fix(install): give the studyloop tool venv the semantic runtime

.github/workflows/nightly-install.yml

@@ -96,6 +96,16 @@ jobs:
           "$UV_TOOL_BIN_DIR/studyloop" --version
           "$UV_TOOL_BIN_DIR/session-export" --help
 
+      - name: Verify the studyloop tool env carries the semantic runtime
+        # `studyloop web` warms the query encoder in-process at boot, inside
+        # the studyloop tool venv (not agent-session-tools' own). Without
+        # these the warm fails at import and the header chip reads
+        # "semantic: failed" -- invisible to the --version/--help checks.
+        env:
+          UV_TOOL_DIR: ${{ runner.temp }}/tools
+        run: |
+          "$UV_TOOL_DIR/studyloop/bin/python" -c "import huggingface_hub, numpy, onnxruntime, sqlite_vec, tokenizers"
+
       - name: Verify installed agent definitions
         # One artefact per planted harness, each a path `install agents`
         # writes for that tool (installers.py _TOOL_LINKS / _configure_*).

CHANGELOG.md

@@ -83,6 +83,16 @@ experience may change before `1.0.0`.
   drained future was already complete, the pump exited without reading that
   future's `StopAsyncIteration`. The pump now retrieves the result of a done
   pull future on every exit path.
+- `studyloop web` started from an installed tool no longer shows
+  **semantic: failed (0.0s)**. The installer co-installed `agent-session-tools`
+  into the `studyloop` tool venv without its extras, so the semantic runtime
+  (tokenizers, onnxruntime, huggingface-hub, numpy, sqlite-vec) never reached
+  the venv that serves the web UI: the boot-time encoder warm failed at import
+  and search silently stayed lexical-only, while `studyloop doctor` in the same
+  venv called the encoder check "does not apply". The co-install now carries
+  `[all]`, and the nightly install job and `scripts/smoke-uv-tool-install.sh`
+  import the runtime in that venv. Existing installs pick it up with
+  `./scripts/install.sh --tools-only`.
 
 ## [0.5.0] - 2026-09-21
 

docs/setup-guide.md

@@ -136,10 +136,15 @@ such as `session-export`, `session-query`, and `session-sync` may not appear on
 ```bash
 uv sync --all-packages
 uv tool install --editable './packages/studyloop[all]' \
-  --with-editable ./packages/agent-session-tools
+  --with-editable './packages/agent-session-tools[all]'
 uv tool install --editable './packages/agent-session-tools[all]'
 ```
 
+The `[all]` on `--with-editable` matters: `studyloop web` runs the semantic
+search layer inside the `studyloop` tool venv, so co-installing
+`agent-session-tools` without its extras leaves the header chip reading
+`semantic: failed`.
+
 Prefer `./scripts/install.sh` or `studyloop install tools` for normal source
 checkout installs because they keep the two tool venvs wired together.
 
@@ -943,7 +948,7 @@ command:
 ```bash
 uv sync --all-packages
 uv tool install --editable './packages/studyloop[all]' \
-  --with-editable ./packages/agent-session-tools \
+  --with-editable './packages/agent-session-tools[all]' \
   --force
 ```
 

packages/studyloop/src/studyloop/installers.py

@@ -1310,7 +1310,14 @@ def install_workspace_tools(
             cmd.append(f"{pkg_dir}[all]")
         elif package_name == "studyloop":
             cmd.append(f"{pkg_dir}[all]")
-            cmd.extend(["--with-editable", str(repo_root / "packages" / "agent-session-tools")])
+            # [all] on the co-installed package too. `studyloop web` imports
+            # agent_session_tools IN THIS venv: the server's boot-time encoder
+            # warm and every hybrid search run tokenizers, onnxruntime,
+            # huggingface_hub, numpy and sqlite_vec here, not in
+            # agent-session-tools' own tool venv. Co-installed bare, the warm
+            # failed at import and the header chip read "semantic: failed".
+            ast_pkg = repo_root / "packages" / "agent-session-tools"
+            cmd.extend(["--with-editable", f"{ast_pkg}[all]"])
         else:
             cmd.append(str(pkg_dir))
         cmd.append("--editable")

packages/studyloop/tests/test_ci_workflow_contract.py

@@ -290,3 +290,24 @@ def test_nightly_installer_job_plants_a_harness_before_running_install_sh() -> N
     assert verify["env"]["HOME"] == "${{ runner.temp }}/home"
     for planted_marker in planted:
         assert planted_marker in verify["run"], f"verify step does not look inside {planted_marker}"
+
+
+def test_nightly_installer_job_proves_the_studyloop_tool_env_carries_the_semantic_runtime() -> None:
+    """`install.sh` gave the studyloop tool venv no semantic runtime, and the
+    job's only checks were `--version` and `--help`, which pass without it --
+    so every install's `studyloop web` failed its encoder warm at import and
+    nothing in CI could see it. The job must import what the warm imports, in
+    the venv that serves `studyloop web`, after the script has run.
+    """
+    steps = _nightly_workflow()["jobs"]["installer"]["steps"]
+    names = [step.get("name") for step in steps]
+    wanted = "Verify the studyloop tool env carries the semantic runtime"
+    assert wanted in names, "the installer job must check the studyloop venv's semantic runtime"
+    assert names.index(wanted) > names.index("Run scripts/install.sh")
+
+    verify = steps[names.index(wanted)]
+    assert verify["env"]["UV_TOOL_DIR"] == "${{ runner.temp }}/tools"
+    assert (
+        '"$UV_TOOL_DIR/studyloop/bin/python" -c '
+        '"import huggingface_hub, numpy, onnxruntime, sqlite_vec, tokenizers"'
+    ) in verify["run"]

