Merge pull request #13 from dayyass/release_v0.1.0

release v0.1.1

.github/workflows/codecov.yml

@@ -0,0 +1,37 @@
+# This workflow will install Python dependencies and run codecov
+# https://github.com/codecov/codecov-action#example-workflowyml-with-codecov-action
+
+name: codecov
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+    steps:
+    - uses: actions/checkout@master
+    - name: Set up Python
+      uses: actions/setup-python@master
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install pytest pytest-cov
+    - name: Generate coverage report
+      run: pytest --cov=./ --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        flags: unittests
+        env_vars: OS,PYTHON
+        fail_ci_if_error: true
+        verbose: true

.github/workflows/linter.yml

@@ -0,0 +1,37 @@
+# This workflow will install Python dependencies and run linter
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+# TODO: update linters
+
+name: linter
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install isort black flake8 mypy
+    - name: Code format check with isort
+      run: isort --check-only --profile black .
+    - name: Code format check with black
+      run: black --check .
+    - name: Code format check with flake8
+      run: flake8 --ignore E501,E203,W503 .
+    - name: Type check with mypy
+      run: mypy --ignore-missing-imports .

.github/workflows/tests.yml

@@ -0,0 +1,30 @@
+# This workflow will install Python dependencies and run tests with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: tests
+
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ['3.7', '3.8', '3.9']
+        os: [ubuntu-latest, macOS-latest, add windows-latest]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Unittests
+      run: python -m unittest discover

.gitignore

@@ -15,3 +15,5 @@ venv
 
 runs
 dayyass
+
+qaner.egg-info

.pre-commit-config.yaml

@@ -29,11 +29,11 @@ repos:
   rev: v0.961
   hooks:
     - id: mypy
-- repo: local
-  hooks:
-    - id: unittest
-      name: unittest
-      entry: venv/bin/python -m unittest discover
-      language: python
-      always_run: true
-      pass_filenames: false
+# - repo: local
+#   hooks:
+#     - id: unittest
+#       name: unittest
+#       entry: venv/bin/python -m unittest discover
+#       language: python
+#       always_run: true
+#       pass_filenames: false

README.md

@@ -1,9 +1,28 @@
+[![tests](https://github.com/dayyass/qaner/actions/workflows/tests.yml/badge.svg)](https://github.com/dayyass/qaner/actions/workflows/tests.yml)
+[![linter](https://github.com/dayyass/qaner/actions/workflows/linter.yml/badge.svg)](https://github.com/dayyass/qaner/actions/workflows/linter.yml)
+<!-- [![codecov](https://codecov.io/gh/dayyass/qaner/branch/main/graph/badge.svg?token=S3UKX8BFP3)](https://codecov.io/gh/dayyass/qaner) -->
+
+[![python 3.7](https://img.shields.io/badge/python-3.7-blue.svg)](https://github.com/dayyass/qaner#requirements)
+[![release (latest by date)](https://img.shields.io/github/v/release/dayyass/qaner)](https://github.com/dayyass/qaner/releases/latest)
+[![license](https://img.shields.io/github/license/dayyass/qaner?color=blue)](https://github.com/dayyass/qaner/blob/main/LICENSE)
+
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-black)](https://github.com/dayyass/qaner/blob/main/.pre-commit-config.yaml)
+[![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
+[![pypi version](https://img.shields.io/pypi/v/qaner)](https://pypi.org/project/qaner)
+[![pypi downloads](https://img.shields.io/pypi/dm/qaner)](https://pypi.org/project/qaner)
+
 # QaNER
 Unofficial implementation of [*QaNER: Prompting Question Answering Models for Few-shot Named Entity Recognition*](https://arxiv.org/abs/2203.01543).
 
 You can adopt this pipeline for arbitrary [BIO-markup](https://github.com/dayyass/QaNER/tree/main/data/conll2003) data.
 
-### CoNLL-2003
+## Installation
+```
+pip install qaner
+```
+
+## CoNLL-2003
 Pipeline results on CoNLL-2003 dataset:
 - [Metrics](https://tensorboard.dev/experiment/FEsbNJdmSd2LGVhga8Ku0Q/)
 - [Trained Hugging Face model](https://huggingface.co/dayyass/qaner-conll-bert-base-uncased)
@@ -12,7 +31,7 @@ Pipeline results on CoNLL-2003 dataset:
 ### Training
 Script for training QaNER model:
 ```
-python qaner/train.py \
+qaner-train \
 --bert_model_name 'bert-base-uncased' \
 --path_to_prompt_mapper 'data/conll2003/prompt_mapper.json' \
 --path_to_train_data 'data/conll2003/train.bio' \
@@ -42,7 +61,7 @@ Optional arguments:
 ### Infrerence
 Script for inference trained QaNER model:
 ```
-python qaner/inference.py \
+qaner-inference \
 --context 'EU rejects German call to boycott British lamb .' \
 --question 'What is the organization?' \
 --path_to_prompt_mapper 'data/conll2003/prompt_mapper.json' \
@@ -78,10 +97,10 @@ Possible inference questions for CoNLL-2003:
 - What is the organization? (ORG)
 - What is the miscellaneous entity? (MISC)
 
