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[pre-commit.ci] pre-commit autoupdate #536

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cbee0e0
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Jul 27, 2026
94d84a9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 27, 2026
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28 changes: 14 additions & 14 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ default_language_version:
python: python3
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.6.0
rev: v6.0.0
hooks:
- id: check-added-large-files
- id: check-byte-order-marker
Expand All @@ -21,69 +21,69 @@ repos:
- id: trailing-whitespace
exclude: .gitignore
- repo: https://github.com/psf/black-pre-commit-mirror
rev: 24.4.2
rev: 26.5.1
hooks:
- id: black-jupyter
- repo: https://github.com/astral-sh/ruff-pre-commit
rev: v0.5.1
rev: v0.16.0
hooks:
- id: ruff
args: [--fix, --exit-non-zero-on-fix]
- repo: https://github.com/rbubley/mirrors-prettier
rev: v3.3.2
rev: v3.9.6
hooks:
- id: prettier
- repo: https://github.com/google/yamlfmt
rev: v0.13.0
rev: v0.21.0
hooks:
- id: yamlfmt
- repo: https://github.com/Yelp/detect-secrets
rev: v1.5.0
hooks:
- id: detect-secrets
- repo: https://github.com/pappasam/toml-sort
rev: v0.23.1
rev: v0.24.4
hooks:
- id: toml-sort-fix
exclude: poetry.lock
- repo: https://github.com/codespell-project/codespell
rev: v2.3.0
rev: v2.4.3
hooks:
- id: codespell
additional_dependencies: [".[toml]"]
- repo: https://github.com/sqlfluff/sqlfluff
rev: 3.1.0
rev: 4.2.2
hooks:
- id: sqlfluff-fix
- repo: https://github.com/hadolint/hadolint
rev: v2.13.0-beta
rev: v2.14.0
hooks:
- id: hadolint-docker
- repo: https://github.com/jsh9/markdown-toc-creator
rev: 0.0.6
rev: 0.1.3
hooks:
- id: markdown-toc-creator
- repo: https://github.com/jumanjihouse/pre-commit-hooks
rev: 3.0.0
hooks:
- id: check-mailmap
- repo: https://github.com/python-poetry/poetry
rev: 1.8.0
rev: 2.4.1
hooks:
- id: poetry-check
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v1.10.1
rev: v2.3.0
hooks:
- id: mypy
additional_dependencies:
- types-requests
- repo: https://github.com/srstevenson/nb-clean
rev: 3.3.0
rev: 4.0.1
hooks:
- id: nb-clean
args: [--preserve-cell-outputs, --remove-empty-cells]
- repo: https://github.com/abravalheri/validate-pyproject
rev: v0.18
rev: v0.25
hooks:
- id: validate-pyproject
additional_dependencies:
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22 changes: 22 additions & 0 deletions code_of_conduct.md
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@@ -1,5 +1,27 @@
# Contributor Covenant Code of Conduct

<!--TOC-->

______________________________________________________________________

**Table of Contents**

- [Our Pledge](#our-pledge)
- [Our Standards](#our-standards)
- [Enforcement Responsibilities](#enforcement-responsibilities)
- [Scope](#scope)
- [Enforcement](#enforcement)
- [Enforcement Guidelines](#enforcement-guidelines)
- [1. Correction](#1-correction)
- [2. Warning](#2-warning)
- [3. Temporary Ban](#3-temporary-ban)
- [4. Permanent Ban](#4-permanent-ban)
- [Attribution](#attribution)

