refactor: poetry to UV (#36)

Author: jannisborn

.github/workflows/ci.yml

@@ -1,4 +1,5 @@
 name: CI
+
 on:
   push:
     branches: [main]
@@ -10,27 +11,25 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v6
+
+      - name: Install uv and Python 3.10
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: "3.10"
-      - name: Install dependencies
-        run: |
-         pip install --upgrade pip
-         pip install poetry
-         poetry install -v
-      
+          enable-cache: true
+
+      - name: Sync dependencies
+        run: uv sync --locked
+
       - name: Run isort
-        run: poetry run isort --profile=black --check-only .
+        run: uv run isort --profile=black --check-only .
 
       - name: Run black
-        run: poetry run black --check .
+        run: uv run black --check .
 
       - name: Check formatting
-        run: |
-         poetry run ruff check .
+        run: uv run ruff check .
 
       - name: Run tests
-        run: |
-         poetry run pytest -sv cmonge
+        run: uv run pytest -sv cmonge

.github/workflows/pypi.yml

@@ -10,35 +10,22 @@ jobs:
     if: ${{ !github.event.release.prerelease }}
 
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v6
 
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      - name: Install uv and Python 3.10
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: '3.10'
-
-      - name: Install Poetry
-        run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
-
-      - name: Configure Poetry
-        run: |
-          poetry config virtualenvs.create false
-
-      - name: Install Dependencies
-        run: |
-          poetry install --no-interaction --no-ansi
+          python-version: "3.10"
 
       - name: Build Package
-        run: |
-          poetry build
+        run: uv build
 
       - name: Publish to PyPI
         env:
-          TWINE_USERNAME: __token__
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          poetry publish --username $TWINE_USERNAME --password $TWINE_PASSWORD
+          UV_PUBLISH_TOKEN: ${{ secrets.PYPI_PASSWORD }}
+        run: uv publish

.gitignore

@@ -91,6 +91,7 @@ celerybeat-schedule
 # Environments
 .env
 .venv
+.uv-cache/
 env/
 venv/
 ENV/

README.md

@@ -21,7 +21,7 @@
 An extension of the [Monge Gap](https://proceedings.mlr.press/v202/uscidda23a.html), an approach to estimate transport maps conditionally on arbitrary context vectors. It is based on a two-step training procedure combining an encoder-decoder architecture with an OT estimator. The model is applied to [4i](https://pubmed.ncbi.nlm.nih.gov/30072512/) and [scRNA-seq](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7289078/) datasets.
 
 ## Systems and software requirements
-Software package requirements and version information can be found in `requirements.txt` and/or the `pyproject.toml`. This package has been tested on Python versions 3.10 and 3.11. 
+Software package requirements and version information are defined in `pyproject.toml` and locked in `uv.lock`. This package has been tested on Python versions 3.10 and 3.11.
 Hardware requirements enough memory (RAM) to process the data and batches. GPU is not needed but does accelerate computation. This software has been tested on HPCs and local machines (iOS). 
 
 ## Installation from PyPI
@@ -33,18 +33,17 @@ pip install cmonge
 which should take about two minutes on a laptop.
 
 ## Development setup & installation
-The package environment is managed by [poetry](https://python-poetry.org/docs/managing-environments/). 
+The package environment is managed by [uv](https://docs.astral.sh/uv/).
 ```sh
-pip install poetry
-git clone git@github.com:AI4SCR/conditional-monge.git
-cd cmonge
-poetry install -v
+curl -LsSf https://astral.sh/uv/install.sh | sh
+git clone https://github.com/AI4SCR/conditional-monge.git
+cd conditional-monge
+uv sync --frozen
 ```
 
 If the installation was successful you can run the tests using pytest
 ```sh
-poetry shell # activate env
-pytest
+uv run pytest
 ```
 
