docugraph 0.1.0__tar.gz

docugraph-0.1.0/.dockerignore

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+# Build context exclusions. The Dockerfile copies narrowly today
+# (`pyproject.toml README.md` and `src/`), so nothing here reaches the image --
+# but the whole tree is still sent to the daemon, and a single future
+# `COPY . .` would otherwise carry a 1.1 GB .venv or a .env into a published
+# image. This file is what makes that copy safe rather than lucky.
+#
+# Docker matches these against the path relative to the context root, so a bare
+# name covers only the root -- `__pycache__` does not match `src/x/__pycache__`.
+# Depth-capable patterns therefore carry `**/`. Patterns that are meaningfully
+# root-only (.venv, .git, data) stay anchored, so a nested `tests/fixtures/data`
+# is not swept up with them.
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# Secrets. Nothing here is tracked, but an untracked .env is exactly what a
+# broad COPY would pick up -- at any depth.
+**/.env
+**/.env.*
+
+# Key material
+**/*.pem
+**/*.key
+**/*.p12
+**/id_rsa*
+
+# VCS
+.git/
+.gitignore
+
+# Caches, test and type-checker output
+**/__pycache__/
+**/*.py[cod]
+**/.pytest_cache/
+**/.ruff_cache/
+**/.mypy_cache/
+**/.cache/
+**/htmlcov/
+**/.coverage
+**/.coverage.*
+**/*.log
+
+# Build output
+build/
+dist/
+wheels/
+**/*.egg-info/
+
+# Local data stores. The container's data dir is a volume
+# (DOCUGRAPH_STORAGE__DATA_DIR=/data/docugraph), never build input.
+data/
+**/*.kuzu
+**/*.lance
+**/*.db
+
+# OS / editor noise
+**/.DS_Store
+
+# tests/, docs/ and examples/ are deliberately NOT excluded: the `development`
+# target installs `.[dev]` and Playwright, so the suite is meant to be runnable
+# inside that container.

docugraph-0.1.0/.github/dependabot.yml

@@ -0,0 +1,101 @@
+# Dependabot is configured rather than switched off.
+#
+# Left as it was, this file opened a PR per dependency per week, which in practice
+# meant a queue of PRs that could not be merged. Five of docugraph's dependencies
+# are held deliberately, and the old grouping covered minor and patch bumps only
+# -- so every major bump, which is exactly where the held-back lines were, arrived
+# as its own PR proposing to lift them. Eight were open at the time of writing.
+#
+# Now the held dependencies are ignored by name with the reason recorded beside
+# each, and the rest arrives as one grouped PR per ecosystem per month: a size a
+# person can review in one sitting.
+#
+# These `ignore` entries restate decisions already written into pyproject.toml.
+# If a pin is lifted there, lift it here too -- otherwise this file goes on
+# suppressing updates that nobody still means to suppress. Note that Dependabot
+# reads this file only from the default branch, so changes here take effect at
+# the next merge to `main`, not at the push.
+#
+# There are deliberately no `labels:` entries. The previous config asked for
+# `dependencies`, `python`, `github-actions` and `docker`, none of which exist in
+# this repository, so every Dependabot PR carried "the following labels could not
+# be found" and no labels at all. Either create them and put the entries back, or
+# leave this as it is; asking for labels that do not exist is worse than not
+# asking.
+
+version: 2
+
+updates:
+  # ------------------------------------------------------------------ Python deps
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    commit-message:
+      prefix: "deps"
+    groups:
+      pip:
+        patterns: ["*"]
+    ignore:
+      # Pinned exactly in pyproject.toml. kuzu is archived upstream -- 0.11.3 is the
+      # final release -- and its file format is not stable before 1.0, so a bump can
+      # leave an existing graph unreadable. Lifting this pin needs a migration step,
+      # not a dependency bump.
+      - dependency-name: "kuzu"
+
+      # Pinned exactly in pyproject.toml, so that a graphiti release cannot change
+      # its kuzu requirement or drop the kuzu driver and break the pin above, with
+      # no change in this repo to explain it. Bump only alongside a re-run of the
+      # ingestion tests.
+      - dependency-name: "graphiti-core"
+
+      # Capped below 2 in pyproject.toml: the 2.x SDK removed the low-level Server
+      # list_tools/call_tool decorators that mcp_server.py is built on.
+      - dependency-name: "mcp"
+        versions: [">= 2.0.0"]
+
+      # Capped below 1.24: newer releases dropped macOS x86_64 wheels, so the
+      # install breaks on an Intel Mac. Same reason as lancedb below.
+      - dependency-name: "onnxruntime"
+        versions: [">= 1.24.0"]
+
+      # Capped below 0.26, for the same dropped-wheel reason.
+      - dependency-name: "lancedb"
+        versions: [">= 0.26.0"]
+
+      # The three cloud SDKs are deliberately *not* ignored here, though they
+      # are still capped in pyproject.toml. They were, and it was the wrong call:
+      # an ignore suppresses the PR that would have shown you the break. The
+      # Anthropic 1.x SDK removed `temperature` from its request type and every
+      # call raised `unexpected keyword argument` -- and because the cap arrived
+      # by hand, the break was discovered rather than announced. A major bump for
+      # any of these now opens a PR that proposes lifting the cap, and CI's
+      # all-extras job runs tests/unit/test_cloud_provider_sdks.py against the
+      # proposed version, which is the only thing that can say whether the new
+      # SDK still accepts the arguments these providers pass. That job exists for
+      # this: read its result before merging, because a green install proves
+      # nothing about the request shape.
+
+  # ----------------------------------------------------------------- GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    commit-message:
+      prefix: "ci"
+    groups:
+      github-actions:
+        patterns: ["*"]
+
+  # ------------------------------------------------------------------ Docker images
+  # Kept from the previous config, now monthly like the others. Nothing is held
+  # here, so it is a plain grouped update of the base image.
+  - package-ecosystem: "docker"
+    directory: "/docker"
+    schedule:
+      interval: "monthly"
+    commit-message:
+      prefix: "docker"
+    groups:
+      docker:
+        patterns: ["*"]

