Agentic workflows, locally indexed search, and CLI (#309)

* add agentic workflow module and cli

* update pyproject.toml and split google into its own import

* remove unused import

* update default search chain

* Update __init__.py

* Update search.py

* move reqs into pyproject.toml, addressing PR comments

* rename search_chain to openai_get_search_query

* remove get_llm_name

* move table_formatter to helpers.py

* Update paperqa/agents/main.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update paperqa/agents/main.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update paperqa/agents/main.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update paperqa/agents/docs.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update paperqa/types.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* rename compute_cost to compute_total_model_token_cost

* remove stream_answer

* rename to stub_manifest, and use Path for all paths

* Update paperqa/llms.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* move SKIP_AGENT_TESTS = False

* nix _ = assignments

* add test comments

* types in conftest.py

* split libs into llms

* link openai chat timeout to query.timeout

* Update paperqa/agents/__init__.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* logging revamp and renaming

* Update tests/test_cli.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update tests/test_cli.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* move vertex import to func call, add docstring to SupportsPickle

* docstring

* remove _ =

* remove bool return type from set

* update gitignore

* add config attribute to baase LLMModel class

* replace get_current_settings -> get_settings

* replace get_current_settings -> get_settings

* PR simplifications

* remove all stream_* functions

* avoid modifying the root logger

* re-organize logger import location

* move hashlib into utils

* refactor strip_answer into Answer object

* label circular imports

* ensure absolute paths are used in index name

* limit select to be used only when DOI is not present in crossref

* Update paperqa/agents/search.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update paperqa/agents/search.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update paperqa/agents/search.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update paperqa/agents/search.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* Update paperqa/agents/models.py

Co-authored-by: James Braza <jamesbraza@gmail.com>

* reconfigure logging to not prevent propagation

* remove newlines in the current year

* use required fields as a subset

* replace . with Path.cwd()

---------

Co-authored-by: James Braza <jamesbraza@gmail.com>

.github/workflows/build.yml

@@ -16,7 +16,7 @@ jobs:
         with:
           python-version: 3.11
           cache: pip
-      - run: pip install .[dev]
+      - run: pip install .[agents,google,dev,llms]
       - name: Build a binary wheel and a source tarball
         run: |
           python -m build --sdist --wheel --outdir dist/ .

.github/workflows/tests.yml

@@ -20,7 +20,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
-      - run: pip install .[dev]
+      - run: pip install .[agents,google,dev,llms]
       - name: Check pre-commit
         run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
       - name: Run Test

.gitignore

@@ -1,3 +1,138 @@
+# Swap
+[._]*.s[a-v][a-z]
+!*.svg  # comment out if you don't need vector files
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+
+# Session
+Session.vim
+Sessionx.vim
+
+# Temporary
+.netrwhist
+*~
+# Auto-generated tag files
+tags
+# Persistent undo
+[._]*.un~
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon[\r]
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -20,7 +155,6 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -50,6 +184,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -72,6 +207,7 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -82,7 +218,9 @@ profile_default/
 ipython_config.py
 
 # pyenv
-.python-version
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -91,7 +229,24 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 
 # Celery stuff
@@ -128,12 +283,23 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# testing files generated
-*.txt.json
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
 
 *.ipynb
 env
 
 # Matching pyproject.toml
 paperqa/version.py
 tests/example*
+tests/test_index/*

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
       - id: mixed-line-ending
       - id: trailing-whitespace
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.0
+    rev: v0.6.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -41,6 +41,7 @@ repos:
           - pydantic~=2.0 # Match pyproject.toml
           - types-requests
           - types-setuptools
+          - types-PyYAML
   - repo: https://github.com/rbubley/mirrors-prettier
     rev: v3.3.2
     hooks: