fix: CI green — all Python versions (3.12 – 3.14t): pytest, persistence, cffi, voyageai

.github/workflows/_reusable-test.yml

@@ -106,7 +106,9 @@ jobs:
             pkg-config \
             python3-dev \
             libffi-dev \
-            libssl-dev
+            libssl-dev \
+            libxml2-dev \
+            libxslt-dev
       - name: Setup Python environment with Mise
         uses: ./.github/actions/setup-mise-env
         with:

.serena/project.yml

@@ -128,7 +128,7 @@ read_only_memory_patterns: []
 # line ending convention to use when writing source files.
 # Possible values: unset (use global setting), "lf", "crlf", or "native" (platform default)
 # This does not affect Serena's own files (e.g. memories and configuration files), which always use native line endings.
-line_ending:
+line_ending: "lf"
 # list of regex patterns for memories to completely ignore.
 # Matching memories will not appear in list_memories or activate_project output
 # and cannot be accessed via read_memory or write_memory.

mise.toml

@@ -236,7 +236,7 @@ run = [
   "mise -y trust --all 2>&1 || true",
   "mise install 2>&1 || true",
   "hk install --mise 2>&1 || mise x hk@latest -- hk install --mise 2>&1 || true",
-  "mise x uv@latest -- uv venv --allow-existing --seed --keyring-provider subprocess --python {{ get_env(name='MISE_PYTHON', default='3.13') }} .venv 2>&1",
+  "mise x uv@latest -- uv venv --allow-existing --seed --keyring-provider subprocess --python {{ get_env(name='PYTHON_VERSION', default='3.13') }} .venv 2>&1",
   "source .venv/bin/activate 2>&1 || true",
   "mise x uv@latest -- uv sync --group dev --group test 2>&1",
   "git config include.path .gitconfig 2>&1 || true",
@@ -553,21 +553,23 @@ if "%usage_cov%"=="true" (
 [tasks.test.env]
 CODEWEAVER_TEST_MODE = "true"
 PYTHONPATH = "src"
+PYTHONWARNINGS = "ignore:Core Pydantic V1:UserWarning"
 
 [tasks.test-cov]
 env.PYTHONPATH = "src"
+env.PYTHONWARNINGS = "ignore:Core Pydantic V1:UserWarning"
 tools.uv = "latest"
 tools.python = '''{{ get_env(name="MISE_PYTHON_VERSION", default="3.13") }}'''
 depends = ["sync"]  # ensure test dependencies are installed
 run = '''
 echo "running test-cov task"
 echo "${CW_PREFIX} Running tests with coverage..."
-uv run pytest tests/ --cov=codeweaver --cov-report=xml --cov-report=term-missing --junit-xml=test-results.xml -v "$@"
+uv run --group test pytest tests/ --cov=codeweaver --cov-report=xml --cov-report=term-missing --junit-xml=test-results.xml -v "$@"
 '''
 run_windows = '''
 echo "running test-cov task"
 echo [codeweaver] Running tests with coverage...
-uv run pytest tests/ --cov=codeweaver --cov-report=xml --cov-report=term-missing --junit-xml=test-results.xml -v %*
+uv run --group test pytest tests/ --cov=codeweaver --cov-report=xml --cov-report=term-missing --junit-xml=test-results.xml -v %*
 '''
 
 [tasks.test-categories]

pyproject.toml

@@ -124,7 +124,7 @@ dependencies = [
   # psutil used for resource governance/limiting by engine
   "psutil>=7.2.2",
   "textcase>=0.4.5",
-  "typing_extensions>=4.15.0",
+  "typing_extensions>=4.15.0; python_version < '3.13'",
   "uuid7>=0.1.0; python_version < '3.14'",
   "uvloop>=0.22.1; python_implementation == 'CPython' and platform_system != 'Windows'",
   # * ================ Core Provider Dependencies ==================*
@@ -148,14 +148,15 @@ dependencies = [
   "cohere==5.20.7",
   "fastembed==0.7.4; python_version < '3.14'",
   "google-genai==1.56.0",
-  # NOTE: We're waiting on pydantic-ai to update to 1.0+ before we can upgrade too
   "huggingface-hub>=1.0.0",
   "mistralai==1.10.0",
   "openai==2.28.0",
   "qdrant-client==1.17.1",
   "pydantic-ai-slim>=1.68.0",
   "sentence-transformers==5.2.0; python_version <= '3.14'",
-  "voyageai==0.3.7",
+  # voyageai declares requires_python: <3.14 — uv respects this automatically,
+  # but pip does not filter by requires_python during install, so we must gate it here.
+  "voyageai==0.3.7; python_version < '3.14'",
   # * ================ Indexing and Engine ==================*
   # Also known as: the land of python rust extensions
   # the core code-weaver-daemon package that keeps indexing continuously updated
@@ -221,37 +222,40 @@ azure-key-vault = ["pydantic-settings[yaml,toml,azure-key-vault]"]
 bedrock = ["pydantic-ai-slim[bedrock]"]
 cohere = ["pydantic-ai-slim[cohere]"]
 # ==== Data Sources ====
-# duckduckgo relies on primp, which needs maturin. Maturin does not yet support python 3.14 free-threaded builds, so we exclude it from python 3.14 installs for now. If you need duckduckgo support on python 3.14, you can install the ddgs package manually in your environment.
-duckduckgo = ["ddgs; python_version < '3.14'"]
+duckduckgo = ["ddgs"]
 exa = ["exa-py"]
+# fastembed blocked on 3.14 by py-rust-stemmers (no cp314/cp314t wheels)
 fastembed = ["fastembed; python_version < '3.14'", "py-cpuinfo"]
 # Requires additional setup, see https://qdrant.github.io/fastembed/examples/FastEmbed_GPU/
 fastembed-gpu = ["fastembed-gpu; python_version < '3.14'", "py-cpuinfo"]
 
 full = [
-  "permit-fastmcp",
-  "ddgs; python_version < '3.14'",
+  "ddgs",
   "eunomia-mcp",
   "exa-py",
   "pydantic-ai-slim[openai,cohere,google,anthropic,groq,mistral,bedrock,huggingface,retries,xai]",
-  # azure-key-vault requires azure-identity, which requires cffi. cffi *does* work on python 3.13, but NOT 3.13 freethreaded
-  # since we have no way to test for freethreaded builds in pyproject.toml and the build breaks with it, we leave it out.
-  # If you need azure-key-vault support on python 3.13, you can install the full group and then manually install azure-identity in your environment to get the missing dependency (with vanilla python).
+  # azure-key-vault → azure-identity → cryptography → cffi. On 3.13t (free-threaded),
+  # cryptography has no pre-built wheel and building from source requires Rust + cffi<2.0.
+  # No PEP 508 marker distinguishes 3.13t from 3.13, so we exclude azure-key-vault on all 3.13.
+  # Standard 3.13 users can install azure-identity manually. The _special-dependencies task
+  # handles this for non-free-threaded 3.13 builds.
   "pydantic-settings[yaml,toml,aws-secrets-manager,gcp-secret-manager]; python_version == '3.13'",
   "pydantic-settings[yaml,toml,aws-secrets-manager,gcp-secret-manager,azure-key-vault]; python_version != '3.13'",
-  "permit-fastmcp",
+  # permit-fastmcp depends on cffi — same 3.13t issue as azure-key-vault
+  "permit-fastmcp; python_version != '3.13'",
   "sentence-transformers",
   "tavily-python",
 ]
 full-gpu = [
-  "permit-fastmcp",
-  "ddgs; python_version < '3.14'",
+  "ddgs",
   "eunomia-mcp",
   "fastembed-gpu; python_version < '3.14'",
-  "permit-fastmcp",
   "exa-py",
   "pydantic-ai-slim[openai,cohere,google,anthropic,groq,mistral,bedrock,huggingface,retries,xai]",
-  "pydantic-settings[yaml,toml,aws-secrets-manager,azure-key-vault,gcp-secret-manager]",
+  # see full extra comments about cffi/cryptography and free-threaded python 3.13
+  "pydantic-settings[yaml,toml,aws-secrets-manager,gcp-secret-manager]; python_version == '3.13'",
+  "pydantic-settings[yaml,toml,aws-secrets-manager,gcp-secret-manager,azure-key-vault]; python_version != '3.13'",
+  "permit-fastmcp; python_version != '3.13'",
   "sentence-transformers",
   # see note below about why this is commented out
   #  "sentence-transformers[onnx-gpu]; python_version>='3.12' and python_version<'3.14'",
@@ -281,16 +285,14 @@ recommended = [
   "sentence-transformers",
   "tokenizers",
   "py-cpuinfo",
-  "voyageai",
-  "ddgs; python_version < '3.14'",
-  "pydantic-ai-slim[openai,anthropic,retries]",
+  "voyageai; python_version < '3.14'",
   "tavily",
 ]
 recommended-local-only = [
   "fastembed; python_version < '3.14'",
   "sentence-transformers",
   "tokenizers",
-  "ddgs; python_version < '3.14'",
+  "ddgs",
   "py-cpuinfo",
   # openai for ollama local models
   "pydantic-ai-slim[openai,retries]",
@@ -313,7 +315,9 @@ tavily = ["tavily"]
 #     "sentence-transformers[openvino]",
 #     "py-cpuinfo",
 # ]
-voyageai = ["voyageai"]
+# voyageai self-excludes on 3.14+ via its own requires_python: <3.14,
+# but pip doesn't filter on requires_python during install, so we gate here too.
+voyageai = ["voyageai; python_version < '3.14'"]
 xai = ["pydantic-ai-slim[xai]"]
 
