Optimized import paths

paperqa/__init__.py

@@ -1,5 +1,5 @@
-from .docs import Answer, Docs, print_callback
-from .llms import (
+from paperqa.docs import Answer, Docs, print_callback
+from paperqa.llms import (
     EmbeddingModel,
     HybridEmbeddingModel,
     LangchainVectorStore,
@@ -11,9 +11,9 @@
     SparseEmbeddingModel,
     embedding_model_factory,
 )
-from .settings import Settings, get_settings
-from .types import Context, Doc, DocDetails, Text
-from .version import __version__
+from paperqa.settings import Settings, get_settings
+from paperqa.types import Context, Doc, DocDetails, Text
+from paperqa.version import __version__
 
 __all__ = [
     "Answer",

paperqa/agents/__init__.py

@@ -7,9 +7,9 @@
 
 from pydantic_settings import CliSettingsSource
 
-from .. import __version__
-from ..settings import Settings
-from ..utils import get_loop, pqa_directory, setup_default_logs
+from paperqa.settings import Settings
+from paperqa.utils import get_loop, pqa_directory, setup_default_logs
+from paperqa.version import __version__
 
 try:
     from rich.console import Console

paperqa/agents/helpers.py

@@ -7,10 +7,9 @@
 
 from rich.table import Table
 
-from .. import (
-    Docs,
-)
-from ..llms import LiteLLMModel
+from paperqa.docs import Docs
+from paperqa.llms import LiteLLMModel
+
 from .models import AnswerResponse
 
 logger = logging.getLogger(__name__)

paperqa/agents/main.py

@@ -14,9 +14,10 @@
 from langchain_openai import ChatOpenAI
 from rich.console import Console
 
-from ..docs import Docs
-from ..types import Answer
-from ..utils import pqa_directory
+from paperqa.docs import Docs
+from paperqa.types import Answer
+from paperqa.utils import pqa_directory
+
 from .helpers import litellm_get_search_query, table_formatter
 from .models import (
     AgentCallback,

paperqa/agents/models.py

@@ -24,10 +24,9 @@
 from typing_extensions import Protocol
 
 from paperqa.llms import LiteLLMModel
-
-from .. import Answer
-from ..settings import Settings
-from ..version import __version__
+from paperqa.settings import Settings
+from paperqa.types import Answer
+from paperqa.version import __version__
 
 logger = logging.getLogger(__name__)
 

paperqa/agents/search.py

@@ -24,10 +24,11 @@
     wait_random_exponential,
 )
 
-from ..docs import Docs
-from ..settings import MaybeSettings, Settings, get_settings
-from ..types import DocDetails
-from ..utils import hexdigest, pqa_directory
+from paperqa.docs import Docs
+from paperqa.settings import MaybeSettings, Settings, get_settings
+from paperqa.types import DocDetails
+from paperqa.utils import hexdigest, pqa_directory
+
 from .models import SupportsPickle
 
 logger = logging.getLogger(__name__)

paperqa/agents/tools.py

@@ -1,13 +1,13 @@
 from __future__ import annotations
+
 import inspect
 import logging
 import re
 import sys
 from typing import ClassVar
-from langchain_core.callbacks import BaseCallbackHandler
 
 from langchain.tools import BaseTool
-from paperqa import Answer, Docs
+from langchain_core.callbacks import BaseCallbackHandler
 from pydantic import BaseModel, ConfigDict, Field
 
 # ruff: noqa: I001
@@ -16,11 +16,14 @@
     Field as FieldV1,
 )
 
+from paperqa.docs import Docs
+from paperqa.llms import EmbeddingModel, LiteLLMModel
+from paperqa.settings import Settings
+from paperqa.types import Answer
+
 from .helpers import get_year
-from .search import get_directory_index
 from .models import QueryRequest, SimpleProfiler
-from ..settings import Settings
-from ..llms import EmbeddingModel, LiteLLMModel
+from .search import get_directory_index
 
 logger = logging.getLogger(__name__)
 

paperqa/clients/__init__.py

@@ -8,8 +8,9 @@
 import aiohttp
 from pydantic import BaseModel, ConfigDict
 
-from ..types import Doc, DocDetails
-from ..utils import gather_with_concurrency
+from paperqa.types import Doc, DocDetails
+from paperqa.utils import gather_with_concurrency
+
 from .client_models import MetadataPostProcessor, MetadataProvider
 from .crossref import CrossrefProvider
 from .journal_quality import JournalQualityPostProcessor

paperqa/clients/client_models.py

@@ -16,9 +16,9 @@
     model_validator,
 )
 
