Skip to content
Permalink

Comparing changes

Choose two branches to see what’s changed or to start a new pull request. If you need to, you can also or learn more about diff comparisons.

Open a pull request

Create a new pull request by comparing changes across two branches. If you need to, you can also . Learn more about diff comparisons here.
base repository: aaronwtr/geneius
Failed to load repositories. Confirm that selected base ref is valid, then try again.
Loading
base: v1.2
Choose a base ref
...
head repository: aaronwtr/geneius
Failed to load repositories. Confirm that selected head ref is valid, then try again.
Loading
compare: main
Choose a head ref
  • 4 commits
  • 4 files changed
  • 1 contributor

Commits on Nov 7, 2023

  1. Copy the full SHA
    58e1656 View commit details
  2. Copy the full SHA
    7a066e4 View commit details
  3. clean up configs

    aaronwtr committed Nov 7, 2023
    Copy the full SHA
    91afc84 View commit details
  4. prepare new version

    aaronwtr committed Nov 7, 2023
    Copy the full SHA
    c86a9af View commit details
Showing with 4 additions and 20 deletions.
  1. +3 −4 setup.py
  2. +0 −2 src/configs/claude.yml
  3. +0 −5 src/configs/pubmed.yml
  4. +1 −9 src/context.py
7 changes: 3 additions & 4 deletions setup.py
Original file line number Diff line number Diff line change
@@ -1,13 +1,12 @@
from setuptools import setup
import io
from setuptools import setup, find_packages

setup(
name='geneius',
version='1.2',
version='1.4',
packages=['src'],
url='https://github.com/aaronwtr/geneius',
description='A tool for disease-gene evidence search and explanation',
long_description=io.open('README.md', 'r', encoding='utf-8').read(),
long_description='More information on the GitHub repository: https://github.com/aaronwtr/geneius',
license='MIT',
author='Aaron Wenteler',
email='a.wenteler@qmul.ac.uk',
2 changes: 0 additions & 2 deletions src/configs/claude.yml

This file was deleted.

5 changes: 0 additions & 5 deletions src/configs/pubmed.yml

This file was deleted.

10 changes: 1 addition & 9 deletions src/context.py
Original file line number Diff line number Diff line change
@@ -1,21 +1,13 @@
from Bio import Entrez

import yaml
from tqdm import tqdm


class PubMedScraper:
def __init__(self):
self.config = self.config()
self.email = self.config['user']['email']
self.email = '123@example.com'
Entrez.email = self.email

@staticmethod
def config():
with open('geneius/configs/pubmed.yml', 'r') as file:
config = yaml.safe_load(file)
return config

@staticmethod
def search_literature(query, num_records):
try: