From 9fe6df5e286e99420cff0eaa55246bdc773f3824 Mon Sep 17 00:00:00 2001
From: svc-bionemo <267129667+svc-bionemo@users.noreply.github.com>
Date: Wed, 3 Jun 2026 05:01:40 -0700
Subject: [PATCH] fix(geneformer): resolve protobuf conflict with
 nvidia-resiliency-ext>=0.6.0
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megatron-core==0.17.1 requires nvidia-resiliency-ext>=0.6.0 at runtime,
but nvidia-resiliency-ext 0.6.0 pulls in grpcio-tools>=1.76.0 which
requires protobuf>=6.30.0 — conflicting with nemo-toolkit==2.4.0 pinning
protobuf~=5.29.5.

Fix by using a .ci_build.sh script that installs nvidia-resiliency-ext
with --no-deps (skipping grpcio-tools) and then installs the package
normally. grpcio-tools is not needed for geneformer test execution.

Signed-off-by: svc-bionemo <267129667+svc-bionemo@users.noreply.github.com>
---
 bionemo-recipes/models/geneformer/.ci_build.sh | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100755 bionemo-recipes/models/geneformer/.ci_build.sh

diff --git a/bionemo-recipes/models/geneformer/.ci_build.sh b/bionemo-recipes/models/geneformer/.ci_build.sh
new file mode 100755
index 0000000000..e1372d368a
--- /dev/null
+++ b/bionemo-recipes/models/geneformer/.ci_build.sh
@@ -0,0 +1,11 @@
+#!/bin/bash
+# nvidia-resiliency-ext>=0.6.0 is required at runtime by megatron-core==0.17.1,
+# but it depends on grpcio-tools>=1.76.0 which requires protobuf>=6.30.0,
+# conflicting with nemo-toolkit==2.4.0 (protobuf~=5.29.5).
+# Install it without deps to avoid the protobuf conflict, then install
+# its safe transitive deps separately.
+pip install --no-deps "nvidia-resiliency-ext>=0.6.0"
+pip install "defusedxml" "httpx>=0.24.0" "nvidia-ml-py>=12.570.86"
+
+# Install the package itself
+PIP_CONSTRAINT= pip install -e .