support None for const char* arg, with minimal overhead #683
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Since pybind11 also accepts None for const char* as an exception among built-in types, remove a paragraph about differences in porting.rst.
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Please report problems when you find them. notes and changes ----------------- Protocol Buffer is currently not supported by nanobind. Adding GridBase.__array__() for NumPy interoperability in many cases works as seemless replacement of the Protocol Buffer. Implicit list->ndarray conversion is also not supported, but is welcomed: wjakob/nanobind#327 None is not accepted by default, an annotation must be added. I may have missed it in some functions - let me know. In case of const char* arg, None is not supported at all; I proposed it upstream: wjakob/nanobind#683 For default nullptr, using nb::arg()=nb::none() instead of =nullptr. Both work, but the latter seems to be more canonical in nanobind. In nanobind 2.x using make_iterator and bind_vector+__getitem__ returns copies, not references, by default. We usually prefer to avoid copying. Added a helper function usual_iterator() that uses old rv_policy. gemmi.ValueSigmaAsuData.value_array: previously had so-called structured data type, now it has shape (N,2) with dtype=float32. Added pickling support for Structure, Model, Chain, Residue, Atom, UnitCell. Notes about pickling of SpaceGroup: wjakob/nanobind#670 In a follow up, picking of SpaceGroup was optimized, replacing xhm() with an index. The gain was modest (pickling and unpickling a list of all SpaceGroups from the built-in table was reduced from ~1ms, to ~0.5ms). It might not be safe - multiple copies of the table may exist. Notes about constructors for PdbWriteOptions and MmcifOutputGroups: see wjakob/nanobind#664 doctests: many changes, mostly because __repr__ of enums and of bind_vector-ed classes in nanobind is different than in pybind11 added alignas(8) to HklValue: in nanobind array bindings, stride is given as a number of elements, not bytes. This was a problem for ComplexAsuData.value_array: sizeof(HklValue) was 20 (3*4+2*4) which is not a multiple of 8. Functions IT92Coef.calculate_sf() and IT92Coef.calculate_density_iso() used to be vectorized (could take numpy array as arg), now they aren't, let me know if you need a vectorized version. Not yet done: *.pyi files with type annotations Planned: unified logging of warnings/errors from various gemmi functions
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Since pybind11 also accepts None for
const char*as an exception among built-in types, remove a paragraph about differences in porting.rst.The overhead is minimal. Checking the size of
test_functions_ext.cpython-311-x86_64-linux-gnu.sobuilt with -O3, it increased only by 32 bytes.I'm aware that it's possible to use
std::optional<const char*>, but to me it looks more awkward thanstd::optional<int>, perhaps becauseconst char*, unlikestd::string, looks already optional.There is a third place in docs where None arg is covered:
nanobind/docs/functions.rst
Lines 178 to 181 in 8e5fd14
Perhaps it's outdated, because having argument such as
int*works fine, just doesn't accept None. Or I misunderstand it. Anyway, I didn't try to edit it.