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fa5cf48
regex splitting logic
anoushka2000 Apr 23, 2026
95e834d
BigSMILES vocab file add
anoushka2000 Apr 23, 2026
821f97e
add vocab_bigsmiles to includes
anoushka2000 Apr 23, 2026
b656edd
fist pass big smiles tokenizer
anoushka2000 Apr 23, 2026
b3f7eac
add big smiles tokenizer to wrapper
anoushka2000 Apr 23, 2026
56002c6
add python tests
anoushka2000 Apr 23, 2026
26d284b
formatting and first pass demo
anoushka2000 Apr 23, 2026
c860816
add additional tokenization and MLM demo in nbk
anoushka2000 Apr 23, 2026
ab85a89
add API ref
anoushka2000 Apr 23, 2026
d7eb1a8
docs: add path to BigSMILES spec
anoushka2000 Apr 26, 2026
3da58ec
add updated vocab generator
anoushka2000 Apr 26, 2026
ba53f9f
add support for abstarct labels and test for spec egs
anoushka2000 Apr 26, 2026
3905621
fix unk handling and add test
anoushka2000 Apr 26, 2026
789b9fb
add missing test for clone
anoushka2000 Apr 26, 2026
e553b15
formatting
anoushka2000 Apr 26, 2026
6a039e3
add rust level test for splitting and init
anoushka2000 Apr 26, 2026
e765b39
remove redundant jupyter notebook dep
anoushka2000 Apr 26, 2026
023b549
add BigSMILES tokenizer to changelog
anoushka2000 Apr 26, 2026
b20b142
serialize BigSMILES version and test save
anoushka2000 Apr 28, 2026
601b36c
fix typo in demo notebook
anoushka2000 Apr 28, 2026
a3f14cf
only support abstract labels when fragment def is provided
anoushka2000 Apr 28, 2026
5bf0d10
regex generator updated for new abstract label logic
anoushka2000 Apr 28, 2026
0af2abc
expand test and test all smiles/ bigsmiles for round trip
anoushka2000 Apr 28, 2026
7ef3e88
clean up test formatting
anoushka2000 Apr 28, 2026
a6e503a
add fragment label handling in docs notebook
anoushka2000 Apr 28, 2026
45e0e2a
fix: link to fragment names in notebook md
anoushka2000 May 6, 2026
0594550
fix dependabot
awadell1 May 10, 2026
8cdf333
use default versioning-strategy
awadell1 May 10, 2026
01e6fca
Bump rdkit from 2024.9.5 to 2026.3.1
dependabot[bot] May 10, 2026
8925a27
Bump actions/upload-artifact from 5 to 7
dependabot[bot] May 10, 2026
a9032f5
Bump actions/attest-build-provenance from 3 to 4
dependabot[bot] May 10, 2026
9736128
Bump actions/upload-pages-artifact from 4 to 5
dependabot[bot] May 10, 2026
4b32738
Bump actions/checkout from 3 to 6
dependabot[bot] May 10, 2026
46bf9a1
Bump actions/deploy-pages from 4 to 5
dependabot[bot] May 10, 2026
6e2b2f0
Bump furo from 2024.8.6 to 2025.12.19
dependabot[bot] May 10, 2026
cb4d2d0
Update datasets requirement from ~=3.3 to >=3.3,<5.0
dependabot[bot] May 11, 2026
e53c426
Update transformers requirement from ~=4.48.2 to >=4.48.2,<4.58.0
dependabot[bot] May 11, 2026
b8c7f43
Update pyo3 requirement from ^0.27 to ^0.28
dependabot[bot] May 10, 2026
9e57f51
fix: renamed allow_threads -> detach
awadell1 May 11, 2026
2003b9c
Update tokenizers requirement from ^0.21 to ^0.23
dependabot[bot] May 11, 2026
9c9014b
fix: token addition for tokenizer v0.23
awadell1 May 11, 2026
fb1d4bb
Bump actions/download-artifact from 6 to 8
dependabot[bot] May 11, 2026
cebed21
Bump astral-sh/setup-uv from 5 to 7
dependabot[bot] May 11, 2026
7787b31
Update myst-nb requirement from ~=1.2.0 to >=1.2,<1.4
dependabot[bot] May 11, 2026
fc69a89
Update pre-commit requirement from ~=4.1.0 to >=4.1,<4.4
dependabot[bot] May 11, 2026
79f7f09
Bump actions/setup-python from 3 to 6
dependabot[bot] May 11, 2026
ace7e79
doc: dep bump changelog entry
awadell1 May 11, 2026
4f96b39
fix: typo in CHANGELOG
awadell1 May 11, 2026
8dd8594
remove redundant jupyter notebook dep
anoushka2000 Apr 26, 2026
0727230
add BigSMILES tokenizer to changelog
anoushka2000 Apr 26, 2026
902a4aa
Merge branch 'main' into feat/big-smiles
anoushka2000 May 13, 2026
54caede
add warning about predefined Common Repeat Units
anoushka2000 May 13, 2026
39a2197
deseralizer rejects all except v1.1
anoushka2000 May 13, 2026
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6 changes: 5 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## Unreleased

### Added

- `SmirkBigSmilesFast` Tokenizer for BigSMILES line notation representation of polymers ([#8](https://github.com/BattModels/smirk/pull/8))

### Changed

- Bumped GitHub Actions, Python, Rust, and documentation dependencies ([#10](https://github.com/BattModels/smirk/pull/10) -- [#24](https://github.com/BattModels/smirk/pull/24))

### Fixed

- Build issue due to leading `./` in included file paths ([#7](https://github.com/BattModels/smirk/pull/7))
- Build issue due to leading `./` in included file paths ([#7](https://github.com/BattModels/smirk/pull/7))
- Fixed Dependabot configuration ([#9](https://github.com/BattModels/smirk/pull/9))

## [v0.2.0](https://github.com/BattModels/smirk/tree/v0.2.0)
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8 changes: 7 additions & 1 deletion docs/api.rst
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,13 @@ API Reference

.. seealso:: :py:meth:`transformers.PreTrainedTokenizerBase.batch_decode` for the 🤗 documentation

.. autofunction:: smirk.SmirkSelfiesFast
.. autoclass:: smirk.SmirkSelfiesFast
:special-members:
:members:

.. autoclass:: smirk.SmirkBigSmilesFast
:special-members:
:members:

.. autodata:: smirk.SPECIAL_TOKENS

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