packages/studyloop/tests/test_installers_workspace_tools.py

@@ -59,7 +59,7 @@ def test_install_workspace_tools_installs_expected_tool_commands(tmp_path: Path)
                 _PY_VER,
                 f"{studyloop_pkg}[all]",
                 "--with-editable",
-                str(agent_pkg),
+                f"{agent_pkg}[all]",
                 "--editable",
                 "--force",
             ],
@@ -68,6 +68,29 @@ def test_install_workspace_tools_installs_expected_tool_commands(tmp_path: Path)
     ]
 
 
+def test_the_studyloop_tool_env_gets_agent_session_tools_with_its_runtime_extras(
+    tmp_path: Path,
+) -> None:
+    """`studyloop web` imports agent_session_tools in-process, in the STUDYLOOP
+    tool venv: the server's boot-time encoder warm and every hybrid search run
+    tokenizers, onnxruntime, huggingface_hub, numpy and sqlite_vec there. The
+    standalone agent-session-tools tool gets ``[all]``, but that is a different
+    venv. Co-installed bare, the studyloop venv had none of them, so the warm
+    failed at import in ~10 ms and the header chip read ``semantic: failed
+    (0.0s)`` -- while `doctor`, running in the same venv, called the encoder
+    check "does not apply".
+    """
+    repo_root = _workspace(tmp_path)
+
+    with patch("studyloop.installers._run") as run:
+        install_workspace_tools(repo_root, sync_workspace=False)
+
+    studyloop_spec = f"{repo_root / 'packages' / 'studyloop'}[all]"
+    command = next(c.args[0] for c in run.call_args_list if studyloop_spec in c.args[0])
+    co_installed = command[command.index("--with-editable") + 1]
+    assert co_installed == f"{repo_root / 'packages' / 'agent-session-tools'}[all]"
+
+
 def test_install_workspace_tools_can_skip_sync_and_force(tmp_path: Path) -> None:
     repo_root = _workspace(tmp_path)
 

packages/studyloop/tests/test_smoke_installed_cli_contract.py

@@ -67,7 +67,14 @@ def test_smoke_uv_tool_install_uses_isolated_tool_home_and_runs_cli_smoke() -> N
         'uv tool install --force --editable --python "$PY_REQUEST" '
         '"$ROOT_DIR/packages/studyloop[all]"'
     ) in script_text
-    assert '--with-editable "$ROOT_DIR/packages/agent-session-tools"' in script_text
+    assert '--with-editable "$ROOT_DIR/packages/agent-session-tools[all]"' in script_text
+    # The studyloop venv serves `studyloop web`, whose encoder warm imports
+    # the semantic runtime in-process. Import level only: the isolated HOME
+    # has no Hugging Face cache, and the ONNX artefact is `doctor --fix`'s job.
+    assert (
+        '"$(uv tool dir)/studyloop/bin/python" -c '
+        '"import huggingface_hub, numpy, onnxruntime, sqlite_vec, tokenizers"'
+    ) in script_text
     assert (
         'uv tool install --force --editable --python "$PY_REQUEST" '
         '"$ROOT_DIR/packages/agent-session-tools[all]"'

scripts/smoke-uv-tool-install.sh

@@ -28,9 +28,14 @@ TOOL_BIN="$UV_TOOL_BIN_DIR"
 PY_REQUEST="$(tr -d '[:space:]' < "$ROOT_DIR/.python-version")"
 
 uv tool install --force --editable --python "$PY_REQUEST" "$ROOT_DIR/packages/studyloop[all]" \
-  --with-editable "$ROOT_DIR/packages/agent-session-tools"
+  --with-editable "$ROOT_DIR/packages/agent-session-tools[all]"
 uv tool install --force --editable --python "$PY_REQUEST" "$ROOT_DIR/packages/agent-session-tools[all]"
 
 test -x "$TOOL_BIN/studyloop"
 test -x "$TOOL_BIN/session-export"
+# The studyloop venv serves `studyloop web`, whose boot-time encoder warm
+# imports the semantic runtime in-process; without it the header chip reads
+# "semantic: failed". Import level only: this isolated HOME has no Hugging
+# Face cache, and fetching the ONNX artefact is `doctor --fix`'s job.
+"$(uv tool dir)/studyloop/bin/python" -c "import huggingface_hub, numpy, onnxruntime, sqlite_vec, tokenizers"
 STUDYLOOP_EXPECT_BIN_DIR="$TOOL_BIN" PATH="$TOOL_BIN:$PATH" "$ROOT_DIR/scripts/smoke-installed-cli.sh"