Fix Atoms.cluster_from_file() in io.feff.inputs giving wrong number of atoms

[kaifengZheng]

Summary

Atoms.cluster_from_file() generates a cluster with a wrong number of atoms because it skips wrong lines when the format of feff input file in the Atom parts is different.
Major changes:

• feature 1(old): skipped 3 lines from the line having "ATOMS"
• fix 1(new): only skip 1 line(ignore ATOMS line)
• feature 2(old): It requires the special format of FEFF input file
• fix 2(new): add a condition to ignore the lines beginning with "*", which is feasible to adapt the different format of Atom parts

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

[janosh]

Suggested change

	if line and line[0].__contains__("*"):
	if line and line.startswith("*"):

[janosh]

why not test for the expected number of atoms?

[kaifengZheng]

Hi Janosh,
The expected number of atoms is 37; how should I specify this value?

[janosh]

Is != a typo?

[janosh]

You're missing one level of indentation to make it a method of the test class.

[kaifengZheng]

Let me fix it. sorry to confuse you. I want it to pass when the expected number of atoms is equal to num_atom and throw an error when the numbers are not equal.

[janosh]

We have 6 or more existing .inp files. Can you reuse those for testing?

[kaifengZheng]

Every updated feff.inp file has the same format. My input file deletes the * lines under ATOMS, which can be used for the test.

[janosh]

You're missing one level of indentation to make it a method of the test class.

[janosh]

This looks almost done but can you fix the failing tests: FileNotFoundError: [Errno 2] No such file or directory: 'ATOMS_test.inp'?