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Fix missing context in ESM2 FT checkpoint #878

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farhadrgh merged 2 commits into
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farhadr/esm2_ft_bug
May 15, 2025
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Fix missing context in ESM2 FT checkpoint #878
farhadrgh merged 2 commits into
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farhadr/esm2_ft_bug

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@farhadrgh farhadrgh commented May 13, 2025 •
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Description

Type of changes

  • 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:

Note

By default, the notebooks validation tests are skipped unless explicitly enabled.

Authorizing CI Runs

We use copy-pr-bot 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.

Usage

TODO: Add code snippet

Pre-submit Checklist

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

farhadrgh added 2 commits May 13, 2025 21:59
@farhadrgh
update tracked config
6b549c6 
Signed-off-by: Farhad Ramezanghorbani <farhadr@nvidia.com>
@farhadrgh
add sequence class inference
a6d061b 
Signed-off-by: Farhad Ramezanghorbani <farhadr@nvidia.com>
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copy-pr-bot Bot commented May 13, 2025

This pull request requires additional validation before any workflows can run on NVIDIA's runners.

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@farhadrgh farhadrgh requested a review from polinabinder1 May 13, 2025 22:02
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farhadrgh commented May 14, 2025

/ok to test a6d061b

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codecov-commenter commented May 14, 2025 •
edited by codecov Bot
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.39%. Comparing base (2e3446f) to head (a6d061b).
⚠️ Report is 428 commits behind head on main.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #878      +/-   ##
==========================================
+ Coverage   84.38%   84.39%   +0.01%     
==========================================
  Files         138      138              
  Lines        8698     8698              
==========================================
+ Hits         7340     7341       +1     
+ Misses       1358     1357       -1
Files with missing lines Coverage Δ
...emo-esm2/src/bionemo/esm2/scripts/finetune_esm2.py 92.45% <100.00%> (ø)

... and 1 file with indirect coverage changes

🚀 New features to boost your workflow:
  • 📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

skothenhill-nv
skothenhill-nv approved these changes May 15, 2025
View reviewed changes
Comment thread sub-packages/bionemo-esm2/src/bionemo/esm2/scripts/finetune_esm2.py
@farhadrgh farhadrgh enabled auto-merge May 15, 2025 16:05
@farhadrgh farhadrgh added this pull request to the merge queue May 15, 2025
Merged via the queue into main with commit 40552ad May 15, 2025
14 checks passed
@farhadrgh farhadrgh deleted the farhadr/esm2_ft_bug branch May 15, 2025 17:20
jwilber pushed a commit that referenced this pull request May 15, 2025
@farhadrgh @jwilber
Fix missing context in ESM2 FT checkpoint (#878)
1719da3 
### Description
<!-- Provide a detailed description of the changes in this PR -->

### Type of changes
<!-- Mark the relevant option with an [x] -->

- [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:

-
[SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci)
- Skip all continuous integration tests
-
[INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests)
- Execute notebook validation tests in pytest
-
[INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests)
- Execute tests labelled as slow in pytest for extensive testing

> [!NOTE]
> By default, the notebooks validation tests are skipped unless
explicitly enabled.

#### 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.

### Usage
<!--- How does a user interact with the changed code -->
```python
TODO: Add code snippet
```

### 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: Farhad Ramezanghorbani <farhadr@nvidia.com>
trvachov pushed a commit that referenced this pull request May 16, 2025
@farhadrgh @trvachov
Fix missing context in ESM2 FT checkpoint (#878)
6f3e588 
### Description
<!-- Provide a detailed description of the changes in this PR -->

### Type of changes
<!-- Mark the relevant option with an [x] -->

- [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:

-
[SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci)
- Skip all continuous integration tests
-
[INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests)
- Execute notebook validation tests in pytest
-
[INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests)
- Execute tests labelled as slow in pytest for extensive testing

> [!NOTE]
> By default, the notebooks validation tests are skipped unless
explicitly enabled.

#### 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.

### Usage
<!--- How does a user interact with the changed code -->
```python
TODO: Add code snippet
```

### 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: Farhad Ramezanghorbani <farhadr@nvidia.com>
camirr-nv pushed a commit that referenced this pull request Jun 26, 2025
@farhadrgh @camirr-nv
Fix missing context in ESM2 FT checkpoint (#878)
94830aa 
### Description
<!-- Provide a detailed description of the changes in this PR -->

### Type of changes
<!-- Mark the relevant option with an [x] -->

- [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:

-
[SKIP_CI](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#skip_ci)
- Skip all continuous integration tests
-
[INCLUDE_NOTEBOOKS_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_notebooks_tests)
- Execute notebook validation tests in pytest
-
[INCLUDE_SLOW_TESTS](https://github.com/NVIDIA/bionemo-framework/blob/main/docs/docs/user-guide/contributing/contributing.md#include_slow_tests)
- Execute tests labelled as slow in pytest for extensive testing

> [!NOTE]
> By default, the notebooks validation tests are skipped unless
explicitly enabled.

#### 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.

### Usage
<!--- How does a user interact with the changed code -->
```python
TODO: Add code snippet
```

### 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: Farhad Ramezanghorbani <farhadr@nvidia.com>
Signed-off-by: Ubuntu <camirr@nvidia.com>
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