Fix import issue (theochem#78)

* Use absolute import path

* Try src folder

* Fix pyci C ext. module import

* Update FanCI to use new C ext. module

---------

Co-authored-by: Michelle Richer <michellericher93@gmail.com>

Author: FanwangM

Makefile

@@ -70,15 +70,15 @@ OBJECTS := $(patsubst %.cpp,%.o,$(wildcard pyci/src/*.cpp))
 # -------------
 
 .PHONY: all
-all: pyci/pyci.so.$(PYCI_VERSION) pyci/pyci.so.$(VERSION_MAJOR) pyci/pyci.so
+all: pyci/_pyci.so.$(PYCI_VERSION) pyci/_pyci.so.$(VERSION_MAJOR) pyci/_pyci.so
 
 .PHONY: test
 test:
 	$(PYTHON) -m pytest -sv ./pyci
 
 .PHONY: clean
 clean:
-	rm -rf pyci/src/*.o pyci/pyci.so*
+	rm -rf pyci/src/*.o pyci/_pyci.so*
 
 .PHONY: cleandeps
 cleandeps:
@@ -94,13 +94,13 @@ compile_flags.txt:
 pyci/src/%.o: pyci/src/%.cpp pyci/include/pyci.h $(DEPS)
 	$(CXX) $(CFLAGS) $(DEFS) -c $(<) -o $(@)
 
-pyci/pyci.so.$(PYCI_VERSION): $(OBJECTS)
+pyci/_pyci.so.$(PYCI_VERSION): $(OBJECTS)
 	$(CXX) $(CFLAGS) $(DEFS) -shared $(^) -o $(@)
 
-pyci/pyci.so.$(VERSION_MAJOR): pyci/pyci.so.$(PYCI_VERSION)
+pyci/_pyci.so.$(VERSION_MAJOR): pyci/_pyci.so.$(PYCI_VERSION)
 	ln -sf $(notdir $(<)) $(@)
 
-pyci/pyci.so: pyci/pyci.so.$(PYCI_VERSION)
+pyci/_pyci.so: pyci/_pyci.so.$(PYCI_VERSION)
 	ln -sf $(notdir $(<)) $(@)
 
 deps/eigen:

pyci/__init__.py

@@ -15,21 +15,20 @@
 
 r"""PyCI module."""
 
-from .pyci import __version__, c_long, c_ulong, c_double, sparse_op
-
-from .pyci import secondquant_op, wavefunction, one_spin_wfn, two_spin_wfn
-from .pyci import doci_wfn, fullci_wfn, genci_wfn, sparse_op
-from .pyci import get_num_threads, set_num_threads, popcnt, ctz
-from .pyci import compute_overlap, compute_rdms, compute_transition_rdms
-from .pyci import add_hci, compute_enpt2
-
-from .utility import make_senzero_integrals, reduce_senzero_integrals, spinize_rdms
-from .utility import odometer_one_spin, odometer_two_spin
-
-from .excitation_ci import add_excitations
-from .seniority_ci import add_seniorities
-from .gkci import add_gkci
-from .cost_ci import add_cost
+from pyci._pyci import __version__, c_long, c_ulong, c_double
+from pyci._pyci import secondquant_op, wavefunction, one_spin_wfn, two_spin_wfn
+from pyci._pyci import doci_wfn, fullci_wfn, genci_wfn, sparse_op
+from pyci._pyci import get_num_threads, set_num_threads, popcnt, ctz
+from pyci._pyci import compute_overlap, compute_rdms, compute_transition_rdms
+from pyci._pyci import add_hci, compute_enpt2
+
+from pyci.utility import make_senzero_integrals, reduce_senzero_integrals, spinize_rdms
+from pyci.utility import odometer_one_spin, odometer_two_spin
+
+from pyci.excitation_ci import add_excitations
+from pyci.seniority_ci import add_seniorities
+from pyci.gkci import add_gkci
+from pyci.cost_ci import add_cost
 
 
 __all__ = [

pyci/cost_ci.py

@@ -15,7 +15,8 @@
 
 r"""PyCI Griebel-Knapek CI module."""
 
-from . import pyci
+from pyci.utility import odometer_one_spin, odometer_two_spin
+import pyci._pyci as pyci
 
 
 __all__ = [
@@ -47,8 +48,8 @@ def add_cost(wfn, cost, q_max, t=-0.5):
     """
     # Run odometer algorithm
     if isinstance(wfn, (pyci.doci_wfn, pyci.genci_wfn)):
-        pyci.odometer_one_spin(wfn, cost, q_max=q_max, t=t)
+        odometer_one_spin(wfn, cost, q_max=q_max, t=t)
     elif isinstance(wfn, pyci.fullci_wfn):
-        pyci.odometer_two_spin(wfn, cost, q_max=q_max, t=t)
+        odometer_two_spin(wfn, cost, q_max=q_max, t=t)
     else:
         raise TypeError(f"invalid `wfn` type `{type(wfn)}`; must be `pyci.wavefunction`")

pyci/fanci/ap1rog.py

@@ -10,7 +10,7 @@
 
 import pyci
 
-from ..pyci import AP1roGObjective
+from pyci._pyci import AP1roGObjective
 from .fanci import FanCI
 
 

pyci/fanci/apig.py

@@ -9,7 +9,7 @@
 
 import pyci
 
-from ..pyci import APIGObjective
+from pyci._pyci import APIGObjective
 from .fanci import FanCI
 
 

pyci/gkci.py

@@ -18,8 +18,7 @@
 import numpy as np
 
 from scipy.special import gammaln, polygamma
-import pyci
-
+import pyci._pyci as pyci
 
 
 __all__ = [

pyci/seniority_ci.py

@@ -19,7 +19,7 @@
 
 import numpy as np
 
-from . import pyci
+import pyci._pyci as pyci
 
 
 __all__ = [

pyci/src/binding.cpp

@@ -26,7 +26,7 @@ using namespace pyci;
 Section: Python C extension.
 */
 
-BEGIN_MODULE(pyci, m)
+BEGIN_MODULE(_pyci, m)
 
 /*
 Section: Initialization

pyci/utility.py

@@ -16,7 +16,7 @@
 r"""PyCI utility module."""
 
 import numpy as np
-import pyci
+import pyci._pyci as pyci
 
 __all__ = [
     "make_senzero_integrals",

pyproject.toml

@@ -82,7 +82,7 @@ packages = [
 [tool.setuptools.package-data]
 # Non-Python files to include in the package
 "pyci" = [
-    "pyci.so",        # Compiled C++ extension
+    "_pyci.so",        # Compiled C++ extension
     "include/*.h",    # C++ header files
     "src/*.cpp"       # C++ source files
 ]