docugraph-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,210 @@
+# Continuous Integration - Run tests and linting
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  # Deliberately no branch filter. With `branches: [main, master]` here, a pull
+  # request whose base is any other branch -- which is how a change is stacked on
+  # another unmerged change -- got no CI at all, and "no checks reported" in the
+  # PR list reads much like "checks passed". Every pull request runs CI.
+  pull_request:
+
+env:
+  # fastembed model cache (bge-small ~130 MB; shared across jobs)
+  FASTEMBED_CACHE_PATH: /home/runner/.cache/fastembed
+
+jobs:
+  # The workflow files are the one thing here with no other gate, and release.yml
+  # is the part that runs rarely and matters most -- so a mistake in it is found
+  # at release time, by everyone. actionlint reads the workflows themselves:
+  # expression syntax, job-graph references, and the shell and Python inside each
+  # `run:` block, through shellcheck and pyflakes, both of which the pinned image
+  # below ships. Run against this tree it reported two SC2086 findings in
+  # release.yml (`>> $GITHUB_OUTPUT` unquoted); both are fixed.
+  actionlint:
+    name: Lint workflows
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Run actionlint
+        uses: docker://rhysd/actionlint:1.7.12
+        with:
+          args: -color
+
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      # --all-extras, not --extra dev. The cloud SDKs are imported conditionally,
+      # so with them absent mypy reports "cannot find implementation or library
+      # stub" and types the calls against `Any` -- which is how a `temperature`
+      # argument the Anthropic SDK had already removed passed type checking while
+      # raising TypeError at runtime for every user of docugraph[cloud].
+      - name: Sync dependencies
+        run: uv sync --all-extras
+
+      # `scripts/` is included, not just `src/`. The live-provider smoke script is
+      # not part of the package but it is part of this repository, and code no gate
+      # reads is code that rots. mypy gets both paths together so it resolves
+      # `docugraph` to this source tree rather than to the installed copy, which it
+      # otherwise reports as an untyped library.
+      - name: Run Ruff linter
+        run: uv run ruff check src/ scripts/
+
+      - name: Run Ruff formatter check
+        run: uv run ruff format --check src/ scripts/
+
+      - name: Run mypy
+        run: uv run mypy src/ scripts/
+
+      # These SDKs are installed in this job and nowhere else in CI, so it is the
+      # only place the cloud request shapes can be checked against the real
+      # libraries rather than against their absence. Skips itself if anthropic
+      # is missing, which is why it belongs to the all-extras job.
+      - name: Check the cloud provider calls against the installed SDKs
+        run: uv run pytest tests/unit/test_cloud_provider_sdks.py -v
+
+  test:
+    name: Test (py${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    needs: lint
+    strategy:
+      # Report every version, rather than cancelling the others when one fails.
+      fail-fast: false
+      matrix:
+        # Every version the package claims, via the pyproject classifiers, now
+        # that 3.13 is among them. 3.14 is excluded by `requires-python`; the
+        # comment there gives the two independent reasons.
+        python-version: ['3.11', '3.12', '3.13']
+    env:
+      # uv otherwise reads .python-version (3.11) and silently builds a 3.11
+      # venv for both legs, so the matrix would prove nothing. This overrides
+      # that file for every uv command in the job, `uv run` included.
+      UV_PYTHON: ${{ matrix.python-version }}
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      # `--extra cloud` as well as dev, so the whole suite runs with the SDKs
