Merge pull request #362 from Future-House/september-2024-release

September 2024 release

Author: whitead

.github/workflows/build.yml

@@ -2,25 +2,19 @@ name: publish
 
 on:
   release:
-    types:
-      - created
+    types: [created]
   workflow_dispatch:
 
 jobs:
   publish:
     runs-on: ubuntu-latest
-
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.11
-          cache: pip
-      - run: pip install .[dev]
+      - name: Set up uv
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+      - run: uv sync
       - name: Build a binary wheel and a source tarball
-        run: |
-          python -m build --sdist --wheel --outdir dist/ .
-      - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        run: uv run python -m build --sdist --wheel --outdir dist/ .
+      - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/tests.yml

@@ -4,27 +4,54 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
 
 jobs:
-  test:
+  pre-commit:
     runs-on: ubuntu-latest
+    if: github.event_name == 'pull_request' # pre-commit-ci/lite-action only runs here
     strategy:
       matrix:
-        python-version: ["3.11"]
-
+        python-version: [3.12] # Our min and max supported Python versions
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-          cache: pip
-      - run: pip install .[dev]
-      - name: Check pre-commit
-        run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
-      - name: Run Test
+      - uses: pre-commit/[email protected]
+      - uses: pre-commit-ci/[email protected]
+        if: always()
+  lint:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11] # Our min supported Python version
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up uv
+        run: |-
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          uv python pin ${{ matrix.python-version }}
+      - run: uv sync --python-preference=only-managed
+      - run: uv run refurb paperqa tests
+      - run: uv run pylint paperqa
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12] # Our min and max supported Python versions
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up uv
+        run: |-
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          uv python pin ${{ matrix.python-version }}
+      - run: uv sync --python-preference=only-managed
+      - uses: google-github-actions/auth@v2
+        with:
+          credentials_json: ${{ secrets.GOOGLE_CREDENTIALS }}
+      - run: uv run pytest -n auto
         env:
           OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
           ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
-        run: pytest
+          SEMANTIC_SCHOLAR_API_KEY: ${{ secrets.SEMANTIC_SCHOLAR_API_KEY }}
+          CROSSREF_API_KEY: ${{ secrets.CROSSREF_API_KEY }}

.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
+.vscode
+
+# 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
+# Version files made by setuptools_scm
+**/version.py
 
-# Matching pyproject.toml
-paperqa/version.py
-tests/example*
+# Tests
+tests/*txt
+tests/*html
+tests/test_index/*

.mailmap

@@ -0,0 +1,8 @@
+Andrew White <[email protected]> <[email protected]>
+James Braza <[email protected]> <[email protected]>
+Geemi Wellawatte <[email protected]> <[email protected]>
+Geemi Wellawatte <[email protected]> <[email protected]>
+Michael Skarlinski <[email protected]> mskarlin <[email protected]>
+Odhran O'Donoghue <[email protected]> odhran-o-d <[email protected]>
+Odhran O'Donoghue <[email protected]> <[email protected]>
+Samantha Cox <[email protected]> <[email protected]>