SinaTools 0.1.38__tar.gz → 0.1.39__tar.gz

{sinatools-0.1.38 → sinatools-0.1.39}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: SinaTools
-Version: 0.1.38
+Version: 0.1.39
 Summary: Open-source Python toolkit for Arabic Natural Understanding, allowing people to integrate it in their system workflow.
 Home-page: https://github.com/SinaLab/sinatools
 License: MIT license
@@ -13,12 +13,17 @@ Requires-Dist: farasapy
 Requires-Dist: tqdm
 Requires-Dist: requests
 Requires-Dist: pathlib
-Requires-Dist: torch==1.13.0
-Requires-Dist: transformers==4.24.0
-Requires-Dist: torchtext==0.14.0
-Requires-Dist: torchvision==0.14.0
+Requires-Dist: transformers==4.47.1
+Requires-Dist: torchvision==0.20.1
 Requires-Dist: seqeval==1.2.2
 Requires-Dist: natsort==7.1.1
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 SinaTools
 ======================

{sinatools-0.1.38 → sinatools-0.1.39}/SinaTools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: SinaTools
-Version: 0.1.38
+Version: 0.1.39
 Summary: Open-source Python toolkit for Arabic Natural Understanding, allowing people to integrate it in their system workflow.
 Home-page: https://github.com/SinaLab/sinatools
 License: MIT license
@@ -13,12 +13,17 @@ Requires-Dist: farasapy
 Requires-Dist: tqdm
 Requires-Dist: requests
 Requires-Dist: pathlib
-Requires-Dist: torch==1.13.0
-Requires-Dist: transformers==4.24.0
-Requires-Dist: torchtext==0.14.0
-Requires-Dist: torchvision==0.14.0
+Requires-Dist: transformers==4.47.1
+Requires-Dist: torchvision==0.20.1
 Requires-Dist: seqeval==1.2.2
 Requires-Dist: natsort==7.1.1
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 SinaTools
 ======================

sinatools-0.1.39/SinaTools.egg-info/requires.txt

@@ -0,0 +1,9 @@
+six
+farasapy
+tqdm
+requests
+pathlib
+transformers==4.47.1
+torchvision==0.20.1
+seqeval==1.2.2
+natsort==7.1.1

{sinatools-0.1.38 → sinatools-0.1.39}/setup.py

@@ -18,10 +18,10 @@ requirements = [
     'requests',
     # 'regex',
     'pathlib',
-    'torch==1.13.0',
-    'transformers==4.24.0',
-    'torchtext==0.14.0',
-    'torchvision==0.14.0',
+    # 'torch==2.5.1',
+    'transformers==4.47.1',
+    # 'torchtext==0.14.0',
+    'torchvision==0.20.1',
     'seqeval==1.2.2',
     'natsort==7.1.1'
 ]

sinatools-0.1.39/sinatools/VERSION

@@ -0,0 +1 @@
+0.1.39

sinatools-0.1.39/sinatools/environment.yml

@@ -0,0 +1,182 @@
+name: dev
+channels:
+  - pytorch
+  - nvidia
+  - defaults
+  - https://repo.anaconda.com/pkgs/main
+  - https://repo.anaconda.com/pkgs/r
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
+  - binutils_impl_linux-64=2.40=h5293946_0
+  - binutils_linux-64=2.40.0=hc2dff05_1
+  - blas=1.0=mkl
+  - brotli-python=1.0.9=py311h6a678d5_8
+  - bzip2=1.0.8=h5eee18b_6
+  - ca-certificates=2024.11.26=h06a4308_0
+  - certifi=2024.12.14=py311h06a4308_0
+  - charset-normalizer=3.3.2=pyhd3eb1b0_0
+  - cuda-cudart=12.4.127=0
+  - cuda-cupti=12.4.127=0
+  - cuda-libraries=12.4.1=0
+  - cuda-nvrtc=12.4.127=0
+  - cuda-nvtx=12.4.127=0
+  - cuda-opencl=12.4.127=0
+  - cuda-runtime=12.4.1=0
+  - cuda-version=11.7=h6a555f7_3
+  - cudatoolkit=11.7.0=hd8887f6_10
+  - ffmpeg=4.3=hf484d3e_0
+  - filelock=3.13.1=py311h06a4308_0
+  - freetype=2.12.1=h4a9f257_0
+  - fsspec=2024.6.1=py311h06a4308_0
+  - gcc_impl_linux-64=11.2.0=h1234567_1
+  - gcc_linux-64=11.2.0=h5c386dc_1
+  - giflib=5.2.2=h5eee18b_0
+  - gmp=6.2.1=h295c915_3
+  - gmpy2=2.1.2=py311hc9b5ff0_0
+  - gnutls=3.6.15=he1e5248_0
+  - gxx_impl_linux-64=11.2.0=h1234567_1
+  - gxx_linux-64=11.2.0=hc2dff05_1
+  - idna=3.7=py311h06a4308_0
+  - intel-openmp=2023.1.0=hdb19cb5_46306
+  - jinja2=3.1.4=py311h06a4308_1
+  - jpeg=9e=h5eee18b_3
+  - kernel-headers_linux-64=3.10.0=h57e8cba_10
+  - lame=3.100=h7b6447c_0
+  - lcms2=2.16=hb9589c4_0
+  - ld_impl_linux-64=2.40=h12ee557_0
+  - lerc=4.0.0=h6a678d5_0
+  - libabseil=20240116.2=cxx17_h6a678d5_0
+  - libcublas=12.4.5.8=0
+  - libcufft=11.2.1.3=0
+  - libcufile=1.9.1.3=0
+  - libcurand=10.3.5.147=0
+  - libcusolver=11.6.1.9=0
+  - libcusparse=12.3.1.170=0
+  - libdeflate=1.22=h5eee18b_0
+  - libffi=3.4.4=h6a678d5_1
+  - libgcc-devel_linux-64=11.2.0=h1234567_1
+  - libgcc-ng=11.2.0=h1234567_1
+  - libgomp=11.2.0=h1234567_1
+  - libiconv=1.16=h5eee18b_3
+  - libidn2=2.3.4=h5eee18b_0
+  - libjpeg-turbo=2.0.0=h9bf148f_0
+  - libnpp=12.2.5.30=0
+  - libnvfatbin=12.4.127=0
+  - libnvjitlink=12.4.127=0
+  - libnvjpeg=12.3.1.117=0
+  - libpng=1.6.39=h5eee18b_0
+  - libprotobuf=4.25.3=he621ea3_0
+  - libstdcxx-devel_linux-64=11.2.0=h1234567_1
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libtasn1=4.19.0=h5eee18b_0
+  - libtiff=4.5.1=hffd6297_1
+  - libunistring=0.9.10=h27cfd23_0
+  - libuuid=1.41.5=h5eee18b_0
+  - libwebp=1.3.2=h11a3e52_0
+  - libwebp-base=1.3.2=h5eee18b_1
+  - llvm-openmp=14.0.6=h9e868ea_0
+  - lz4-c=1.9.4=h6a678d5_1
+  - markupsafe=2.1.3=py311h5eee18b_0
+  - mkl=2023.1.0=h213fc3f_46344
+  - mkl-service=2.4.0=py311h5eee18b_1
+  - mkl_fft=1.3.11=py311h5eee18b_0
+  - mkl_random=1.2.8=py311ha02d727_0
