - cd pyclaw/src/pyclaw
-  - nosetests --first-pkg-wins --with-doctest --exclude=limiters --exclude=sharpclaw --exclude=io --exclude=example --with-coverage --cover-package=clawpack.pyclaw
+  - nosetests --first-pkg-wins --with-doctest --exclude=limiters --exclude=sharpclaw --exclude=fileio --exclude=example --with-coverage --cover-package=clawpack.pyclaw
   - mv .coverage temp
   - if [[ "${TEST_PACKAGE}" == "pyclaw" ]]; then
         nosetests -v --first-pkg-wins --exclude=limiters --exclude=sharpclaw --with-coverage --cover-package=clawpack.pyclaw --include=IOTest;
     fi
   - if [[ "${TEST_PACKAGE}" == "petclaw" ]]; then
-       mpirun -n 4 nosetests -v --first-pkg-wins --exclude=limiters --exclude=sharpclaw --exclude=io;
+       mpirun -n 4 nosetests -v --first-pkg-wins --exclude=limiters --exclude=sharpclaw --exclude=fileio;
     fi
   - if [[ "${TEST_PACKAGE}" == "petclaw" ]]; then
        cd ../petclaw/tests;
@@ -65,6 +72,13 @@ script:
   - if [[ "${TEST_PACKAGE}" == "petclaw" ]]; then
        cd ../../pyclaw;
     fi
+  - if [[ "${TEST_PACKAGE}" == "forestclaw" ]]; then
+       cd ../forestclaw ;
+       nosetests --first-pkg-wins --exclude=limiters --exclude=sharpclaw --with-coverage --cover-package=clawpack.forestclaw;
+    fi
+  - if [[ "${TEST_PACKAGE}" == "forestclaw" ]]; then
+         cd ../../pyclaw ;
+    fi
   - mv temp .coverage.doctest
   - coverage combine
 

src/forestclaw/__init__.py

@@ -0,0 +1,43 @@
+"""Additions for ForestClaw support"""
+
+from __future__ import absolute_import
+import os
+import logging
+import logging.config
+
+# Default logging configuration file
+_DEFAULT_LOG_CONFIG_PATH = os.path.join(os.path.dirname(__file__),
+                                        '../pyclaw/log.config')
+del os
+
+# Setup loggers
+logging.config.fileConfig(_DEFAULT_LOG_CONFIG_PATH)
+
+__all__ = []
+
+# Module imports - Note the only difference here is the geometry module
+__all__.extend(['Controller', 'Dimension', 'Patch', 'Domain', 'Solution',
+                'State', 'CFL'])#, 'plot'])
+from clawpack.forestclaw.controller import Controller
+from clawpack.forestclaw.solution import Solution
+from clawpack.forestclaw.geometry import Dimension, Patch, Domain
+from clawpack.forestclaw.state import State
+from clawpack.forestclaw.cfl import CFL
+
+# from clawpack.pyclaw import plot
+
+# The below are not yet needed
+# __all__.extend(['ClawSolver1D', 'ClawSolver2D', 'ClawSolver3D',
+#                 'SharpClawSolver1D', 'SharpClawSolver2D', 'SharpClawSolver3D'])
+# from clawpack.pyclaw.classic.solver import ClawSolver1D, ClawSolver2D, ClawSolver3D
+# from clawpack.pyclaw.sharpclaw.solver import SharpClawSolver1D, SharpClawSolver2D
+# from clawpack.pyclaw.sharpclaw.solver import SharpClawSolver2D, SharpClawSolver3D
+
+
+# Sub-packages
+# from clawpack.pyclaw import limiters
+# from clawpack.pyclaw.limiters import *
+# __all__.extend(limiters.__all__)
+
+# __all__.append('BC')
+# from clawpack.pyclaw.solver import BC

src/forestclaw/cfl.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Module containing the ForestClaw CFL class.
+"""
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+from clawpack.pyclaw.cfl import CFL

src/forestclaw/controller.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Module containing the ForestClaw Controller class.
+"""
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+from clawpack.pyclaw.controller import Controller

src/forestclaw/fileio/__init__.py

@@ -0,0 +1,11 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+"""I/O support for ForestClaw"""
+
+from __future__ import absolute_import
+import logging
+logger = logging.getLogger('pyclaw.fileio')
+
+from . import ascii
+__all__ = ["ascii.read", "ascii.write"]

src/forestclaw/fileio/ascii.py

@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Routines for reading and writing an ascii output file from ForestClaw
+"""
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+import logging
+import numpy as np
+
+import clawpack.forestclaw as forestclaw
+from clawpack.pyclaw.fileio.ascii import write
+from clawpack.pyclaw.fileio.ascii import read
+from clawpack.pyclaw.util import read_data_line
+
+logger = logging.getLogger('pyclaw.fileio')
+
+
+def write_patch_header(f, patch):
+    f.write("%5i                  patch_number\n" % patch.patch_index)
+    f.write("%5i                  AMR_level\n" % patch.level)
+    f.write("%5i                  block_number\n" % patch.block_number)
+    f.write("%5i                  mpi_rank\n" % patch.mpi_rank)
+    for dim in patch.dimensions:
+        f.write("%5i                  m%s\n" % (dim.num_cells, dim.name))
+    for dim in patch.dimensions:
+        f.write("%18.8e     %slow\n" % (dim.lower, dim.name))
+    for dim in patch.dimensions:
+        f.write("%18.8e     d%s\n" % (dim.delta, dim.name))
+
+    f.write("\n")
+
+
+def read_patch_header(f, num_dim):
+    r"""Read header describing the next patch
+
+    :Input:
+     - *f* - (file) Handle to open file
+     - *num_dim* - (int) Number of dimensions
+
+    :Output:
+     - *patch* - (clawpack.pyclaw.geometry.Patch) Initialized patch represented
+       by the header data.
+    """
+
+    n = np.zeros((num_dim))
+    d = np.zeros((num_dim))
+    lower = np.zeros((num_dim))
+
+    patch_index = read_data_line(f, data_type=int)
+    level = read_data_line(f, data_type=int)
+    block_number = read_data_line(f, data_type=int)
+    mpi_rank = read_data_line(f, data_type=int)
+    for i in range(num_dim):
+        n[i] = read_data_line(f, data_type=int)
+    for i in range(num_dim):
+        lower[i] = read_data_line(f)
+    for i in range(num_dim):
+        d[i] = read_data_line(f)
+
+    blank = f.readline()
+
+    # Construct the patch
+    # Since we do not have names here, we will construct the patch with
+    # dimension names x,y,z
+    names = ['x', 'y', 'z']
+    dimensions = [forestclaw.geometry.Dimension(lower[i], lower[i] + n[i] * d[i],
+                  n[i], name=names[i]) for i in range(num_dim)]
+    patch = forestclaw.geometry.Patch(dimensions)
+
+    # Add AMR attributes:
+    patch.patch_index = patch_index
+    patch.level = level
+
+    # Add ForestClaw attributes
+    patch.block_number = block_number
+    patch.mpi_rank = mpi_rank
+
+    return patch
+
+# # Replace the ascii module functions with those defined above
+# # ascii.read_patch_header = read_patch_header
+# # ascii.write_patch_header = write_patch_header
+# read = ascii.read
+# write = ascii.write

