Merge branch 'main' into dependabot/pip/numpy-gte-2-and-lt-2.5

Author: brownjuly2003-code

.github/dependabot.yml

@@ -64,6 +64,23 @@ updates:
         update-types: ["version-update:semver-major"]
       - dependency-name: "dagster"
         update-types: ["version-update:semver-major"]
+      # mcp 2.x's lowlevel Server drops the list_tools/call_tool decorators
+      # integrations/agentflow_integrations/mcp/server.py is built on (checked
+      # against 2.2.0), so a major bump is a port, not an update. PR #244
+      # proposed <3 and was closed on that basis; the ignore stops it coming
+      # back weekly. Same NOTE above applies: the safety/pip-audit jobs still
+      # scan mcp and fail on a CVE that only a major fixes.
+      - dependency-name: "mcp"
+        update-types: ["version-update:semver-major"]
+      # pyiceberg-core is pinned to the release PyIceberg pairs with, not to
+      # the newest one. PyIceberg 0.11.1 declares pyiceberg-core>=0.5.1,<0.9.0;
+      # the only step up inside that window is 0.8.0, published as
+      # requires-python <3.13, which the 3.11-3.13 resolution environments in
+      # pyproject.toml rule out. Bumps only make sense when PyIceberg raises
+      # its own range, and that arrives as a pyiceberg PR. PR #245 proposed
+      # <0.11 and was closed on that basis.
+      - dependency-name: "pyiceberg-core"
+        update-types: ["version-update:semver-minor"]
 
   # ── Python: Flink runtime image manifest ───────────────────────────
   # Not an extra of the root project (its beam chain can never co-install
@@ -120,6 +137,12 @@ updates:
       - dependencies
       - python
       - integrations
+    ignore:
+      # The other half of the mirrored mcp pin (see the root pip entry): the
+      # ceiling is what the integration's decorators need, so leaving this
+      # ecosystem unignored just reopens the same PR from the other directory.
+      - dependency-name: "mcp"
+        update-types: ["version-update:semver-major"]
 
   # ── npm: TypeScript SDK ────────────────────────────────────────────
   - package-ecosystem: npm

.github/workflows/ci.yml

@@ -247,6 +247,7 @@ jobs:
         with:
           python-version: "3.11"
       - name: Install dependencies
+        id: install
         run: |
           bash scripts/ci_sync.sh test-integrations
       - name: Verify SDK/integrations joint installability
@@ -264,22 +265,27 @@ jobs:
       - name: Enforce changed-code coverage
         run: diff-cover .artifacts/coverage/coverage.xml --compare-branch=origin/main --fail-under=80
       - name: Run quality validators coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           python -m pytest tests/unit/test_validators.py -v --tb=short --cov=agentflow_runtime.quality.validators --cov-report=term-missing --cov-fail-under=90
       - name: Run freshness monitor coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           python -m pytest tests/unit/test_freshness_monitor.py -v --tb=short --cov=agentflow_runtime.quality.monitors.freshness_monitor --cov-report=term-missing --cov-fail-under=90
       - name: Run event producer coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           python -m pytest tests/unit/test_event_producer.py -v --tb=short --cov=agentflow_runtime.ingestion.producers.event_producer --cov-report=term-missing --cov-fail-under=90
       - name: Run SQL guard coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           # Security-critical NL->SQL guard: validate_nl_sql (SELECT-only, no DML,
           # tenant table allow-list, recursive-CTE shadow reject). test_sql_guard
           # plus test_sql_guard_mutation give full module coverage (100% local);
           # the 90% gate keeps a 10pp regression cushion.
           python -m pytest tests/unit/test_sql_guard.py tests/unit/test_sql_guard_mutation.py -v --tb=short --cov=agentflow_runtime.serving.semantic_layer.sql_guard --cov-report=term-missing --cov-fail-under=90
       - name: Run rate limiter coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           # Security-critical sliding-window rate limiter (Redis + in-memory
           # fail-closed fallback); local module coverage is 98% (only the optional
@@ -297,6 +303,7 @@ jobs:
             -k "not auth_middleware" -v --tb=short -p no:schemathesis -p no:cov
           python -m coverage report --include="*/serving/api/rate_limiter.py" --show-missing --fail-under=90
       - name: Run auth manager coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           # Security-critical auth manager (key match/verify, tenant isolation,
           # rate-limit/failed-auth windows, rotation grace) and a mutmut target;
@@ -331,6 +338,7 @@ jobs:
             -p no:schemathesis
           python -m coverage report --include="*/serving/api/auth/manager.py" --show-missing --fail-under=90
       - name: Run key rotation coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           # Security-critical key-rotation lifecycle (create/rotate/revoke,
           # grace-period scheduling, rotation status) and a mutmut target. Like
@@ -353,6 +361,7 @@ jobs:
             -p no:schemathesis
           python -m coverage report --include="*/serving/api/auth/key_rotation.py" --show-missing --fail-under=90
       - name: Run outbox coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           # Security/reliability-critical at-least-once outbox dispatch loop
           # (delivery, retry/backoff, poison-to-failed, mark-sent transactions)
@@ -362,6 +371,7 @@ jobs:
           python -m coverage run -m pytest tests/unit/test_outbox_processor.py tests/unit/test_outbox_connection_guard.py -p no:schemathesis
           python -m coverage report --include="*/processing/outbox.py" --show-missing --fail-under=90
       - name: Run query package coverage gate
+        if: ${{ !cancelled() && steps.install.outcome == 'success' }}
         run: |
           # The NL->SQL orchestration surface (engine, entity/metric/NL query
           # mixins, SQL builder) and a mutmut target set; the old single-file

