deepspeed deps (#33)

* deps

* deps

* changes

* changes

* push

* changes

* testing

* wip

* wip

---------

Co-authored-by: freyn6 <[email protected]>
Co-authored-by: Joseph Kleinhenz <[email protected]>

.github/workflows/push.yml

@@ -45,43 +45,6 @@ jobs:
         with:
           args: "format --check"
           version: 0.7.3
-  # pypi:
-  #   environment:
-  #     name: "pypi.org"
-  #     url: "https://pypi.org/project/lbster"
-  #   if: "startsWith(github.ref, 'refs/tags/')"
-  #   needs:
-  #     - "build"
-  #   permissions:
-  #     id-token: "write"
-  #   runs-on: "ubuntu-latest"
-  #   steps:
-  #     - uses: "actions/download-artifact@v3"
-  #       with:
-  #         name: "python-package-distributions"
-  #         path: "dist/"
-  #     - uses: "pypa/gh-action-pypi-publish@release/v1"
-  # release:
-  #   needs:
-  #     - "pypi"
-  #   permissions:
-  #     contents: "write"
-  #     id-token: "write"
-  #   runs-on: "ubuntu-latest"
-  #   steps:
-  #     - uses: "actions/download-artifact@v3"
-  #       with:
-  #         name: "python-package-distributions"
-  #         path: "dist/"
-  #     - uses: "sigstore/[email protected]"
-  #       with:
-  #         inputs: "./dist/*.tar.gz ./dist/*.whl"
-  #     - env:
-  #         GITHUB_TOKEN: "${{ github.token }}"
-  #       run: "gh release create '${{ github.ref_name }}' --notes '' --repo '${{ github.repository }}'"
-  #     - env:
-  #         GITHUB_TOKEN: "${{ github.token }}"
-  #       run: "gh release upload '${{ github.ref_name }}' dist/** --repo '${{ github.repository }}'"
   testpypi:
     environment:
       name: "test.pypi.org"

env.yml

@@ -6,9 +6,8 @@ channels:
   - bioconda
 dependencies:
   - pip
-  - python==3.10.*
+  - python==3.12.*
   - setuptools
   - git-lfs
   - pip:
-    - -r requirements.in
-    - -r requirements-dev.in
+    - -r requirements.txt

pyproject.toml

@@ -3,7 +3,7 @@ name = "lbster"
 readme = "README.md"
 description = "Language models for Biological Sequence Transformation and Evolutionary Representation."
 authors = [{name = "Nathan C. Frey", email = "[email protected]"}]
-dynamic = ["version", "optional-dependencies"]
+dynamic = ["version"]
 requires-python = ">=3.10"
 dependencies = [
     "pooch",
@@ -35,10 +35,10 @@ dependencies = [
     "edlib",
     "onnx",
     "onnxscript",
-    "fair-esm",
     "einops",
     "flash-attn; sys_platform == 'linux'",
     "beignet[datasets,mdtraj]",
+    "deepspeed",
 ]
 
 [build-system]
@@ -54,12 +54,11 @@ lobster_intervene_multiproperty = "lobster.cmdline:intervene_multiproperty"
 lobster_perplexity = "lobster.cmdline:perplexity"
 lobster_eval = "lobster.cmdline:eval_embed"
 
-[tool.setuptools.dynamic]
-dependencies = {file = ["requirements.in"]}
-
-[tool.setuptools.dynamic.optional-dependencies]
-dev = {file = ["requirements-dev.in"]}
-mgm = {file = ["requirements-mgm.in"]}
+[project.optional-dependencies]
+mgm = [
+    "rdkit>=2024.9.4",
+    "selfies>=2.1.2",
+]
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -112,7 +111,6 @@ ignore = [
 [tool.uv]
 environments = ["sys_platform == 'darwin'", "sys_platform == 'linux'"]
 constraint-dependencies = ["torch==2.5.1"]
-cache-keys = [{file = "requirements.in"}, {file = "requirements-dev.in"}, {file = "requirements-mgm.in"}]
 
 [tool.uv.sources]
 flash_attn = [
@@ -122,3 +120,13 @@ flash_attn = [
   { url = "https://github.com/Dao-AILab/flash-attention/releases/download/v2.7.3/flash_attn-2.7.3+cu12torch2.5cxx11abiFalse-cp313-cp313-linux_x86_64.whl", marker = "sys_platform == 'linux' and python_version == '3.13'"}
 ]
 beignet = { git = "https://github.com/Genentech/beignet" }
+
+[dependency-groups]
+dev = [
+    "ipykernel>=6.29.5",
+    "mypy>=1.14.1",
+    "pre-commit>=4.0.1",
+    "pytest>=8.3.4",
+    "pytest-cov>=6.0.0",
+    "ruff>=0.9.1",
+]