Paper-qa

What's Changed

* Renamed to PQASession type by whitead in https://github.com/Future-House/paper-qa/pull/653
* Lock file maintenance by renovate in https://github.com/Future-House/paper-qa/pull/657
* Ability to zero-shot `gen_answer` by jamesbraza in https://github.com/Future-House/paper-qa/pull/658
* Lock file maintenance by renovate in https://github.com/Future-House/paper-qa/pull/659
* Moving to `uv` dependency groups by jamesbraza in https://github.com/Future-House/paper-qa/pull/660
* Lock file maintenance by renovate in https://github.com/Future-House/paper-qa/pull/664
* Convert citation to formatted_citation usage where necessary by mskarlin in https://github.com/Future-House/paper-qa/pull/666
* Catch edge case where externalIds field is None by mskarlin in https://github.com/Future-House/paper-qa/pull/668
* Made o1 temperature issue a warning, instead of valueerror by whitead in https://github.com/Future-House/paper-qa/pull/669
* Added train and eval splits' questions and DOIs by jamesbraza in https://github.com/Future-House/paper-qa/pull/662
* `fake` agent allowing timeouts or exceptions, by jamesbraza in https://github.com/Future-House/paper-qa/pull/672
* Optional `AnswerSetting.max_answer_attempts` to allow a new unsure branch by jamesbraza in https://github.com/Future-House/paper-qa/pull/673
* Made it so you do not die on invalid tool by whitead in https://github.com/Future-House/paper-qa/pull/670
* Allowing latest `pydantic-settings` and regenerated cassettes by jamesbraza in https://github.com/Future-House/paper-qa/pull/674
* Empty tool calls leading to `done` condition by jamesbraza in https://github.com/Future-House/paper-qa/pull/671
* Changed it to be debug for source quality by whitead in https://github.com/Future-House/paper-qa/pull/675

**Full Changelog**: https://github.com/Future-House/paper-qa/compare/v5.3.2...v5.4.0

Prevents parallel tool calls from clobbering the env. state.

**Full Changelog**: https://github.com/Future-House/paper-qa/compare/v5.3.2...v5.3.3

What's Changed

* Printing the `text` in a failed `llm_parse_json` by jamesbraza in https://github.com/Future-House/paper-qa/pull/629
* Change S2 client logic to use arxiv doi if it's defined by mskarlin in https://github.com/Future-House/paper-qa/pull/632
* Increased retry count for `ClientConnectorDNSError` errors by jamesbraza in https://github.com/Future-House/paper-qa/pull/639
* Make string similarity case insensitive by default by mskarlin in https://github.com/Future-House/paper-qa/pull/640
* Pulling in latest `fhaviary`, `mypy`, `ruff` by jamesbraza in https://github.com/Future-House/paper-qa/pull/647
* Add an after model validator ensuring temp=1 for o1 models by dakoner in https://github.com/Future-House/paper-qa/pull/649
* Fixing crash due to `None` author by jamesbraza in https://github.com/Future-House/paper-qa/pull/650
* Fixing flaky test `test_minimal_fields_filtering` by jamesbraza in https://github.com/Future-House/paper-qa/pull/651
* Fixing flaky tests `test_code` and `test_minimal_fields_filtering` by jamesbraza in https://github.com/Future-House/paper-qa/pull/652
* Lock file maintenance by renovate in https://github.com/Future-House/paper-qa/pull/648

New Contributors

* dakoner made their first contribution in https://github.com/Future-House/paper-qa/pull/649

**Full Changelog**: https://github.com/Future-House/paper-qa/compare/v5.3.1...v5.3.2

What's Changed
* Exposed `LDPRolloutCallback` and `on_agent_action_callback` for `fake` agent by jamesbraza in https://github.com/Future-House/paper-qa/pull/612
* Fixed `NumpyVectorStore.__eq__`'s `NotImplemented` case by jamesbraza in https://github.com/Future-House/paper-qa/pull/613
* Implemented `__deepcopy__` on all `Environment`s by jamesbraza in https://github.com/Future-House/paper-qa/pull/614
* Made embedding default by whitead in https://github.com/Future-House/paper-qa/pull/615
* Lock file maintenance by renovate in https://github.com/Future-House/paper-qa/pull/617
* Pulled in latest PyMuPDF for `set_messages` by jamesbraza in https://github.com/Future-House/paper-qa/pull/618
* Fixed crash due to DOI being a `list` by jamesbraza in https://github.com/Future-House/paper-qa/pull/619
* Added configuration to adjust how contexts are displayed by whitead in https://github.com/Future-House/paper-qa/pull/620
* Fixing CI by regenerating `test_pdf_reader_match_doc_details` cassette by jamesbraza in https://github.com/Future-House/paper-qa/pull/625
* Retrying flaky test `test_propagate_options` by jamesbraza in https://github.com/Future-House/paper-qa/pull/626
* Regression protection in `embedding_model_factory` by jamesbraza in https://github.com/Future-House/paper-qa/pull/622
* Added `writer.wait_merging_threads` call by jamesbraza in https://github.com/Future-House/paper-qa/pull/628
* Caching opened `tantivy.Index`es in the package by jamesbraza in https://github.com/Future-House/paper-qa/pull/627


**Full Changelog**: https://github.com/Future-House/paper-qa/compare/v5.3.0...v5.3.1

What's Changed
* Add callback support in settings and tools by nadolskit in https://github.com/Future-House/paper-qa/pull/590
* Moved `validate_sources` to include all `sources` not found by jamesbraza in https://github.com/Future-House/paper-qa/pull/595
* Cleaning up citations by jamesbraza in https://github.com/Future-House/paper-qa/pull/598
* Validating sources with case insensitive DOI matching by jamesbraza in https://github.com/Future-House/paper-qa/pull/600
* Added sentence transformers embedding model by whitead in https://github.com/Future-House/paper-qa/pull/604
* Cleaned and clarified deferred embeddings code by jamesbraza in https://github.com/Future-House/paper-qa/pull/597
* Fixed `NumpyVectorStore.clear` from not clearing `text_hashes` by jamesbraza in https://github.com/Future-House/paper-qa/pull/608
* Moved Pydantic `model_config` to top of each class by jamesbraza in https://github.com/Future-House/paper-qa/pull/607
* Testing we can use `~` as `paper_directory` by jamesbraza in https://github.com/Future-House/paper-qa/pull/610
* Increased testing of `NumpyVectorStore` and `defer_embeddings` by jamesbraza in https://github.com/Future-House/paper-qa/pull/606
* Expose env class to run_agent functions by mskarlin in https://github.com/Future-House/paper-qa/pull/611


**Full Changelog**: https://github.com/Future-House/paper-qa/compare/v5.2.1...v5.3.0