Restore Python bindings on current Python

.github/workflows/python-package.yml

@@ -56,3 +56,70 @@ jobs:
           path: |
             coverage.txt
             coverage.xml
+
+  bindings:
+    name: Python bindings
+    runs-on: ubuntu-22.04
+    timeout-minutes: 30
+    env:
+      CMAKE_POLICY_VERSION_MINIMUM: "3.5"
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Set up Python 3.14
+        uses: actions/setup-python@v7
+        with:
+          python-version: "3.14"
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            bison \
+            build-essential \
+            flex \
+            libboost-dev \
+            libeigen3-dev \
+            liblapack-dev \
+            libopenblas-serial-dev \
+            libreadline-dev \
+            libsuitesparse-dev \
+            swig
+          git clone --depth 1 https://github.com/Electrostatics/metis-fork.git /tmp/metis
+          cd /tmp/metis
+          make config prefix=/usr/local
+          sudo make install
+
+      - name: Configure Python bindings
+        run: |
+          cmake -S . -B build-bindings \
+            -DAPBS_STATIC_BUILD=OFF \
+            -DBLA_VENDOR=OpenBLAS \
+            -DBUILD_DOC=OFF \
+            -DBUILD_SHARED_LIBS=ON \
+            -DBUILD_TOOLS=ON \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DCMAKE_INSTALL_PREFIX="$PWD/build-bindings/install" \
+            -DENABLE_BEM=OFF \
+            -DENABLE_GEOFLOW=OFF \
+            -DENABLE_iAPBS=OFF \
+            -DENABLE_PBAM=OFF \
+            -DENABLE_PBSAM=OFF \
+            -DENABLE_PYGBE=OFF \
+            -DENABLE_PYTHON=ON \
+            -DENABLE_TESTS=OFF \
+            -DGET_NanoShaper=OFF \
+            -DPYTHON_VERSION=3.14
+
+      - name: Build and install Python bindings
+        run: cmake --build build-bindings --parallel 2 --target install
+
+      - name: Test Python bindings
+        run: |
+          cd /tmp
+          PYTHONPATH="$GITHUB_WORKSPACE/build-bindings/install/lib" \
+            python "$GITHUB_WORKSPACE/tools/python/test_bindings.py"

CMakeLists.txt

@@ -170,6 +170,16 @@ set(FETK_VERSION "57195e55351e04ce6ee0ef56a143c996a9aee7e2" CACHE STRING "Versio
 include(ImportFETK)
 import_fetk(${FETK_VERSION})
 
+if(NOT APBS_STATIC_BUILD)
+    find_package(BLAS REQUIRED)
+    if(TARGET cgcode)
+        target_link_libraries(cgcode PRIVATE vf2c BLAS::BLAS)
+    endif()
+    if(TARGET superlu)
+        target_link_libraries(superlu PRIVATE BLAS::BLAS)
+    endif()
+endif()
+
 if(APPLE AND CMAKE_C_COMPILER_ID MATCHES "AppleClang|Clang" AND TARGET vf2c)
     target_compile_options(vf2c PRIVATE -Wno-error=implicit-int)
 endif()

tools/python-pybind/CMakeLists.txt

@@ -1,5 +1,17 @@
 
-find_package(pybind11 REQUIRED)
+set(PYBIND11_FINDPYTHON ON)
+find_package(pybind11 CONFIG QUIET)
+if(NOT TARGET pybind11::module)
+  if(NOT EXISTS ${CMAKE_SOURCE_DIR}/externals/pybind11/CMakeLists.txt)
+    message(FATAL_ERROR "pybind11 was not found and its submodule is unavailable")
+  endif()
+  add_subdirectory(
+    ${CMAKE_SOURCE_DIR}/externals/pybind11
+    ${CMAKE_BINARY_DIR}/externals/pybind11
+    EXCLUDE_FROM_ALL
+    )
+endif()
+
 add_library(apbs_pybind
   MODULE
   module.cpp

tools/python-pybind/bind_nosh.cpp

@@ -1,17 +1,18 @@
 #include "bind_nosh.hpp"
 #include "bind_valist.hpp"
 