 [dependency-groups]
@@ -322,17 +326,17 @@ dev = [
   "black>=26.3.1",
   "ruff>=0.15.6",
   "serena>=0.9.1",
-  "ty>=0.0.23",
-  "uv>=0.10.11",
+  "ty>=0.0.25",
+  "uv>=0.11.1",
 ]
-build = ["hatchling>=1.28.0", "twine>=6.2.0", "uv-dynamic-versioning>=0.12.0"]
+build = ["hatchling>=1.28.0", "twine>=6.2.0", "uv-dynamic-versioning>=0.14.0"]
 dev-helpers = [
   "ipython>=9.11.0",
   "jsonlines>=4.0.0",
   "memory-profiler>=0.61.0",
   "pdbpp>=0.12.1",
   "pyperclip>=1.11.0",
-  "superclaude>=4.2.0",
+  "superclaude>=4.3.0",
 ]
 docs = [
   "griffe>=2.0.0",
@@ -344,7 +348,7 @@ test = [
   "hypothesis>=6.151.9",
   "pytest>=9.0.2",
   "pytest-asyncio>=1.3.0",
-  "pytest-cov>=7.0.0",
+  "pytest-cov>=7.1.0",
   "pytest-env>=1.6.0",
   "pytest-examples>=0.0.18",
   "pytest-flakefinder>=1.1.0",
@@ -356,26 +360,57 @@ test = [
 [build-system]
 requires = [
   "hatchling>=1.29.0",
-  "twine>=6.2.0",
-  "uv-dynamic-versioning>=0.13.0",
+  "uv-dynamic-versioning>=0.14.0",
 ]
 build-backend = "hatchling.build"
 
 # TODO: Integrate hatch plugins for:
 #  - readme: https://github.com/hynek/hatch-fancy-pypi-readme
 
 [tool.coverage.run]
+concurrency = ["multiprocessing", "thread"]
+patch = ["_exit", "subprocess"]
+relative_files = true
+parallel = true
 omit = [
-  "scripts/*",
-  "mise-tasks/*",
-  "typings/*",
-  ".venv/*",
-  "tests/*",
-  "vendored/*",
-  "src/codeweaver/__init__.py",
-  "src/codeweaver/**/__init__.py",
-  "src/codeweaver/**/types/*",
-  "src/codeweaver/**/types.py",
+  "*/scripts/*",
+  "*/mise-tasks/*",
+  "*/tests/*",
+  "*/__init__.py",
+  "*/__main__.py",
+  "*/_version.py",
+]
+
+[tool.coverage.report]
+skip_empty = true
+sort = "-cover"
+omit = [
+  "*/scripts/*",
+  "*/mise-tasks/*",
+  "*/tests/*",
+  "*/__init__.py",
+  "*/__main__.py",
+  "*/_version.py",
+]
+exclude_also = [
+  '@(abc\.)?abstractmethod',
+  '@(dataclasses\.)?dataclass',
+  '@(typing\.)?overload',
+  '@(typing\.)?override',
+  '@(typing\.)?runtime_checkable',
+  '@(typing\.)?type_check_only',
+  '[ \t]+?pass\n',
+  'class .*\bProtocol\):',
+  "def __repr__",
+  "if __name__ == .__main__.:",
+  "if 0:",
+  "if self.debug:",
+  "if settings.DEBUG",
+  "if TYPE_CHECKING:",
+  "no cover: start(?s:.)*?no cover: stop",
+  "raise AssertionError",
+  "raise NotImplementedError",
+  '\s*def .*\)\s*->\s*TypeIs\[.+\]:[\n\sA-za-z0-9_-]+?\n\n',
 ]
 
