fix: non-zero exit code when a workflow run ends failed or aborted

workflow run and workflow resume printed Status: failed (or emitted the
--json payload) and exited 0, so scripts and CI could not rely on the
process exit code. Map terminal outcomes: failed|aborted -> 1,
completed|paused -> 0, on both the text and --json paths.

The previous exit-0-on-failed behavior was pinned by
test_workflow_run_failing_yaml_without_project; the pin is updated to
the new contract.

Fixes #2958

Author: doquanghuy

src/specify_cli/__init__.py

@@ -2756,6 +2756,16 @@ def _workflow_run_payload(state: Any) -> dict[str, Any]:
     }
 
 
+def _run_outcome_exit_code(status_value: str) -> int:
+    """Exit code for a finished run/resume: non-zero on terminal failure.
+
+    ``failed`` and ``aborted`` map to 1 so scripts and orchestrators can
+    rely on the process exit code; ``completed`` and ``paused`` map to 0
+    (paused is a legitimate waiting state, not a failure).
+    """
+    return 1 if status_value in ("failed", "aborted") else 0
+
+
 def _emit_workflow_json(payload: dict[str, Any]) -> None:
     """Write a workflow payload as machine-readable JSON to stdout.
 
@@ -2868,7 +2878,7 @@ def workflow_run(
 
     if json_output:
         _emit_workflow_json(_workflow_run_payload(state))
-        return
+        raise typer.Exit(_run_outcome_exit_code(state.status.value))
 
     status_colors = {
         "completed": "green",
@@ -2883,6 +2893,8 @@ def workflow_run(
     if state.status.value == "paused":
         console.print(f"\nResume with: [cyan]specify workflow resume {state.run_id}[/cyan]")
 
+    raise typer.Exit(_run_outcome_exit_code(state.status.value))
+
 
 @workflow_app.command("resume")
 def workflow_resume(
@@ -2921,7 +2933,7 @@ def workflow_resume(
 
     if json_output:
         _emit_workflow_json(_workflow_run_payload(state))
-        return
+        raise typer.Exit(_run_outcome_exit_code(state.status.value))
 
     status_colors = {
         "completed": "green",
@@ -2932,6 +2944,8 @@ def workflow_resume(
     color = status_colors.get(state.status.value, "white")
     console.print(f"\n[{color}]Status: {state.status.value}[/{color}]")
 
+    raise typer.Exit(_run_outcome_exit_code(state.status.value))
+
 
 @workflow_app.command("status")
 def workflow_status(

tests/test_workflow_run_without_project.py

@@ -162,7 +162,9 @@ def test_workflow_run_failing_yaml_without_project(self, tmp_path):
             ], catch_exceptions=False)
         finally:
             os.chdir(old_cwd)
-        assert result.exit_code == 0, f"workflow run failed unexpectedly: {result.output}"
+        # A failed workflow now maps to a non-zero process exit code so
+        # scripts and CI can rely on $? (the CLI itself still ran fine).
+        assert result.exit_code == 1, f"expected exit 1 on failed run: {result.output}"
         assert "Status: failed" in result.output
 
     def test_workflow_run_yaml_rejects_symlinked_specify_dir(self, tmp_path):

tests/test_workflows.py

@@ -3944,3 +3944,71 @@ def fake_open_url(url, timeout=None, extra_headers=None):
         asset_calls = [(url, h) for url, h in captured_urls if "releases/assets/" in url]
         assert len(asset_calls) >= 1
         assert asset_calls[0][1] == {"Accept": "application/octet-stream"}
+
+
+class TestWorkflowRunExitCodes:
+    """CLI-level tests for the run/resume process exit codes."""
+
+    _WF_OK = """
+schema_version: "1.0"
+workflow:
+  id: "exit-ok"
+  name: "Exit OK"
+  version: "1.0.0"
+steps:
+  - id: fine
+    type: shell
+    run: "true"
+"""
+
+    _WF_FAIL = """
+schema_version: "1.0"
+workflow:
+  id: "exit-fail"
+  name: "Exit Fail"
+  version: "1.0.0"
+steps:
+  - id: boom
+    type: shell
+    run: "false"
+"""
+
+    def _write(self, tmp_path, content):
+        path = tmp_path / "wf.yml"
+        path.write_text(content, encoding="utf-8")
+        return path
+
+    def test_run_completed_exits_zero(self, tmp_path, monkeypatch):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        monkeypatch.chdir(tmp_path)
+        runner = CliRunner()
+        result = runner.invoke(app, ["workflow", "run", str(self._write(tmp_path, self._WF_OK))])
+        assert result.exit_code == 0
+        assert "Status: completed" in result.stdout
+
+    def test_run_failed_exits_nonzero(self, tmp_path, monkeypatch):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        monkeypatch.chdir(tmp_path)
+        runner = CliRunner()
+        result = runner.invoke(app, ["workflow", "run", str(self._write(tmp_path, self._WF_FAIL))])
+        assert "Status: failed" in result.stdout
+        assert result.exit_code == 1
+
+    def test_run_failed_exits_nonzero_with_json(self, tmp_path, monkeypatch):
+        import json as _json
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        monkeypatch.chdir(tmp_path)
+        runner = CliRunner()
+        result = runner.invoke(
+            app,
+            ["workflow", "run", str(self._write(tmp_path, self._WF_FAIL)), "--json"],
+        )
+        payload = _json.loads(result.stdout)
+        assert payload["status"] == "failed"
+        assert result.exit_code == 1