fix: restore logger levels after silencing machine output

.github/CONTRIBUTING.md

@@ -223,6 +223,7 @@ Adding a new language has a dedicated recipe, see
 - Add tests for new features and bug fixes
 - Place tests in `tests/unit/` or `tests/integration/`
 - Run the full suite with `uv run pytest`
+- A test asserting on a `caplog` record needs `caplog.set_level(logging.INFO, logger="<the module's full logger name>")` (or the level you're asserting on) — setting the root logger's level is not enough when an ancestor logger (e.g. `repowise.core`, `repowise.server`) has its own level raised, since Python resolves the *effective* level from the nearest ancestor that has one set, not from root.
 
 ## Pull Request Guidelines
 

packages/cli/src/repowise/cli/commands/_tool_adapters.py

@@ -139,8 +139,8 @@ def run(repo_path: Path, factory: Callable[[], Awaitable[dict]], tool_name: str)
     from repowise.cli.helpers import silence_logs_for_machine_output
     from repowise.cli.tool_bridge import call_tool
 
-    silence_logs_for_machine_output()
-    return call_tool(repo_path, factory, tool_name)
+    with silence_logs_for_machine_output():
+        return call_tool(repo_path, factory, tool_name)
 
 
 #: MCP tool name -> the CLI command that now does the same thing.

packages/cli/src/repowise/cli/commands/doctor_cmd/command.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import contextlib
 import json
 
 import click
@@ -61,96 +62,95 @@ def doctor_command(
             "--repair is not supported with --format json (json mode is read-only)."
         )
 
-    if fmt != "table":
-        silence_logs_for_machine_output()
+    silencer = silence_logs_for_machine_output() if fmt != "table" else contextlib.nullcontext()
+    with silencer:
+        status = err_console if fmt != "table" else console
 
-    status = err_console if fmt != "table" else console
-
-    target = resolve_command_target(
-        path=path,
-        workspace_flag=workspace,
-        no_workspace_flag=no_workspace,
-    )
-    target.notice(status, command="doctor")
+        target = resolve_command_target(
+            path=path,
+            workspace_flag=workspace,
+            no_workspace_flag=no_workspace,
+        )
+        target.notice(status, command="doctor")
 
-    if fmt == "table":
-        # Advisory CLI update check, printed once above the repo check table(s).
-        _print_cli_version_status()
+        if fmt == "table":
+            # Advisory CLI update check, printed once above the repo check table(s).
+            _print_cli_version_status()
+
+        if not target.is_workspace:
+            assert target.repo_path is not None
+            all_ok, checks = _run_repo_checks(target.repo_path, repair, fmt=fmt)
+            if fmt != "table":
+                payload = {"ok": all_ok, "checks": [c._asdict() for c in checks]}
+                click.echo(json.dumps(payload, indent=2))
+                if not all_ok:
+                    raise SystemExit(1)
+            return
+
+        # Workspace mode — iterate over every entry, run workspace-level
+        # validation, and report a summary table at the end so the user knows
+        # which repos need attention.
+        assert target.ws_root is not None and target.ws_config is not None
+        ws_root = target.ws_root
+        ws_config = target.ws_config
+
+        ws_issues = _run_workspace_checks(ws_root, ws_config, repair=repair, fmt=fmt)
+
+        overall_ok = True
+        not_indexed: list[str] = []
+        all_checks: list[DoctorCheck] = []
+        for entry in ws_config.repos:
+            abs_path = (ws_root / entry.path).resolve()
+            if not abs_path.is_dir():
+                continue
+            if not (abs_path / ".repowise").is_dir():
+                not_indexed.append(entry.alias)
+                continue
+            if fmt == "table":
+                console.print()
+                console.print(
+                    f"[bold]── {entry.alias}[/bold]  "
+                    f"[dim]({entry.path})[/dim]"
+                    + (
+                        "  [bold cyan](primary)[/bold cyan]"
+                        if entry.alias == ws_config.default_repo
+                        else ""
+                    )
+                )
+            ok, checks = _run_repo_checks(abs_path, repair, fmt=fmt)
+            overall_ok = overall_ok and ok
+            all_checks.extend(DoctorCheck(f"{entry.alias}: {c.name}", c.ok, c.detail) for c in checks)
 
-    if not target.is_workspace:
-        assert target.repo_path is not None
-        all_ok, checks = _run_repo_checks(target.repo_path, repair, fmt=fmt)
         if fmt != "table":
-            payload = {"ok": all_ok, "checks": [c._asdict() for c in checks]}
+            all_ok = overall_ok and not ws_issues and not not_indexed
+            payload = {
+                "ok": all_ok,
+                "checks": [c._asdict() for c in all_checks],
+                "workspace": {
+                    "checked": True,
+                    "issues": list(ws_issues),
+                    "not_indexed": not_indexed,
+                },
+            }
             click.echo(json.dumps(payload, indent=2))
             if not all_ok:
                 raise SystemExit(1)
-        return
-
-    # Workspace mode — iterate over every entry, run workspace-level
-    # validation, and report a summary table at the end so the user knows
-    # which repos need attention.
-    assert target.ws_root is not None and target.ws_config is not None
-    ws_root = target.ws_root
-    ws_config = target.ws_config
-
-    ws_issues = _run_workspace_checks(ws_root, ws_config, repair=repair, fmt=fmt)
-
-    overall_ok = True
-    not_indexed: list[str] = []
-    all_checks: list[DoctorCheck] = []
-    for entry in ws_config.repos:
-        abs_path = (ws_root / entry.path).resolve()
-        if not abs_path.is_dir():
-            continue
-        if not (abs_path / ".repowise").is_dir():
-            not_indexed.append(entry.alias)
-            continue
-        if fmt == "table":
-            console.print()
+            return
+
+        console.print()
+        if not_indexed:
+            console.print(f"[yellow]Not indexed:[/yellow] {', '.join(not_indexed)}")
+            console.print("  Run [bold]repowise update --workspace[/bold] to index them.")
+        if ws_issues and not repair:
             console.print(
-                f"[bold]── {entry.alias}[/bold]  "
-                f"[dim]({entry.path})[/dim]"
-                + (
-                    "  [bold cyan](primary)[/bold cyan]"
-                    if entry.alias == ws_config.default_repo
-                    else ""
-                )
+                f"[yellow]{len(ws_issues)} workspace-level issue(s); "
+                f"rerun with [bold]--repair[/bold] to attempt fixes.[/yellow]"
             )
-        ok, checks = _run_repo_checks(abs_path, repair, fmt=fmt)
-        overall_ok = overall_ok and ok
-        all_checks.extend(DoctorCheck(f"{entry.alias}: {c.name}", c.ok, c.detail) for c in checks)
-
-    if fmt != "table":
-        all_ok = overall_ok and not ws_issues and not not_indexed
-        payload = {
-            "ok": all_ok,
-            "checks": [c._asdict() for c in all_checks],
-            "workspace": {
-                "checked": True,
-                "issues": list(ws_issues),
-                "not_indexed": not_indexed,
-            },
-        }
-        click.echo(json.dumps(payload, indent=2))
-        if not all_ok:
-            raise SystemExit(1)
-        return
-
-    console.print()
-    if not_indexed:
-        console.print(f"[yellow]Not indexed:[/yellow] {', '.join(not_indexed)}")
-        console.print("  Run [bold]repowise update --workspace[/bold] to index them.")
-    if ws_issues and not repair:
-        console.print(
-            f"[yellow]{len(ws_issues)} workspace-level issue(s); "
-            f"rerun with [bold]--repair[/bold] to attempt fixes.[/yellow]"
-        )
 
-    workspace_clean = not ws_issues and overall_ok and not not_indexed
-    if workspace_clean:
-        console.print("[bold green]Workspace healthy.[/bold green]")
-    elif overall_ok and not ws_issues:
-        console.print("[bold yellow]All indexed repos healthy; some repos unindexed.[/bold yellow]")
-    else:
-        console.print("[bold yellow]Some checks failed across the workspace.[/bold yellow]")
+        workspace_clean = not ws_issues and overall_ok and not not_indexed
+        if workspace_clean:
+            console.print("[bold green]Workspace healthy.[/bold green]")
+        elif overall_ok and not ws_issues:
+            console.print("[bold yellow]All indexed repos healthy; some repos unindexed.[/bold yellow]")
+        else:
+            console.print("[bold yellow]Some checks failed across the workspace.[/bold yellow]")