CLI Fixes

paperqa/agents/__init__.py

@@ -3,7 +3,6 @@
 import argparse
 import logging
 import os
-from datetime import datetime
 from typing import Any
 
 from pydantic_settings import CliSettingsSource
@@ -16,7 +15,7 @@
     from rich.console import Console
     from rich.logging import RichHandler
 
-    from .main import agent_query, search
+    from .main import agent_query, index_search
     from .models import AnswerResponse, QueryRequest
     from .search import SearchIndex, get_directory_index
 
@@ -44,6 +43,8 @@ def configure_cli_logging(verbosity: int = 0) -> None:
             "paperqa.agents.models": logging.WARNING,
             "paperqa.agents.search": logging.INFO,
             "litellm": logging.WARNING,
+            "LiteLLM Router": logging.WARNING,
+            "LiteLLM Proxy": logging.WARNING,
         }
     }
 
@@ -59,6 +60,8 @@ def configure_cli_logging(verbosity: int = 0) -> None:
         "paperqa.models": logging.DEBUG,
         "paperqa.agents.search": logging.DEBUG,
         "litellm": logging.INFO,
+        "LiteLLM Router": logging.INFO,
+        "LiteLLM Proxy": logging.INFO,
     }
 
     verbosity_map[3] = verbosity_map[2] | {
@@ -90,22 +93,6 @@ def configure_cli_logging(verbosity: int = 0) -> None:
         print(f"PaperQA version: {__version__}")
 
 
-def get_file_timestamps(path: os.PathLike | str) -> dict[str, str]:
-    # Get the stats for the file/directory
-    stats = os.stat(path)
-
-    # Get created time (ctime)
-    created_time = datetime.fromtimestamp(stats.st_ctime)
-
-    # Get modified time (mtime)
-    modified_time = datetime.fromtimestamp(stats.st_mtime)
-
-    return {
-        "created_at": created_time.strftime("%Y-%m-%d %H:%M:%S"),
-        "modified_at": modified_time.strftime("%Y-%m-%d %H:%M:%S"),
-    }
-
-
 def ask(query: str, settings: Settings) -> AnswerResponse:
     """Query PaperQA via an agent."""
     configure_cli_logging(verbosity=settings.verbosity)
@@ -138,7 +125,7 @@ def search_query(
         index_name = settings.get_index_name()
     loop = get_loop()
     return loop.run_until_complete(
-        search(
+        index_search(
             query,
             index_name=index_name,
             index_directory=settings.index_directory,
@@ -147,13 +134,20 @@ def search_query(
 
 
 def build_index(
+    index_name: str,
+    directory: str | os.PathLike,
     settings: Settings,
 ) -> SearchIndex:
     """Build a PaperQA search index, this will also happen automatically upon using `ask`."""
+    if index_name == "default":
+        index_name = settings.get_index_name()
     configure_cli_logging(verbosity=settings.verbosity)
+    settings.paper_directory = directory
     loop = get_loop()
 
-    return loop.run_until_complete(get_directory_index(settings=settings))
+    return loop.run_until_complete(
+        get_directory_index(index_name=index_name, settings=settings)
+    )
 
 
 def save_settings(
@@ -190,6 +184,10 @@ def main():
         help="Named settings to use. Will search in local, pqa directory, and package last",
     )
 
+    parser.add_argument(
+        "--index", "-i", default="default", help="Index name to search or create"
+    )
+
     subparsers = parser.add_subparsers(
         title="commands", dest="command", description="Available commands"
     )
@@ -208,12 +206,14 @@ def main():
     search_parser = subparsers.add_parser(
         "search",
         help="Search the index specified by --index."
-        " Pass --index answers to search previous answers.",
+        " Pass `--index answers` to search previous answers.",
     )
     search_parser.add_argument("query", help="Keyword search")
-    search_parser.add_argument(
-        "-i", dest="index", default="default", help="Index to search"
+
+    build_parser = subparsers.add_parser(
+        "index", help="Build a search index from given directory"
     )
+    build_parser.add_argument("directory", help="Directory to build index from")
 
     # Create CliSettingsSource instance
     cli_settings = CliSettingsSource(Settings, root_parser=parser)
@@ -237,7 +237,7 @@ def main():
         case "search":
             search_query(args.query, args.index, settings)
         case "index":
-            build_index(args.verbosity)
+            build_index(args.index, args.directory, settings)
         case _:
             commands = ", ".join({"view", "ask", "search", "index"})
             brief_help = f"\nRun with commands: {{{commands}}}\n\n"

paperqa/agents/helpers.py

@@ -56,10 +56,6 @@ async def litellm_get_search_query(
             f"The current year is {get_year()}."
         )
 