+  - mpc=1.1.0=h10f8cd9_1
+  - mpfr=4.0.2=hb69a4c5_1
+  - mpmath=1.3.0=py311h06a4308_0
+  - ncurses=6.4=h6a678d5_0
+  - nettle=3.7.3=hbbd107a_1
+  - networkx=3.2.1=py311h06a4308_0
+  - numpy=2.0.1=py311h08b1b3b_1
+  - numpy-base=2.0.1=py311hf175353_1
+  - openh264=2.1.1=h4ff587b_0
+  - openjpeg=2.5.2=he7f1fd0_0
+  - openssl=3.0.15=h5eee18b_0
+  - pillow=11.0.0=py311hcea889d_1
+  - pip=24.2=py311h06a4308_0
+  - pysocks=1.7.1=py311h06a4308_0
+  - python=3.11.11=he870216_0
+  - pytorch=2.5.1=py3.11_cuda12.4_cudnn9.1.0_0
+  - pytorch-cuda=12.4=hc786d27_7
+  - pytorch-mutex=1.0=cuda
+  - pyyaml=6.0.2=py311h5eee18b_0
+  - readline=8.2=h5eee18b_0
+  - requests=2.32.3=py311h06a4308_1
+  - setuptools=75.1.0=py311h06a4308_0
+  - sqlite=3.45.3=h5eee18b_0
+  - sysroot_linux-64=2.17=h57e8cba_10
+  - tbb=2021.8.0=hdb19cb5_0
+  - tk=8.6.14=h39e8969_0
+  - torchaudio=2.5.1=py311_cu124
+  - torchtriton=3.1.0=py311
+  - torchvision=0.20.1=py311_cu124
+  - typing_extensions=4.12.2=py311h06a4308_0
+  - urllib3=2.2.3=py311h06a4308_0
+  - wheel=0.44.0=py311h06a4308_0
+  - xz=5.4.6=h5eee18b_1
+  - yaml=0.2.5=h7b6447c_0
+  - zlib=1.2.13=h5eee18b_1
+  - zstd=1.5.6=hc292b87_0
+  - pip:
+      - absl-py==2.1.0
+      - accelerate==1.2.1
+      - aiohappyeyeballs==2.4.4
+      - aiohttp==3.11.11
+      - aiosignal==1.3.2
+      - annotated-types==0.7.0
+      - attrs==24.3.0
+      - datasets==3.2.0
+      - deepspeed==0.16.2
+      - dill==0.3.8
+      - einops==0.8.0
+      - flash-attn==2.7.2.post1
+      - frozenlist==1.5.0
+      - grpcio==1.70.0
+      - hjson==3.1.0
+      - huggingface-hub==0.27.0
+      - joblib==1.4.2
+      - markdown==3.7
+      - markdown-it-py==3.0.0
+      - mdurl==0.1.2
+      - mpi4py==4.0.1
+      - msgpack==1.1.0
+      - multidict==6.1.0
+      - multiprocess==0.70.16
+      - natsort==8.4.0
+      - ninja==1.11.1.3
+      - nvidia-ml-py==12.560.30
+      - packaging==24.2
+      - pandas==2.2.3
+      - peft==0.14.0
+      - propcache==0.2.1
+      - protobuf==6.30.0
+      - psutil==6.1.1
+      - py-cpuinfo==9.0.0
+      - pyarrow==18.1.0
+      - pydantic==2.10.4
+      - pydantic-core==2.27.2
+      - pygments==2.18.0
+      - python-dateutil==2.9.0.post0
+      - pytz==2024.2
+      - regex==2024.11.6
+      - rich==13.9.4
+      - safetensors==0.4.5
+      - scikit-learn==1.6.1
+      - scipy==1.15.2
+      - seqeval==1.2.2
+      - six==1.17.0
+      - sympy==1.13.1
+      - tensorboard==2.19.0
+      - tensorboard-data-server==0.7.2
+      - threadpoolctl==3.5.0
+      - tokenizers==0.21.0
+      - tqdm==4.67.1
+      - transformers==4.47.1
+      - trl==0.12.0
+      - tzdata==2024.2
+      - werkzeug==3.1.3
+      - xxhash==3.5.0
+      - yarl==1.18.3
+

