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Update for Python 3.12 #26

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3 changes: 1 addition & 2 deletions rxnfp/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@
import logging
import random
import warnings
import pkg_resources
import sklearn

from transformers import (
Expand Down Expand Up @@ -562,4 +561,4 @@ def __init__(
continue
elif 'pooler' in name:
continue
param.requires_grad = False
param.requires_grad = False
12 changes: 4 additions & 8 deletions rxnfp/tokenization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,7 @@
import re
import numpy as np
from rdkit import Chem

import pkg_resources
from importlib.resources import files

from typing import List

Expand All @@ -21,11 +20,8 @@
SMI_REGEX_PATTERN = r"(\%\([0-9]{3}\)|\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\||\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"

def get_default_tokenizer():
default_vocab_path = (
pkg_resources.resource_filename(
"rxnfp",
"models/transformers/bert_ft_10k_25s/vocab.txt"
)
default_vocab_path = str(
files("rxnfp") / "models/transformers/bert_ft_10k_25s/vocab.txt"
)
return SmilesTokenizer(default_vocab_path, do_lower_case=False)

Expand Down Expand Up @@ -150,4 +146,4 @@ def process_reaction(rxn):

joined_precursors = ".".join(sorted(precursors))
joined_products = ".".join(sorted(products))
return f"{joined_precursors}>>{joined_products}"
return f"{joined_precursors}>>{joined_products}"
16 changes: 5 additions & 11 deletions rxnfp/transformer_fingerprints.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@

# Cell
import torch
import pkg_resources
import numpy as np
from importlib.resources import files
from typing import List
from tqdm import tqdm
from itertools import islice
Expand Down Expand Up @@ -109,16 +109,10 @@ def convert_batch(self, rxn_smiles_list: List[str]):

def get_default_model_and_tokenizer(model='bert_ft', force_no_cuda=False):

model_path = pkg_resources.resource_filename(
"rxnfp",
f"models/transformers/{model}"
)
model_path = str(files("rxnfp") / f"models/transformers/{model}")

tokenizer_vocab_path = (
pkg_resources.resource_filename(
"rxnfp",
f"models/transformers/{model}/vocab.txt"
)
tokenizer_vocab_path = str(
files("rxnfp") / f"models/transformers/{model}/vocab.txt"
)
device = torch.device("cuda" if (torch.cuda.is_available() and not force_no_cuda) else "cpu")

Expand All @@ -142,4 +136,4 @@ def generate_fingerprints(rxns: List[str], fingerprint_generator:FingerprintGene
fps_batch = fingerprint_generator.convert_batch(batch)

fps += fps_batch
return np.array(fps)
return np.array(fps)
4 changes: 2 additions & 2 deletions settings.ini
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Original file line number Diff line number Diff line change
Expand Up @@ -9,13 +9,13 @@ author_email = phs@zurich.ibm.com
copyright = RXN for Chemistry team / University of Bern
branch = master
version = 0.1.0
min_python = 3.6
min_python = 3.9
audience = Developers
language = English
custom_sidebar = True
license = mit
status = 2
requirements = transformers>=4.5.0 torch>=1.6 scipy==1.4.1 scikit-learn==0.23.1 matplotlib==3.2.2 faerun==0.3.20
requirements = transformers torch scipy scikit-learn matplotlib faerun
nbs_path = nbs
doc_path = docs
doc_host = https://rxn4chemistry.github.io
Expand Down
7 changes: 3 additions & 4 deletions setup.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
from pkg_resources import parse_version
from packaging.version import Version
from configparser import ConfigParser
import setuptools
assert parse_version(setuptools.__version__)>=parse_version('36.2')
assert Version(setuptools.__version__) >= Version("36.2")

# note: all settings are in settings.ini; edit there, not here
config = ConfigParser(delimiters=['='])
Expand All @@ -19,7 +19,7 @@
}
statuses = [ '1 - Planning', '2 - Pre-Alpha', '3 - Alpha',
'4 - Beta', '5 - Production/Stable', '6 - Mature', '7 - Inactive' ]
py_versions = '2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8'.split()
py_versions = "2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 3.10 3.11 3.12".split()

requirements = cfg.get('requirements','').split()
lic = licenses[cfg['license']]
Expand All @@ -45,4 +45,3 @@
zip_safe = False,
entry_points = { 'console_scripts': cfg.get('console_scripts','').split() },
**setup_cfg)