Linting refactoring/3 manual fixes flagged by ruff

[mcocdawc]

Only merge after the current test-suite is fixed #53 Adresses one task in #54 merge after #55 and #56

made manual fixes of which I am sure and ignore E741

• I fixed many of the reported warnings/errors, but the unused/undeclared variables still pose a problem for the following reasons:

  1. Sometimes they come from function calls that have side effects, i.e. the function call has to be retained (perhaps)

  2. They seem like typos or inconsisten casing, e.g. COUL vs. coul, that appears later in the code

  Overall fixing these reported problems requires some deeper knowledge of the surrounding code.

• ignore E741 in ruff linting https://docs.astral.sh/ruff/rules/ambiguous-variable-name/

[mcocdawc]

Just to give some exemplary easily avoided bugs that were found by the linting:

eritransform_parallel

    from molbe.external.eri_transform import get_emb_eri_fast_gdf

in kbe.pbe.eritransform_parallel would fail, because the submodule does not even exists. Moving all imports to the top and using libdmet.basis_transform.eri_transform.get_emb_eri_fast_gdf throughout fixes it.

examples.kbe_polyacetylene

# Define fragment in the supercell
kfrag = fragpart(be_type="be2", mol=cell, kpt=kpt, frozen_core=True)
# Initialize BE
mykbe = BE(kmf, fobj, kpts=kpts)

# here the fobj is undefined and should be kfrag

examples.molbe_pp.py

mf = scf.RHF(mol)
mf.conv_tol = 1e-12
mf.kernel()

# Define fragments; use IAO scheme with 'sto-3g' as the minimal basis set
fobj = fragpart(be_type="be2", mol=mol, valence_basis="sto-3g", frozen_core=True)

# Initialize BE
mybe = BE(mg, fobj, lo_method="iao")

# here the mg is not defined and should be mf

[mcocdawc]

Examples for constructs that raised a warning, but were not yet fixed because they require a deeper inspection and background knowlege:

molbe.ube

In the following code the dm_init is never used.

dm_init = fobj_b.get_nsocc(self.S, self.C_b, self.Nocc[1], ncore=self.ncore)

Since get_nsocc has unfortunately side-effects, it requires more careful inspection if the line can be removed or replaced with:

fobj_b.get_nsocc(self.S, self.C_b, self.Nocc[1], ncore=self.ncore)

i.e. call get_nsocc purely for its side-effect.

kbe.lo

There is a line

ovlp_ciao = uciao[k].conj().T @ self.S[k] @ Ciao[k]

The name uciao is undefined, most likely it should be

ovlp_ciao = Ciao[k].conj().T @ self.S[k] @ Ciao[k]

but one has to make sure this was actually intended.

kbe.pbe

The variable ECOUL is unused and initialized to 0.0

        ECOUL = 0.0

lateron in the code a variable ecoul is used. Most likely this was a typo and mismatched lower- vs upper-case.

molbe.external.jac_utils

In the function get_dt1ao_an the variable deov is assigned to but never used.

Since someone actually chose a name for it

deov = get_Dia_r(dmoe, no)

it might actually be relevant for later expressions and was just forgotten.

[mcocdawc]

PR is postponed