.github/workflows/publish-pypi.yml

@@ -79,8 +79,14 @@ jobs:
               env.write(f"IS_RC={str('-rc' in release_version).lower()}\n")
           PY
 
+      # build 1.5.1 was yanked upstream ("considers breaking changes, will
+      # discuss re-releasing as a new major version"). A yanked release still
+      # installs when pinned exactly, so this kept working -- it just meant
+      # every published artifact came out of a withdrawn builder. 1.6.0 is the
+      # supported successor; uv.lock carries the same version for the wheels
+      # CI builds in python-compat.
       - name: Install build tooling
-        run: python -m pip install --upgrade build==1.5.1 twine==6.2.0
+        run: python -m pip install --upgrade build==1.6.0 twine==6.2.0
 
       - name: Clean previous distributions
         run: rm -rf dist sdk/dist

CHANGELOG.md

@@ -4,6 +4,61 @@ All notable changes to AgentFlow are documented in this file.
 
 ## [Unreleased]
 
+### CI — a red coverage gate no longer hides the gates behind it
+
+* **Steps in a job stop at the first failure**, and `test-unit` runs nine
+  per-module coverage gates in a row. While an earlier step was failing, the
+  auth-manager gate never ran at all — which is how that module drifted from
+  94% to 82% for two weeks with a gate supposedly holding it at 90%, and how
+  the key-rotation gate reached 89.6% (passing only because coverage rounds
+  before it compares). Both were found by running the gates by hand.
+* **Each gate now runs whenever the environment installed**
+  (`if: !cancelled() && steps.install.outcome == 'success'`). They measure
+  different modules and share nothing but the venv, so there was never a
+  reason for one to gate the next. Every gate still fails the job on its own;
+  the difference is that one run now reports all nine verdicts instead of
+  stopping at the first.
+* **A ratchet keeps it that way.**
+  `test_coverage_policy.py::test_every_coverage_gate_runs_even_after_an_earlier_one_fails`
+  fails if a gate is added without the condition, or if the install step
+  loses the `id` the condition refers to.
+
+### Supply chain — releases were being built by a yanked builder
+
+* **`build` 1.5.1 is yanked upstream** ("considers breaking changes, will
+  discuss re-releasing as a new major version"), and it was pinned in two
+  places: `uv.lock`, which builds the wheels CI smoke-tests in
+  `python-compat`, and `.github/workflows/publish-pypi.yml`, which builds the
+  artifacts that go to PyPI. A yanked release still installs when pinned
+  exactly, so nothing failed — every `uv lock` just printed the warning and
+  every release came out of a withdrawn builder.
+* **Both now use 1.6.0**, the supported successor. `requirements-docker.lock`
+  is unchanged (`build` is a `dev` dependency, not part of the
+  cloud/postgres export), and `tests/unit/test_publish_workflows.py` pins the
+  new command so the two cannot drift apart.
+
+### Dependencies — the two version ceilings that keep coming back are now explained
+
