uv

.github/workflows/pre-commit.yml

@@ -0,0 +1,14 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.1

.github/workflows/unit.yml

@@ -0,0 +1,22 @@
+name: unit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+
+jobs:
+  unit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        run: uv run pytest -svv --cov=cortex tests

.gitignore

@@ -3,3 +3,5 @@
 __pycache__
 *.egg-info
 docs/build
+temp
+.coverage

.pre-commit-config.yaml

@@ -17,10 +17,11 @@ repos:
     rev: 0.6.0
     hooks:
       - id: nbstripout
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.2.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.9.7
     hooks:
+      # Run the linter.
       - id: ruff
-        name: ruff
-        args: [ --fix ]
+      # Run the formatter.
       - id: ruff-format

README.md

@@ -17,23 +17,11 @@ Rather than tack on auxiliary abstractions to a single input --> single task mod
 
 Note: conda/mamba are no longer actively supported. We recommend using `uv` for package management.
 
-Note: Support for Python versions > 3.10 is blocked by the current dependency on `pytorch-lightning==1.9.5`.
-
 ```bash
-uv venv -n ~/.venv/cortex --python 3.10
+uv sync
 source ~/.venv/cortex/bin/activate
-uv pip install pytorch-cortex
 ```
 
-
-If you have a package version issue we provide pinned versions of all dependencies in `requirements.txt`.
-To update the frozen dependencies run
-
-```bash
-uv pip freeze > requirements.txt
-```
-
-
 ## Running
 
 Use `cortex_train_model --config-name <CONFIG_NAME>` to train, e.g.:
@@ -57,14 +45,14 @@ Contributions are welcome!
 ### Install dev requirements and pre-commit hooks
 
 ```bash
-python -m pip install -r requirements-dev.in
-pre-commit install
+uv sync --dev
+uv run pre-commit install
 ```
 
 ### Testing
 
 ```bash
-python -m pytest -v --cov-report term-missing --cov=./cortex ./tests
+uv run pytest -v --cov-report term-missing --cov=./cortex ./tests
 ```
 
 ### Build and browse docs locally

cortex/data/dataset/_data_frame_dataset.py

@@ -53,9 +53,7 @@ def __init__(
                 remove_archive=True,
             )
         else:
-            raise ValueError(
-                f"Dataset not found at {path}. " "If `download` is `True`, the dataset will be downloaded."
-            )
+            raise ValueError(f"Dataset not found at {path}. If `download` is `True`, the dataset will be downloaded.")
         self._data = self._read_data(path, dedup=dedup, train=train, random_seed=random_seed, **kwargs)
 
     def _read_data(self, path: str, dedup: bool, train: bool, random_seed: int, **kwargs: Any) -> DataFrame:

cortex/model/elemental/_ddp_standardize.py

@@ -81,7 +81,7 @@ def forward(self, Y: Tensor, Yvar: Optional[Tensor] = None) -> tuple[Tensor, Opt
                     f"Y.shape[:-2]={Y.shape[:-2]}."
                 )
             if Y.size(-1) != self._m:
-                raise RuntimeError(f"Wrong output dimension. Y.size(-1) is {Y.size(-1)}; expected " f"{self._m}.")
+                raise RuntimeError(f"Wrong output dimension. Y.size(-1) is {Y.size(-1)}; expected {self._m}.")
             stdvs = Y.std(dim=-2, keepdim=True)
             stdvs = stdvs.where(stdvs >= self._min_stdv, torch.full_like(stdvs, 1.0))
             means = Y.mean(dim=-2, keepdim=True)

pyproject.toml

@@ -1,13 +1,36 @@
 [project]
 name = "pytorch-cortex"
-dynamic = ["version", "readme", "dependencies", "optional-dependencies"]
+dynamic = ["version"]
+readme = "README.md"
 description = "A modular architecture for deep learning systems."
 authors = [{name = "Samuel Stanton", email = "stanton.samuel@gene.com"}]
 classifiers=[
     "Development Status :: 3 - Alpha",
     "Intended Audience :: Science/Research",
     "Programming Language :: Python :: 3",
 ]
+requires-python = ">=3.10"
+dependencies = [
+    "boto3>=1.37.1",
+    "botorch>=0.9.4",
+    "cachetools>=5.5.2",
+    "edlib>=1.3.9.post1",
+    "hydra-core>=1.2.0",
+    "lightning>=2.0",
+    "numpy>=2",
+    "omegaconf>=2.3.0",
+    "pandas>=2",
+    "pyarrow>=19.0.1",
+    "pytorch-warmup>=0.2.0",
+    "s3fs>=2025.3.2",
+    "tabulate>=0.9.0",
+    "torch>=2.5.1",
+    "torchvision",
+    "tqdm>=4.67.1",
+    "transformers>=4.24.0",
+    "universal-pathlib>=0.2.6",
+    "wandb>=0.19.9",
+]
 
 [project.scripts]
 cortex_train_model = "cortex.cmdline.train_cortex_model:main"
@@ -19,11 +42,6 @@ cortex_generate_designs = "cortex.cmdline.generate_designs:main"
 requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools.dynamic]
-dependencies = {file = ["requirements.in"]}
-optional-dependencies = {dev = {file = ["requirements-dev.in"]}}
-readme = {file = "README.rst"}
-
 [tool.setuptools.packages.find]
 include = ["cortex*"]
 
@@ -39,6 +57,11 @@ fallback_version = "0.0.0"
 
 [tool.ruff]
 line-length = 120
+extend-exclude = [
+  "*.ipynb",
+  "**/torchinductor/**/*.py",
+  "notebooks",
+]
 
 [tool.ruff.lint]
 select = [
@@ -61,5 +84,14 @@ ignore = [
     "F401", # MODULE IMPORTED BUT UNUSED
 ]
 
-[tool.uv]
-cache-keys = [{file = "requirements.in"}, {file = "requirements-dev.in"}]
+[dependency-groups]
+dev = [
+    "ipykernel>=6.29.5",
+    "ipython>=8.34.0",
+    "pre-commit>=4.2.0",
+    "pytest>=8.3.5",
+    "pytest-cov>=6.1.0",
+    "sphinx>=8.1.3",
+    "sphinx-autoapi>=3.6.0",
+    "sphinx-rtd-theme>=3.0.2",
+]