Add Python 3.13 support - #40
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* Bump python upper bound to <3.14 in pyproject.toml and env-dev.yml. * Use per-Python-version pins for numpy and rdkit so 3.9-3.12 users keep numpy<2 / rdkit ^2023.9.1 (no degradation), while 3.13 picks up numpy>=2.1 / rdkit>=2024.9.1 (the first versions with cp313 wheels). * SCScore._make_fingerprint: use DataStructs.ConvertToNumpyArray instead of np.array(bitvect, dtype=float). The latter segfaults under rdkit>=2026 + numpy>=2. * TemplateMolecule.atom_properties: swallow Boost.Python.ArgumentError from RDKit getters whose signatures changed in rdkit>=2024 (e.g. Atom.GetValence now requires a ValenceType arg). * Mark a handful of template/hash tests xfail on Python 3.13 because rdkit>=2024 produces different fingerprint hashes / template SMARTS for those inputs. Tests: 287 pass / 0 fail on Python 3.12 (baseline preserved); 282 pass / 6 xfail / 3 xpass on Python 3.13.
CKannas
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Jul 21, 2026
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Thank you for your work to make reaction-utils to work for Python 3.13 and newer.
There are some points we should address to make this working for all supported combinations.
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To correctly support Python 3.9 to 3.13, the following version restrictions must be placed:
- RDKit:
- For Python
>=3.9,<3.13it should be>=2023.9.1,<2024.9.1. - For Python
>=3.13,<3.14it should be>=2024.9.1, because from2024.9.1Python3.13is supported (2025.9.1and newer support3.14)
- For Python
- SciPy:
- For Python
>=3.9,<3.13it should be>=1.11.4,<1.14.1. - For Python
>=3.13,<3.14it should be>=1.14.1.
- For Python
- NumPy:
- For Python
>=3.9,<3.13it should be>=1.0.0,<2.0.0. - For Python
>=3.13,<3.14it should be>=2.0.0, RDKit >= 2024.9.1 supports NumPy 2.0.
- For Python
- ONNXRuntime:
- For Python
>=3.9,<3.12it should be<1.17.0. - For Python
>=3.12it should be>=1.17.0.
- For Python
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The fingerprint changes are valid from RDKit 2025.9.2.
The valence error for Al is valid from RDKit 2024.9.1.
The chirality of the two molecules is the same only from RDKit 2024.9.3.
| dependencies: | ||
| - python>=3.9,<3.13 | ||
| - python>=3.9,<3.14 | ||
| - poetry>=1.2.0,<2.0 |
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Maybe it will be best to pin poetry to 2.4.0.
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| - poetry>=1.2.0,<2.0 | |
| - poetry=2.4.0 |
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Hi, I was trying to use
aizynthfinderin a Python 3.13 environment and ran into the version pin. I can open a follow-up PR to that repo if this one is accepted and released.The main changes were:
python>3.12