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rename framework to recipes
Signed-off-by: Peter St. John <pstjohn@nvidia.com>
1 parent d52b0b9 commit 5237c87

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‎ci/lepton/model_convergence/configs/base.yaml‎

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@@ -100,8 +100,8 @@ commit_sha: ""
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############################################################
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checkout_script: |
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set -euo pipefail
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git clone https://github.com/NVIDIA/bionemo-framework.git
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cd bionemo-framework
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git clone https://github.com/NVIDIA-BioNeMo/bionemo-recipes.git
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cd bionemo-recipes
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if [ -n "${commit_sha}" ]; then
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echo "Checking out commit: ${commit_sha}"
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git checkout "${commit_sha}"

‎ci/lepton/model_convergence/configs/recipes/codonfm_ptl_te.yaml‎

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# edit these
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max_steps: 200
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out_dir: "/workspace/bionemo-framework/recipes/codonfm_ptl_te"
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out_dir: "/workspace/bionemo-recipes/recipes/codonfm_ptl_te"
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learning_rate: 1e-4
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train_batch_size: 32
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val_batch_size: 32
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############################################################
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checkout_script: |
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cd /workspace
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git clone https://github.com/NVIDIA/bionemo-framework.git
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cd bionemo-framework
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git clone https://github.com/NVIDIA-BioNeMo/bionemo-recipes.git
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cd bionemo-recipes
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if [ -n "${commit_sha}" ]; then
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echo "Checking out commit: ${commit_sha}"
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git checkout "${commit_sha}"

‎ci/lepton/model_convergence/launchers/convergence_tests.sh‎

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RC=$?
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set -e
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echo "commit in bionemo-framework"
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(cd bionemo-framework && git log -1 || true)
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# Always grab the exact commit currently checked out in the framework repo
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COMMIT_SHA="$(cd bionemo-framework && git rev-parse HEAD 2>/dev/null || true)"
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echo "Resolved framework commit: ${COMMIT_SHA:-<none>}"
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echo "commit in bionemo-recipes"
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(cd bionemo-recipes && git log -1 || true)
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# Always grab the exact commit currently checked out in the recipes repo
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COMMIT_SHA="$(cd bionemo-recipes && git rev-parse HEAD 2>/dev/null || true)"
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echo "Resolved recipes commit: ${COMMIT_SHA:-<none>}"
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# Authenticate to Lepton
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pip install -q leptonai >/dev/null 2>&1 || pip install -q leptonai || true
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ALL_CONFIG_JSON_UPDATED='{}'
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fi
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# Inject/overwrite the resolved framework commit (only if we actually got one)
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# Inject/overwrite the resolved recipes commit (only if we actually got one)
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if [ -n "${COMMIT_SHA:-}" ]; then
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ALL_CONFIG_JSON_UPDATED="$(printf '%s' "$ALL_CONFIG_JSON_UPDATED" | jq -c --arg commit "$COMMIT_SHA" '.commit_sha = $commit')"
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# Find which branch contains this commit
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RESOLVED_BRANCH="$(cd bionemo-framework && git branch -r --contains "$COMMIT_SHA" | grep 'origin/' | head -1 | sed 's|.*origin/||' || true)"
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RESOLVED_BRANCH="$(cd bionemo-recipes && git branch -r --contains "$COMMIT_SHA" | grep 'origin/' | head -1 | sed 's|.*origin/||' || true)"
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if [ -n "$RESOLVED_BRANCH" ] && [ "$RESOLVED_BRANCH" != "HEAD" ]; then
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ALL_CONFIG_JSON_UPDATED="$(printf '%s' "$ALL_CONFIG_JSON_UPDATED" | jq -c --arg branch "$RESOLVED_BRANCH" '.branch = $branch')"
@@ -180,7 +180,7 @@ NVIDIA_DRIVER_INFO="$(jq -n --arg dv "$DRIVER_VERSION" --arg cv "$CUDA_VERSION"
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set -e
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# Look for W&B files
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WANDB_DIR="/workspace/bionemo-framework/recipes/$RECIPE_SUBDIR/wandb"
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WANDB_DIR="/workspace/bionemo-recipes/recipes/$RECIPE_SUBDIR/wandb"
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WANDB_FOUND=0
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WANDB_SUMMARY=""

‎docs/conftest.py‎

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# limitations under the License.
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# FIXME: remove this notebooks from ignore when this issue is fixed: https://github.com/NVIDIA/bionemo-framework/issues/778
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# FIXME: remove this notebooks from ignore when this issue is fixed: https://github.com/NVIDIA-BioNeMo/bionemo-recipes/issues/778
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collect_ignore = ["docs/user-guide/examples/bionemo-geneformer/geneformer_cellxgene_tutorial.ipynb"]

‎docs/docs/main/FAQ.md‎

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## How do I install BioNeMo Recipes?
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You can install individual recipe directories from within BioNeMo Recipes by following the corresponding
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README pages the [BioNeMo Recipes GitHub](https://github.com/NVIDIA-BioNeMo/bionemo-framework).
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README pages in the [BioNeMo Recipes GitHub repository](https://github.com/NVIDIA-BioNeMo/bionemo-recipes).
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## What are the system requirements for BioNeMo Recipes?
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## How do I report bugs or suggest new features?
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To report a bug or suggest a new feature, open an issue on the
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[BioNeMo Recipes GitHub site](https://github.com/NVIDIA-BioNeMo/bionemo-framework/issues). For the fastest turnaround,
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[BioNeMo Recipes GitHub site](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/issues). For the fastest turnaround,
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thoroughly describe your issue, including any steps and/or _minimal_ data sets necessary to reproduce (when possible),
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as well as the expected behavior.
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‎docs/docs/models/ESM-2/pre-training.md‎

