Scikit-mol

Improved Parallelism via joblib and software development flow improvements

Parallel Execution Improvements & API Changes

The codebase has been updated to improve parallel execution, now handled via joblib. This migration simplifies the underlying implementation, enhances robustness, and significantly improves performance, especially on Windows, reducing test run times from approximately 7 minutes to 1.5 minutes.

**API Change:**
The parallel argument has been replaced with n_jobs to align with scikit-learn’s API.
If you previously used parallel=True, update your code to n_jobs=-1 to utilize all available cores.
Note: n_jobs now only accepts integer values—boolean values are no longer supported.

**Bug Fix:**
Resolved a potential issue with safe_inference during parallel executions.

**Other Updates:**
Python 3.8 is deprecated as it is no longer supported.
Migrated to uv and hatchling for build and dependency management. See CONTRIBUTING.md for details.
Added plotting.py for parallel benchmark visualization and updated Notebook 7 with new benchmarks.


What's Changed
* Migration to joblib + new build system + separate reusable publish workflow by asiomchen in https://github.com/EBjerrum/scikit-mol/pull/58

**Full Changelog**: https://github.com/EBjerrum/scikit-mol/compare/v0.4.5...v0.4.6

New transformer class, AvalonFingerprintTransformer.

**Renaming of modules and classes for consistency**

Module and Class renaming for better consistency.
This will break imports in existing scripts, but better now than later.

Fingerprints are now in the fingerprints module rather than in the transformers module
(all are transformers, so this is more descriptive)

_Fingerprint_ consistently spelled out in the class names, e.g. not FP, but Fingerprint

Descriptors in the descriptors module

Smiles2Mol is now in a new module called conversions

Also:
New transformer available: MHFingerprintTransformer

Parallel transformations, see [https://github.com/EBjerrum/scikit-mol/blob/main/notebooks/07_parallel_transforms.ipynb](https://github.com/EBjerrum/scikit-mol/blob/main/notebooks/07_parallel_transforms.ipynb) for example and guidelines for use.

Merged the documentation branch to the main, and re-releasing tagged version.

What's Changed
* Documentation by EBjerrum in https://github.com/EBjerrum/scikit-mol/pull/23


**Full Changelog**: https://github.com/EBjerrum/scikit-mol/compare/v0.0.4...v0.1.1

Updated notebooks and Readme's, as well as various bug fixes.

What's Changed
* Fixed a bug in Standardize script by son-ha-264 in https://github.com/EBjerrum/scikit-mol/pull/21
* minor fixes, test script and adding toy data to run test by adrienchaton in https://github.com/EBjerrum/scikit-mol/pull/12
* Integration test by EBjerrum in https://github.com/EBjerrum/scikit-mol/pull/22

New Contributors
* adrienchaton made their first contribution in https://github.com/EBjerrum/scikit-mol/pull/12

**Full Changelog**: https://github.com/EBjerrum/scikit-mol/compare/v0.0.3...v0.1.0