Merge pull request #20 from gjkennedy/cython

fixed cython interface

Makefile

@@ -13,7 +13,7 @@ default:
 	    echo "making $@ in $$subdir"; \
 	    echo; (cd $$subdir && $(MAKE) TMR_DIR=${TMR_DIR}) || exit 1; \
 	done
-	${CXX} ${SO_LINK_FLAGS} ${TMR_OBJS} ${TMR_EXTERN_LIBS} -o ${TMR_DIR}/lib/libtmr.${SO_EXT} 
+	${CXX} ${SO_LINK_FLAGS} ${TMR_OBJS} ${TMR_EXTERN_LIBS} -o ${TMR_DIR}/lib/libtmr.${SO_EXT}
 
 debug:
 	echo "Building Real TMR"
@@ -24,7 +24,7 @@ debug:
 	${CXX} ${SO_LINK_FLAGS} ${TMR_OBJS} ${TMR_EXTERN_LIBS} -o ${TMR_DIR}/lib/libtmr.${SO_EXT}
 
 interface:
-	${PYTHON} setup.py build_ext --inplace
+	pip install -e .
 
 clean:
 	${RM} lib/*.a lib/*.so

examples/egads/crm/dcel.py

@@ -1,6 +1,7 @@
 """
 Implementation of a DECL data structure
 """
+
 import numpy as np
 
 

examples/poisson/poisson_agg_error.py

@@ -2,6 +2,7 @@
 Plot the aggregation error as a function of rho for the KS and p-norm
 functionals
 """
+
 from __future__ import print_function
 import tikzplots as tkz
 import numpy as np

examples/pygeometryloader/plate/plate.py

@@ -3,6 +3,7 @@
 
 To run the defaults: mpirun -np 2 python plate.py
 """
+
 # imports
 import os
 from mpi4py import MPI

examples/pytacsadapt/plate/plate_adapt.py

@@ -13,6 +13,7 @@
 3. run `mpirun -np 4 python plate_adapt.py --niters 10 --strategy fixed_growth --ref_factor 0.1`
 4. compare the results of uniform and adaptive refinement between step 2 and 3
 """
+
 import os
 import argparse
 from mpi4py import MPI

examples/smooth/smooth_stl.py

@@ -1,6 +1,7 @@
 """
 Imports a STL file and applies a smoothing to it
 """
+
 from __future__ import print_function
 
 # Import the locate point code

examples/topology_optimization/eigenvalue/lbracket_eigenvalue.py

@@ -2,6 +2,7 @@
 Solve the eigenvalue-constrained optimization problem
 
 """
+
 from mpi4py import MPI
 from tmr import TMR, TopOptUtils
 from paropt import ParOpt, ParOptEig

examples/topology_optimization/qn-correction/compliance/comp-min.py

@@ -397,9 +397,9 @@ def evalObjConGrad(self, x, g, gcon):
                 prob.driver.opt_settings["Minor print level"] = 0
 
                 if max_iterations > 1 and step == max_iterations - 1:
-                    prob.driver.opt_settings[
-                        "Major iterations limit"
-                    ] = args.niter_finest
+                    prob.driver.opt_settings["Major iterations limit"] = (
+                        args.niter_finest
+                    )
                 else:
                     prob.driver.opt_settings["Major iterations limit"] = args.max_iter
 

examples/topology_optimization/qn-correction/eigenvalue/eig-max-lite.py

@@ -1,6 +1,7 @@
 """
 This script performs eigenvalue minimization with mass constraint
 """
+
 import numpy as np
 from mpi4py import MPI
 import argparse

examples/topology_optimization/qn-correction/frequency-baseline/baseline.py

@@ -1,6 +1,7 @@
 """
 Compute the base frequencies for different domains with concentrated mass
 """
+
 from tmr import TMR, TopOptUtils
 from tacs import TACS, constitutive
 

examples/topology_optimization/qn-correction/refactor_compfreq/compfreq.py

@@ -475,9 +475,9 @@ def evalObjConGrad(self, x, g, gcon):
                 omprob.driver.opt_settings["Minor print level"] = 0
 
                 if args.n_mesh_refine > 1 and step == args.n_mesh_refine - 1:
-                    omprob.driver.opt_settings[
-                        "Major iterations limit"
-                    ] = args.niter_finest
+                    omprob.driver.opt_settings["Major iterations limit"] = (
+                        args.niter_finest
+                    )
                 else:
                     omprob.driver.opt_settings["Major iterations limit"] = args.max_iter
 

examples/topology_optimization/qn-correction/refactor_frequency/refactor_frequency.py

@@ -447,9 +447,9 @@ def evalObjConGrad(self, x, g, gcon):
                 omprob.driver.opt_settings["Minor print level"] = 0
 
                 if n_refine_steps > 1 and step == n_refine_steps - 1:
-                    omprob.driver.opt_settings[
-                        "Major iterations limit"
-                    ] = args.niter_finest
+                    omprob.driver.opt_settings["Major iterations limit"] = (
+                        args.niter_finest
+                    )
                 else:
                     omprob.driver.opt_settings["Major iterations limit"] = args.max_iter
 

setup.py

@@ -2,17 +2,16 @@
 from subprocess import check_output
 import sys
 
-# Numpy/mpi4py must be installed prior to installing TACS
+# Numpy/mpi4py must be installed prior to installing
 import numpy
 import mpi4py
 
 # Import distutils
-from setuptools import setup
+from setuptools import setup, find_packages
 from distutils.core import Extension as Ext
 from Cython.Build import cythonize
 from Cython.Compiler import Options
 
-Options.embedsignature = True
 Options.docstrings = True
 
 
@@ -77,6 +76,7 @@ def get_mpi_flags():
 if "tacs" in sys.modules:
     inc_dirs.extend(tacs.get_include())
     inc_dirs.extend(tacs.get_cython_include())
+    inc_dirs.append(os.path.split(tacs.get_cython_include()[0])[0])
     tacs_lib_dirs, tacs_libs = tacs.get_libraries()
     lib_dirs.extend(tacs_lib_dirs)
     libs.extend(tacs_libs)
@@ -88,6 +88,7 @@ def get_mpi_flags():
 if "paropt" in sys.modules:
     inc_dirs.extend(paropt.get_include())
     inc_dirs.extend(paropt.get_cython_include())
+    inc_dirs.append(os.path.split(paropt.get_cython_include()[0])[0])
     paropt_lib_dirs, paropt_libs = paropt.get_libraries()
     lib_dirs.extend(paropt_lib_dirs)
     libs.extend(paropt_libs)
@@ -99,6 +100,7 @@ def get_mpi_flags():
 if "egads4py" in sys.modules:
     inc_dirs.extend(egads4py.get_include())
     inc_dirs.extend(egads4py.get_cython_include())
+    inc_dirs.append(os.path.split(egads4py.get_cython_include()[0])[0])
     egads4py_lib_dirs, egads4py_libs = egads4py.get_libraries()
     lib_dirs.extend(egads4py_lib_dirs)
     libs.extend(egads4py_libs)
@@ -127,16 +129,16 @@ def get_mpi_flags():
 
 for e in exts:
     e.cython_directives = {
-        "language_level": "3",
         "embedsignature": True,
         "binding": True,
     }
 
 setup(
     name="tmr",
-    version=0.1,
+    version=1.0,
     description="Parallel mesh generation utilities",
     author="Graeme J. Kennedy",
     author_email="graeme.kennedy@ae.gatech.edu",
+    packages=find_packages(include=["tmr*"]),
     ext_modules=cythonize(exts, include_path=inc_dirs),
 )