+* **`mcp<2` is load-bearing.** mcp 2.x's lowlevel `Server` no longer defines
+  `list_tools` or `call_tool` (checked against 2.2.0), and
+  `integrations/agentflow_integrations/mcp/server.py` builds its whole surface
+  out of `@server.list_tools()` and `@server.call_tool()`. Taking mcp 2 means
+  porting that module first. Both halves of the mirrored pin
+  (`pyproject.toml` and `integrations/pyproject.toml`) now say so.
+* **`pyiceberg-core<0.8` is not a stale ceiling.** PyIceberg 0.11.1 declares
+  `pyiceberg-core>=0.5.1,<0.9.0`, so 0.8.0 is the only step up inside the
+  pairing upstream supports — and 0.8.0 is the one release in the line
+  published as `requires-python <3.13`, which the 3.11–3.13 resolution
+  `environments` rule out. 0.9+ restored 3.13 but sits outside PyIceberg's
+  declared window. Nothing in that window is installable, so the ceiling
+  moves when PyIceberg raises its own.
+* **Dependabot stops re-proposing both.** `.github/dependabot.yml` ignores
+  `mcp` majors (in the root *and* integrations ecosystems, which own the two
+  halves of the same pin) and `pyiceberg-core` minors, each with the reason
+  and the exit condition. The existing NOTE about `ignore` also suppressing
+  security updates still applies: `safety` and `pip-audit` scan both
+  packages and fail on a CVE that only a blocked bump would fix.
+
 ### Quality — the key-rotation coverage gate was passing on a rounding margin
 
 * **89.6% rounds to 90.** The gate on `serving/api/auth/key_rotation.py` ran

Dockerfile.api

@@ -21,7 +21,7 @@ COPY packaging /build/packaging
 # a reproducibility input for the artifact: with --no-isolation its only job is
 # installing these two pinned distributions.
 RUN pip install --no-cache-dir --upgrade pip \
-    && pip install --no-cache-dir build==1.5.1 hatchling==1.31.0 \
+    && pip install --no-cache-dir build==1.6.0 hatchling==1.31.0 \
     && python -m build --wheel --no-isolation --outdir /tmp/dist
 
 FROM python:3.11-slim@sha256:9c900dea9e8fb7e16277c179b555cc72d29a352dbc33cff48ad5a0412fd5bfc7

deploy/hf-space/Dockerfile

@@ -32,7 +32,7 @@ WORKDIR /src
 # Mirrors Dockerfile.api: pinned build backend, and --no-isolation so the pin is
 # what builds the wheel instead of a fresh PyPI download inside build's venv.
 RUN pip install --no-cache-dir --upgrade pip \
-    && pip install --no-cache-dir build==1.5.1 hatchling==1.31.0 \
+    && pip install --no-cache-dir build==1.6.0 hatchling==1.31.0 \
     && python -m build --wheel --no-isolation --outdir /tmp/dist
 
 FROM python:3.11-slim@sha256:9c900dea9e8fb7e16277c179b555cc72d29a352dbc33cff48ad5a0412fd5bfc7

integrations/pyproject.toml

@@ -26,7 +26,9 @@ dependencies = [
 
 [project.optional-dependencies]
 mcp = [
-    # MCP 2 removes the low-level Server decorators used by this integration.
+    # mcp 2.x's lowlevel Server drops the list_tools/call_tool decorators
+    # server.py is built on (checked against 2.2.0). Port the module before
+    # moving this pin; the root pyproject mirrors it.
     "mcp>=1.0,<2",
 ]
 

pyproject.toml

@@ -40,8 +40,14 @@ dependencies = [
 cloud = [
     "boto3>=1.35,<2",
     "pyiceberg>=0.7,<1",
-    # PyIceberg 0.11 write paths require native transforms. Core 0.8 excludes
-    # Python 3.13, while 0.7 provides a stable-ABI wheel across Python 3.11-3.13.
+    # PyIceberg 0.11 write paths require native transforms, and 0.7 is the
+    # only core release that can serve them here. PyIceberg 0.11.1 declares
+    # pyiceberg-core>=0.5.1,<0.9.0, so 0.8.0 is the only step up inside the
+    # pairing upstream supports -- and 0.8.0 is the one release in the line
+    # published as requires-python <3.13, which the 3.11-3.13 resolution
+    # environments below rule out. (0.9+ restored 3.13 but sits outside
+    # PyIceberg's declared window; nothing in that window is installable.)
+    # The ceiling moves when PyIceberg raises its own, not before.
     "pyiceberg-core>=0.7,<0.8",
 ]
 postgres = [
@@ -77,8 +83,11 @@ integrations = [
     "llama-index-core>=0.12,<1",
     # Mirrors integrations/pyproject.toml [mcp]: locking it here lets CI
     # install the editable integrations package with --no-deps from the
-    # frozen root resolution (audit F-05). MCP 2 removes the low-level
-    # Server decorators the integration uses.
+    # frozen root resolution (audit F-05). The ceiling is load-bearing:
+    # mcp 2.x's lowlevel Server no longer defines list_tools or call_tool
+    # (checked against 2.2.0), and integrations/.../mcp/server.py builds its
+    # whole surface out of @server.list_tools() and @server.call_tool().
+    # Taking mcp 2 means porting that module first, not moving this pin.
     "mcp>=1.0,<2",
 ]
 contract = [

tests/unit/test_coverage_policy.py

@@ -177,3 +177,36 @@ def test_ci_has_scoped_query_package_coverage_gate() -> None:
     assert "coverage run" in gate_step["run"]
     assert "*/serving/semantic_layer/query/*" in gate_step["run"]
     assert "--fail-under=90" in gate_step["run"]
+
+
+def test_every_coverage_gate_runs_even_after_an_earlier_one_fails() -> None:
+    """A red gate must not hide the gates behind it.
+
+    Steps in a job stop at the first failure, so for two weeks the
+    auth-manager gate never ran: an earlier step in test-unit was failing, and
+    the module drifted from 94% to 82% with nothing to report it. Each gate
+    measures a different module and depends on nothing the others produce, so
+    each one runs whenever the environment installed -- and still fails the
+    job on its own.
+    """
+    workflow = yaml.safe_load(
+        (PROJECT_ROOT / ".github" / "workflows" / "ci.yml").read_text(encoding="utf-8")
+    )
+    steps = workflow["jobs"]["test-unit"]["steps"]
+
+    install = next(step for step in steps if step.get("name") == "Install dependencies")
+    assert install.get("id") == "install", "the gate condition references steps.install"
+
+    gates = [
+        step
+        for step in steps
+        if str(step.get("name", "")).startswith("Run ")
+        and str(step.get("name", "")).endswith(" coverage gate")
+    ]
+    assert len(gates) >= 9, f"expected the per-module gates, found {len(gates)}"
+
+    for gate in gates:
+        condition = gate.get("if")
+        assert condition is not None, f"{gate['name']} has no if: condition"
+        assert "!cancelled()" in condition, gate["name"]
+        assert "steps.install.outcome == 'success'" in condition, gate["name"]

tests/unit/test_publish_workflows.py

@@ -121,7 +121,7 @@ def test_python_publish_checks_artifacts_with_pinned_tooling_before_upload():
     names = [step.get("name") for step in steps if isinstance(step, dict)]
     commands = _step_commands(workflow)
 
-    assert "python -m pip install --upgrade build==1.5.1 twine==6.2.0" in commands
+    assert "python -m pip install --upgrade build==1.6.0 twine==6.2.0" in commands
     assert "python scripts/check_release_artifacts.py dist/* sdk/dist/*" in commands
     assert names.index("Reject unsafe release artifacts") < names.index(
         "Dry-run build and twine check"