From 628715993b123b2c185e1fc9baa9900fe7c8fc4b Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Wed, 17 Sep 2025 23:22:24 +1000 Subject: [PATCH 1/2] prepend stdout to stderr when raising Docker errors --- pydra/environments/docker.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pydra/environments/docker.py b/pydra/environments/docker.py index 3c6da919a..2ef7d09d1 100644 --- a/pydra/environments/docker.py +++ b/pydra/environments/docker.py @@ -37,7 +37,7 @@ def execute(self, job: "Job[shell.Task]") -> dict[str, ty.Any]: output = dict(zip(keys, values)) if output["return_code"]: if output["stderr"]: - raise RuntimeError(output["stderr"]) + raise RuntimeError(output["stdout"] + "\n" + output["stderr"]) else: raise RuntimeError(output["stdout"]) return output From 5f396e3dd96fc136b81a9411fbd06ad14e5b4327 Mon Sep 17 00:00:00 2001 From: "Thomas G. Close" Date: Mon, 13 Oct 2025 15:36:19 +1100 Subject: [PATCH 2/2] fix up mrtrix3 import path --- docs/source/tutorial/6-workflow.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/tutorial/6-workflow.ipynb b/docs/source/tutorial/6-workflow.ipynb index 73e61afac..8ace36945 100644 --- a/docs/source/tutorial/6-workflow.ipynb +++ b/docs/source/tutorial/6-workflow.ipynb @@ -481,7 +481,7 @@ "from pathlib import Path\n", "import numpy as np\n", "from fileformats.medimage import Nifti1\n", - "import fileformats.medimage_mrtrix3 as mrtrix3\n", + "import fileformats.vendor.mrtrix3.medimage as mrtrix3\n", "from pydra.environments import docker\n", "from pydra.compose import workflow, python\n", "from pydra.tasks.mrtrix3.v3_0 import MrConvert, MrThreshold\n",