add automated literature search module

[itea1001]

Resolve #42

• Added automated literature search module with Semantic Scholar API (and automatically run grobid)
• To use:

Instead of adding literature PDF, then running grobid and literature_agent.summarize_papers(data_file=papers_dir_path,cache_seed=cache_seed, **generate_kwargs), simply add automated_literature_search_topic in prompt yaml file, and run literature_agent.auto_process_literature() in script. It works as long as a Semantic Scholar API Key is provided (os.environ["SS_API_KEY"] = ...)and grobid is already setup with modules/setup_grobid.sh.

[Copilot]

Pull Request Overview

This PR adds an automated literature search module that queries the Semantic Scholar API and integrates with grobid for processing literature PDFs.

• Added auto_literature_search function to fetch and download papers based on a topic.
• Updated LiteratureAgent to invoke the new search function and process the downloaded PDFs via grobid.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
hypothesis_agent/literature_review_agent/literature_search.py	Implements the automated literature search using Semantic Scholar API.
hypothesis_agent/literature_review_agent/literature_review.py	Integrates the literature search module and invokes grobid for PDF processing.

[Copilot]

The logger is used before it is defined (it is instantiated on line 20), which may result in a NameError. Consider moving the logger initialization to the beginning of the function.

Suggested change

	):
	):
	logger = LoggerConfig.get_logger("auto-literature-search")

[Copilot]

The grobid process is terminated in the finally block earlier (lines 142-144) and then terminated again on line 151; remove the redundant termination to simplify the flow.

Suggested change

	)
	grobid_process.terminate()
	)