Allow specify workflow run to execute YAML files without a project

src/specify_cli/commands/init.py

@@ -113,6 +113,7 @@ def init(
         branch_numbering: str = typer.Option(None, "--branch-numbering", help="Branch numbering strategy: 'sequential' (001, 002, …, 1000, … — expands past 999 automatically) or 'timestamp' (YYYYMMDD-HHMMSS)"),
         integration: str = typer.Option(None, "--integration", help="Use the new integration system (e.g. --integration copilot). Mutually exclusive with --ai."),
         integration_options: str = typer.Option(None, "--integration-options", help='Options for the integration (e.g. --integration-options="--commands-dir .myagent/cmds")'),
+        workflow: str = typer.Option(None, "--workflow", help="Run a workflow YAML file after project initialization"),
     ):
         """
         Initialize a new Specify project.
@@ -673,6 +674,45 @@ def init(
         console.print(tracker.render())
         console.print("\n[bold green]Project ready.[/bold green]")
 
+        if workflow:
+            workflow_path = Path(workflow)
+            if not workflow_path.is_absolute():
+                workflow_path = Path.cwd() / workflow_path
+            if not workflow_path.exists():
+                console.print(f"[red]Error:[/red] Workflow file not found: {workflow}")
+                raise typer.Exit(1)
+            console.print(f"\n[bold cyan]Running post-init workflow:[/bold cyan] {workflow}")
+            try:
+                from ..workflows.engine import WorkflowEngine
+                engine = WorkflowEngine(project_path)
+                engine.on_step_start = lambda sid, label: console.print(f"  ▸ [{sid}] {label} …")
+                definition = engine.load_workflow(str(workflow_path))
+                errors = engine.validate(definition)
+                if errors:
+                    console.print("[red]Workflow validation failed:[/red]")
+                    for err in errors:
+                        console.print(f"  • {err}")
+                    raise typer.Exit(1)
+                state = engine.execute(definition)
+                status_colors = {
+                    "completed": "green",
+                    "paused": "yellow",
+                    "failed": "red",
+                    "aborted": "red",
+                }
+                color = status_colors.get(state.status.value, "white")
+                console.print(f"\n[{color}]Workflow status: {state.status.value}[/{color}]")
+                if state.status.value == "paused":
+                    console.print(f"\nResume with: [cyan]specify workflow resume {state.run_id}[/cyan]")
+                elif state.status.value in ("failed", "aborted"):
+                    console.print("[red]Post-init workflow did not complete successfully.[/red]")
+                    raise typer.Exit(1)
+            except (typer.Exit, SystemExit):
+                raise
+            except Exception as wf_exc:
+                console.print(f"[red]Post-init workflow failed:[/red] {wf_exc}")
+                raise typer.Exit(1)
+
         agent_config = AGENT_CONFIG.get(selected_ai)
         if agent_config:
             agent_folder = ai_commands_dir if selected_ai == "generic" else agent_config["folder"]

tests/test_init_workflow.py

@@ -0,0 +1,133 @@
+"""Tests for --workflow flag on specify init."""
+
+import os
+
+import yaml
+
+
+class TestInitWorkflowFlag:
+    """Tests for the --workflow option on specify init."""
+
+    def test_workflow_flag_missing_file_errors(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        runner = CliRunner()
+        project = tmp_path / "wf-test"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = runner.invoke(app, [
+                "init", "--here", "--integration", "copilot",
+                "--script", "sh", "--no-git",
+                "--workflow", str(tmp_path / "nonexistent.yml"),
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code != 0
+        assert "Workflow file not found" in result.output
+
+    def test_workflow_flag_runs_workflow_after_init(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        runner = CliRunner()
+        project = tmp_path / "wf-run-test"
+        project.mkdir()
+
+        # Create a minimal workflow YAML that runs a simple shell step
+        workflow_file = tmp_path / "post-init.yml"
+        workflow_content = {
+            "schema_version": "1.0",
+            "workflow": {
+                "id": "post-init-test",
+                "name": "Post Init Test",
+                "version": "1.0.0",
+                "description": "A test post-init workflow",
+            },
+            "steps": [
+                {
+                    "id": "create-marker",
+                    "type": "shell",
+                    "run": "echo done > marker.txt",
+                },
+            ],
+        }
+        workflow_file.write_text(yaml.dump(workflow_content), encoding="utf-8")
+
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = runner.invoke(app, [
+                "init", "--here", "--integration", "copilot",
+                "--script", "sh", "--no-git",
+                "--workflow", str(workflow_file),
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0, f"init failed: {result.output}"
+        assert "Running post-init workflow" in result.output
+        assert "Workflow status: completed" in result.output
+        # The shell step should have created the marker file
+        assert (project / "marker.txt").exists()
+
+    def test_workflow_flag_failing_workflow_exits_nonzero(self, tmp_path):
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        runner = CliRunner()
+        project = tmp_path / "wf-fail-test"
+        project.mkdir()
+
+        # Create a workflow that fails
+        workflow_file = tmp_path / "bad-workflow.yml"
+        workflow_content = {
+            "schema_version": "1.0",
+            "workflow": {
+                "id": "bad-wf",
+                "name": "Bad Workflow",
+                "version": "1.0.0",
+                "description": "A failing workflow",
+            },
+            "steps": [
+                {
+                    "id": "fail-step",
+                    "type": "shell",
+                    "run": "exit 1",
+                },
+            ],
+        }
+        workflow_file.write_text(yaml.dump(workflow_content), encoding="utf-8")
+
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = runner.invoke(app, [
+                "init", "--here", "--integration", "copilot",
+                "--script", "sh", "--no-git",
+                "--workflow", str(workflow_file),
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code != 0
+
+    def test_init_without_workflow_flag_works_normally(self, tmp_path):
+        """Ensure that omitting --workflow does not change existing behavior."""
+        from typer.testing import CliRunner
+        from specify_cli import app
+
+        runner = CliRunner()
+        project = tmp_path / "no-wf-test"
+        project.mkdir()
+        old_cwd = os.getcwd()
+        try:
+            os.chdir(project)
+            result = runner.invoke(app, [
+                "init", "--here", "--integration", "copilot",
+                "--script", "sh", "--no-git",
+            ], catch_exceptions=False)
+        finally:
+            os.chdir(old_cwd)
+        assert result.exit_code == 0, f"init failed: {result.output}"
+        assert "Running post-init workflow" not in result.output