{sinatools-0.1.38 → sinatools-0.1.39}/sinatools/ner/data/datasets.py

@@ -37,7 +37,11 @@ class Token:
         :return: str
         """
         gold_tags = "|".join(self.gold_tag)
-        pred_tags = "|".join([pred_tag["tag"] for pred_tag in self.pred_tag])
+
+        if self.pred_tag:
+            pred_tags = "|".join([pred_tag["tag"] for pred_tag in self.pred_tag])
+        else:
+            pred_tags = ""
 
         if self.gold_tag:
             r = f"{self.text}\t{gold_tags}\t{pred_tags}"
@@ -139,8 +143,8 @@ class NestedTagsDataset(Dataset):
         masks = torch.cat(masks)
 
         # Pad the tags, do the padding for each tag type
-        tags = [torch.nn.ConstantPad1d((0, subwords.shape[-1] - tag.shape[-1]), vocab.get_stoi()["<pad>"])(tag)
+        tags = [torch.nn.ConstantPad1d((0, subwords.shape[-1] - tag.shape[-1]), vocab.get_stoi()["O"])(tag)
                 for tag, vocab in zip(tags, self.vocab.tags[1:])]
         tags = torch.cat(tags)
 
-        return subwords, tags, tokens, masks, valid_len
+        return subwords, tags, tokens, masks, valid_len

{sinatools-0.1.38 → sinatools-0.1.39}/sinatools/ner/data_format.py

@@ -1,16 +1,30 @@
 from torch.utils.data import DataLoader
-from torchtext.vocab import vocab
 from collections import Counter, namedtuple
 import logging
 import re
 import itertools
 from sinatools.ner.helpers import load_object
-from sinatools.ner.datasets import Token
-from sinatools.utils.tokenizers_words import simple_word_tokenize
+from sinatools.ner.data.datasets import Token
 
 logger = logging.getLogger(__name__)
 
 
+class Vocab:
+    def __init__(self, counter, specials=[]) -> None:
+        self.itos = list(counter.keys()) + specials
+        self.stoi = {s: i for i, s in enumerate(self.itos)}
+        self.word_count = counter
+
+    def get_itos(self) -> list[str]:
+        return self.itos
+
+    def get_stoi(self) -> dict[str, int]:
+        return self.stoi
+
+    def __len__(self):
+        return len(self.itos)
+
+
 def conll_to_segments(filename):
     """
     Convert CoNLL files to segments. This return list of segments and each segment is
@@ -60,8 +74,8 @@ def parse_conll_files(data_paths):
 
     # Generate vocabs for tags and tokens
     tag_vocabs = tag_vocab_by_type(tags)
-    tag_vocabs.insert(0, vocab(Counter(tags)))
-    vocabs = vocabs(tokens=vocab(Counter(tokens), specials=["UNK"]), tags=tag_vocabs)
+    tag_vocabs.insert(0, Vocab(Counter(tags)))
+    vocabs = vocabs(tokens=Vocab(Counter(tokens), specials=["UNK"]), tags=tag_vocabs)
     return tuple(datasets), vocabs
 
 
@@ -72,9 +86,9 @@ def tag_vocab_by_type(tags):
     tag_types = sorted(list(set([tag.split("-", 1)[1] for tag in tag_names if "-" in tag])))
 
     for tag_type in tag_types:
-        r = re.compile(".*-" + tag_type)
+        r = re.compile(".*-" + tag_type + "$")
         t = list(filter(r.match, tags)) + ["O"]
-        vocabs.append(vocab(Counter(t), specials=["<pad>"]))
+        vocabs.append(Vocab(Counter(t)))
 
     return vocabs
 
@@ -83,13 +97,11 @@ def text2segments(text):
     """
     Convert text to a datasets and index the tokens
     """
-    #dataset = [[Token(text=token, gold_tag=["O"]) for token in text.split()]]
-    list_of_tokens = simple_word_tokenize(text)
-    dataset = [[Token(text=token, gold_tag=["O"]) for token in list_of_tokens]]
+    dataset = [[Token(text=token, gold_tag=["O"]) for token in text.split()]]
     tokens = [token.text for segment in dataset for token in segment]
 
     # Generate vocabs for the tokens
-    segment_vocab = vocab(Counter(tokens), specials=["UNK"])
+    segment_vocab = Vocab(Counter(tokens), specials=["UNK"])
     return dataset, segment_vocab
 
 
@@ -121,4 +133,4 @@ def get_dataloaders(
         logger.info("%s batches found", len(dataloader))
         dataloaders.append(dataloader)
 
