make gemmi work with pybind11 2.3.0

.travis.yml

@@ -41,7 +41,7 @@ matrix:
 install:
 - |
   $PYTHON -m pip --version || $PYTHON -m ensurepip --user
-  $PYTHON -m pip install --user pybind11==2.2.4
+  $PYTHON -m pip install --user pybind11
   $PYTHON -c "import pybind11; print('headers: ' + pybind11.get_include(True))"
 script:
   - $COMPILER --version

examples/matthews.py

@@ -27,7 +27,8 @@ def gather_data():
     for path in util.get_file_paths_from_args():
         block = cif.read(path).sole_block()
         code = cif.as_string(block.find_value('_entry.id'))
-        na = sum('nucleotide' in t[0] for t in block.find('_entity_poly.type'))
+        na = sum('nucleotide' in t[0]
+                 for t in block.find_values('_entity_poly.type'))
         vs = block.find_value('_exptl_crystal.density_percent_sol')
         vm = block.find_value('_exptl_crystal.density_Matthews')
         d_min = block.find_value('_refine.ls_d_res_high')

examples/simple_search.py

@@ -7,6 +7,6 @@
 
 for path in get_file_paths_from_args():
     block = cif.read(path).sole_block()
-    anis = block.find("_atom_site_anisotrop.id")
+    anis = block.find_values("_atom_site_anisotrop.id")
     if len(anis) > 50000:
         print(block.name, len(anis))

python/unitcell.cpp

@@ -73,15 +73,15 @@ void add_unitcell(py::module& m) {
     .def("apply", &FTransform::apply);
 
 
-  py::class_<SymImage> symimage(m, "SymImage");
-  symimage
+  py::class_<SymImage>(m, "SymImage")
     .def("dist", &SymImage::dist)
     .def("__repr__", [](const SymImage& self) {
         return "<gemmi.SymImage cell:[" +
           triple(self.box[0], self.box[1], self.box[2]) +
           "] sym:" + std::to_string(self.sym_id) + ">";
     });
-  py::enum_<SameAsu>(symimage, "Asu")
+
+  py::enum_<SameAsu>(m, "Asu")
     .value("Same", SameAsu::Yes)
     .value("Different", SameAsu::No)
     .value("Any", SameAsu::Any);
@@ -108,8 +108,10 @@ void add_unitcell(py::module& m) {
     .def("fractionalize", &UnitCell::fractionalize)
     .def("orthogonalize", &UnitCell::orthogonalize)
     .def("volume_per_image", &UnitCell::volume_per_image)
+    // since pybind11 2.3.0 having =SameAsu::Any causes "import gemmi" to fail:
+    // ImportError: TypeError: __int__ returned non-int (type str)
     .def("find_nearest_image", &UnitCell::find_nearest_image,
-        py::arg("ref"), py::arg("pos"), py::arg("asu")=SameAsu::Any)
+         py::arg("ref"), py::arg("pos"), py::arg("asu")/*=SameAsu::Any*/)
     .def("is_special_position", &UnitCell::is_special_position,
          py::arg("pos"), py::arg("max_dist")=0.8)
     .def("calculate_1_d2", &UnitCell::calculate_1_d2,

setup.py

@@ -155,7 +155,7 @@ def build_extensions(self):
     ext_modules=ext_modules,
     packages=['gemmi-examples'],
     package_dir={'gemmi-examples': 'examples'},
-    install_requires=['pybind11==2.2.4'],
+    install_requires=['pybind11>=2.3.0'],
     cmdclass={'build_ext': BuildExt},
     zip_safe=False,
     license='MPL-2.0',

tests/test_mol.py

@@ -372,7 +372,8 @@ def test_ncs(self):
         ne2 = st[0].sole_residue('A', gemmi.SeqId('63'))['NE2']
         direct_dist = first_atom.pos.dist(ne2.pos)
         self.assertAlmostEqual(direct_dist, 34.89, delta=1e-2)
-        nearest_image = st.cell.find_nearest_image(first_atom.pos, ne2.pos)
+        nearest_image = st.cell.find_nearest_image(first_atom.pos, ne2.pos,
+                                                   gemmi.Asu.Any)
         nearest_dist = nearest_image.dist()
         self.assertAlmostEqual(nearest_dist, 8.02, delta=1e-2)
 

tools/upstream-check.py

@@ -8,7 +8,7 @@
 import urllib
 
 TAGGED_REPOS = {
-    'pybind/pybind11': 'v2.2.4',
+    'pybind/pybind11': 'v2.3.0',
     'taocpp/PEGTL': '2.4.0',
     'cxong/tinydir': '1.2.4',
     'madler/zlib': 'v1.2.11',