From 4e8eb7142eb1cda7338a5ff5242f05dc58713e85 Mon Sep 17 00:00:00 2001
From: Graeme Kennedy <graeme.kennedy@ae.gatech.edu>
Date: Wed, 6 Mar 2024 17:34:27 -0500
Subject: [PATCH] updated cython

---
 Makefile    |  2 +-
 setup.py    |  3 +++
 tmr/TMR.pxd | 47 +++++++++++++++++++++++++++++++++++------------
 tmr/TMR.pyx |  4 +++-
 4 files changed, 42 insertions(+), 14 deletions(-)

diff --git a/Makefile b/Makefile
index c32c27e..8f35eeb 100644
--- a/Makefile
+++ b/Makefile
@@ -24,7 +24,7 @@ debug:
 	${CXX} ${SO_LINK_FLAGS} ${TMR_OBJS} ${TMR_EXTERN_LIBS} -o ${TMR_DIR}/lib/libtmr.${SO_EXT}
 
 interface:
-	pip install -e .\[all\]
+	pip install -e .
 
 clean:
 	${RM} lib/*.a lib/*.so
diff --git a/setup.py b/setup.py
index 471c395..78cfc43 100644
--- a/setup.py
+++ b/setup.py
@@ -76,6 +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)
@@ -87,6 +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)
@@ -98,6 +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)
diff --git a/tmr/TMR.pxd b/tmr/TMR.pxd
index 7a7d36a..721e573 100644
--- a/tmr/TMR.pxd
+++ b/tmr/TMR.pxd
@@ -19,7 +19,6 @@
 # limitations under the License.
 
 # For MPI
-from mpi4py.libmpi cimport *
 cimport mpi4py.MPI as MPI
 
 # Import numpy
@@ -29,21 +28,45 @@ import numpy as np
 # Import TACS
 from tacs import TACS
 from tacs cimport TACS
-from tacs.TACS import *
-from tacs.TACS cimport *
-from tacs.constitutive import *
-from tacs.constitutive cimport *
+from tacs.TACS import Vec, VecInterp, Assembler, Mg, Element, Function, Pc
+from tacs.TACS cimport (
+    Vec,
+    VecInterp,
+    Assembler,
+    Mg,
+    Element,
+    Function,
+    Pc,
+    TACSFunction,
+    TACSBVec,
+    TACSBVecInterp,
+    TACSAssembler,
+    TACSMg,
+    _init_Vec,
+    _init_VecInterp,
+    _init_Assembler,
+    _init_Mg,
+    _dynamicTACSMg,
+)
+from tacs.constitutive import (
+    PlaneStressConstitutive,
+    SolidConstitutive,
+    MaterialProperties,
+)
+from tacs.constitutive cimport (
+    PlaneStressConstitutive,
+    SolidConstitutive,
+    MaterialProperties,
+    TACSMaterialProperties,
+)
 
 # Import ParOpt
-from paropt.ParOpt import *
-from paropt.ParOpt cimport *
+from paropt.ParOpt import PVec, ProblemBase
+from paropt.ParOpt cimport PVec, ProblemBase, ParOptVec, _init_PVec
 
 # Import EGADS
-from egads4py.egads import *
-from egads4py.egads cimport *
-
-# Import all of the TMR header files
-from tmr.cpp_headers.TMR cimport *
+from egads4py.egads import pyego
+from egads4py.egads cimport pyego
 
 cdef inline char* tmr_convert_str_to_chars(s):
    if isinstance(s, unicode):
diff --git a/tmr/TMR.pyx b/tmr/TMR.pyx
index 31e6484..346f72c 100644
--- a/tmr/TMR.pyx
+++ b/tmr/TMR.pyx
@@ -19,7 +19,6 @@
 # limitations under the License.
 
 # # For the use of MPI
-from mpi4py.libmpi cimport *
 cimport mpi4py.MPI as MPI
 
 # Import numpy
@@ -41,6 +40,9 @@ from libcpp cimport bool
 # Import C methods for python
 from cpython cimport PyObject, Py_INCREF
 
+# Import all of the TMR header files
+from tmr.cpp_headers.TMR cimport *
+
 cdef tmr_init():
     if not TMRIsInitialized():
         TMRInitialize()