-### Requirements
+## Requirements
 Python >= 3.7
 
-### Citation
+## Citation
 ```bibtex
 @misc{liu2022qaner,
     title         = {QaNER: Prompting Question Answering Models for Few-shot Named Entity Recognition},

qaner/__init__.py

@@ -1 +1 @@
-# TODO
+__version__ = "0.1.1"

qaner/dataset.py

@@ -2,9 +2,10 @@
 
 import torch
 import transformers
-from data_utils import Instance, Span
 from tqdm import tqdm
 
+from qaner.data_utils import Instance, Span
+
 
 # TODO: add documentation
 class Dataset(torch.utils.data.Dataset):

qaner/inference.py

@@ -2,11 +2,12 @@
 from typing import Any, Dict
 
 import torch
-from arg_parse import get_inference_args
-from data_utils import Instance
-from inference_utils import get_top_valid_spans
 from transformers import AutoModelForQuestionAnswering, AutoTokenizer
-from utils import set_global_seed
+
+from qaner.arg_parse import get_inference_args
+from qaner.data_utils import Instance
+from qaner.inference_utils import get_top_valid_spans
+from qaner.utils import set_global_seed
 
 
 # TODO: add batch inference
@@ -71,7 +72,13 @@ def predict(
     return prediction
 
 
-if __name__ == "__main__":
+def main() -> int:
+    """
+    Main inference function.
+
+    Returns:
+        int: exit code.
+    """
 
     # argparse
     args = get_inference_args()
@@ -113,3 +120,9 @@ def predict(
     print(f"\nquestion: {prediction.question}\n")
     print(f"context: {prediction.context}")
     print(f"\nanswer: {prediction.answer}\n")
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()

qaner/inference_utils.py

@@ -3,7 +3,8 @@
 import numpy as np
 import torch
 import transformers
-from data_utils import Span
+
+from qaner.data_utils import Span
 
 
 def get_top_valid_spans(
@@ -85,7 +86,7 @@ def get_top_valid_spans(
                 span = Span(
                     token=context[start_context_char_char:end_context_char_char],
                     label=inv_prompt_mapper[  # TODO: add inference exception
-                        question_list[i].lstrip("What is the ").rstrip("?")
+                        question_list[i].split(r"What is the ")[-1].rstrip(r"?")
                     ],
                     start_context_char_pos=start_context_char_char,
                     end_context_char_pos=end_context_char_char,

qaner/metrics.py

@@ -1,7 +1,8 @@
 from typing import Dict, List
 
 import numpy as np
-from data_utils import Span
+
+from qaner.data_utils import Span
 
 
 # TODO: add metrics over label types
@@ -33,7 +34,7 @@ def compute_metrics(
     confusion_matrix_pred_denominator = np.zeros(len(entity_mapper))
 
     for span_true, span_pred in zip(spans_true_batch, spans_pred_batch_top_1):
-        span_pred = span_pred[0]
+        span_pred = span_pred[0]  # type: ignore
 
         i = entity_mapper[span_true.label]
         j = entity_mapper[span_pred.label]  # type: ignore

qaner/train.py

@@ -1,15 +1,23 @@
 import json
 
 import torch
-from arg_parse import get_train_args
-from data_utils import prepare_sentences_and_spans, read_bio_markup
-from dataset import Collator, Dataset
 from torch.utils.tensorboard import SummaryWriter
-from train_utils import train
 from transformers import AutoModelForQuestionAnswering, AutoTokenizer
-from utils import set_global_seed
 
-if __name__ == "__main__":
+from qaner.arg_parse import get_train_args
+from qaner.data_utils import prepare_sentences_and_spans, read_bio_markup
+from qaner.dataset import Collator, Dataset
+from qaner.train_utils import train
+from qaner.utils import set_global_seed
+
+
+def main() -> int:
+    """
+    Main train function.
+
+    Returns:
+        int: exit code.
+    """
 
     # argparse
     args = get_train_args()
@@ -105,3 +113,9 @@
 
     model.save_pretrained(args.path_to_save_model)
     tokenizer.save_pretrained(args.path_to_save_model)
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()

qaner/train_utils.py

@@ -2,13 +2,14 @@
 
 import numpy as np
 import torch
-from data_utils import Span
-from inference_utils import get_top_valid_spans
-from metrics import compute_metrics
 from torch.utils.tensorboard import SummaryWriter
 from tqdm import tqdm
 from transformers import AutoModelForQuestionAnswering
 
+from qaner.data_utils import Span
+from qaner.inference_utils import get_top_valid_spans
+from qaner.metrics import compute_metrics
+
 
 # TODO: add metrics calculation
 def train(

setup.py

@@ -0,0 +1,33 @@
+from setuptools import setup
+
+from qaner import __version__
+
+with open("README.md", mode="r", encoding="utf-8") as fp:
+    long_description = fp.read()
+
+
+setup(
+    name="qaner",
+    version=__version__,
+    description="Unofficial implementation of QaNER: Prompting Question Answering Models for Few-shot Named Entity Recognition.",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    author="Dani El-Ayyass",
+    author_email="[email protected]",
+    license_files=["LICENSE"],
+    url="https://github.com/dayyass/qaner",
+    packages=["qaner"],
+    entry_points={
+        "console_scripts": [
+            "qaner-train = qaner.train:main",
+            "qaner-inference = qaner.inference:main",
+        ],
+    },
+    install_requires=[
+        "numpy==1.21.6",
+        "tensorboard==2.9.0",
+        "torch==1.8.1",
+        "tqdm==4.64.0",
+        "transformers==4.19.2",
+    ],
+)