-int parseInputFromString(NOsh *nosh, std::string str)
+int parseInputFromString(NOsh *nosh, const std::string& str)
 {
   int ret, bufsize;
   Vio *sock;
 
   startVio();
 
-  VASSERT( bufsize <= VMAX_BUFSIZE );
+  VASSERT( str.size() <= VMAX_BUFSIZE );
+  bufsize = static_cast<int>(str.size());
   sock = Vio_ctor("BUFF","ASC",VNULL,"0","r");
 
-  Vio_bufTake(sock, const_cast<char*>(str.c_str()), str.size());
+  Vio_bufTake(sock, const_cast<char*>(str.c_str()), bufsize);
 
   ret = NOsh_parseInput(nosh, sock); 
   sock->VIObuffer = VNULL;
@@ -59,20 +60,7 @@ void bind_nosh(py::module& m)
     .def("parseInputFromString",
         [] (NOsh& self, std::string str) -> int
         {
-          int ret, bufsize;
-          Vio *sock;
-
-          startVio();
-
-          VASSERT( bufsize <= VMAX_BUFSIZE );
-          sock = Vio_ctor("BUFF","ASC",VNULL,"0","r");
-
-          Vio_bufTake(sock, const_cast<char*>(str.c_str()), str.size());
-
-          ret = NOsh_parseInput(&self, sock); 
-          sock->VIObuffer = VNULL;
-          Vio_dtor(&sock);
-          return ret;
+          return parseInputFromString(&self, str);
         })
     .def("__del__",
         [] (NOsh* self)

tools/python/CMakeLists.txt

@@ -3,7 +3,7 @@ if (${CMAKE_VERSION} VERSION_GREATER "3.13")
 	CMAKE_POLICY(SET CMP0086 OLD)
 endif()
 
-FIND_PACKAGE(SWIG REQUIRED)
+FIND_PACKAGE(SWIG 4.0 REQUIRED)
 INCLUDE(${SWIG_USE_FILE})
 
 
@@ -36,18 +36,9 @@ endif(APPLE)
 
 SWIG_LINK_LIBRARIES(apbslib ${APBS_LIBS} ${APBS_INTERNAL_LIBS} ${Python3_LIBRARIES})
 
-if(WIN32)
-	add_custom_command(TARGET _apbslib POST_BUILD
-		COMMAND ${CMAKE_COMMAND} -E
-			copy ${CMAKE_CURRENT_BINARY_DIR}/apbslib.py ${CMAKE_SOURCE_DIR}/../pdb2pqr/pdb2pka
-		COMMAND ${CMAKE_COMMAND} -E
-			copy ${LIBRARY_OUTPUT_PATH}/$<CONFIG>/_apbslib.pyd ${CMAKE_SOURCE_DIR}/../pdb2pqr/pdb2pka
-		)
-else()
-	add_custom_command(TARGET _apbslib POST_BUILD
-		COMMAND ${CMAKE_COMMAND} -E
-			copy ${CMAKE_CURRENT_BINARY_DIR}/apbslib.py ${CMAKE_SOURCE_DIR}/../pdb2pqr/pdb2pka
-		COMMAND ${CMAKE_COMMAND} -E
-			copy ${LIBRARY_OUTPUT_PATH}/_apbslib${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_SOURCE_DIR}/../pdb2pqr/pdb2pka
-	)
-endif()
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/apbslib.py
+        DESTINATION lib
+        COMPONENT python)
+install(TARGETS ${SWIG_MODULE_apbslib_REAL_NAME}
+	LIBRARY DESTINATION lib COMPONENT python
+	RUNTIME DESTINATION lib COMPONENT python)

tools/python/apbslib.i

@@ -272,18 +272,18 @@ void set_entry(double *array, int i, double val){
 
 %inline %{
 
-int parseInputFromString(NOsh *nosh, PyObject *string){
+int parseInputFromString(NOsh *nosh, const char *string){
 
     int ret, bufsize;
     Vio *sock;
 
     startVio();
-    bufsize = PyString_Size(string);
+  bufsize = strlen(string);
 
