From 569a152299393eb1460b2c432c102ea588d9b1d1 Mon Sep 17 00:00:00 2001
From: svc-bionemo <267129667+svc-bionemo@users.noreply.github.com>
Date: Thu, 4 Jun 2026 05:07:15 -0700
Subject: [PATCH] fix(geneformer): add nvidia-resiliency-ext>=0.6.0 dependency
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megatron-core now requires nvidia-resiliency-ext>=0.6.0 at import time
(via dist_checkpointing.strategies.nvrx.has_nvrx_async_support). The
base container image (nvcr.io/nvidia/pytorch:26.04-py3) ships an older
version, causing an AssertionError during test collection for all tests
that import geneformer.convert (which transitively imports nemo.lightning
→ megatron.core).

Add the explicit dependency pin so pip installs the required version
during the Docker build.

Signed-off-by: svc-bionemo <267129667+svc-bionemo@users.noreply.github.com>
---
 bionemo-recipes/models/geneformer/pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bionemo-recipes/models/geneformer/pyproject.toml b/bionemo-recipes/models/geneformer/pyproject.toml
index 2de37ed6b3..168cb7485e 100644
--- a/bionemo-recipes/models/geneformer/pyproject.toml
+++ b/bionemo-recipes/models/geneformer/pyproject.toml
@@ -16,6 +16,7 @@ dependencies = [
     "nemo_toolkit[lightning]==2.4.0",
     "fiddle",
     "megatron-core",
+    "nvidia-resiliency-ext>=0.6.0",
     "pytest",
     "requests",
     "hydra-core",