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## Training with BioNeMo Recipes
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Active ESM-2 training code lives in
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[`recipes/esm2_native_te`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/recipes/esm2_native_te).
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[`recipes/esm2_native_te`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/recipes/esm2_native_te).
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See the recipe README for setup instructions, supported training scripts (`train_ddp.py`,
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`train_fsdp2.py`), and benchmark results.
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An Accelerate-based variant is also available at
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[`recipes/esm2_accelerate_te`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/recipes/esm2_accelerate_te).
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[`recipes/esm2_accelerate_te`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/recipes/esm2_accelerate_te).
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## Model Convergence
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‎docs/docs/models/amplify.md‎

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## Model Overview
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Training code for this model is in
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[`recipes/esm2_native_te`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/recipes/esm2_native_te)
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[`recipes/esm2_native_te`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/recipes/esm2_native_te)
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and
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[`recipes/esm2_accelerate_te`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/recipes/esm2_accelerate_te);
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[`recipes/esm2_accelerate_te`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/recipes/esm2_accelerate_te);
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use an AMPLIFY model tag such as `nvidia/AMPLIFY_120M`. Use
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[`models/amplify`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/models/amplify)
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[`models/amplify`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/models/amplify)
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for checkpoint conversion and model implementation details.
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### Description
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The model is fully compatible with weights distributed via HuggingFace, i.e.,
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[chandar-lab/AMPLIFY_120M](https://huggingface.co/chandar-lab/AMPLIFY_120M). See
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[`models/amplify`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/models/amplify)
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[`models/amplify`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/models/amplify)
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for checkpoint conversion utilities and usage examples.
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## Training & Evaluation
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Use the recipe READMEs for current training entrypoints:
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- [`models/amplify`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/models/amplify)
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- [`recipes/esm2_native_te`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/recipes/esm2_native_te)
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- [`recipes/esm2_accelerate_te`](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main/recipes/esm2_accelerate_te)
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- [`models/amplify`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/models/amplify)
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- [`recipes/esm2_native_te`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/recipes/esm2_native_te)
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- [`recipes/esm2_accelerate_te`](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main/recipes/esm2_accelerate_te)
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| Model Size | GPUs | Batch Size (per GPU) | Training Step Time (s) |
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| ---------- | ---------------- | -------------------- | ---------------------- |

‎docs/docs/models/index.md‎

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State-of-the-art models are continually integrated into BioNeMo Recipes. BioNeMo Recipes currently offers the following pre-trained models:
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| **Model** | **Modality** | **Uses** | **Training Location** |
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| ----------------------------- | ------------ | ----------------------- | -------------------------------------------------------------------------------- |
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| [AMPLIFY](./amplify.md) | Protein | Representation Learning | [BioNeMo Recipes](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main) |
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| [ESM-2](./ESM-2/index.md) | Protein | Representation Learning | [BioNeMo Recipes](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main) |
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| [Evo2](./evo2.md) | DNA | Generative AI | [BioNeMo Recipes](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main) |
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| [Geneformer](./geneformer.md) | Single Cell | Representation Learning | [BioNeMo Recipes](https://github.com/NVIDIA-BioNeMo/bionemo-framework/tree/main) |
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| **Model** | **Modality** | **Uses** | **Training Location** |
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| ----------------------------- | ------------ | ----------------------- | ------------------------------------------------------------------------------ |
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| [AMPLIFY](./amplify.md) | Protein | Representation Learning | [BioNeMo Recipes](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main) |
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| [ESM-2](./ESM-2/index.md) | Protein | Representation Learning | [BioNeMo Recipes](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main) |
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| [Evo2](./evo2.md) | DNA | Generative AI | [BioNeMo Recipes](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main) |
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| [Geneformer](./geneformer.md) | Single Cell | Representation Learning | [BioNeMo Recipes](https://github.com/NVIDIA-BioNeMo/bionemo-recipes/tree/main) |
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<!-- TODO: MolMIM has not yet been ported to BioNeMo Recipes. Add a model card entry here once a recipe is available. -->
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‎docs/mkdocs.yml‎

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site_name: BioNeMo
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site_url: https://nvidia-bionemo.github.io/bionemo-framework
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repo_url: https://github.com/NVIDIA-BioNeMo/bionemo-framework
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repo_name: NVIDIA-BioNeMo/bionemo-framework
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site_url: https://nvidia-bionemo.github.io/bionemo-recipes
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repo_url: https://github.com/NVIDIA-BioNeMo/bionemo-recipes
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repo_name: NVIDIA-BioNeMo/bionemo-recipes
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theme:
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name: "material"
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extra:
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social:
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- icon: fontawesome/brands/github
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link: https://github.com/NVIDIA-BioNeMo/bionemo-framework
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link: https://github.com/NVIDIA-BioNeMo/bionemo-recipes
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version:
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provider: mike
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default: latest
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alias: true
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github_url: https://github.com/NVIDIA-BioNeMo/bionemo-framework
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github_url: https://github.com/NVIDIA-BioNeMo/bionemo-recipes
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copyright: |
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&copy; Copyright 2023-2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.

‎docs/scripts/gen_ref_pages.py‎

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}
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SUPPORT_FILE_NAMES = {"Dockerfile", "LICENSE", "Makefile", "requirements.txt"}
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SKIP_SUPPORT_DIRS = {"assets", "examples", "notebooks", ".venv", "__pycache__", ".pytest_cache"}
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GITHUB_BLOB_BASE = "https://github.com/NVIDIA-BioNeMo/bionemo-framework/blob/main"
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GITHUB_BLOB_BASE = "https://github.com/NVIDIA-BioNeMo/bionemo-recipes/blob/main"
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def _rewrite_relative_links(

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