chore: update PyTorch base container from 26.03-py3 to 26.04-py3

Update all Dockerfiles and CI workflow references to use the new
pytorch 26.04-py3 base container. The squashed image has been pushed
to svcbionemo023/bionemo-framework:pytorch26.04-py3-squashed.

Resolves BIO-405.

Signed-off-by: svc-bionemo <267129667+svc-bionemo@users.noreply.github.com>

Author: svc-bionemo

.devcontainer/Dockerfile

@@ -1,6 +1,6 @@
 # Uncomment to use the latest TE from the NGC registry for debugging changes with latest TE.
 # FROM gitlab-master.nvidia.com/dl/transformerengine/transformerengine:main-pytorch-py3-base
-FROM nvcr.io/nvidia/pytorch:26.03-py3
+FROM nvcr.io/nvidia/pytorch:26.04-py3
 
 # FIXME: Fix for "No such file or directory: /workspace/TransformerEngine"
 #  Remove once bug has been addressed in the nvidia/pytorch container.

.github/workflows/unit-tests-framework.yml

@@ -232,7 +232,7 @@ jobs:
       )
     name: "unit-tests (${{ matrix.pkg.name }})"
     container:
-      image: svcbionemo023/bionemo-framework:pytorch26.03-py3-squashed
+      image: svcbionemo023/bionemo-framework:pytorch26.04-py3-squashed
       options: --shm-size=16G
       env:
         CI: true
@@ -329,7 +329,7 @@ jobs:
         )
     name: "slow-tests (${{ matrix.pkg.name }})"
     container:
-      image: svcbionemo023/bionemo-framework:pytorch26.03-py3-squashed
+      image: svcbionemo023/bionemo-framework:pytorch26.04-py3-squashed
       options: --shm-size=16G
       env:
         CI: true
@@ -405,7 +405,7 @@ jobs:
         )
     name: "notebook-tests (${{ matrix.pkg.name }})"
     container:
-      image: svcbionemo023/bionemo-framework:pytorch26.03-py3-squashed
+      image: svcbionemo023/bionemo-framework:pytorch26.04-py3-squashed
       options: --shm-size=16G
       env:
         CI: true

.github/workflows/unit-tests-mbridge-recipes.yaml

@@ -113,7 +113,7 @@ jobs:
             map({
               dir: .,
               name: (. | sub("^bionemo-recipes/"; "")),
-              image: "svcbionemo023/bionemo-framework:pytorch26.03-py3-squashed"
+              image: "svcbionemo023/bionemo-framework:pytorch26.04-py3-squashed"
             })
           ')
           echo "dirs=$DIRS_WITH_IMAGES" >> $GITHUB_OUTPUT

.github/workflows/unit-tests-recipes.yml

@@ -95,8 +95,8 @@ jobs:
           # Currently, AMPLIFY is the only folder that needs a custom base image, since we have to support both TE and
           # xformers-based models for golden value testing. The rest of the models use the default pytorch image.
 
-          # This uses a squashed version of the pytorch:26.03-py3 image, generated with `docker-squash
-          # nvcr.io/nvidia/pytorch:26.03-py3 -t svcbionemo023/bionemo-framework:pytorch26.03-py3-squashed --output
+          # This uses a squashed version of the pytorch:26.04-py3 image, generated with `docker-squash
+          # nvcr.io/nvidia/pytorch:26.04-py3 -t svcbionemo023/bionemo-framework:pytorch26.04-py3-squashed --output
           # type=registry,compression=zstd,force-compression=true,oci-mediatypes=true,compression-level=15` and pushed
           # to the dockerhub registry. Our github actions are able to cache image pulls from dockerhub but not nvcr, so
           # hopefully this cuts down slightly on CI time at the expense of having a slightly in-directed image location.
@@ -109,8 +109,8 @@ jobs:
                 if . == "bionemo-recipes/models/amplify" then
                   "svcbionemo023/bionemo-framework:amplify-model-devcontainer-082025"
                 else
-                  # "nvcr.io/nvidia/pytorch:26.03-py3"
-                  "svcbionemo023/bionemo-framework:pytorch26.03-py3-squashed"
+                  # "nvcr.io/nvidia/pytorch:26.04-py3"
+                  "svcbionemo023/bionemo-framework:pytorch26.04-py3-squashed"
                 end
               )
             })

bionemo-recipes/models/esm2/Dockerfile

@@ -1,4 +1,4 @@
-FROM nvcr.io/nvidia/pytorch:26.03-py3
+FROM nvcr.io/nvidia/pytorch:26.04-py3
 WORKDIR /workspace/bionemo
 COPY . .
 RUN --mount=type=cache,target=/root/.cache/pip \

bionemo-recipes/models/geneformer/Dockerfile

@@ -1,4 +1,4 @@
-FROM nvcr.io/nvidia/pytorch:26.03-py3
+FROM nvcr.io/nvidia/pytorch:26.04-py3
 WORKDIR /workspace/bionemo
 COPY . .
 RUN --mount=type=cache,target=/root/.cache/pip \

bionemo-recipes/models/qwen/Dockerfile

@@ -1,4 +1,4 @@
-FROM nvcr.io/nvidia/pytorch:26.03-py3
+FROM nvcr.io/nvidia/pytorch:26.04-py3
 WORKDIR /workspace/bionemo
 COPY . .
 RUN --mount=type=cache,target=/root/.cache/pip \

bionemo-recipes/recipes/README.md

@@ -85,7 +85,7 @@ recipes/{recipe_name}/
 Your `Dockerfile` should create a complete, reproducible training environment:
 
 ```dockerfile
-FROM nvcr.io/nvidia/pytorch:26.03-py3
+FROM nvcr.io/nvidia/pytorch:26.04-py3
 
 # Install dependencies with caching for faster builds
 RUN --mount=type=cache,target=/root/.cache/pip \

bionemo-recipes/recipes/codonfm_native_te/Dockerfile

@@ -1,5 +1,5 @@
 # syntax=docker/dockerfile:1.4
-FROM nvcr.io/nvidia/pytorch:26.03-py3
+FROM nvcr.io/nvidia/pytorch:26.04-py3
 
 RUN --mount=type=cache,target=/root/.cache/pip \
     --mount=type=bind,source=requirements.txt,target=/requirements.txt \

bionemo-recipes/recipes/eden_megatron/Dockerfile

@@ -1,5 +1,5 @@
 # syntax=docker/dockerfile:1.4
-FROM nvcr.io/nvidia/pytorch:26.03-py3
+FROM nvcr.io/nvidia/pytorch:26.04-py3
 
 # uv is pre-installed in the nvcr.io/nvidia/pytorch base image.
 # If using a base image without uv, uncomment the following line: