From 892d031b92d91bb4c4e3878000a3e9b386606745 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Apr 2025 21:06:49 +0000 Subject: [PATCH 1/8] specify deps in pyproject.toml and add uv.lock --- pyproject.toml | 41 +- requirements-dev.in | 7 - requirements.in | 19 - requirements.txt | 141 -- uv.lock | 3234 +++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 3267 insertions(+), 175 deletions(-) delete mode 100644 requirements-dev.in delete mode 100644 requirements.in delete mode 100644 requirements.txt create mode 100644 uv.lock diff --git a/pyproject.toml b/pyproject.toml index fe6edcc..00ee9f8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,7 @@ [project] name = "pytorch-cortex" -dynamic = ["version", "readme", "dependencies", "optional-dependencies"] +dynamic = ["version"] +readme = "README.rst" description = "A modular architecture for deep learning systems." authors = [{name = "Samuel Stanton", email = "stanton.samuel@gene.com"}] classifiers=[ @@ -8,6 +9,27 @@ classifiers=[ "Intended Audience :: Science/Research", "Programming Language :: Python :: 3", ] +requires-python = ">=3.10" +dependencies = [ + "botorch>=0.9.4", + "cachetools>=5.5.2", + "edlib>=1.3.9.post1", + "hydra-core>=1.2.0", + "lightning>=2.0", + "numpy>=2.2.4", + "omegaconf>=2.3.0", + "pandas>=2.2.3", + "pyarrow>=19.0.1", + "pytorch-warmup>=0.2.0", + "s3fs>=2025.3.2", + "tabulate>=0.9.0", + "torch>=2.6.0", + "torchvision>=0.21.0", + "tqdm>=4.67.1", + "transformers>=4.50.3", + "universal-pathlib>=0.2.6", + "wandb>=0.19.9", +] [project.scripts] cortex_train_model = "cortex.cmdline.train_cortex_model:main" @@ -19,11 +41,6 @@ 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*"] @@ -61,5 +78,13 @@ 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", + "pytest>=8.3.5", + "pytest-cov>=6.1.0", + "sphinx>=8.1.3", + "sphinx-autoapi>=3.6.0", + "sphinx-rtd-theme>=3.0.2", +] diff --git a/requirements-dev.in b/requirements-dev.in deleted file mode 100644 index 253e028..0000000 --- a/requirements-dev.in +++ /dev/null @@ -1,7 +0,0 @@ -pytest -pip-tools -pytest-cov -pre-commit -sphinx -sphinx-rtd-theme -sphinx-autoapi diff --git a/requirements.in b/requirements.in deleted file mode 100644 index 26238a0..0000000 --- a/requirements.in +++ /dev/null @@ -1,19 +0,0 @@ -boto3 -botorch >= 0.9.4 -cachetools -edlib -hydra-core >= 1.2.0 -lightning>=2.0 -numpy -omegaconf -pandas -pyarrow -pytorch_warmup -s3fs -tabulate -torch -torchvision -transformers -tqdm 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2/8] pre-commit and lint --- .pre-commit-config.yaml | 9 +-- cortex/data/dataset/_data_frame_dataset.py | 4 +- cortex/model/elemental/_ddp_standardize.py | 2 +- pyproject.toml | 6 ++ tests/cortex/metrics/test_blosum.py | 2 +- uv.lock | 68 ++++++++++++++++++++++ 6 files changed, 82 insertions(+), 9 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 265f8db..e0b62e3 100644 --- a/.pre-commit-config.yaml +++ b/.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 diff --git a/cortex/data/dataset/_data_frame_dataset.py b/cortex/data/dataset/_data_frame_dataset.py index dbb7563..c014222 100644 --- a/cortex/data/dataset/_data_frame_dataset.py +++ b/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: diff --git a/cortex/model/elemental/_ddp_standardize.py b/cortex/model/elemental/_ddp_standardize.py index 7797941..cad252d 100644 --- a/cortex/model/elemental/_ddp_standardize.py +++ b/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. 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.github/workflows/ci.yml create mode 100644 .github/workflows/pre-commit.yml create mode 100644 .github/workflows/unit.