From fd99448aa44d2b59e89799d84fb3202324029d8f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Apr 2026 20:02:35 +0000
Subject: [PATCH] build(deps): bump the pip group across 1 directory with 9
 updates

Bumps the pip group with 9 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [biopython](https://github.com/biopython/biopython) | `1.81` | `1.87` |
| [black](https://github.com/psf/black) | `22.3.0` | `26.3.1` |
| [deepspeed](https://github.com/deepspeedai/DeepSpeed) | `0.8.0` | `0.15.1` |
| [protobuf](https://github.com/protocolbuffers/protobuf) | `4.21.12` | `5.29.6` |
| [pydantic](https://github.com/pydantic/pydantic) | `1.10.4` | `1.10.13` |
| [pytest](https://github.com/pytest-dev/pytest) | `7.3.1` | `9.0.3` |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.2.1` | `1.5.0` |
| [sentry-sdk](https://github.com/getsentry/sentry-python) | `1.15.0` | `1.45.1` |
| [tqdm](https://github.com/tqdm/tqdm) | `4.64.1` | `4.66.3` |



Updates `biopython` from 1.81 to 1.87
- [Changelog](https://github.com/biopython/biopython/blob/master/NEWS.rst)
- [Commits](https://github.com/biopython/biopython/commits)

Updates `black` from 22.3.0 to 26.3.1
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](https://github.com/psf/black/compare/22.3.0...26.3.1)

Updates `deepspeed` from 0.8.0 to 0.15.1
- [Release notes](https://github.com/deepspeedai/DeepSpeed/releases)
- [Commits](https://github.com/deepspeedai/DeepSpeed/compare/v0.8.0...v0.15.1)

Updates `protobuf` from 4.21.12 to 5.29.6
- [Release notes](https://github.com/protocolbuffers/protobuf/releases)
- [Commits](https://github.com/protocolbuffers/protobuf/commits)

Updates `pydantic` from 1.10.4 to 1.10.13
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](https://github.com/pydantic/pydantic/compare/v1.10.4...v1.10.13)

Updates `pytest` from 7.3.1 to 9.0.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/7.3.1...9.0.3)

Updates `scikit-learn` from 1.2.1 to 1.5.0
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](https://github.com/scikit-learn/scikit-learn/compare/1.2.1...1.5.0)

Updates `sentry-sdk` from 1.15.0 to 1.45.1
- [Release notes](https://github.com/getsentry/sentry-python/releases)
- [Changelog](https://github.com/getsentry/sentry-python/blob/1.45.1/CHANGELOG.md)
- [Commits](https://github.com/getsentry/sentry-python/compare/1.15.0...1.45.1)

Updates `tqdm` from 4.64.1 to 4.66.3
- [Release notes](https://github.com/tqdm/tqdm/releases)
- [Commits](https://github.com/tqdm/tqdm/compare/v4.64.1...v4.66.3)

---
updated-dependencies:
- dependency-name: biopython
  dependency-version: '1.87'
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: black
  dependency-version: 26.3.1
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: deepspeed
  dependency-version: 0.15.1
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: protobuf
  dependency-version: 5.29.6
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: pydantic
  dependency-version: 1.10.13
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: pytest
  dependency-version: 9.0.3
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: scikit-learn
  dependency-version: 1.5.0
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: sentry-sdk
  dependency-version: 1.45.1
  dependency-type: direct:production
  dependency-group: pip
- dependency-name: tqdm
  dependency-version: 4.66.3
  dependency-type: direct:production
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements.txt | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index c52639a..65d6c73 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,10 @@
 antlr4-python3-runtime==4.9.3
-biopython==1.81
-black==22.3.0
+biopython==1.87
+black==26.3.1
 blessed==1.20.0
 click==8.1.3
 contextlib2==21.6.0
-deepspeed==0.8.0
+deepspeed==0.15.1
 docker-pycreds==0.4.0
 fair-esm==2.0.0
 gitdb==4.0.10
@@ -27,21 +27,21 @@ omegaconf==2.3.0
 omegaconf==2.3.0
 pathtools==0.1.2
 pre-commit==2.19.0
-protobuf==4.21.12
+protobuf==5.29.6
 py-cpuinfo==9.0.0
-pydantic==1.10.4
-pytest==7.3.1
-pytest==7.3.1
+pydantic==1.10.13
+pytest==9.0.3
+pytest==9.0.3
 pytest-cov==4.0.0
 pytest-mock==3.11.1
 pytest-xdist==3.2.1
 ruff==0.0.231
 s3fs==2023.1.0
-scikit-learn==1.2.1
-sentry-sdk==1.15.0
+scikit-learn==1.5.0
+sentry-sdk==1.45.1
 setproctitle==1.3.2
 smmap==5.0.0
 threadpoolctl==3.1.0
 tmtools==0.0.2
-tqdm==4.64.1
+tqdm==4.66.3
 types-tqdm==4.65.0.1