replace poetry with uv (#872)

* add log message

* move to uv

* update lint sections

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update urls

* update tests to use uv

* updates

* add h5py

* build documentation test in CI

* update rtd to use uv

* add `dvc-s3`

* add sphinx

* add furo

* add docs packages

* install pandoc

* use sudo

* add publish action

* add missing sections

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/publish.yaml

@@ -0,0 +1,19 @@
+name: Release
+on:
+  release:
+    types:
+      - created
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Publish
+        env:
+          PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          uv build
+          uv publish --token $PYPI_TOKEN

.github/workflows/test.yaml

@@ -17,10 +17,10 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
+          - "3.13"
           - "3.12"
           - "3.11"
           - "3.10"
-          - 3.9
         os:
           - ubuntu-latest
 
@@ -49,31 +49,24 @@ jobs:
 
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-      - name: Install package
-        run: |
-          poetry run pip install aim
-          poetry install --no-interaction
+      - name: Install the project
+        run: uv sync --all-extras --dev
       - name: Setup git user
         run: |
           git config --global user.name "John Doe"
           git config --global user.email [email protected]
           git config --global init.defaultBranch "main"
       - name: Pytest
         run: |
-          poetry run python --version
-          poetry run coverage run -m pytest --benchmark-autosave -vv
-          poetry run coverage xml
-          poetry run coverage lcov
-          poetry run py.test-benchmark compare --csv=export.csv
+          uv run python --version
+          uv run coverage run -m pytest --benchmark-autosave -vv
+          uv run coverage xml
+          uv run coverage lcov
+          uv run py.test-benchmark compare --csv=export.csv
       - name: Coveralls
         uses: coverallsapp/github-action@master
         with:
@@ -110,25 +103,26 @@ jobs:
   #       run: |
   #         poetry run pytest --nbmake ./examples
 
-  # doctest:
-  #   runs-on: ubuntu-latest
-  #   needs: [ pytest, nbtest ]
-  #   steps:
-  #     - uses: actions/checkout@v2
-  #     - name: Set up Python 3.11
-  #       uses: actions/setup-python@v4
-  #       with:
-  #         python-version: "3.11"
-  #     - name: Install Poetry
-  #       uses: snok/install-poetry@v1
-  #       with:
-  #         virtualenvs-create: true
-  #         virtualenvs-in-project: true
-  #     - name: Install package
-  #       run: |
-  #         sudo apt install pandoc
-  #         poetry install --with=docs
-  #     - name: Build documentation
-  #       run: |
-  #         cd ./docs
-  #         poetry run make html
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install uv and set the python version
+      uses: astral-sh/setup-uv@v5
+      with:
+        python-version: "3.12"
+    - name: Install the project
+      run: uv sync --all-extras --dev
+    - name: Install pandoc
+      run: |
+        sudo apt update
+        sudo apt install pandoc
+    - name: Setup git user
+      run: |
+        git config --global user.name "John Doe"
+        git config --global user.email [email protected]
+        git config --global init.defaultBranch "main"
+    - name: Build documentation
+      run: |
+        cd docs
+        uv run make html

.python-version

@@ -0,0 +1 @@
+3.11

.readthedocs.yaml

@@ -10,16 +10,10 @@ build:
   tools:
     python: "3.11"
   jobs:
-    post_create_environment:
-      # Install poetry
-      # https://python-poetry.org/docs/#installing-manually
-      - pip install poetry
     post_install:
-      # Install dependencies with 'docs' dependency group
-      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
-      # VIRTUAL_ENV needs to be set manually for now.
-      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+      # see https://github.com/astral-sh/uv/issues/10074
+      - pip install uv
+      - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --all-extras --group docs --link-mode=copy
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

pyproject.toml

@@ -1,64 +1,53 @@
-[tool.poetry]
+[project]
 name = "zntrack"
 version = "0.8.2"
 description = "Create, Run and Benchmark DVC Pipelines in Python"
-authors = ["zincwarecode <[email protected]>"]
+authors = [
+    { name = "Fabian Zills", email = "[email protected]" },
+]
 license = "Apache-2.0"
 keywords=["data-science", "data-version-control", "machine-learning", "reproducibility", "collaboration"]
 readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "dvc>=3.59.0",
+    "pandas>=2.2.3",
+    "pyyaml>=6.0.2",
+    "tqdm>=4.67.1",
+    "typer>=0.15.1",
+    "znfields>=0.1.2",
+    "znflow>=0.2.4",
+    "znjson>=0.2.6",
+]
 
+[project.scripts]
+zntrack = 'zntrack.cli:app'
+
+[project.urls]
+Repository = "https://github.com/zincware/zntrack"
+Releases = "https://github.com/zincware/zntrack/releases"
+Documentation = "https://zntrack.readthedocs.io"
+
+[dependency-groups]
+dev = [
+    "coverage>=7.6.10",
+    "dvc-s3>=3.2.0",
+    "furo>=2024.8.6",
+    "h5py>=3.12.1",
+    "mlflow>=2.20.0",
+    "nbsphinx>=0.9.6",
+    "nbsphinx-link>=1.3.1",
+    "pytest>=8.3.4",
+    "pytest-benchmark>=5.1.0",
+    "sphinx>=8.1.3",
+    "sphinx-copybutton>=0.5.2",
+]
 
-[tool.poetry.dependencies]
-python = ">=3.10,<4"
-dvc = "^3.50"
-pyyaml = "^6"
-tqdm = "^4"
-
-znjson = "^0.2"
-znflow = "^0.2.3"
-typer = "^0.13"
-znfields = "^0.1.2"
-pandas = "^2"
-
-
-[tool.poetry.urls]
-documentation = "https://zntrack.readthedocs.io"
-repository = "https://github.com/zincware/ZnTrack"
-
-
-[tool.poetry.scripts]
-zntrack = "zntrack.cli:app"
-
-[tool.poetry.group.dev.dependencies]
-pytest-benchmark = "^3"
-pytest = "^7"
-numpy = "^1"
-matplotlib = "^3"
-ase = "^3"
-pre-commit = "^2"
-coverage = "^6"
-pytest-xdist = "^2"
-optuna = "^3"
-scikit-learn = "^1"
-nbmake = "^1"
-mlflow = "^2.16"
-dvc-s3 = "^3.2.0"
-h5py = "^3"
-
-[tool.poetry.group.notebook.dependencies]
-jupyterlab = "^3"
-
-[tool.poetry.group.docs.dependencies]
-furo = "^2022"
-sphinx-copybutton = "^0.5"
-sphinx = "^6"
-nbsphinx = "^0.8"
-nbsphinx-link = "^1"
 
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
 
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
 [tool.black]
 line-length = 90