Improve types for electronic_structure.{bandstructure/cohp}

[DanielYang59]

Summary

• Improve type annotations and docstring for electronic_structure
  • bandstructure
  • cohp
• Replace unnecessary single-item list extend with append in 8e25238 for performance

Caution

Change the cell translation vector translation from list[float] to tuple[float, float, float] (Vector3D) in 9551db2 and 5fcf236

New custom type

• Add a custom type SpinLike:

  pymatgen/pymatgen/electronic_structure/cohp.py

  Lines 120 to 121 in c83d5d5

  	spin: Spin. Can be parsed as spin object, integer (-1/1)
  	or str ("up"/"down")

Script for testing lobsterpy

Bash script

#!/bin/bash -l

CONDA_PROFILE="/opt/anaconda3/etc/profile.d/conda.sh"
ENV_NAME="test_lobster"
PYTHON_VERSION="3.11"
PMG_REPO="https://github.com/DanielYang59/pymatgen.git"
PMG_BRANCH="type-elec-struct"
LOBSTERPY_REPO="https://github.com/JaGeo/LobsterPy.git"

# Functions
function create_and_activate_env() {
  conda create -y -n $ENV_NAME python=$PYTHON_VERSION
  conda activate $ENV_NAME
}

function clone_and_install_pymatgen() {
  git clone --depth 1 -b $PMG_BRANCH $PMG_REPO
  cd pymatgen
  pip install .
  cd ..
}

function clone_and_install_lobsterpy() {
  git clone --depth 1 $LOBSTERPY_REPO
  cd LobsterPy
  pip install -e '.[featurizer,dev,tests]'
  pip install pytest-xdist
  cd ..
}

function run_pytest() {
  cd LobsterPy
  pytest tests --maxfail=1000
  cd ..
}

function remove_env() {
  conda deactivate
  conda env remove -n $ENV_NAME -y
}

# Main Script
source $CONDA_PROFILE
create_and_activate_env
clone_and_install_pymatgen
clone_and_install_lobsterpy
run_pytest
remove_env

[DanielYang59]

Need a closer look at this type error, perhaps it's because mypy might be false-positive in determining overlapping types python/mypy#4020.

[DanielYang59]

It's a bit unclear to me what is translation? Is it a 3D vector?

[JaGeo]

Same wording is used as in Lobster. It describes the unit cell in which the atom is in. [0 0 0] is the normal cell, but the atom might be translated to the neighboring cell

[DanielYang59]

Thanks for clarifying! I just searched the wrong documentation ;) I searched Lobster_FAQ_5.0.0 instead of Lobster_Users_Guide_5.0.0.

If atoms are not located in the original unit cell, the corresponding translation vector can be added by the keyword "cell" like this:
cobiBetween atom 1 atom 2 atom 3 cell 1 0 0

Update: clarified in 0e75e0d

[janosh]

thanks a lot @DanielYang59 for your continued clean up efforts! 👍

[DanielYang59]

All good, thanks for reviewing. I would clean up the merge conflicts in #3880 to get it ready for review. Thanks for your time :)