fix(geneformer): resolve protobuf conflict with nvidia-resiliency-ext>=0.6.0#1598
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pstjohn merged 1 commit intoJun 5, 2026
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…>=0.6.0 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>
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Problem
The geneformer nightly CI fails because megatron-core==0.17.1 asserts nvidia-resiliency-ext>=0.6.0 at import time, but that version isn't installed in the CI container.
Simply adding nvidia-resiliency-ext>=0.6.0 to pyproject.toml creates an unresolvable pip conflict:
Fix
Add a
.ci_build.shthat installs nvidia-resiliency-ext>=0.6.0 with--no-deps(skipping grpcio-tools which is not needed for test execution), then installs the package normally.The CI workflow already supports
.ci_build.shas a hook — if the file exists, it runs that instead of the defaultpip install -e ..Root Cause
nvidia-resiliency-ext 0.6.0 added grpcio/grpcio-tools as hard dependencies (for its new gRPC-based fault tolerance features), but these are incompatible with nemo-toolkit 2.4.0's protobuf pin. This will resolve when nemo-toolkit relaxes its protobuf constraint.