Adds CodonFM Recipe to BioNeMo Recipes (#1279)

### Description

Adds the codonFM recipe

Does not add top level readme edits.

#### Usage

<!--- How does a user interact with the changed code -->

```python
TODO: Add code snippet
```

### Type of changes

<!-- Mark the relevant option with an [x] -->

- [ ] Bug fix (non-breaking change which fixes an issue)
- [ ] New feature (non-breaking change which adds functionality)
- [ ] Refactor
- [ ] Documentation update
- [ ] Other (please describe):

### CI Pipeline Configuration

Configure CI behavior by applying the relevant labels. By default, only
basic unit tests are run.

-
[ciflow:skip](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:skip)
- Skip all CI tests for this PR
-
[ciflow:notebooks](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:notebooks)
- Run Jupyter notebooks execution tests for bionemo2
-
[ciflow:slow](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:slow)
- Run slow single GPU integration tests marked as @pytest.mark.slow for
bionemo2
-
[ciflow:all](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:all)
- Run all tests (unit tests, slow tests, and notebooks) for bionemo2.
This label can be used to enforce running tests for all bionemo2.
-
[ciflow:all-recipes](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/main/contributing/contributing.md#ciflow:all-recipes)
- Run tests for all recipes (under bionemo-recipes). This label can be
used to enforce running tests for all recipes.

Unit tests marked as `@pytest.mark.multi_gpu` or
`@pytest.mark.distributed` are not run in the PR pipeline.

For more details, see [CONTRIBUTING](CONTRIBUTING.md)

> [!NOTE]
> By default, only basic unit tests are run. Add appropriate labels to
enable an additional test coverage.

#### Authorizing CI Runs

We use
[copy-pr-bot](https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/#automation)
to manage authorization of CI
runs on NVIDIA's compute resources.

- If a pull request is opened by a trusted user and contains only
trusted changes, the pull request's code will
automatically be copied to a pull-request/ prefixed branch in the source
repository (e.g. pull-request/123)
- If a pull request is opened by an untrusted user or contains untrusted
changes, an NVIDIA org member must leave an
`/ok to test` comment on the pull request to trigger CI. This will need
to be done for each new commit.

### Pre-submit Checklist

<!--- Ensure all items are completed before submitting -->

- [ ] I have tested these changes locally
- [ ] I have updated the documentation accordingly
- [ ] I have added/updated tests as needed
- [ ] All existing tests pass successfully

---------

Signed-off-by: Jonathan Mitchell <[email protected]>
Co-authored-by: Yang Zhang <[email protected]>
Co-authored-by: Cory Ye <[email protected]>
Co-authored-by: Peter St. John <[email protected]>
Co-authored-by: Timur Rvachov <[email protected]>

Author: 5 people

bionemo-recipes/recipes/codonfm_ptl_te/.devcontainer/devcontainer.json

@@ -0,0 +1,54 @@
+{
+	"name": "Codo AI Dev Container",
+	"runArgs": [
+		"--gpus=all",
+		"--ipc=host",
+		"--net=host"
+	],
+	"hostname": "localhost",
+	"mounts": [
+		"source=${localEnv:HOME}/.ssh,target=/home/${localEnv:USER}/.ssh,type=bind,readonly",
+		"source=${localEnv:HOME}/.aws,target=/home/${localEnv:USER}/.aws,type=bind,consistency=cached",
+		"source=${localEnv:HOME}/.ngc,target=/home/${localEnv:USER}/.ngc,type=bind,consistency=cached",
+		"source=${localEnv:HOME}/.cache,target=/home/${localEnv:USER}/.cache,type=bind,consistency=cached",
+		"source=${localEnv:HOME}/.netrc,target=/home/${localEnv:USER}/.netrc,readonly,type=bind,consistency=cached",
+		"source=${localEnv:HOME}/.bash_history_devcontainer,target=/home/${localEnv:USER}/.bash_history,type=bind,consistency=cached"
+	],
+	"forwardPorts": [8888],
+	"containerEnv": {
+		"TMPDIR": "/tmp",
+		"NUMBA_CACHE_DIR": "/tmp/"
+	},
+	"build": {
+		"context": "${localWorkspaceFolder}",
+		"dockerfile": "${localWorkspaceFolder}/Dockerfile",
+		"target": "development",
+		"args": {
+			// These values will be filled automatically at build time by devcontainer.
+			"USERNAME": "${localEnv:USER}",
+			"USER_UID": "${localEnv:USER_UID}",
+			"USER_GID": "${localEnv:USER_GID}"
+		}
+	},
+	"workspaceMount": "source=${localWorkspaceFolder},target=/workspace/codonfm,type=bind,consistency=cached",
+	"workspaceFolder": "/workspace/codonfm",
+	"postCreateCommand": "./.devcontainer/postCreateCommand.sh",
+	"remoteUser": "${localEnv:USER}",
+	"updateRemoteUserUID": true,
+	"initializeCommand": "./.devcontainer/initializeCommand.sh",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-python.python",
+				"ms-python.vscode-pylance",
+				"eamodio.gitlens",
+				"streetsidesoftware.code-spell-checker",
+				"ms-azuretools.vscode-docker",
+				"charliermarsh.ruff",
+				"njpwerner.autodocstring",
+				"ms-toolsai.jupyter",
+				"tamasfe.even-better-toml"
+			]
+		}
+	}
+}