 [tool.hatch.build.hooks.version]
@@ -412,7 +447,6 @@ artifacts = ["*.so", "src/**", "vendored/**", "packages/**"]
 [tool.hatch.build.targets.sdist]
 include = [
   ".gitignore",
-  "ARCHITECTURE.md",
   "CHANGELOG.md",
   "CONTRIBUTORS_LICENSE_AGREEMENT.py",
   "LICENSE",
@@ -428,7 +462,7 @@ include = [
   "packages/**",
   "pyproject.toml",
   "sbom.spdx",
-  "schema/**",
+  "schema/latest/*",
   "src/**",
   "tests/**",
   "typings/**",
@@ -519,7 +553,7 @@ markers = [
   "requires_fastembed: Tests requiring fastembed package (not available on Python 3.14+)",
   "requires_gpu: Tests requiring GPU hardware for execution",
   "requires_models: Tests requiring ML model downloads and local model files",
-  "requires_voyageai: Tests requiring voyageai package (has pydantic v1 issues on Python 3.14+)",
+  "requires_voyageai: Tests requiring voyageai package (upstream requires_python caps at <3.14)",
   "retry: Tests that may need retries",
   "search: Tests related to search functionality",
   "server: Tests related to server functionality",
@@ -813,6 +847,24 @@ conflicts = [
   ],
 ]
 preview = true
+override-dependencies = [
+  # cffi 2.0 segfaults on free-threaded 3.13 (sync primitive differences vs 3.14t).
+  # No PEP 508 marker distinguishes 3.13t from 3.13, so this applies to both —
+  # harmless on standard 3.13 since cryptography has pre-built wheels there.
+  "cffi==1.17.1; python_version == '3.13'",
+  # Pin cryptography to 45.0.7 on 3.13: its build-system.requires uses cffi>=1.12,
+  # compatible with our cffi pin. cryptography 46+ requires cffi>=2.0.0 to build,
+  # which conflicts with the cffi<2.0 build constraint needed for 3.13t.
+  # On 3.14+, cryptography 46+ resolves naturally (has pre-built wheels + cffi 2.0 works).
+  "cryptography==45.0.7; python_version == '3.13'",
+]
+# Constrain cffi in build isolation environments. override-dependencies only affects
+# runtime resolution; when cryptography builds from source on 3.13t, its build env
+# pulls cffi>=1.12 independently. This prevents cffi 2.0 from entering build envs.
+build-constraint-dependencies = [
+  "cffi<2.0; python_version == '3.13'",
+]
+prerelease = "allow"
 
 [tool.uv.workspace]
 members = ["packages/*"]

src/codeweaver/providers/vector_stores/inmemory.py

@@ -18,6 +18,7 @@
 from pydantic import PrivateAttr
 
 from codeweaver.core import (
+    DEFAULT_PERSIST_INTERVAL,
     CodeChunk,
     PersistenceError,
     Provider,
@@ -77,15 +78,22 @@ async def _init_provider(self) -> None:
         from codeweaver.core import is_test_environment
 
         # Logic for auto_persist:
-        # 1. If explicitly provided in config, use that value.
-        # 2. If not provided, disable in test mode, enable otherwise.
+        # 1. In test environments, always disable — even if the config explicitly says True.
+        #    _default_memory_config() hardcodes auto_persist=True, which would otherwise
+        #    trigger handle_persistence() after every upsert and race-fail on the .tmp path.
+        # 2. If not provided (None), default based on environment (disabled in tests).
+        # 3. If explicitly provided and not in a test environment, use the config value.
         auto_persist = self.config.in_memory_config.get("auto_persist")
-        if auto_persist is None:
+        if auto_persist is None or is_test_environment():
             auto_persist = not is_test_environment()
 
-        persist_interval = self.config.in_memory_config.get("persist_interval")
-        if persist_interval is None:
-            persist_interval = 300
+        persist_interval: int | None
+        in_memory_config = self.config.in_memory_config
+        if "persist_interval" not in in_memory_config:
+            persist_interval = DEFAULT_PERSIST_INTERVAL
+        else:
+            # Explicit None means "disable periodic persistence"
+            persist_interval = in_memory_config.get("persist_interval")
 
         # Store as private attributes
         object.__setattr__(self, "_persist_path", self.config.in_memory_config.get("persist_path"))
@@ -119,8 +127,9 @@ async def _init_provider(self) -> None:
         if await AsyncPath(str(self.persist_path)).exists():
             await self._restore_from_disk()
 
-        # Set up periodic persistence if configured
-        if auto_persist:
+        # Set up periodic persistence if configured (disabled in test environments
+        # or when persist_interval is explicitly set to None)
+        if auto_persist and persist_interval is not None and not is_test_environment():
             periodic_task = asyncio.create_task(self._periodic_persist_task())
             object.__setattr__(self, "_periodic_task", periodic_task)
 
@@ -215,7 +224,7 @@ async def _periodic_persist_task(self) -> None:
         """
         while not self._shutdown:
             try:
-                await asyncio.sleep(self._persist_interval or 300)
+                await asyncio.sleep(self._persist_interval or DEFAULT_PERSIST_INTERVAL)
                 if not self._shutdown:
                     await self._persist_to_disk()
             except asyncio.CancelledError:

tests/conftest.py

@@ -7,6 +7,12 @@
 """Global pytest configuration and fixtures for CodeWeaver tests."""
 
 import contextlib
+import warnings
+
+
+# Suppress pydantic v1 compat warnings from transitive deps (langsmith, voyageai)
+# on Python 3.14+ — fires at import time before pytest filterwarnings takes effect
+warnings.filterwarnings("ignore", message="Core Pydantic V1", category=UserWarning)
 
 from collections.abc import Generator, Sequence
 from pathlib import Path