install gprMax as a module

gprMax/__init__.py

@@ -1 +1,4 @@
-from gprMax._version import __version__
+from ._version import __version__
+from .gprMax import api as run
+
+__name__ = 'gprMax'

gprMax/gprMax.py

@@ -18,33 +18,38 @@
 
 """gprMax.gprMax: provides entry point main()."""
 
-import argparse, datetime, itertools, os, psutil, sys
-from time import perf_counter
-from enum import Enum
+import argparse
+import datetime
+import itertools
+import os
+import psutil
+import sys
 
 import numpy as np
 
-import gprMax
-from gprMax.constants import c, e0, m0, z0, floattype
-from gprMax.exceptions import GeneralError
-from gprMax.fields_update import update_electric, update_magnetic, update_electric_dispersive_multipole_A, update_electric_dispersive_multipole_B, update_electric_dispersive_1pole_A, update_electric_dispersive_1pole_B
-from gprMax.grid import FDTDGrid, dispersion_check
-from gprMax.input_cmds_geometry import process_geometrycmds
-from gprMax.input_cmds_file import process_python_include_code, write_processed_file, check_cmd_names
-from gprMax.input_cmds_multiuse import process_multicmds
-from gprMax.input_cmds_singleuse import process_singlecmds
-from gprMax.materials import Material
-from gprMax.writer_hdf5 import prepare_hdf5, write_hdf5
-from gprMax.pml import build_pmls, update_electric_pml, update_magnetic_pml
-from gprMax.utilities import update_progress, logo, human_size
-from gprMax.yee_cell_build import build_electric_components, build_magnetic_components
+from time import perf_counter
+from enum import Enum
+from ._version import __version__
+from .constants import c, e0, m0, z0
+from .exceptions import GeneralError
+from .fields_update import update_electric, update_magnetic, update_electric_dispersive_multipole_A, update_electric_dispersive_multipole_B, update_electric_dispersive_1pole_A, update_electric_dispersive_1pole_B
+from .grid import FDTDGrid, dispersion_check
+from .input_cmds_geometry import process_geometrycmds
+from .input_cmds_file import process_python_include_code, write_processed_file, check_cmd_names
+from .input_cmds_multiuse import process_multicmds
+from .input_cmds_singleuse import process_singlecmds
+from .materials import Material
+from .writer_hdf5 import prepare_hdf5, write_hdf5
+from .pml import build_pmls, update_electric_pml, update_magnetic_pml
+from .utilities import update_progress, logo, human_size
+from .yee_cell_build import build_electric_components, build_magnetic_components
 
 
 def main():
     """This is the main function for gprMax."""
 
     # Print gprMax logo, version, and licencing/copyright information
-    logo(gprMax.__version__ + ' (Bowmore)')
+    logo(__version__ + ' (Bowmore)')
 
     # Parse command line arguments
     parser = argparse.ArgumentParser(prog='gprMax', description='Electromagnetic modelling software based on the Finite-Difference Time-Domain (FDTD) method')
@@ -57,6 +62,31 @@ def main():
     parser.add_argument('--write-processed', action='store_true', default=False, help='write an input file after any Python code and include commands in the original input file have been processed')
     parser.add_argument('--opt-taguchi', action='store_true', default=False, help='optimise parameters using the Taguchi optimisation method')
     args = parser.parse_args()
+
+    run_main(args)
+
+
+def api(inputfile, n=1, mpi=False, benchmark=False, geometry_only=False, geometry_fixed=False, write_processed=False, opt_taguchi=False):
+    """If you have installed gprMax as a module this is the entry point"""
+    class ImportArguments:
+        pass
+
+    args = ImportArguments()
+
+    args.inputfile = inputfile
+    args.n = n
+    args.mpi = mpi
+    args.benchmark = benchmark
+    args.geometry_only = geometry_only
+    args.geometry_fixed = geometry_fixed
+    args.write_processed = write_processed
+    args.opt_taguchi = opt_taguchi
+
+    run_main(args)
+
+
+def run_main(args):
+
     numbermodelruns = args.n
     inputdirectory = os.path.dirname(os.path.abspath(args.inputfile))
     inputfile = os.path.abspath(os.path.join(inputdirectory, os.path.basename(args.inputfile)))

gprMax/writer_hdf5.py

@@ -17,26 +17,25 @@
 # along with gprMax.  If not, see <http://www.gnu.org/licenses/>.
 
