Merge remote-tracking branch 'origin/main' into jwilber/codon-gene-enrichment-eval

Author: jwilber

.devcontainer/recipes/Dockerfile .devcontainer/Dockerfile.devcontainer/recipes/Dockerfile renamed to .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:26.02-py3
+FROM nvcr.io/nvidia/pytorch:26.03-py3
 
 # FIXME: Fix for "No such file or directory: /workspace/TransformerEngine"
 #  Remove once bug has been addressed in the nvidia/pytorch container.

.devcontainer/recipes/README.md .devcontainer/README.md.devcontainer/recipes/README.md renamed to .devcontainer/README.md

@@ -1,5 +1,5 @@
 {
-    "name": "BioNeMo Recipes Dev Container",
+    "name": "BioNeMo Dev Container",
     "build": {
         "dockerfile": "Dockerfile"
     },
@@ -14,8 +14,8 @@
         "source=${localEnv:HOME}/.netrc,target=/home/ubuntu/.netrc,type=bind,consistency=cached",
         "source=${localEnv:HOME}/.ssh,target=/home/ubuntu/.ssh,readonly,type=bind,consistency=cached"
     ],
-    "postCreateCommand": ".devcontainer/recipes/postCreateCommand.sh",
-    "initializeCommand": ".devcontainer/recipes/initializeCommand.sh",
+    "postCreateCommand": ".devcontainer/postCreateCommand.sh",
+    "initializeCommand": ".devcontainer/initializeCommand.sh",
     "remoteUser": "ubuntu",
     "runArgs": [
         "--gpus=all",

.devcontainer/recipes/devcontainer.json .devcontainer/devcontainer.json.devcontainer/recipes/devcontainer.json renamed to .devcontainer/devcontainer.json

@@ -1,15 +1,15 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-# Launch the recipes devcontainer headlessly (no VS Code / Cursor required).
+# Launch the devcontainer headlessly (no VS Code / Cursor required).
 # All mounts, runArgs, containerEnv, and lifecycle commands are parsed at
 # runtime from devcontainer.json so the two definitions never drift apart.
 
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-REPO_ROOT="$(cd "${SCRIPT_DIR}/../.." && pwd)"
+REPO_ROOT="$(cd "${SCRIPT_DIR}/.." && pwd)"
 DEVCONTAINER_JSON="${SCRIPT_DIR}/devcontainer.json"
-CONTAINER_NAME="${BIONEMO_CONTAINER_NAME:-bionemo-recipes-devcontainer}"
-IMAGE_NAME="${BIONEMO_IMAGE_NAME:-bionemo-recipes-devcontainer:latest}"
+CONTAINER_NAME="${BIONEMO_CONTAINER_NAME:-bionemo-devcontainer}"
+IMAGE_NAME="${BIONEMO_IMAGE_NAME:-bionemo-devcontainer:latest}"
 
 # ---------------------------------------------------------------------------
 # Helpers