Breakig changes in dependencies

[chrisjonesBSU]

I tried removing all of the pins in environment.yml to see where breaking changes are happening

These packages seem to be the bottle neck at the moment. I'm sure other dependency issues might pop up once these are updated (probably at least numpy 2.0)

pyscf
Installed version: 2.11
Old version: 1.7
Error: ModuleNotFoundError: No module named 'pyscf.semiempirical
pyscf is also pins python to <3.8, so updating to 2.x should let us use newer versions of python

h5py 3
Installed version: 3.7
Old version: 2.10
Error: ValueError: Using default_file_mode other than 'r' is no longer supported. Pass the mode to h5py.File() instead.

libcint
Installed version: 6.1.3
Old version: 4.0
Error: OSError: libcint.so.4: cannot open shared object file: No such file or directory

@StephMcCallum We need to see what replaced pyscf.semiempirical in pyscf 2, and make a PR that uses that in morphct. I bet the libcint issue will be resolved once pyscf 2 is supported, and we can bump libcint back up to version 6.x

[jennyfothergill]

I think pyscf needs to be installed with pip

pip install 'pyscf[semiempirical]'

python -c "import pyscf.semiempirical"

works on my mac with pyscf 2.11.0. I think the libcint and h5py packages/pins can be safely removed--a lot of that was trial and error trying to get the pyscf conda package to work IIRC.