From 0b769caeabed98e2a9c60180ed346db32a3dd5d4 Mon Sep 17 00:00:00 2001 From: Jannis Born Date: Sun, 29 Mar 2026 16:17:37 +0200 Subject: [PATCH] refactor: poetry to UV --- .github/workflows/ci.yml | 29 +- .github/workflows/pypi.yml | 33 +- .gitignore | 1 + README.md | 15 +- poetry.lock | 2850 ------------------------------------ pyproject.toml | 104 +- requirements.txt | 21 - uv.lock | 1840 +++++++++++++++++++++++ 8 files changed, 1930 insertions(+), 2963 deletions(-) delete mode 100644 poetry.lock delete mode 100644 requirements.txt create mode 100644 uv.lock diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9b2d29e..53c7a24 100644 --- a/.github/workflows/ci.yml +++ b/.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 diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml index 1d45980..2b6450b 100644 --- a/.github/workflows/pypi.yml +++ b/.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 diff --git a/.gitignore b/.gitignore index 4e2467e..afa2725 100644 --- a/.gitignore +++ b/.gitignore @@ -91,6 +91,7 @@ celerybeat-schedule # Environments .env .venv +.uv-cache/ env/ venv/ ENV/ diff --git a/README.md b/README.md index 01a4c4b..adc031a 100644 --- a/README.md +++ b/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 diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index 503e545..0000000 --- a/poetry.lock +++ /dev/null @@ -1,2850 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. - 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