-from paperqa.clients.exceptions import DOINotFoundError
+from paperqa.types import DocDetails
 
-from ..types import DocDetails
+from .exceptions import DOINotFoundError
 
 logger = logging.getLogger(__name__)
 

paperqa/clients/crossref.py

@@ -11,16 +11,17 @@
 
 import aiohttp
 
-from ..clients.exceptions import DOINotFoundError
-from ..types import CITATION_FALLBACK_DATA, DocDetails
-from ..utils import (
+from paperqa.types import CITATION_FALLBACK_DATA, DocDetails
+from paperqa.utils import (
     bibtex_field_extract,
     create_bibtex_key,
     remove_substrings,
     strings_similarity,
     union_collections_to_ordered_list,
 )
+
 from .client_models import DOIOrTitleBasedProvider, DOIQuery, TitleAuthorQuery
+from .exceptions import DOINotFoundError
 
 logger = logging.getLogger(__name__)
 

paperqa/clients/journal_quality.py

@@ -7,7 +7,8 @@
 
 from pydantic import ValidationError
 
-from ..types import DocDetails
+from paperqa.types import DocDetails
+
 from .client_models import JournalQuery, MetadataPostProcessor
 
 logger = logging.getLogger(__name__)

paperqa/clients/semantic_scholar.py

@@ -11,13 +11,14 @@
 
 import aiohttp
 
-from ..types import DocDetails
-from ..utils import (
+from paperqa.types import DocDetails
+from paperqa.utils import (
     _get_with_retrying,
     clean_upbibtex,
     strings_similarity,
     union_collections_to_ordered_list,
 )
+
 from .client_models import DOIOrTitleBasedProvider, DOIQuery, TitleAuthorQuery
 from .crossref import doi_to_bibtex
 from .exceptions import DOINotFoundError

paperqa/clients/unpaywall.py

@@ -8,11 +8,9 @@
 import aiohttp
 from pydantic import BaseModel, ConfigDict, ValidationError
 
-from ..types import DocDetails
-from ..utils import (
-    _get_with_retrying,
-    strings_similarity,
-)
+from paperqa.types import DocDetails
+from paperqa.utils import _get_with_retrying, strings_similarity
+
 from .client_models import DOIOrTitleBasedProvider, DOIQuery, TitleAuthorQuery
 from .exceptions import DOINotFoundError
 

paperqa/contrib/zotero.py

@@ -1,4 +1,5 @@
-# This file gets PDF files from the user's Zotero library
+"""This module gets PDF files from the user's Zotero library."""
+
 import logging
 import os
 from pathlib import Path
@@ -8,10 +9,13 @@
 
 try:
     from pyzotero import zotero
-except ImportError:
-    raise ImportError("Please install pyzotero: `pip install pyzotero`")  # noqa: B904
-from ..paths import PAPERQA_DIR
-from ..utils import StrPath, count_pdf_pages
+except ImportError as e:
+    raise ImportError(
+        "zotero requires the 'zotero' extra for 'pyzotero'. Please:"
+        " `pip install aviary[zotero]`."
+    ) from e
+from paperqa.paths import PAPERQA_DIR
+from paperqa.utils import StrPath, count_pdf_pages
 
 
 class ZoteroPaper(BaseModel):

paperqa/core.py

@@ -5,9 +5,9 @@
 from collections.abc import Callable
 from typing import Any
 
-from .llms import Chain
-from .types import Context, LLMResult, Text
-from .utils import extract_score, strip_citations
+from paperqa.llms import Chain
+from paperqa.types import Context, LLMResult, Text
+from paperqa.utils import extract_score, strip_citations
 
 
 def llm_parse_json(text: str) -> dict:

paperqa/docs.py

@@ -20,18 +20,13 @@
     field_validator,
 )
 