     VASSERT( bufsize <= VMAX_BUFSIZE );
     sock = Vio_ctor("BUFF","ASC",VNULL,"0","r");
 
-    Vio_bufTake(sock, PyString_AsString(string), bufsize);
+    Vio_bufTake(sock, (char *)string, bufsize);
 
     ret = NOsh_parseInput(nosh, sock);
     sock->VIObuffer = VNULL;
@@ -441,9 +441,9 @@ PyObject *getForces(AtomForce **atomForce, Valist *alist){
     dbholder = PyList_New(3);
     ibholder = PyList_New(3);
 
-    qf = PyString_FromString("qf");
-    db = PyString_FromString("db");
-    ib = PyString_FromString("ib");
+    qf = PyUnicode_FromString("qf");
+    db = PyUnicode_FromString("db");
+    ib = PyUnicode_FromString("ib");
 
     for (i=0;i<Valist_getNumberAtoms(alist);i++){
         for (j=0;j<3;j++){

tools/python/main.py

@@ -77,7 +77,6 @@
     Vcom_rank,
     Vcom_size,
     Vmem_ctor,
-    atomForce,
     delete_Com,
     delete_Mem,
     delete_Nosh,
@@ -126,7 +125,6 @@
     wrap_forceMG,
     writedataMG,
     writematMG,
-    xrange,
 )
 import sys
 import time
@@ -271,7 +269,7 @@ def main():
     atomforce = new_atomforcelist(NOSH_MAXCALC)
 
     # Start the main timer
-    main_timer_start = time.clock()
+    main_timer_start = time.perf_counter()
 
     # Check invocation
     stdout.write(getHeader())
@@ -324,10 +322,10 @@ def main():
 
     stdout.write("Preparing to run %d PBE calculations. \n" % nosh.ncalc)
 
-    for icalc in xrange(nosh.ncalc):
+    for icalc in range(nosh.ncalc):
         totEnergy.append(0.0)
 
-    for icalc in xrange(nosh.ncalc):
+    for icalc in range(nosh.ncalc):
         stdout.write("---------------------------------------------\n")
         calc = NOsh_getCalc(nosh, icalc)
         mgparm = calc.mgparm
@@ -419,19 +417,19 @@ def main():
     if nosh.nprint > 0:
         stdout.write("---------------------------------------------\n")
         stdout.write("PRINT STATEMENTS\n")
-    for iprint in xrange(nosh.nprint):
+    for iprint in range(nosh.nprint):
         if NOsh_printWhat(nosh, iprint) == NPT_ENERGY:
             printEnergy(com, nosh, totEnergy, iprint)
         elif NOsh_printWhat(nosh, iprint) == NPT_FORCE:
             printForce(com, nosh, nforce, atomforce, iprint)
         elif NOsh_printWhat(nosh, iprint) == NPT_ELECENERGY:
             printElecEnergy(com, nosh, totEnergy, iprint)
         elif NOsh_printWhat(nosh, iprint) == NPT_ELECFORCE:
-            printElecForce(com, nosh, nforce, atomForce, iprint)
+            printElecForce(com, nosh, nforce, atomforce, iprint)
         elif NOsh_printWhat(nosh, iprint) == NPT_APOLENERGY:
             printApolEnergy(nosh, iprint)
         elif NOsh_printWhat(nosh, iprint) == NPT_APOLFORCE:
-            printApolForce(com, nosh, nforce, atomForce, iprint)
+            printApolForce(com, nosh, nforce, atomforce, iprint)
         else:
             stdout.write("Undefined PRINT keyword!\n")
             break
@@ -472,7 +470,7 @@ def main():
     stdout.write("Thanks for using APBS!\n\n")
 