-    if "gpt" not in llm:
-        raise ValueError(
-            f"Invalid llm: {llm}, note a GPT model must be used for the fake agent search."
-        )
     model = LiteLLMModel(name=llm)
     model.config["model_list"][0]["litellm_params"].update({"temperature": temperature})
     chain = model.make_chain(prompt=search_prompt, skip_system=True)
@@ -91,9 +87,11 @@ def table_formatter(
         table.add_column("Title", style="cyan")
         table.add_column("File", style="magenta")
         for obj, filename in objects:
-            table.add_row(
-                cast(Docs, obj).texts[0].doc.title[:max_chars_per_column], filename  # type: ignore[attr-defined]
-            )
+            try:
+                display_name = cast(Docs, obj).texts[0].doc.title  # type: ignore[attr-defined]
+            except AttributeError:
+                display_name = cast(Docs, obj).texts[0].doc.citation
+            table.add_row(display_name[:max_chars_per_column], filename)
         return table
     raise NotImplementedError(
         f"Object type {type(example_object)} can not be converted to table."

paperqa/agents/main.py

@@ -298,16 +298,23 @@ async def aplan_with_injected_callbacks(
     return answer, agent_status
 
 
-async def search(
+async def index_search(
     query: str,
     index_name: str = "answers",
     index_directory: str | os.PathLike | None = None,
 ) -> list[tuple[AnswerResponse, str] | tuple[Any, str]]:
+    fields = [*SearchIndex.REQUIRED_FIELDS]
+    if index_name == "answers":
+        fields.append("question")
     search_index = SearchIndex(
-        ["file_location", "body", "question"],
+        fields=fields,
         index_name=index_name,
         index_directory=index_directory or pqa_directory("indexes"),
-        storage=SearchDocumentStorage.JSON_MODEL_DUMP,
+        storage=(
+            SearchDocumentStorage.JSON_MODEL_DUMP
+            if index_name == "answers"
+            else SearchDocumentStorage.PICKLE_COMPRESSED
+        ),
     )
 
     results = [
@@ -320,6 +327,7 @@ async def search(
         # Render the table to a string
         console.print(table_formatter(results))
     else:
-        agent_logger.info("No results found.")
+        count = await search_index.count
+        agent_logger.info(f"No results found. Searched {count} docs")
 
     return results

paperqa/agents/search.py

@@ -160,6 +160,10 @@ async def searcher(self) -> Searcher:
             self._searcher = index.searcher()
         return self._searcher
 
+    @property
+    async def count(self) -> int:
+        return (await self.searcher).num_docs
+
     @property
     async def index_files(self) -> dict[str, str]:
         if not self._index_files:
@@ -284,7 +288,7 @@ async def get_saved_object(
         return None
 
     def clean_query(self, query: str) -> str:
-        for replace in ("*", "[", "]"):
+        for replace in ("*", "[", "]", ":", "(", ")", "{", "}", "~"):
             query = query.replace(replace, "")
         return query
 
@@ -395,6 +399,7 @@ async def process_file(
 
 
 async def get_directory_index(
+    index_name: str | None = None,
     sync_index_w_directory: bool = True,
     settings: MaybeSettings = None,
 ) -> SearchIndex:
@@ -403,6 +408,7 @@ async def get_directory_index(
 
     Args:
         sync_index_w_directory: Sync the index with the directory. (i.e. delete files not in directory)
+        index_name: Name of the index. If not given, the name will be taken from the settings
         settings: Application settings.
     """
     _settings = get_settings(settings)
@@ -415,7 +421,7 @@ async def get_directory_index(
 
     search_index = SearchIndex(
         fields=[*SearchIndex.REQUIRED_FIELDS, "title", "year"],
-        index_name=_settings.get_index_name(),
+        index_name=index_name or _settings.get_index_name(),
         index_directory=_settings.index_directory,
     )
 

paperqa/clients/client_models.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import asyncio
 import logging
 from abc import ABC, abstractmethod
 from collections.abc import Collection
@@ -115,7 +116,7 @@ async def query(self, query: dict) -> DocDetails | None:
                 f"{client_query.doi if isinstance(client_query, DOIQuery) else client_query.title}"
                 f" in {self.__class__.__name__}."
             )
-        except TimeoutError:
+        except (TimeoutError, asyncio.exceptions.TimeoutError):
             logger.warning(
                 f"Request to {self.__class__.__name__} for "
                 f"{client_query.doi if isinstance(client_query, DOIQuery) else client_query.title}"

