python extension module is now installed into site-packages/gemmi/

and it's organized in a peculiar way, as advised here:
wjakob/nanobind#730

CMakeLists.txt

@@ -492,7 +492,9 @@ if (USE_PYTHON)
   else()
     target_link_libraries(gemmi_py PRIVATE gemmi_cpp)
   endif()
-  set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME gemmi)
+  set_property(TARGET gemmi_py PROPERTY OUTPUT_NAME _gemmi)
+  set_property(TARGET gemmi_py PROPERTY LIBRARY_OUTPUT_DIRECTORY py/gemmi)
+  configure_file(python/gemmi/__init__.py py/gemmi/__init__.py COPYONLY)
 
   # nanobind gives warnings with -Wpedantic and -Wshadow
   if(CMAKE_CXX_FLAGS MATCHES "-Wshadow")
@@ -526,7 +528,7 @@ if (USE_PYTHON)
     nanobind_add_stub(
       gemmi_stub
       MODULE gemmi
-      OUTPUT __init__.pyi
+      OUTPUT py/gemmi/__init__.pyi
       PYTHON_PATH $<TARGET_FILE_DIR:gemmi_py>
       DEPENDS gemmi_py
       PATTERN_FILE "${CMAKE_CURRENT_SOURCE_DIR}/python/stubs.pat"
@@ -535,7 +537,7 @@ if (USE_PYTHON)
     nanobind_add_stub(
       gemmi_cif_stub
       MODULE gemmi.cif
-      OUTPUT cif.pyi
+      OUTPUT py/gemmi/cif.pyi
       PYTHON_PATH $<TARGET_FILE_DIR:gemmi_py>
       DEPENDS gemmi_py
     )
@@ -588,22 +590,22 @@ if (USE_PYTHON)
     if (DEFINED SKBUILD)
       # When building via pip, Python_SITEARCH is /tmp.../wheel/platlib,
       # different from the actual install path. Best guess:
-      set(rpath_rel "../../../${CMAKE_INSTALL_LIBDIR}")
+      set(rpath_rel "../../../../${CMAKE_INSTALL_LIBDIR}")
     else()
       file(RELATIVE_PATH rpath_rel
-           "${Python_SITEARCH}" "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+           "${Python_SITEARCH}/gemmi" "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
     endif()
     set_target_properties(gemmi_py PROPERTIES INSTALL_RPATH "${origin}/${rpath_rel}")
   endif()
-  install(TARGETS gemmi_py DESTINATION "${Python_SITEARCH}" COMPONENT py)
+  install(TARGETS gemmi_py DESTINATION "${Python_SITEARCH}/gemmi" COMPONENT py)
   install(DIRECTORY examples DESTINATION "${Python_SITEARCH}/gemmi" COMPONENT py
           FILES_MATCHING PATTERN "*.py"
           PATTERN "[._]*" EXCLUDE)
   if (GENERATE_STUBS AND NOT CMAKE_CROSSCOMPILING)
     install(FILES
-            "${CMAKE_CURRENT_BINARY_DIR}/py.typed"
-            "${CMAKE_CURRENT_BINARY_DIR}/__init__.pyi"
-            "${CMAKE_CURRENT_BINARY_DIR}/cif.pyi"
+            "${CMAKE_CURRENT_BINARY_DIR}/py/py.typed"
+            "${CMAKE_CURRENT_BINARY_DIR}/py/__init__.pyi"
+            "${CMAKE_CURRENT_BINARY_DIR}/py/cif.pyi"
             DESTINATION "${Python_SITEARCH}/gemmi" COMPONENT py)
   endif()
 endif()

docs/install.rst

@@ -249,7 +249,7 @@ Code derived from the following projects is used in the library:
 * `QCProt <https://theobald.brandeis.edu/qcp/>`_ -- superposition method
   in `qcp.hpp` is taken from QCProt and adapted to our project. License: BSD.
 * `Larch <https://github.com/xraypy/xraylarch>`_ -- calculation of f' and f"
-  in `fprime.hpp` is based on CromerLiberman code from Larch.
+  in `fprime.cpp` is based on CromerLiberman code from Larch.
   License: 2-clause BSD.
 
 Projects included under `third_party/` that are not used in the library

python/gemmi.cpp

@@ -153,7 +153,8 @@ void add_misc(nb::module_& m) {
   }, nb::arg("nbins"), nb::arg("obs"), nb::arg("calc"));
 }
 
-NB_MODULE(gemmi, mg) {
+NB_MODULE(_gemmi, mg_) {
+  nb::module_ mg = nb::module_::import_("gemmi");
   mg.doc() = "Python bindings to GEMMI - a library used in macromolecular\n"
              "crystallography and related fields";
   mg.attr("__version__") = GEMMI_VERSION;

python/gemmi/__init__.py

@@ -0,0 +1,2 @@
+# Importing C++ extension populates this module.
+from . import _gemmi

run-tests.sh

@@ -6,7 +6,7 @@
 # PYTHONPATH. Locally, I'm using bash function "gpy" that starts python with
 # gemmi imported ("gpy" for interactive mode, "gpy file.py" for script):
 #   echo "import gemmi" > $HOME/.import-gemmi.py
-#   gpy() { PYTHONPATH=$HOME/gemmi/gemmi/build PYTHONSTARTUP=$HOME/.import-gemmi.py python3 -q "$@"; }
+#   gpy() { PYTHONPATH=$HOME/gemmi/gemmi/build/py PYTHONSTARTUP=$HOME/.import-gemmi.py python3 -q "$@"; }
 
 # set up variables
 set -eu
@@ -33,19 +33,19 @@ if [ $# != 0 ] && [ $1 = n ]; then
     shift
 else
     (cd $BUILD_DIR && make -j4 all check)
-    ./tools/cmp-size.py build/gemmi build/*gemmi*.so
+    ./tools/cmp-size.py build/gemmi build/libgemmi_cpp.so build/py/gemmi/_gemmi*
     ./tools/docs-help.sh
 fi
 ./tools/header-list.py >docs/headers.rst
 (cd docs && make -j4 html SPHINXOPTS="-q -n")
 
 # Run tests and checks.
 if [ $# = 0 ] || [ $1 != i ]; then
-    export PYTHONPATH=$BUILD_DIR
+    export PYTHONPATH=$BUILD_DIR/py
     export PATH="$BUILD_DIR:$PATH"
 fi
 $PYTHON -m unittest discover -s tests
-grep :: $BUILD_DIR/*.pyi ||:
+grep :: $BUILD_DIR/py/gemmi/*.pyi ||:
 
 if [ -z "${NO_DOCTEST-}" ]; then
     # 'make doctest' works only if sphinx-build was installed for python3.