Superpose3d

In the previous release, I forgot to update the version numbers in the setup.py file. This small update fixes that. (It was necessary to do that to upload the changes to pypi.)

This version fixes a bug that prevented "c" (the scale factor) from being calculated correctly. This bug was caused by a typo introduced in v1.1.0 (commit 91d30b8) when converting the for-loops into compact numpy expressions.
Hopefully scale factors are being calculated correctly now.

This fixes a bug which was introduced in v1.1.0.

When we first began using numpy to speed up the matrix operations (introduced in v1.1.0), we forgot to incorporate weights in one part of the code. So the python code worked when uniform weights were used (which occurs by default). But we forgot to make sure that non-uniform weights are working.

This code has finally been fixed, and the testing code has been updated.

The first entry in the output of Superpose3D() is now a number instead of a rank-0 tensor. The previous behavior (rank-0 tensor) was a mistake which my automated tests failed to catch. Changing this might break backward compatibility for some users, but this new behavior is simpler and is consistent with the documentation.

Very small update. After updating to the latest version of *jacobi_pd*, a few namespaces and include files needed to be updated ("*matrix_alloc*"->"*matrix_alloc_jpd*"). (Both *superpose3d.hpp* and *test_superpose3d.cpp* borrow the short routines for allocating 2D arrays located in the "*matrix_alloc_jpd.hpp*" include file.)

Replaced "vector" with "std::vector".
Thanks to github user KeeganBruer for reporting this.