-from .clients import DEFAULT_CLIENTS, DocMetadataClient
-from .core import llm_parse_json, map_fxn_summary
-from .llms import (
-    EmbeddingModel,
-    LLMModel,
-    NumpyVectorStore,
-    VectorStore,
-)
-from .paths import PAPERQA_DIR
-from .readers import read_doc
-from .settings import MaybeSettings, get_settings
-from .types import (
+from paperqa.clients import DEFAULT_CLIENTS, DocMetadataClient
+from paperqa.core import llm_parse_json, map_fxn_summary
+from paperqa.llms import EmbeddingModel, LLMModel, NumpyVectorStore, VectorStore
+from paperqa.paths import PAPERQA_DIR
+from paperqa.readers import read_doc
+from paperqa.settings import MaybeSettings, get_settings
+from paperqa.types import (
     Answer,
     Doc,
     DocDetails,
@@ -40,7 +35,7 @@
     Text,
     set_llm_answer_ids,
 )
-from .utils import (
+from paperqa.utils import (
     gather_with_concurrency,
     get_loop,
     maybe_is_html,

paperqa/llms.py

@@ -12,9 +12,9 @@
 from litellm import Router, aembedding, token_counter
 from pydantic import BaseModel, ConfigDict, Field, model_validator
 
-from .prompts import default_system_prompt
-from .types import Doc, Embeddable, LLMResult, Text
-from .utils import is_coroutine_callable
+from paperqa.prompts import default_system_prompt
+from paperqa.types import Doc, Embeddable, LLMResult, Text
+from paperqa.utils import is_coroutine_callable
 
 Chain = Callable[
     [dict, list[Callable[[str], None]] | None, str | None],

paperqa/readers.py

@@ -7,8 +7,8 @@
 import html2text
 import tiktoken
 
-from .types import ChunkMetadata, Doc, ParsedMetadata, ParsedText, Text
-from .version import __version__ as pqa_version
+from paperqa.types import ChunkMetadata, Doc, ParsedMetadata, ParsedText, Text
+from paperqa.version import __version__ as pqa_version
 
 
 def parse_pdf_fitz_to_pages(path: Path) -> ParsedText:

paperqa/settings.py

@@ -13,8 +13,8 @@
 from pydantic import BaseModel, ConfigDict, Field, computed_field, field_validator
 from pydantic_settings import BaseSettings, CliSettingsSource, SettingsConfigDict
 
-from .llms import EmbeddingModel, LiteLLMModel, embedding_model_factory
-from .prompts import (
+from paperqa.llms import EmbeddingModel, LiteLLMModel, embedding_model_factory
+from paperqa.prompts import (
     citation_prompt,
     default_system_prompt,
     qa_prompt,
@@ -24,8 +24,8 @@
     summary_json_system_prompt,
     summary_prompt,
 )
-from .utils import hexdigest, pqa_directory
-from .version import __version__
+from paperqa.utils import hexdigest, pqa_directory
+from paperqa.version import __version__
 
 
 class AnswerSettings(BaseModel):
@@ -232,7 +232,7 @@ def check_pre(cls, v: str | None) -> str | None:
     def check_post(cls, v: str | None) -> str | None:
         if v is not None:
             # kind of a hack to get list of attributes in answer
-            from .types import Answer
+            from paperqa.types import Answer
 
             attrs = set(Answer.model_fields.keys())
             if not set(get_formatted_variables(v)).issubset(attrs):
@@ -311,7 +311,7 @@ def validate_tool_names(cls, v: set[str] | None) -> set[str] | None:
         if v is None:
             return None
         # imported here to avoid circular imports
-        from .agents.main import GenerateAnswerTool
+        from paperqa.agents.main import GenerateAnswerTool
 
         answer_tool_name = GenerateAnswerTool.__fields__["name"].default
         if answer_tool_name not in v:

paperqa/types.py

@@ -24,13 +24,13 @@
     model_validator,
 )
 
-from .utils import (
+from paperqa.utils import (
     create_bibtex_key,
     encode_id,
     format_bibtex,
     get_citenames,
 )
-from .version import __version__ as pqa_version
+from paperqa.version import __version__ as pqa_version
 
 # Just for clarity
 # also in case one day we want to narrow

pyproject.toml

@@ -70,6 +70,9 @@ typing = [
     "types-requests",
     "types-setuptools",
 ]
+zotero = [
+    "pyzotero",
+]
 
 [project.scripts]
 pqa = "paperqa.agents:main"
@@ -336,7 +339,6 @@ ignore = [
     "TCH003",
     "TD002",  # Don't care for TODO author
     "TD003",  # Don't care for TODO links
-    "TID252",  # Allow relative imports for packaging
     "TRY003",  # Overly pedantic
 ]
 preview = true