 ## Data

poetry.lock

@@ -1,18 +1,26 @@
-[tool.poetry]
+[build-system]
+requires = ["hatchling>=1.27.0"]
+build-backend = "hatchling.build"
+
+[project]
 name = "cmonge"
 version = "0.1.3"
 description = "Extension of the Monge Gap to learn conditional optimal transport maps"
-authors = ["Alice Driessen <adr@zurich.ibm.com>", "Benedek Harsanyi <hben.0204@gmail.com>", "Jannis Born <jab@zurich.ibm.com>"]
 readme = "README.md"
+requires-python = ">=3.10,<3.12"
+license = { file = "LICENSE" }
+authors = [
+    { name = "Alice Driessen", email = "adr@zurich.ibm.com" },
+    { name = "Benedek Harsanyi", email = "hben.0204@gmail.com" },
+    { name = "Jannis Born", email = "jab@zurich.ibm.com" },
+]
 keywords = [
     "Machine Learning",
     "Optimal Transport",
     "Neural OT",
     "Monge Gap",
-    "Conditional Distribution Learning"
+    "Conditional Distribution Learning",
 ]
-homepage = "https://github.com/AI4SCR/conditional-monge"
-repository = "https://github.com/AI4SCR/conditional-monge"
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
@@ -21,53 +29,57 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
-    "Topic :: Scientific/Engineering :: Artificial Intelligence"
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+dependencies = [
+    "anndata>=0.10.5.post1,<0.11",
+    "chex>=0.1.85,<0.2",
+    "dotmap>=1.3.30,<2",
+    "flax>=0.10.2,<0.11",
+    "jax>=0.4.36,<0.5",
+    "jaxlib>=0.4.36,<0.5",
+    "loguru>=0.7.2,<0.8",
+    "optax>=0.2.4,<0.3",
+    "optuna>=3.5.0,<4",
+    "ott-jax>=0.5.0,<0.6",
+    "pandas>=2.0.0,<3",
+    "pyyaml>=6.0",
+    "rdkit>=2023.9.5,<2024",
+    "scanpy>=1.9.8,<2",
+    "scikit-learn>=1.4.0,<2",
+    "scipy==1.12.0",
+    "seaborn>=0.13.2,<0.14",
+    "typer>=0.9.0,<1",
+    "umap-learn>=0.5.5,<0.6",
 ]
 
+[project.urls]
+Homepage = "https://github.com/AI4SCR/conditional-monge"
+Repository = "https://github.com/AI4SCR/conditional-monge"
 
-[tool.poetry.group.dev.dependencies]
-ruff = "*"
-pytest = "*"
-pre-commit = "*"
-
-[tool.poetry.dependencies]
-python = ">=3.10,<3.12"
-flax = "^0.10.2"
-optax = "^0.2.4"
-ott-jax = "^0.5.0"
-scikit-learn = "^1.4.0"
-typer = "^0.9.0"
-loguru = "^0.7.2"
-optuna = "^3.5.0"
-pandas = "^2.0.0"
-seaborn = "^0.13.2"
-dotmap = "^1.3.30"
-umap-learn = "^0.5.5"
-jaxlib = "^0.4.36"
-anndata = "^0.10.5.post1"
-scanpy = "^1.9.8"
-chex = "^0.1.85"
-rdkit = "^2023.9.5"
-jax = "^0.4.36"
-isort = "^5.13.2"
-black = "^24.4.2"
-ruff = "^0.5.4"
-types-pyyaml = "^6.0.12.20240311"
-scipy = "1.12.0"
-
-[[tool.poetry.source]]
-name = "jax"
-url = "https://storage.googleapis.com/jax-releases/jax_releases.html"
-priority = "primary"
+[dependency-groups]
+dev = [
+    "black>=24.4.2,<25",
+    "isort>=5.13.2,<6",
+    "pre-commit",
+    "pytest",
+    "ruff>=0.5.4,<0.6",
+    "types-pyyaml>=6.0.12.20240311",
+]
 
+[tool.hatch.build.targets.sdist]
+include = [
+    "/cmonge",
+    "/LICENSE",
+    "/README.md",
+    "/pyproject.toml",
+]
 
-[[tool.poetry.source]]
-name = "PyPI"
-priority = "primary"
+[tool.hatch.build.targets.wheel]
+packages = ["cmonge"]
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[tool.uv]
+find-links = ["https://storage.googleapis.com/jax-releases/jax_releases.html"]
 
 [tool.ruff]
 line-length = 88