Dropped PyCryptodome and build dependencies (#426)

.github/workflows/build.yml

@@ -13,8 +13,7 @@ jobs:
       - 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: uv run python -m build --sdist --wheel --outdir dist/ .
+      - run: uv build --sdist --wheel --out-dir dist/ .
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}

pyproject.toml

@@ -17,7 +17,6 @@ classifiers = [
     "Programming Language :: Python",
 ]
 dependencies = [
-    "PyCryptodome",
     "PyMuPDF>=1.24.3",  # python -c "import pymupdf" won't run before version 1.24.3
     "aiohttp",  # TODO: remove in favor of httpx
     "anyio",
@@ -235,6 +234,7 @@ filterwarnings = [
     "ignore:'imghdr' is deprecated and slated for removal in Python 3.13:DeprecationWarning",  # SEE: https://github.com/BerriAI/litellm/issues/2929#issuecomment-2345224633
     "ignore:Support for class-based `config` is deprecated, use ConfigDict instead",  # SEE: https://github.com/BerriAI/litellm/issues/5648
     'ignore:open_text is deprecated. Use files\(\) instead:DeprecationWarning',  # SEE: https://github.com/BerriAI/litellm/issues/5647
+    'ignore:pkg_resources is deprecated as an API.:DeprecationWarning:pybtex',  # SEE: https://bitbucket.org/pybtex-devs/pybtex/issues/169/replace-pkg_resources-with
 ]
 # List of directories that should be searched for tests when no specific directories,
 # files or test ids are given in the command line when executing pytest from the rootdir
@@ -396,10 +396,9 @@ trailing_comma_inline_array = true
 
 [tool.uv]
 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[datasets,ldp,typing]",
+    "paper-qa[datasets,ldp,typing,zotero]",
     "pre-commit~=3.4",  # Pin to keep recent
     "pydantic~=2.0",
     "pylint-pydantic",
@@ -412,7 +411,5 @@ dev-dependencies = [
     "pytest-xdist",
     "pytest>=8",  # Pin to keep recent
     "python-dotenv",
-    "pyzotero",
     "refurb>=2",  # Pin to keep recent
-    "requests",
 ]

tests/test_agents.py

@@ -263,7 +263,7 @@ async def test_gather_evidence_rejects_empty_docs() -> None:
     assert response.status == AgentStatus.FAIL, "Agent should have registered a failure"
 
 
-@pytest.mark.flaky(reruns=3, only_rerun=["AssertionError"])
+@pytest.mark.flaky(reruns=3, only_rerun=["AssertionError", "EmptyDocsError"])
 @pytest.mark.asyncio
 async def test_agent_sharing_state(
     agent_test_settings: Settings, subtests: SubTests