bionemo-recipes folder restructure (#1151)

Moves bionemo-recipes content, including the models/ and recipes/
directories, into a top-level `bionemo-recipes/` folder

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
  - THD (Flash Attention) input support for ESM2 TE models.
- New MLM data collator that packs sequences and provides FlashAttention
metadata.

- **Documentation**
  - BioNeMo Recipes README link updated to the repository subdirectory.

- **Tests**
- Added THD parity and end-to-end tests; enhanced fixtures and an
autouse debug fixture.

- **Chores**
- CI/workflows and local test scripts updated to use bionemo-recipes
paths.
  - Lint configuration refinements.

- **Refactor**
  - Removed deprecated contact-prediction public API.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Peter St. John <pstjohn@nvidia.com>

Author: pstjohn

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

@@ -44,8 +44,7 @@ jobs:
           base_sha: ${{ steps.merge-base.outputs.merge-base }}
           files: |
             **
-            !models/**
-            !recipes/**
+            !bionemo-recipes/**
             !**.md
             !.github/**
             !.gitignore

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

@@ -51,10 +51,10 @@ jobs:
           matrix: true
           base_sha: ${{ steps.merge-base.outputs.merge-base }}
           dir_names: true
-          dir_names_max_depth: 2
+          dir_names_max_depth: 3
           files: |
-            models/**
-            recipes/**
+            bionemo-recipes/models/**
+            bionemo-recipes/recipes/**
 
       - id: set-dirs
         name: Determine which directories to run
@@ -64,7 +64,7 @@ jobs:
           CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}
         run: |
           # Get all recipe and model directories
-          ALL_DIRS=$(ls -d recipes/*/ models/*/ 2>/dev/null | jq -R -s -c 'split("\n")[:-1] | map(rtrimstr("/"))')
+          ALL_DIRS=$(ls -d bionemo-recipes/models/*/ bionemo-recipes/recipes/*/ 2>/dev/null | jq -R -s -c 'split("\n")[:-1] | map(rtrimstr("/"))')
 
           # Determine which directories to run: all for schedule, filtered for other events
           if [[ "$EVENT_NAME" == "schedule" ]]; then
@@ -102,8 +102,9 @@ jobs:
           DIRS_WITH_IMAGES=$(echo "$DIRS" | jq -c '
             map({
               dir: .,
+              name: (. | sub("^bionemo-recipes/"; "")),
               image: (
-                if . == "models/amplify" then
+                if . == "bionemo-recipes/models/amplify" then
                   "svcbionemo023/bionemo-framework:amplify-model-devcontainer-082025"
                 else
                   "svcbionemo023/bionemo-framework:pytorch25.06-py3-squashed-zstd"
@@ -129,6 +130,7 @@ jobs:
     needs: changed-dirs
     runs-on: linux-amd64-gpu-l4-latest-1
     if: ${{ needs.changed-dirs.outputs.dirs != '[]' }}
+    name: "unit-tests (${{ matrix.recipe.name }})"
     container:
       image: ${{ matrix.recipe.image }}
       options: --shm-size=16G
@@ -138,7 +140,6 @@ jobs:
       fail-fast: false
 
     steps:
-
       - name: Show GPU info
         run: nvidia-smi
       - name: Setup proxy cache