+      # present. Without it the two `importorskip("openai")` tests in
+      # tests/unit/test_embeddings.py skipped here -- and they ran nowhere else,
+      # because the all-extras job runs only tests/unit/test_cloud_provider_sdks.py.
+      # One of the two is the guard on the auto-embedding fix: a key in the
+      # environment must not be read as a request to send documents to OpenAI.
+      # A regression guard that never runs is a comment.
+      #
+      # `ollama` is deliberately not included: no test imports it, and the three
+      # ollama tests in tests/unit/test_llm_preflight.py monkeypatch the probe.
+      - name: Sync dependencies
+        run: uv sync --extra dev --extra cloud
+
+      - name: Cache fastembed models
+        uses: actions/cache@v4
+        with:
+          path: /home/runner/.cache/fastembed
+          key: fastembed-bge-small-en-v1.5
+
+      - name: Run tests
+        run: uv run pytest tests/unit/ tests/integration/ tests/e2e/ -v --tb=short
+
+  docker:
+    # Builds the image but never publishes it: docker-publish.yml owns pushing,
+    # and that only triggers on a tag. This job exists so a dependency change
+    # cannot break the image without anyone noticing between releases.
+    name: Docker (production image)
+    runs-on: ubuntu-latest
+    needs: lint
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Build the production target
+        run: docker build --file docker/Dockerfile --target production --tag docugraph:ci .
+
+      - name: Handshake over stdio
+        # Initialise, then let stdin close. A missing LLM does not stop the
+        # server from identifying itself -- that is the point of the
+        # degradation work -- so this needs no credentials.
+        run: |
+          printf '%s\n' \
+            '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"ci-handshake","version":"0"}}}' \
+            | timeout 300 docker run -i --rm docugraph:ci \
+                > /tmp/handshake.jsonl 2> /tmp/handshake.err \
+            || echo "docker run exit: $?"
+          echo "--- container stderr (tail) ---"
+          tail -20 /tmp/handshake.err || true
+
+      - name: Assert the handshake
+        run: |
+          python3 - <<'PY'
+          import json, pathlib, sys
+
+          EXPECTED = "0.1.0"  # the version this repo publishes; pinned deliberately
+          raw = pathlib.Path("/tmp/handshake.jsonl").read_text()
+
+          # stdout carries the JSON-RPC stream and nothing else. A stray line
+          # here corrupts the protocol, so it fails rather than being skipped.
+          messages = []
+          for n, line in enumerate(raw.splitlines(), 1):
+              if not line.strip():
+                  continue
+              try:
+                  messages.append(json.loads(line))
+              except json.JSONDecodeError as e:
+                  sys.exit(f"stdout line {n} is not JSON: {line[:160]!r} ({e})")
+
+          infos = [
+              m["result"]["serverInfo"]
+              for m in messages
+              if isinstance(m.get("result"), dict) and "serverInfo" in m["result"]
+          ]
+          if not infos:
+              sys.exit(f"no serverInfo in {len(messages)} message(s): {messages!r}")
+          if infos[0].get("version") != EXPECTED:
+              sys.exit(f"serverInfo.version is {infos[0].get('version')!r}, expected {EXPECTED!r}")
+
+          print(f"stdout: {len(messages)} JSON-RPC message(s), 0 stray lines")
+          print(f"serverInfo: {infos[0]}")
+          PY
+
+  test-summary:
+    name: Test Summary
+    runs-on: ubuntu-latest
+    needs: test
+    if: always()
+
+    steps:
+      - name: Check test results
+        run: |
+          if [ "${{ needs.test.result }}" == "success" ]; then
+            echo "All tests passed!"
+          else
+            echo "Some tests failed"
+            exit 1
+          fi

docugraph-0.1.0/.github/workflows/docker-publish.yml

@@ -0,0 +1,85 @@
+# Build and publish Docker images to GitHub Container Registry
+name: Docker Publish
+
+on:
+  # Manual only. Publishing a release goes through release.yml, which builds the
+  # same production image and tags it with the release version; a `v*` tag used
+  # to fire this file as well, building that image a second time under a second
+  # set of tags. Branch pushes deliberately do not trigger it either: an image
+  # for every push to main is noise, and it made the first push to a new
+  # repository fail a multi-platform build before anything was released.
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      # The arm64 half of the multi-platform build runs under emulation on the
+      # amd64 runners, which requires QEMU registered with binfmt. Without this
+      # step the arm64 build fails.
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels)
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            # The tag as pushed (v1.2.3)
+            type=ref,event=tag
+            # Semver components (1.2.3, 1.2, 1)
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+            # Short SHA, so a manual run is traceable
+            type=sha,prefix=sha-
+            # `latest` only for a version tag, never for a manual run
+            type=raw,value=latest,enable=${{ startsWith(github.ref, 'refs/tags/v') }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./docker/Dockerfile
+          target: production
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          platforms: linux/amd64,linux/arm64
+
+      - name: Build and push development image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./docker/Dockerfile
+          target: development
+          push: true
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:dev
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          platforms: linux/amd64,linux/arm64

docugraph-0.1.0/.github/workflows/live-provider-smoke.yml

@@ -0,0 +1,77 @@
+# One real call per cloud provider, weekly and on demand.
+#
+# This is the only job in this repository that talks to a provider for real.
+# Everything else runs offline, and the unit tests that cover request shape use a
+# mocked transport -- deliberately, because that is what makes them fast and
+# deterministic, and also what makes them unable to answer the one question only
+# a live call can: does the model the operator configured still exist, and does
+# the provider still accept the request this package builds for it? Vendors
+# retire model ids on their own schedule, and no amount of local testing notices.
+#
+# So it is deliberately not in the push and PR gate. It needs secrets, it spends a
+# fraction of a cent, and it fails for reasons that have nothing to do with the
+# commit under test -- a red X on every PR would train people to ignore it. It
+# runs on `main` only, weekly and by hand, and its failures are a signal about the
+# world rather than about a diff.
+#
+#   Models  come from repository *variables*  (Settings -> Secrets and variables
+#           -> Actions -> Variables): OPENAI_MODEL, ANTHROPIC_MODEL, COHERE_MODEL.
+#           A model id is not a credential, and being able to read it in the
+#           settings page is what makes a failure diagnosable.
+#   Keys    come from repository *secrets* (OPENAI_API_KEY, ANTHROPIC_API_KEY,
+#           COHERE_API_KEY).
+#
+# A provider with no key or no model is reported as skipped, and the job stays
+# green -- but a run where *nothing* was configured fails, because a smoke test
+# that passes by testing nothing is worse than one that never ran.
+name: Live provider smoke
+
+on:
+  # Manual: Actions -> Live provider smoke -> Run workflow.
+  workflow_dispatch:
+  schedule:
+    # Mondays at 07:13 UTC. Off the hour on purpose: the top of the hour is when
+    # most of the world's scheduled jobs fire, and GitHub queues behind them.
+    - cron: '13 7 * * 1'
+
+# Read-only: this job runs provider SDKs against a checked-out tree and writes
+# nothing back.
+permissions:
+  contents: read
+
+jobs:
+  smoke:
+    name: One call per provider
+    runs-on: ubuntu-latest
+    # `main` only, including for a manual dispatch, which can otherwise be
+    # started from any branch. The point is to check what users have: a branch may
+    # name a model that is not the released default, and a green run there would
+    # say nothing about the published package. Scheduled runs are already pinned
+    # to the default branch.
+    if: github.ref == 'refs/heads/main'
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      # --all-extras so every provider's SDK is present; without it the ones that
+      # are missing report as skipped, which reads identically to unconfigured.
+      - name: Sync dependencies
+        run: uv sync --all-extras
+
+      - name: One tiny call per provider
+        env:
+          OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+          COHERE_API_KEY: ${{ secrets.COHERE_API_KEY }}
+          OPENAI_MODEL: ${{ vars.OPENAI_MODEL }}
+          ANTHROPIC_MODEL: ${{ vars.ANTHROPIC_MODEL }}
+          COHERE_MODEL: ${{ vars.COHERE_MODEL }}
+        run: uv run python scripts/live_provider_smoke.py