     # Stop the main timer
-    main_timer_stop = time.clock()
+    main_timer_stop = time.perf_counter()
     stdout.write(
         "Total execution time:  %1.6e sec\n"
         % (main_timer_stop - main_timer_start)

tools/python/noinput.py

@@ -94,11 +94,9 @@
     wrap_forceMG,
     writedataMG,
     writematMG,
-    xrange,
 )
 import sys
 import time
-import string
 import re
 from sys import stdout, stderr
 
@@ -317,7 +315,7 @@ def printResults(energyList, potList, forceList):
 
     factor = getUnitConversion()
 
-    for i in xrange(len(potList)):
+    for i in range(len(potList)):
         list = potList[i]
         print(f"\nPer-atom potentials from calculation {i}")
         for j in range(len(list)):
@@ -384,7 +382,7 @@ def runAPBS(PQR, INPUT):
     atomforce = new_atomforcelist(NOSH_MAXCALC)
 
     # Start the main timer
-    main_timer_start = time.clock()
+    main_timer_start = time.perf_counter()
 
     # Parse the input file
     nosh = NOsh_ctor(rank, size)
@@ -400,7 +398,7 @@ def runAPBS(PQR, INPUT):
     # the need for an actual PQR file from stdin
 
     alist = new_valist(NOSH_MAXMOL)
-    atoms = string.split(PQR, "\n")
+    atoms = PQR.split("\n")
     for i in range(len(atoms)):
         atom = atoms[i]
         if not (atom.startswith("ATOM") or atom.startswith("HETATM")):
@@ -413,7 +411,7 @@ def runAPBS(PQR, INPUT):
         if re.compile(r"( [A-Z]{3} [A-Z]{1} *\d+)").findall(atom) != []:
             haschain = 1
 
-        params = string.split(atom)
+        params = atom.split()
         x.append(float(params[5 + haschain]))
         y.append(float(params[6 + haschain]))
         z.append(float(params[7 + haschain]))
@@ -576,7 +574,7 @@ def runAPBS(PQR, INPUT):
     if nosh.nprint > 0:
         stdout.write("---------------------------------------------\n")
         stdout.write("PRINT STATEMENTS\n")
-    for iprint in xrange(nosh.nprint):
+    for iprint in range(nosh.nprint):
         if NOsh_printWhat(nosh, iprint) == NPT_ENERGY:
             printEnergy(com, nosh, totEnergy, iprint)
         elif NOsh_printWhat(nosh, iprint) == NPT_FORCE:
@@ -621,7 +619,7 @@ def runAPBS(PQR, INPUT):
     stdout.write("Thanks for using APBS!\n\n")
 
     # Stop the main timer
-    main_timer_stop = time.clock()
+    main_timer_stop = time.perf_counter()
     stdout.write(
         "Total execution time:  %1.6e sec\n"
         % (main_timer_stop - main_timer_start)

tools/python/test_bindings.py

@@ -0,0 +1,40 @@
+"""Smoke tests for the installed APBS Python extension modules."""
+
+import ast
+from importlib import import_module
+from pathlib import Path
+
+
+def load_example_input():
+    """Load the input string without executing the legacy driver."""
+    source = Path(__file__).with_name("noinput.py").read_text(encoding="utf-8")
+    tree = ast.parse(source)
+    for node in tree.body:
+        if not isinstance(node, ast.Assign):
+            continue
+        if any(
+            isinstance(target, ast.Name) and target.id == "INPUT"
+            for target in node.targets
+        ):
+            return ast.literal_eval(node.value)
+    raise RuntimeError("Could not find INPUT in noinput.py")
+
+
+def main():
+    """Parse the same APBS input through both binding implementations."""
+    apbs = import_module("apbs")
+    apbslib = import_module("apbslib")
+    input_text = load_example_input()
+
+    legacy_nosh = apbslib.NOsh_ctor(0, 1)
+    try:
+        assert apbslib.parseInputFromString(legacy_nosh, input_text) == 1
+    finally:
+        apbslib.delete_Nosh(legacy_nosh)
+
+    modern_nosh = apbs.NOsh()
+    assert modern_nosh.parseInputFromString(input_text) == 1
+
+
+if __name__ == "__main__":
+    main()