Add CrystalToolkitAnimationScene to phonon component (#476)

* add atom index to _meta

* Revert "add atom index to _meta"

This reverts commit 56497f2.

* add index to _meta

* remove empty line

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* ruff format

* add retain_atom_idx

* add animation component

* add .venv to .gitignore

* linting

* linting

* fix irregular bonding

---------

Co-authored-by: Chiu Peter <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Chiu Peter <[email protected]>
Co-authored-by: Patrick Huck <[email protected]>

Author: 5 people

.gitignore

@@ -13,3 +13,6 @@ build/*
 *.egg-info
 dist/*
 .vscode
+
+.venv/
+_version.py