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index fa0a52b..0000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,50 +0,0 @@ -name: CI - -on: - pull_request: - push: - branches: - - main - -jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - with: - python-version: "3.x" - cache: 'pip' - - uses: pre-commit/action@v3.0.0 - - linux_checks: - - runs-on: ubuntu-latest - strategy: - matrix: - python-version: - - "3.10" - fail-fast: false - steps: - - - uses: actions/checkout@v4 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v4 - with: - python-version: ${{ matrix.python-version }} - cache: 'pip' - - - name: Install test requirements - shell: bash -l {0} - run: | - set -vxeuo pipefail - python -m pip install -r requirements.txt - python -m pip install .[dev] - python -m pip list - - - name: Test with pytest - shell: bash -l {0} - run: | - set -vxeuo pipefail - pytest -v --cov=cortex diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml new file mode 100644 index 0000000..2b11178 --- /dev/null +++ b/.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 diff --git a/.github/workflows/unit.yml b/.github/workflows/unit.yml new file mode 100644 index 0000000..04fac24 --- /dev/null +++ b/.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 From aeaf9b1635711861d0c54f017d60077fcca39040 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Apr 2025 21:20:16 +0000 Subject: [PATCH 4/8] add missing dep --- pyproject.toml | 1 + uv.lock | 28 ++++++++++++++++++++++++++++ 2 files changed, 29 insertions(+) diff --git a/pyproject.toml b/pyproject.toml index 768fe12..68b86e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,6 +11,7 @@ classifiers=[ ] requires-python = ">=3.10" dependencies = [ + "boto3>=1.37.1", "botorch>=0.9.4", "cachetools>=5.5.2", "edlib>=1.3.9.post1", diff --git a/uv.lock b/uv.lock index c262721..c080469 100644 --- a/uv.lock +++ b/uv.lock @@ -221,6 +221,20 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/b7/b8/3fe70c75fe32afc4bb507f75563d39bc5642255d1d94f1f23604725780bf/babel-2.17.0-py3-none-any.whl", hash = "sha256:4d0b53093fdfb4b21c92b5213dba5a1b23885afa8383709427046b21c366e5f2", size = 10182537 }, ] +[[package]] +name = "boto3" +version = "1.37.1" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "botocore" }, + { name = "jmespath" }, + { name = "s3transfer" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/21/8c/c2af03daafaacea1db1823d23073facffa75818b61d376c3be77dd297ae8/boto3-1.37.1.tar.gz", hash = "sha256:96d18f7feb0c1fcb95f8837b74b6c8880e1b4e35ce5f8a8f8cb243a090c278ed", size = 111175 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/63/ec/e722c53c9dc41e8df094587c32e19409bace8b43b5eb31fe3536ca57a38b/boto3-1.37.1-py3-none-any.whl", hash = "sha256:4320441f904435a1b85e6ecb81793192e522c737cc9ed6566014e29f0a11cb22", size = 139338 }, +] + [[package]] name = "botocore" version = "1.37.1" @@ -2018,6 +2032,7 @@ wheels = [ name = "pytorch-cortex" source = { editable = "." } dependencies = [ + { name = "boto3" }, { name = "botorch" }, { name = "cachetools" }, { name = "edlib" }, @@ -2054,6 +2069,7 @@ dev = [ [package.metadata] requires-dist = [ + { name = "boto3", specifier = ">=1.37.1" }, { name = "botorch", specifier = ">=0.9.4" }, { name = "cachetools", specifier = ">=5.5.2" }, { name = "edlib", specifier = ">=1.3.9.post1" }, @@ -2369,6 +2385,18 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/66/e1/4db0388df5655de92ce5f9b60d2bef220a58dde130e0453e5433c579986e/s3fs-2025.3.2-py3-none-any.whl", hash = "sha256:81eae3f37b4b04bcc08845d7bcc607c6ca45878813ef7e6a28d77b2688417130", size = 30485 }, ] +[[package]] +name = "s3transfer" +version = "0.11.3" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "botocore" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/39/24/1390172471d569e281fcfd29b92f2f73774e95972c965d14b6c802ff2352/s3transfer-0.11.3.tar.gz", hash = "sha256:edae4977e3a122445660c7c114bba949f9d191bae3b34a096f18a1c8c354527a", size = 148042 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/e4/81/48c41b554a54d75d4407740abb60e3a102ae416284df04d1dbdcbe3dbf24/s3transfer-0.11.3-py3-none-any.whl", hash = "sha256:ca855bdeb885174b5ffa95b9913622459d4ad8e331fc98eb01e6d5eb6a30655d", size = 84246 }, +] + [[package]] name = "safetensors" version = "0.5.3" From cd6f20af9daa70a5cdaeb49468a58587d634b7a7 Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Apr 2025 21:23:36 +0000 Subject: [PATCH 5/8] update readme --- README.md | 20 ++++---------------- 1 file changed, 4 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index fb6a5a2..9dfc70c 100644 --- a/README.md +++ b/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 ` 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 From 140ed958a337b373570f5842719f505f5815f61f Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Apr 2025 21:23:50 +0000 Subject: [PATCH 6/8] remove setup.cfg --- setup.cfg | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 setup.cfg diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index d9675f2..0000000 --- a/setup.cfg +++ /dev/null @@ -1,8 +0,0 @@ -[flake8] -ignore = E203, E266, E501, W503, F403, F401, W605, E231, C417, B950, B024, C408 -max-line-length = 120 -max-complexity = 18 -select = B,C,E,F,W,T4,B9 -exclude = - __init__.py, - .git From 682d5eccaa05354001f1eb44be6476ee1c9d73da Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Apr 2025 21:24:59 +0000 Subject: [PATCH 7/8] cleanup --- .gitignore | 2 ++ README.rst | 0 pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 1 deletion(-) delete mode 100644 README.rst diff --git a/.gitignore b/.gitignore index f8093a2..c339a42 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,5 @@ __pycache__ *.egg-info docs/build +temp +.coverage diff --git a/README.rst b/README.rst deleted file mode 100644 index e69de29..0000000 diff --git a/pyproject.toml b/pyproject.toml index 68b86e6..adf06b1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [project] name = "pytorch-cortex" dynamic = ["version"] -readme = "README.rst" +readme = "README.md" description = "A modular architecture for deep learning systems." authors = [{name = "Samuel Stanton", email = "stanton.samuel@gene.com"}] classifiers=[ From 5daaa9a566e60ac6e7618dd0f593b1a5ff2eb9dd Mon Sep 17 00:00:00 2001 From: Joseph Kleinhenz Date: Thu, 3 Apr 2025 21:32:51 +0000 Subject: [PATCH 8/8] relax some version bounds --- pyproject.toml | 10 +++++----- uv.lock | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index adf06b1..daa67bf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,17 +17,17 @@ dependencies = [ "edlib>=1.3.9.post1", "hydra-core>=1.2.0", "lightning>=2.0", - "numpy>=2.2.4", + "numpy>=2", "omegaconf>=2.3.0", - "pandas>=2.2.3", + "pandas>=2", "pyarrow>=19.0.1", "pytorch-warmup>=0.2.0", "s3fs>=2025.3.2", "tabulate>=0.9.0", - "torch>=2.6.0", - "torchvision>=0.21.0", + "torch>=2.5.1", + "torchvision", "tqdm>=4.67.1", - "transformers>=4.50.3", + "transformers>=4.24.0", "universal-pathlib>=0.2.6", "wandb>=0.19.9", ] diff --git a/uv.lock b/uv.lock index c080469..c2de539 100644 --- a/uv.lock +++ b/uv.lock @@ -2075,17 +2075,17 @@ requires-dist = [ { name = "edlib", specifier = ">=1.3.9.post1" }, { name = "hydra-core", specifier = ">=1.2.0" }, { name = "lightning", specifier = ">=2.0" }, - { name = "numpy", specifier = ">=2.2.4" }, + { name = "numpy", specifier = ">=2" }, { name = "omegaconf", specifier = ">=2.3.0" }, - { name = "pandas", specifier = ">=2.2.3" }, + { name = "pandas", specifier = ">=2" }, { name = "pyarrow", specifier = ">=19.0.1" }, { name = "pytorch-warmup", specifier = ">=0.2.0" }, { name = "s3fs", specifier = ">=2025.3.2" }, { name = "tabulate", specifier = ">=0.9.0" }, - { name = "torch", specifier = ">=2.6.0" }, - { name = "torchvision", specifier = ">=0.21.0" }, + { name = "torch", specifier = ">=2.5.1" }, + { name = "torchvision" }, { name = "tqdm", specifier = ">=4.67.1" }, - { name = "transformers", specifier = ">=4.50.3" }, + { name = "transformers", specifier = ">=4.24.0" }, { name = "universal-pathlib", specifier = ">=0.2.6" }, { name = "wandb", specifier = ">=0.19.9" }, ]