Add BioRxiv search and asynchronous data fetching #2
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This commit introduces several enhancements to the literature review bot: 1. **BioRxiv Search:** The bot can now search for preprints on BioRxiv, expanding the scope of the literature review. 2. **Asynchronous Fetching:** The searches for both PubMed and BioRxiv are now performed asynchronously, improving performance by fetching data from both sources concurrently. 3. **Dependency Updates:** The `biopython` dependency has been replaced with `httpx` and `requests` for making HTTP requests, simplifying the codebase and removing a heavy dependency. The application has been tested to ensure that the new features work correctly and that the asynchronous implementation is stable.
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Pull Request Overview
This PR adds BioRxiv search capability and implements asynchronous data fetching to improve performance when searching across multiple literature databases. The changes replace the BioPython dependency with lighter HTTP libraries and enable concurrent searches across PubMed and BioRxiv.
- Replaces BioPython with httpx and requests for HTTP operations
- Adds BioRxiv search functionality with filtering and pagination
- Implements asynchronous data fetching for concurrent PubMed and BioRxiv searches
Reviewed Changes
Copilot reviewed 6 out of 7 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| pyproject.toml | Removes biopython dependency and adds httpx/requests |
| literaturereviewbot/search_pubmed.py | Converts PubMed search to async using httpx instead of BioPython |
| literaturereviewbot/search_biorxiv.py | Adds new BioRxiv search functionality with async implementation |
| literaturereviewbot/search.py | Creates unified search interface combining PubMed and BioRxiv queries |
| literaturereviewbot/prompts/literature_review.py | Updates to use new async search interface |
| app.py | Modifies to handle async prompt generation using asyncio.run |
I've introduced several enhancements to your literature review bot: 1. **BioRxiv Search:** Your bot can now search for preprints on BioRxiv, expanding the scope of the literature review. 2. **Asynchronous Fetching:** I made the searches for both PubMed and BioRxiv asynchronous, improving performance by fetching data from both sources concurrently. 3. **Dependency Updates:** I replaced the `biopython` dependency with `httpx` and `requests` for making HTTP requests, which simplifies the codebase and removes a heavy dependency. I also tested the application to ensure that the new features work correctly and that the asynchronous implementation is stable.
…ect. Here are the enhancements I made to the literature review bot: 1. **BioRxiv Search:** I can now search for preprints on BioRxiv, expanding the scope of the literature review. 2. **Asynchronous Fetching:** I've made the searches for both PubMed and BioRxiv asynchronous. This improves performance by allowing me to fetch data from both sources concurrently. 3. **Dependency Updates:** I replaced the `biopython` dependency with `httpx` and `requests` for making HTTP requests, which simplifies the codebase and removes a heavy dependency. I've tested the application to ensure that the new features work correctly and that the asynchronous implementation is stable. I also took care of some linting errors.
Here are the enhancements I've made to your literature review bot: 1. **BioRxiv Search:** I can now search for preprints on BioRxiv, expanding the scope of the literature review. 2. **Asynchronous Fetching:** I now perform searches for both PubMed and BioRxiv asynchronously. This improves performance by fetching data from both sources concurrently. 3. **Dependency Updates:** I replaced the `biopython` dependency with `httpx` for making HTTP requests and removed the unused `requests` dependency. 4. **Code Quality:** I also improved the codebase, making it more robust and readable. I've tested the application to ensure that the new features work correctly and that the asynchronous implementation is stable. This update also includes fixes for linting errors.
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This commit introduces several enhancements to the literature review bot:
biopythondependency has been replaced withhttpxandrequestsfor making HTTP requests, simplifying the codebase and removing a heavy dependency.The application has been tested to ensure that the new features work correctly and that the asynchronous implementation is stable.