______________________________________________________________________

<!--TOC-->

## Our Pledge

We as members, contributors, and leaders pledge to make participation in our
Expand Down
3 changes: 1 addition & 2 deletions data/natural/preprocess_msds.py
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Expand Up @@ -44,6 +44,5 @@ def get_text(d, text="", level=1, linebreaks=2):
print(f"Output file already exists, please check: {path_jsonl_out}")
else:
with open(path_jsonl_out, "a") as fout:
for sample in data:
fout.write(json.dumps(sample) + "\n")
fout.writelines(json.dumps(sample) + "\n" for sample in data)
print(f"JSONL saved to: {path_jsonl_out}")
64 changes: 32 additions & 32 deletions data/tabular/RedDB/transform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -214,46 +214,46 @@ def read_dataset():
journal = {Nature Scientific Data}""",
],
"templates": [
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {solubilityAqSolPred__names__noun} of {solubilityAqSolPred#} {solubilityAqSolPred__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {molecularSurface__names__noun} of {molecularSurface#} {molecularSurface__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {reactionFieldEnergy__names__noun} of {reactionFieldEnergy#} {reactionFieldEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {solventAccessSurface__names__noun} of {solventAccessSurface#} {solventAccessSurface__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {cavityEnergy__names__noun} of {cavityEnergy#} {cavityEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {gasEnergy__names__noun} of {gasEnergy#} {gasEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {gasHomo__names__noun} of {gasHomo#} {gasHomo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {gasLumo__names__noun} of {gasLumo#} {gasLumo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {solutionEnergy__names__noun} of {solutionEnergy#} {solutionEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {solutionLumo__names__noun} of {solutionLumo#} {solutionLumo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {nuclearRepulsionEnergy__names__noun} of {nuclearRepulsionEnergy#} {nuclearRepulsionEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {optGasEnergy__names__noun} of {optGasEnergy#} {optGasEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {optGasHomo__names__noun} of {optGasHomo#} {optGasHomo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {optGasLumo__names__noun} of {optGasLumo#} {optGasLumo__units}.""" # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {solubilityAqSolPred__names__noun} of {solubilityAqSolPred#} {solubilityAqSolPred__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {molecularSurface__names__noun} of {molecularSurface#} {molecularSurface__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {reactionFieldEnergy__names__noun} of {reactionFieldEnergy#} {reactionFieldEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {solventAccessSurface__names__noun} of {solventAccessSurface#} {solventAccessSurface__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {cavityEnergy__names__noun} of {cavityEnergy#} {cavityEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {gasEnergy__names__noun} of {gasEnergy#} {gasEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {gasHomo__names__noun} of {gasHomo#} {gasHomo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {gasLumo__names__noun} of {gasLumo#} {gasLumo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {solutionEnergy__names__noun} of {solutionEnergy#} {solutionEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {solutionLumo__names__noun} of {solutionLumo#} {solutionLumo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {nuclearRepulsionEnergy__names__noun} of {nuclearRepulsionEnergy#} {nuclearRepulsionEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {optGasEnergy__names__noun} of {optGasEnergy#} {optGasEnergy__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {optGasHomo__names__noun} of {optGasHomo#} {optGasHomo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {optGasLumo__names__noun} of {optGasLumo#} {optGasLumo__units}.""", # noqa: E501
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {solubilityAqSolPred__names__noun} of {solubilityAqSolPred#} {solubilityAqSolPred__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {molecularSurface__names__noun} of {molecularSurface#} {molecularSurface__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {reactionFieldEnergy__names__noun} of {reactionFieldEnergy#} {reactionFieldEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {solventAccessSurface__names__noun} of {solventAccessSurface#} {solventAccessSurface__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {cavityEnergy__names__noun} of {cavityEnergy#} {cavityEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {gasEnergy__names__noun} of {gasEnergy#} {gasEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {gasHomo__names__noun} of {gasHomo#} {gasHomo__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {gasLumo__names__noun} of {gasLumo#} {gasLumo__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {solutionEnergy__names__noun} of {solutionEnergy#} {solutionEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {solutionLumo__names__noun} of {solutionLumo#} {solutionLumo__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {nuclearRepulsionEnergy__names__noun} of {nuclearRepulsionEnergy#} {nuclearRepulsionEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {optGasEnergy__names__noun} of {optGasEnergy#} {optGasEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {optGasHomo__names__noun} of {optGasHomo#} {optGasHomo__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} has a {optGasLumo__names__noun} of {optGasLumo#} {optGasLumo__units}."""
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {solubilityAqSolPred__names__noun} of {solubilityAqSolPred#} {solubilityAqSolPred__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {molecularSurface__names__noun} of {molecularSurface#} {molecularSurface__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {reactionFieldEnergy__names__noun} of {reactionFieldEnergy#} {reactionFieldEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {solventAccessSurface__names__noun} of {solventAccessSurface#} {solventAccessSurface__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {cavityEnergy__names__noun} of {cavityEnergy#} {cavityEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {gasEnergy__names__noun} of {gasEnergy#} {gasEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {gasHomo__names__noun} of {gasHomo#} {gasHomo__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {gasLumo__names__noun} of {gasLumo#} {gasLumo__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {solutionEnergy__names__noun} of {solutionEnergy#} {solutionEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {solutionLumo__names__noun} of {solutionLumo#} {solutionLumo__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {nuclearRepulsionEnergy__names__noun} of {nuclearRepulsionEnergy#} {nuclearRepulsionEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {optGasEnergy__names__noun} of {optGasEnergy#} {optGasEnergy__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {optGasHomo__names__noun} of {optGasHomo#} {optGasHomo__units}.""",
"""The {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} {#representation of |!}{InChI#} has a {optGasLumo__names__noun} of {optGasLumo#} {optGasLumo__units}.""",
"""Task: Please {#give me|create|generate!} a {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} based on the {#text |!}description{# below|!}.
Description: It has an {solubilityAqSolPred__names__noun} {solubilityAqSolPred#} {solubilityAqSolPred__units} and a {cavityEnergy__names__noun} of {cavityEnergy#} {cavityEnergy__units}.
Result: {SMILES#}""", # noqa: E501
Result: {SMILES#}""",
"""Task: Please {#give me|create|generate!} a {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} based on the {#text |!}description{# below|!}.
Description: It has an {solubilityAqSolPred__names__noun} {solubilityAqSolPred#} {solubilityAqSolPred__units} and a {cavityEnergy__names__noun} of {cavityEnergy#} {cavityEnergy__units}.
Result: {InChI#}""", # noqa: E501
Result: {InChI#}""",
"""Task: Please {#give me|create|generate!} a {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} based on the {#text |!}description{# below|!}.
Description: It has an {solutionLumo__names__noun} {solutionLumo#} {solutionLumo__units} and a {solutionHomo__names__noun} of {solutionHomo#} {solutionHomo__units}.
Result: {SMILES#}""", # noqa: E501
Result: {SMILES#}""",
"""Task: Please {#give me|create|generate!} a {#molecule|compound|chemical|molecular species|chemical compound!} with the {InChI__description} based on the {#text |!}description{# below|!}.
Description: It has an {solutionLumo__names__noun} {solutionLumo#} {solutionLumo__units} and a {solutionHomo__names__noun} of {solutionHomo#} {solutionHomo__units}.
Result: {InChI#}""", # noqa: E501
Result: {InChI#}""",
],
}

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6 changes: 3 additions & 3 deletions data/tabular/SIDER/transform.py
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Expand Up @@ -74,19 +74,19 @@ def write_meta(column_ids: pd.Index, descriptions: List[str], num_points: int) -
]

templates = [
"The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description}" # noqa: E501
"The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description}"
+ " {#representation of |!}{SMILES#} is {"
+ col_id
+ "#not a &a }"
+ "{#potential cause|potential reason!} for {"
+ col_id
+ "__names__noun}." # noqa: E501
+ "__names__noun}."
for col_id in column_ids[1:]
]

meta = {
"name": "SIDER", # unique identifier, we will also use this for directory names
"description": f"""Database of marketed drugs and adverse drug reactions (ADR), grouped into {len(column_ids[1:])} system organ classes.""", # noqa: E501
"description": f"""Database of marketed drugs and adverse drug reactions (ADR), grouped into {len(column_ids[1:])} system organ classes.""",
"identifiers": [
{
"id": "SMILES", # column name
Expand Down
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