-    return dataloaders
+    return dataloaders

sinatools-0.1.39/sinatools/ner/helpers.py

@@ -0,0 +1,117 @@
+import os
+import sys
+import logging
+import importlib
+import shutil
+import torch
+import pickle
+import json
+import random
+import numpy as np
+from argparse import Namespace
+
+
+def logging_config(log_file=None):
+    """
+    Initialize custom logger
+    :param log_file: str - path to log file, full path
+    :return: None
+    """
+    handlers = [logging.StreamHandler(sys.stdout)]
+
+    if log_file:
+        handlers.append(logging.FileHandler(log_file, "w", "utf-8"))
+        print("Logging to {}".format(log_file))
+
+    logging.basicConfig(
+        level=logging.INFO,
+        handlers=handlers,
+        format="%(levelname)s\t%(name)s\t%(asctime)s\t%(message)s",
+        datefmt="%a, %d %b %Y %H:%M:%S",
+        force=True
+    )
+
+
+def load_object(name, kwargs):
+    """
+    Load objects dynamically given the object name and its arguments
+    :param name: str - object name, class name or function name
+    :param kwargs: dict - keyword arguments
+    :return: object
+    """
+    object_module, object_name = name.rsplit(".", 1)
+    object_module = importlib.import_module(object_module)
+    fn = getattr(object_module, object_name)(**kwargs)
+    return fn
+
+
+def make_output_dirs(path, subdirs=[], overwrite=True):
+    """
+    Create root directory and any other sub-directories
+    :param path: str - root directory
+    :param subdirs: List[str] - list of sub-directories
+    :param overwrite: boolean - to overwrite the directory or not
+    :return: None
+    """
+    if overwrite:
+        shutil.rmtree(path, ignore_errors=True)
+
+    os.makedirs(path)
+
+    for subdir in subdirs:
+        os.makedirs(os.path.join(path, subdir))
+
+
+def load_checkpoint(model_path):
+    """
+    Load model given the model path
+    :param model_path: str - path to model
+    :return: tagger - arabiner.trainers.BaseTrainer - the tagger model
+             vocab - arabicner.utils.data.Vocab - indexed tags
+             train_config - argparse.Namespace - training configurations
+    """
+    with open(os.path.join(model_path, "tag_vocab.pkl"), "rb") as fh:
+        tag_vocab = pickle.load(fh)
+
+    # Load train configurations from checkpoint
+    train_config = Namespace()
+    with open(os.path.join(model_path, "args.json"), "r") as fh:
+        train_config.__dict__ = json.load(fh)
+
+    # Initialize the loss function, not used for inference, but evaluation
+    loss = load_object(train_config.loss["fn"], train_config.loss["kwargs"])
+
+    # Load BERT tagger
+    model = load_object(train_config.network_config["fn"], train_config.network_config["kwargs"])
+    model = torch.nn.DataParallel(model)
+
+    if torch.cuda.is_available():
+        model = model.cuda()
+
+    # Update arguments for the tagger
+    # Attach the model, loss (used for evaluations cases)
+    train_config.trainer_config["kwargs"]["model"] = model
+    train_config.trainer_config["kwargs"]["loss"] = loss
+
+    tagger = load_object(train_config.trainer_config["fn"], train_config.trainer_config["kwargs"])
+    tagger.load(os.path.join(model_path, "checkpoints"))
+    return tagger, tag_vocab, train_config
+
+
+def set_seed(seed):
+    """
+    Set the seed for random intialization and set
+    CUDANN parameters to ensure determmihstic results across
+    multiple runs with the same seed
+
+    :param seed: int
+    """
+    np.random.seed(seed)
+    random.seed(seed)
+    torch.manual_seed(seed)
+    torch.cuda.manual_seed(seed)
+    torch.cuda.manual_seed_all(seed)
+
+    torch.backends.cudnn.deterministic = True
+    torch.backends.cudnn.benchmark = False
+    torch.backends.cudnn.enabled = False

{sinatools-0.1.38 → sinatools-0.1.39}/sinatools/ner/trainers/BaseTrainer.py

@@ -113,5 +113,5 @@ class BaseTrainer:
         logger.info("Loading checkpoint %s", checkpoint_path)
 
         device = None if torch.cuda.is_available() else torch.device('cpu')
-        checkpoint = torch.load(checkpoint_path, map_location=device)
-        self.model.load_state_dict(checkpoint["model"], strict=False)
+        checkpoint = torch.load(checkpoint_path, map_location=device, weights_only=False)
+        self.model.load_state_dict(checkpoint["model"], strict=False)