 import h5py
-import numpy as np
 
-import gprMax
+from ._version import __version__
 from gprMax.constants import floattype
 from gprMax.grid import Ix, Iy, Iz
 
 
 def prepare_hdf5(outputfile, G):
     """Prepares an output file in HDF5 format for writing.
-        
+
     Args:
         outputfile (str): Name of the output file.
         G (class): Grid class instance - holds essential parameters describing the model.
-        
+
     Returns:
-        f (file object): File object for the file to be written to. 
+        f (file object): File object for the file to be written to.
     """
 
     f = h5py.File(outputfile, 'w')
-    f.attrs['gprMax'] = gprMax.__version__
+    f.attrs['gprMax'] = __version__
     f.attrs['Title'] = G.title
     f.attrs['Iterations'] = G.iterations
     f.attrs['nx, ny, nz'] = (G.nx, G.ny, G.nz)
@@ -47,7 +46,7 @@ def prepare_hdf5(outputfile, G):
     f.attrs['nrx'] = len(G.rxs)
     f.attrs['srcsteps'] = (G.srcstepx, G.srcstepy, G.srcstepz)
     f.attrs['rxsteps'] = (G.rxstepx, G.rxstepy, G.rxstepz)
-    
+
 
     # Create group for sources (except transmission lines); add type and positional data attributes
     srclist = G.voltagesources + G.hertziandipoles + G.magneticdipoles
@@ -55,7 +54,7 @@ def prepare_hdf5(outputfile, G):
         grp = f.create_group('/srcs/src' + str(srcindex + 1))
         grp.attrs['Type'] = type(src).__name__
         grp.attrs['Position'] = (src.xcoord * G.dx, src.ycoord * G.dy, src.zcoord * G.dz)
-    
+
     # Create group for transmission lines; add positional data, line resistance and line discretisation attributes; initialise arrays for line voltages and currents
     if G.transmissionlines:
         for tlindex, tl in enumerate(G.transmissionlines):
@@ -68,7 +67,7 @@ def prepare_hdf5(outputfile, G):
             grp['Iinc'] = tl.Iinc
             grp.create_dataset('Vtotal', (G.iterations, ), dtype=floattype)
             grp.create_dataset('Itotal', (G.iterations, ), dtype=floattype)
-    
+
     # Create group and add positional data and initialise field component arrays for receivers
     for rxindex, rx in enumerate(G.rxs):
         grp = f.create_group('/rxs/rx' + str(rxindex + 1))
@@ -83,7 +82,7 @@ def prepare_hdf5(outputfile, G):
 
 def write_hdf5(f, timestep, Ex, Ey, Ez, Hx, Hy, Hz, G):
     """Writes field component values to an output file in HDF5 format.
-        
+
     Args:
         f (file object): File object for the file to be written to.
         timestep (int): Current iteration number.
@@ -116,4 +115,3 @@ def write_hdf5(f, timestep, Ex, Ey, Ez, Hx, Hy, Hz, G):
         for tlindex, tl in enumerate(G.transmissionlines):
             f['/tls/tl' + str(tlindex + 1) + '/Vtotal'][timestep] = tl.voltage[tl.antpos]
             f['/tls/tl' + str(tlindex + 1) + '/Itotal'][timestep] = tl.current[tl.antpos]
-

setup.py

@@ -27,28 +27,30 @@ try:
 except ImportError:
     raise ImportError('gprMax requires the NumPy package.')
 
-import glob, os, shutil, sys
+import glob
+import os
+import shutil
+import sys
+import re
+
+# Importing _version__.py before building can cause issues.
+with open('gprMax/_version.py', 'r') as fd:
+    version = re.search(r'^__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
+        fd.read(), re.MULTILINE).group(1)
+
+"""
+  Parse package name from init file. Importing __init__.py / gprMax will
+  break as gprMax depends on compiled .pyx files.
+"""
+with open('gprMax/__init__.py', 'r') as fd:
+    packagename = re.search(r'^__name__\s*=\s*[\'"]([^\'"]*)[\'"]',
+        fd.read(), re.MULTILINE).group(1)
 
 # Python version
 if sys.version_info[:2] < (3, 4):
     print('gprMax requires Python 3.4 or newer')
     sys.exit(-1)
 
-import gprMax
-
-# Package name
-packagename = gprMax.__name__
-
-# Package version
-version = gprMax.__version__
-
-# Process 'install' command line argument
-if 'install' in sys.argv:
-    print("'install' is not required for this package, running 'build_ext --inplace' instead.")
-    sys.argv.remove('install')
-    sys.argv.append('build_ext')
-    sys.argv.append('--inplace')
-
 # Process 'build' command line argument
 if 'build' in sys.argv:
     print("'build' is not required for this package, running 'build_ext --inplace' instead.")
@@ -118,7 +120,7 @@ elif sys.platform == 'darwin':
     compile_args = ['-O3', '-w', '-fstrict-aliasing', '-fno-common', '-fopenmp']
     linker_args = ['-fopenmp']
     extra_objects = []
-    
+
     # If user is cwarren do static linking as this is for binaries uploaded to GitHub
 #    if os.getlogin() == 'cwarren':
 #        linker_args = ['-static-libgcc']
@@ -176,4 +178,5 @@ setup(name=packagename,
                    'Topic :: Scientific/Engineering'
                    ],
       ext_modules=extensions,
+      packages=['gprMax'],
       include_dirs=[np.get_include()])