Remove ESM2, Amplify from 5D. This is now in bionemo-recipes (#1336)

### Description

Remove 5D codepaths that are now covered by bionemo-recipes

#### 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: Timur Rvachov <trvachov@nvidia.com>

Author: trvachov

.devcontainer/framework/devcontainer.json

@@ -41,13 +41,10 @@
 			],
 			"settings": {
 				"python.analysis.extraPaths": [
-					"./sub-packages/bionemo-fw/src",
 					"./sub-packages/bionemo-core/src",
-					"./sub-packages/bionemo-esm2/src",
 					"./sub-packages/bionemo-geneformer/src",
 					"./sub-packages/bionemo-llm/src",
 					"./sub-packages/bionemo-testing/src",
-					"./sub-packages/bionemo-amplify/src",
 					"./sub-packages/bionemo-example_model/src",
 					"./3rdparty/NeMo",
 					"./3rdparty/Megatron-LM"

.secrets.baseline

@@ -148,9 +148,9 @@
         "filename": "pyproject.toml",
         "hashed_secret": "79670e9c9d1c7ea5b81a96a2053d81437712c78e",
         "is_verified": false,
-        "line_number": 44
+        "line_number": 42
       }
     ]
   },
-  "generated_at": "2025-09-25T15:59:12Z"
+  "generated_at": "2025-12-02T22:57:51Z"
 }

CODEOWNERS

@@ -58,16 +58,12 @@ ci/ @dorotat-nv @pstjohn @trvachov @jwilber @jomitchellnv @jstjohn
 #
 ## LIBRARY CODE
 #
-sub-packages/bionemo-fw @DejunL @dorotat-nv @farhadrgh @jstjohn @pstjohn @skothenhill-nv
-
 sub-packages/bionemo-testing @dorotat-nv @farhadrgh @jstjohn @pstjohn @skothenhill-nv
 
 sub-packages/bionemo-core @DejunL @dorotat-nv @farhadrgh @jstjohn @pstjohn @skothenhill-nv
 
 sub-packages/bionemo-llm @farhadrgh @dorotat-nv @jstjohn @pstjohn @skothenhill-nv
 
-sub-packages/bionemo-esm2 @pstjohn @jstjohn @skothenhill-nv @jomitchellnv @farhadrgh @yzhang123 @polinabinder1
-
 sub-packages/bionemo-example_model @jstjohn @skothenhill-nv
 
 sub-packages/bionemo-geneformer @jstjohn @skothenhill-nv

README.md

@@ -78,17 +78,14 @@ A core use-case of the BioNeMo Framework is to help digital biology scientists a
 <summary><b>(Click to expand) <code>sub-packages</code> models support matrix</b></summary>
 <small>
 
-| Directory               | Description                         | Support        | 5D Parallel | Megatron-FSDP | TE  | Sequence Packing | FP8 | Context Parallel |
-| ----------------------- | ----------------------------------- | -------------- | ----------- | ------------- | --- | ---------------- | --- | ---------------- |
-| `bionemo-amplify`       | 5D parallel model                   | 🔧 Maintenance | ✅          | ❌            | ✅  | ❌               | ✅  | ✅               |
-| `bionemo-core`          | Model Config/test data utils        | ✅ Active      | ✅          | N/A           | ✅  | ❌               | N/A | N/A              |
-| `bionemo-esm2`          | 5D parallel model                   | ✅ Active      | ✅          | ❌            | ✅  | ❌               | ✅  | ✅               |
-| `bionemo-evo2`          | 5D parallel model                   | ✅ Active      | ✅          | ❌            | ✅  | ❌               | ✅  | ✅               |
-| `bionemo-example_model` | Example 5D parallel model           | 🔧 Maintenance | ✅          | ❌            | ✅  | ❌               | ✅  | ✅               |
-| `bionemo-fw`            | Meta package to pull other packages | ✅ Active      | ✅          | N/A           | N/A | ❌               | ✅  | N/A              |
-| `bionemo-geneformer`    | 5D parallel model                   | 🔧 Maintenance | ✅          | ❌            | ✅  | ❌               | ✅  | ✅               |
-| `bionemo-llm`           | 5D parallel base model (BioBert)    | ✅ Active      | ✅          | ❌            | ✅  | ✅               | ✅  | ✅               |
-| `bionemo-testing`       | Testing Utilities                   | ✅ Active      | ✅          | N/A           | N/A | N/A              | N/A | N/A              |
+| Directory               | Description                      | Support        | 5D Parallel | Megatron-FSDP | TE  | Sequence Packing | FP8 | Context Parallel |
+| ----------------------- | -------------------------------- | -------------- | ----------- | ------------- | --- | ---------------- | --- | ---------------- |
+| `bionemo-core`          | Model Config/test data utils     | ✅ Active      | ✅          | N/A           | ✅  | ❌               | N/A | N/A              |
+| `bionemo-evo2`          | 5D parallel model                | ✅ Active      | ✅          | ❌            | ✅  | ❌               | ✅  | ✅               |
+| `bionemo-example_model` | Example 5D parallel model        | 🔧 Maintenance | ✅          | ❌            | ✅  | ❌               | ✅  | ✅               |
+| `bionemo-geneformer`    | 5D parallel model                | 🔧 Maintenance | ✅          | ❌            | ✅  | ❌               | ✅  | ✅               |
+| `bionemo-llm`           | 5D parallel base model (BioBert) | ✅ Active      | ✅          | ❌            | ✅  | ✅               | ✅  | ✅               |
+| `bionemo-testing`       | Testing Utilities                | ✅ Active      | ✅          | N/A           | N/A | N/A              | N/A | N/A              |
 
 </small>
 </details>