docugraph-0.1.0/.github/workflows/live-reranker.yml

@@ -0,0 +1,91 @@
+# The opt-in cross-encoder, run against the real weights, weekly and on demand.
+#
+# `tests/unit/test_reranker.py` is skipped on every push and pull request,
+# because bge-reranker-v2-m3 is ~2.3 GB and a download on every run would make
+# the fast offline suite slow and flaky. The consequence was that nothing ever
+# exercised the real model: the one test that proves registration, download
+# wiring and inference work together ran *never*. A gate that has never once
+# been satisfied is not a gate; it is a comment.
+#
+# So this job runs it -- weekly, on `main`, with the weights cached between
+# runs. It is deliberately separate from `live-provider-smoke.yml`, which talks
+# to a cloud provider and says so in its header; this job talks to the Hugging
+# Face hub and runs a model locally, and keeping them apart keeps each header
+# true. The skip in the test file stays, because CI on a pull request must not
+# download 2.3 GB.
+#
+# A *skip* fails this job. The weights are fetched in the step above the test,
+# so nothing here can legitimately skip; if the test does skip, the cache is
+# not where the test looks, and green would mean "checked nothing".
+name: Live reranker
+
+on:
+  # Manual: Actions -> Live reranker -> Run workflow.
+  workflow_dispatch:
+  schedule:
+    # Tuesdays at 07:41 UTC. Off the hour, and the day after the provider smoke,
+    # so a bad Monday there does not hide a bad Tuesday here.
+    - cron: '41 7 * * 2'
+
+# Read-only: this job downloads weights, runs a model and writes nothing back.
+permissions:
+  contents: read
+
+jobs:
+  reranker:
+    name: Real cross-encoder inference
+    runs-on: ubuntu-latest
+    # `main` only, including for a manual dispatch, which can otherwise be
+    # started from any branch. The point is to check what users run: a branch
+    # may name a different model, and a green run there would say nothing about
+    # the released default. Scheduled runs are already pinned to the default
+    # branch.
+    if: github.ref == 'refs/heads/main'
+    env:
+      # The same path ci.yml uses, so both workflows cache fastembed weights in
+      # one place. Set explicitly because fastembed's own default is a
+      # subdirectory of the system temp dir -- unkeyable for the cache step
+      # below and different on every runner. The test resolves the directory
+      # through fastembed's own `define_cache_dir`, so it reads this value
+      # rather than assuming it.
+      FASTEMBED_CACHE_PATH: /home/runner/.cache/fastembed
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      # Keyed on the model, not on a hash of anything: the weights at a given
+      # revision never change, and the job accesses the entry weekly so it does
+      # not age out under GitHub's eviction policy.
+      - name: Restore the reranker weights
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.FASTEMBED_CACHE_PATH }}
+          key: fastembed-bge-reranker-v2-m3
+
+      - name: Sync dependencies
+        run: uv sync --all-extras
+
+      # Cold cache: this is where the ~2.3 GB download happens, and where a
+      # retired repository or a broken ModelSource is caught.
+      - name: Fetch the weights if the cache was cold
+        run: uv run python -c "from docugraph.retrieval.reranker import FastembedReranker; FastembedReranker()"
+
+      # `pipefail` so a failing pytest fails the step; `tee` so the log survives
+      # the grep. Verbose because the assertion below is on the test's own
+      # verdict, and a skip exits 0.
+      - name: Run the reranker tests
+        run: |
+          set -o pipefail
+          uv run pytest tests/unit/test_reranker.py -v | tee /tmp/reranker.log
+          if ! grep -qE "TestFastembedRerankerLive.*PASSED" /tmp/reranker.log; then
+            echo "::error::the live reranker test did not pass -- it skipped, so this run checked nothing"
+            exit 1
+          fi