Changed to default factor for new dataclass syntax

Nle lc (ur-whitelab#133)

* Added langchain and improve NLE

* Tweaked prompt

* Updated notebook

* Added correlation direction

* More work on prompt

* Updated prompt for single vs multi molecules

* More prompt refinement

* Model changes

* Removed oai key dependency

* Updated notebook experiments

* Fixed old text generate code

* Addded OAI key

* Added openai to dev requirements

* Added OAI Key and uncommented explains

Removed tildes coming from synspace

They indicate anybond, so I assume singles. Not perfect, but SMIRKS are poorly defined.
Just need better SMIRKS for the retrosynthesis.

Added date to release

Nle improvements (ur-whitelab#119)

* Improve NLEs

* Added NLE info to tutorial

* Fixed T-statistic computation

* Made presence be majority for multiple bases

* Changed presence computation

* Reverse presence threshold

* Removed none names

* Added openai to code

* updated changelog

* Fixed wording on openai method

* Added sorting

* Made it so at least one POS example is included after merge

* Update build.yml

* Addressed corner case of no explanations

* Made it smarter about including weak descriptors

* Fixed pos_count

* Improved similarity plots to use new plotting code

* Made similarity plots overlap with more atoms

* fixed bug affecting paper2 notebooks

* Updated sklearn requirements

Merge of code for text explanation results (ur-whitelab#114)

* Created text explanations

* Incorporated code from other branches

* Added ECFP names to plots


Co-authored-by: Heta Gandhi <[email protected]>

Fixed plotting bug (ur-whitelab#107)



* Fixed plotting and added tutorial

Co-authored-by: Heta Gandhi <[email protected]>

Easier usage of lime_explain (ur-whitelab#105)

* Fixed doc string

* MACCS is default, saving is default behavior for plotting

* descriptor_type is inferred for plotting

* fixed svg display

* only throw an error for ecfp

* not saving for maccs and classic

* fixed mypy complains

* Made it still possible to save a figure

* ran pre-commit

* Bumpbed version

Co-authored-by: Andrew White <[email protected]>

Fixed run_stoned default alphabet

Merge branch 'main' of github.com:ur-whitelab/exmol into main