bionemo-recipes/recipes/codonfm_ptl_te/.devcontainer/initializeCommand.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+# Create the mounted config directories if they don't already exist
+
+mkdir -p ~/.aws
+mkdir -p ~/.ngc
+mkdir -p ~/.cache
+mkdir -p ~/.ssh
+[ ! -f ~/.netrc ] && touch ~/.netrc
+
+# Create the ~/.bash_history_devcontainer file if it doesn't exist
+[ ! -f ~/.bash_history_devcontainer ] && touch ~/.bash_history_devcontainer
+
+exit 0

bionemo-recipes/recipes/codonfm_ptl_te/.devcontainer/postCreateCommand.sh

@@ -0,0 +1 @@
+pip install -e .

bionemo-recipes/recipes/codonfm_ptl_te/.dockerignore

@@ -0,0 +1,18 @@
+# Exclude heavy or local-only artifacts from image build context
+
+# Requested exclusions
+wandb/
+**/wandb/**
+checkpoints/
+**/checkpoints/**
+results/
+**/results/**
+.env
+**/.env/**
+Dockerfile
+README.md
+__pycache__
+.dockerignore
+
+./data
+./.git

bionemo-recipes/recipes/codonfm_ptl_te/.ruff.toml

@@ -0,0 +1,24 @@
+extend = "../.ruff.toml"
+[lint.extend-per-file-ignores]
+"**/*.ipynb" = [
+    "C411",
+    "C416",
+    "C901",
+    "D101",
+    "D102",
+    "E402",
+    "E722",
+    "F402",
+    "FURB187",
+    "NPY002",
+    "PERF401",
+    "PERF402",
+    "PLW0127",
+    "PLW2901",
+    "RUF003",
+    "RUF005",
+    "RUF015",
+    "RUF017",
+    "RUF059",
+    "RUF100",
+]

bionemo-recipes/recipes/codonfm_ptl_te/Dockerfile

@@ -0,0 +1,66 @@
+# To build a production image:
+# docker build -t <image_name> --target production .
+#
+# To build a development image:
+# docker build -t <image_name> --target development --build-arg USERNAME=$(whoami) --build-arg USER_UID=$(id -u) --build-arg USER_GID=$(id -g) .
+
+ARG FROM_IMAGE_NAME=nvcr.io/nvidia/pytorch:25.08-py3
+FROM ${FROM_IMAGE_NAME} AS base
+
+ENV CUDA_HOME=/usr/local/cuda
+ENV PATH=$CUDA_HOME/bin:$PATH
+ENV LD_LIBRARY_PATH=$CUDA_HOME/lib64:$LD_LIBRARY_PATH
+
+WORKDIR /workspace/codonfm
+
+# Copy requirements first for better layer caching
+COPY ./requirements.txt .
+
+# Install dependencies
+RUN pip install -r requirements.txt \
+    && apt-get update \
+    && apt-get install -y libsndfile1 ffmpeg
+
+
+
+# ----------------- Production Stage -----------------
+FROM base AS production
+
+WORKDIR /workspace/codonfm
+COPY . .
+# Add a CMD for production if you have a main script to run
+# e.g., CMD ["python", "app.py"]
+
+
+# ----------------- Development Stage -----------------
+FROM base AS development
+
+WORKDIR /workspace/codonfm
+
+# Install development specific packages
+RUN apt-get update && apt-get install -y htop rsync
+
+# Create a non-root user for development (robust to empty args)
+ARG USERNAME
+ARG USER_UID
+ARG USER_GID
+
+RUN set -eux; \
+    USERNAME_EFF="${USERNAME:-vscode}"; \
+    USER_UID_EFF="${USER_UID:-1001}"; \
+    USER_GID_EFF="${USER_GID:-1001}"; \
+    if ! getent group "$USER_GID_EFF" >/dev/null 2>&1; then \
+      groupadd --gid "$USER_GID_EFF" "$USERNAME_EFF"; \
+    fi; \
+    if ! id -u "$USERNAME_EFF" >/dev/null 2>&1; then \
+      useradd -l --uid "$USER_UID_EFF" --gid "$USER_GID_EFF" -m "$USERNAME_EFF"; \
+    fi  # noqa: E702
+
+# Copy source code into the image for development
+COPY . .
+
+# Ensure developer owns the app directory
+RUN chown -R ${USERNAME:-vscode}:${USERNAME:-vscode} /workspace/codonfm
+
+# Switch to the non-root user
+USER $USERNAME

bionemo-recipes/recipes/codonfm_ptl_te/LICENSE

@@ -0,0 +1,202 @@
+
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and  # noqa: E702
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and  # noqa: E702
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and  # noqa: E702
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or  # noqa: E702
+          documentation, if provided along with the Derivative Works; or,  # noqa: E702
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright 2025 NVIDIA
+
+   Licensed under the Apache License, Version 2.0 (the "License");  # noqa: E703
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.