Remove Open Babel support

[RMeli]

Description

Close #149. Open Babel seems to be abandoned, especially from the Python side.

Checklist

• Tests
• Documentation
• Changelog

[Copilot]

Pull request overview

This PR removes support for Open Babel from the spyrmsd library, focusing exclusively on RDKit for molecule I/O operations. The change is motivated by Open Babel being abandoned, particularly on the Python side.

• Removed the entire spyrmsd/optional/obabel.py module
• Updated import logic to only use RDKit for molecular operations
• Removed the molformat() utility function that was specific to Open Babel

Reviewed changes

Copilot reviewed 39 out of 39 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
spyrmsd/optional/obabel.py	Deleted entire Open Babel integration module
spyrmsd/io.py	Simplified import logic to only try RDKit, removed nested fallback
spyrmsd/utils.py	Removed molformat() function used for Open Babel format conversion
spyrmsd/optional/rdkit.py	Changed from utils.molformat() to utils.format(), updated docstring reference
spyrmsd/molecule.py	Removed from_obabel() class method, updated docstring
spyrmsd/__main__.py	Updated error message to only mention RDKit requirement
setup.py	Removed openbabel from extras_require
tests/test_utils.py	Removed test_molformat() test function
tests/test_molecule.py	Removed test_from_obmol() test function
docs/source/tutorials/tutorial.rst	Updated to remove Open Babel references, changed section headings
docs/source/tutorials/tutorial.ipynb	Updated notebook to remove Open Babel references
docs/source/installation.rst	Removed Open Babel from installation instructions
docs/source/api/*.rst	Standardized order of autodoc directives, removed obabel module docs
devtools/conda-envs/*.yaml	Removed Open Babel test environments and dependency
.github/workflows/pytest.yml	Removed Open Babel from test matrix
.github/workflows/pre-commit.yml	Updated Python version matrix
README.md	Updated to remove Open Babel references
CHANGELOG.md	Added entry for Open Babel removal

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.