src/forestclaw/fileio/test.py

@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Test suite for forestclaw.io
+"""
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+import os
+import shutil
+import tempfile
+import shutil
+
+import numpy
+import nose
+
+import clawpack.forestclaw as forestclaw
+
+
+def test_forestclaw_input():
+    """Simple test to read in a ForestClaw ASCII file"""
+
+    # Create test solution
+    x = forestclaw.geometry.Dimension(0.0, 1.0, 100, name='x')
+    state = forestclaw.State(forestclaw.Patch(x), 1)
+    state.q = numpy.zeros((1, x.num_cells))
+    sol = forestclaw.Solution(state, forestclaw.geometry.Domain(x))
+
+    # Test specific extensions to Patch
+    sol.domain.patches[0].block_number = 2
+    sol.domain.patches[0].mpi_rank = 2
+
+    # Create temporary directory to write to and read from
+    try:
+        temp_path = tempfile.mkdtemp()
+
+        # Real test
+        sol.write(0, path=temp_path)
+        read_sol = forestclaw.Solution(0, path=temp_path,
+                                       file_format='forestclaw')
+        nose.tools.assert_equal(sol, read_sol,
+                                "ForestClaw IO read/write test failed, " +
+                                "solutions are not equal.")
+    except:
+        shutil.copy(os.path.join(temp_path, 'fort.q0000'), os.getcwd())
+    finally:
+        shutil.rmtree(temp_path)
+
+if __name__ == '__main__':
+    nose.main()

src/forestclaw/geometry.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Module containing forestclaw.geometry.
+"""
+
+from __future__ import absolute_import
+
+from clawpack import pyclaw
+from clawpack.pyclaw import geometry as pyclaw_geometry
+from clawpack.pyclaw.geometry import Dimension
+from clawpack.pyclaw.geometry import Domain
+
+
+class Patch(pyclaw_geometry.Patch):
+    """Patch class with specific ForestClaw attributes.
+    """
+
+    __doc__ += pyclaw.util.add_parent_doc(pyclaw_geometry.Patch)
+
+    def __init__(self, dimensions):
+
+        super(Patch, self).__init__(dimensions)
+
+        self.block_number = 0
+        r"""(int) - Block number of current patch, ``default = 0``"""
+        self.mpi_rank = 0
+        r"""(int) - MPI rank this patch belongs to, ``default = 0``"""

src/forestclaw/setup.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+
+from __future__ import absolute_import
+def configuration(parent_package='',top_path=None):
+    from numpy.distutils.misc_util import Configuration
+
+    config = Configuration('forestclaw', parent_package, top_path)
+    config.add_data_files('log.config')
+    config.add_subpackage('classic')
+    config.add_subpackage('sharpclaw')
+    config.add_subpackage('limiters')
+    config.add_subpackage('fileio')
+    return config
+
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(**configuration(top_path='').todict())

src/forestclaw/solution.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Module containing the ForestClaw Solution class.
+"""
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+from clawpack.pyclaw.solution import Solution

src/forestclaw/state.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Module containing the ForestClaw State class.
+"""
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+from clawpack.pyclaw.state import State

src/forestclaw/test.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Test suite for forestclaw
+"""
+
+from __future__ import absolute_import
+
+from .geometry import Patch, Dimension
+
+
+def test_forestclaw_patch():
+    """Test the simple extension of the pyclaw.Patch class"""
+
+    patch = Patch(Dimension(0.0, 1.0, 10))
+    patch.block_number = 2
+    patch.mpi_rank = 3
+
+
+if __name__ == '__main__':
+    import nose
+    nose.main()

src/petclaw/io/__init__.py → src/petclaw/fileio/__init__.py

@@ -1,16 +1,10 @@
 #!/usr/bin/env python
 # encoding: utf-8
-#  ======================================================================
-#  Package:     pyclaw.io
-#  File:        __init__.py
-#  Created:     Feb 10, 2008
-#  Author:      Kyle Mandli
-#  ======================================================================
-"""Output package for Pyclaw"""
+"""Output package for PetClaw"""
 
 from __future__ import absolute_import
 import logging
-from clawpack.pyclaw.io import ascii
+from clawpack.pyclaw.fileio import ascii
 __all__ = ['ascii.read','ascii.write']
 
 # Check for HDF 5 support
@@ -24,7 +18,7 @@
 # Check for netcdf support
 try:
     import netCDF4
-    from clawpack.pyclaw.io import netcdf 
+    from clawpack.pyclaw.fileio import netcdf 
     __all__ += ['netcdf.read','netcdf.write']
 except(ImportError):
     logging.debug("No netcdf4 support found.")