paperqa/docs.py

@@ -327,7 +327,6 @@ async def aadd(  # noqa: PLR0912
                     doi = citation_doi
                 if citation_author := citation_json.get("authors"):
                     authors = citation_author
-
         # see if we can upgrade to DocDetails
         # if not, we can progress with a normal Doc
         # if "overwrite_fields_from_metadata" is used:
@@ -349,7 +348,6 @@ async def aadd(  # noqa: PLR0912
                 query_kwargs["authors"] = authors
             if title:
                 query_kwargs["title"] = title
-
             doc = await metadata_client.upgrade_doc_to_doc_details(
                 doc, **(query_kwargs | kwargs)
             )

paperqa/utils.py

@@ -479,6 +479,8 @@ def setup_default_logs() -> None:
                 "httpx": {"level": "WARNING"},
                 # SEE: https://github.com/BerriAI/litellm/issues/2256
                 "LiteLLM": {"level": "WARNING"},
+                "LiteLLM Router": {"level": "WARNING"},
+                "LiteLLM Proxy": {"level": "WARNING"},
             },
         }
     )

pyproject.toml

@@ -47,31 +47,23 @@ requires-python = ">=3.10"
 
 [project.optional-dependencies]
 agents = [
-    "anthropic",
     "anyio",
     "langchain",
     "langchain-community",
     "langchain-core",
     "langchain-openai",
     "pymupdf",
+    "pymupdf",
     "requests",
     "tantivy",
     "typer",
     "typing_extensions",
 ]
-google = [
-    "langchain-google-vertexai",
-    "vertexai",
-]
 llms = [
-    "anthropic",
     "faiss-cpu",
     "langchain-community",
     "langchain-core",
     "langchain-openai",
-    "pymupdf",
-    "sentence_transformers",
-    "voyageai",
 ]
 typing = [
     "types-PyYAML",
@@ -155,8 +147,6 @@ module = [
     "fitz",
     "litellm",  # SEE: https://github.com/BerriAI/litellm/issues/825
     "pyzotero",  # SEE: https://github.com/urschrei/pyzotero/issues/110
-    "sentence_transformers",  # SEE: https://github.com/UKPLab/sentence-transformers/issues/1723
-    "voyageai.*",  # SEE: https://github.com/voyage-ai/voyageai-python/issues/8
 ]
 
 [tool.pylint]
@@ -402,9 +392,10 @@ dev-dependencies = [
     "build",  # TODO: remove after https://github.com/astral-sh/uv/issues/6278
     "ipython>=8",  # Pin to keep recent
     "mypy>=1.8",  # Pin for mutable-override
-    "paper-qa[agents,google,llms]",
+    "paper-qa[agents,llms,typing]",
     "pre-commit~=3.4",  # Pin to keep recent
     "pytest-asyncio",
+    "pytest-mock",
     "pytest-recording",
     "pytest-rerunfailures",
     "pytest-subtests",

tests/test_cli.py

@@ -0,0 +1,65 @@
+import io
+import os
+import sys
+from pathlib import Path
+
+import pytest
+
+from paperqa.settings import Settings
+from paperqa.utils import pqa_directory
+
+try:
+    from paperqa.agents import ask, build_index, main, search_query
+    from paperqa.agents.models import AnswerResponse
+except ImportError:
+    pytest.skip("agents module is not installed", allow_module_level=True)
+
+
+def test_can_modify_settings():
+    old_argv = sys.argv
+    old_stdout = sys.stdout
+    captured_output = io.StringIO()
+    try:
+        sys.argv = "paperqa -s debug --llm=my-model-foo save unit_test".split()
+        main()
+
+        sys.stdout = captured_output
+        assert Settings.from_name("unit_test").llm == "my-model-foo"
+
+        sys.argv = "paperqa -s unit_test view".split()
+        main()
+
+        output = captured_output.getvalue().strip()
+        assert "my-model-foo" in output
+    finally:
+        sys.argv = old_argv
+        sys.stdout = old_stdout
+        os.unlink(pqa_directory("settings") / "unit_test.json")
+
+
+def test_cli_ask(agent_index_dir: Path, stub_data_dir: Path):
+    settings = Settings.from_name("debug")
+    settings.index_directory = agent_index_dir
+    settings.paper_directory = stub_data_dir
+    response = ask(
+        "How can you use XAI for chemical property prediction?", settings=settings
+    )
+    assert response.answer.formatted_answer
+
+    search_result = search_query(
+        " ".join(response.answer.formatted_answer.split()[:5]),
+        "answers",
+        settings,
+    )
+    found_answer = search_result[0][0]
+    assert isinstance(found_answer, AnswerResponse)
+    assert found_answer.model_dump_json() == response.model_dump_json()
+
+
+def test_cli_can_build_and_search_index(agent_index_dir: Path, stub_data_dir: Path):
+    settings = Settings.from_name("debug")
+    settings.index_directory = agent_index_dir
+    index_name = "test"
+    build_index(index_name, stub_data_dir, settings)
+    search_result = search_query("XAI", index_name, settings)
+    assert search_result