migrate to uv (#164)

* migrate to `uv`

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

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

* move actions to uv

* bump version

---------

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

.github/workflows/benchmark.yaml

@@ -7,26 +7,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
+      - name: Install uv and set the python version
+        uses: astral-sh/setup-uv@v5
       - uses: actions/setup-node@v1
         with:
           node-version: '16'
       - uses: iterative/setup-cml@v1
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
       - name: Install package
         run: |
-          poetry install --no-interaction
+          uv sync --all-extras --dev
       - name: Run pytest
         run: |
-          poetry run python --version
-          poetry run pytest --benchmark-histogram benchmark -m benchmark
+          uv run python --version
+          uv run pytest --benchmark-histogram benchmark -m benchmark
       - name: Create report
         env:
           REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/publish.yaml

@@ -9,14 +9,15 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.12"
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: build frontend
+        run: |
+          npm install -g bun
+          cd app && bun install && bun vite build && cd ..
       - name: Publish
         env:
           PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
         run: |
-          poetry config pypi-token.pypi $PYPI_TOKEN
-          poetry publish --build
+          uv build
+          uv publish --token $PYPI_TOKEN

.github/workflows/pytest.yaml

@@ -15,6 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
+          - "3.13"
           - "3.12"
           - "3.11"
           - "3.10"
@@ -23,23 +24,18 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - 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 install --no-interaction
+          uv sync --all-extras --dev
       - name: Run pytest
         run: |
-          poetry run python --version
-          poetry run coverage run -m pytest
-          poetry run coverage lcov
+          uv run python --version
+          uv run coverage run -m pytest
+          uv run coverage lcov
       - name: Coveralls
         uses: coverallsapp/github-action@master
         with:

.python-version

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

pyproject.toml

@@ -1,42 +1,31 @@
-[tool.poetry]
+[project]
 name = "znh5md"
-version = "0.4.3"
+version = "0.4.4"
 description = "ASE Interface for the H5MD format."
-authors = ["zincwarecode <[email protected]>"]
+authors = [
+    { name = "Fabian Zills", email = "[email protected]" },
+]
 license = "Apache-2.0"
 readme = "README.md"
+requires-python = ">=3.10"
+dependencies = [
+    "ase>=3.24.0",
+    "h5py>=3.12.1",
+    "tqdm>=4.67.1",
+    "typer>=0.15.1",
+]
 
-[tool.poetry.dependencies]
-python = "^3.10"
-h5py = "^3"
-ase = "^3.23"
-tqdm = "^4"
-typer = {extras = ["all"], version = "^0"}
-
-[tool.poetry.group.dev.dependencies]
-pytest = "^7.2.0"
-pre-commit = "^2.20.0"
-ruff = "^0.4"
-mdanalysis = "^2.8"
-coverage = "^7.5.3"
-pyh5md = "^1.0.0"
-pytest-benchmark = {extras = ["histogram"], version = "^4.0.0"}
-networkx = "^3.3"
-rdkit2ase = "^0.1.4"
-
-
-[tool.poetry.group.benchmark.dependencies]
-pandas = "^2.2.2"
-chemfiles = "^0.10.4"
-mdtraj = "^1.10.0"
-
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
-[tool.poetry.scripts]
-znh5md = 'znh5md.cli:app'
+[project.scripts]
+znh5md = "znh5md.cli:app"
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[project.urls]
+Repository = "https://github.com/zincware/ZnH5MD"
+Releases = "https://github.com/zincware/ZnH5MD/releases"
+Discord = "https://discord.gg/7ncfwhsnm4"
 
 [tool.ruff.lint]
 select = ["E", "F", "N", "C", "I"]
@@ -50,5 +39,20 @@ skip = "poetry.lock,*.ipynb"
 [tool.pytest.ini_options]
 addopts = "-m 'not benchmark'"
 
-[tool.poetry.plugins."ase.ioformats"]
+[dependency-groups]
+dev = [
+    "chemfiles>=0.10.4",
+    "coverage>=7.6.10",
+    "mdanalysis>=2.8.0",
+    "mdtraj>=1.10.2",
+    "networkx>=3.4.2",
+    "numpy<2",
+    "pandas>=2.2.3",
+    "pyh5md>=1.0.0",
+    "pytest>=8.3.4",
+    "pytest-benchmark[histogram]>=5.1.0",
+    "rdkit2ase>=0.1.4",
+]
+
+[project.entry-points."ase.ioformats"]
 znh5md = "znh5md.ase_plugin:znh5md_format"

tests/test_timestep.py

@@ -1,5 +1,6 @@
+import warnings
+
 import ase.build
-import pytest
 
 import znh5md
 
@@ -69,7 +70,7 @@ def test_no_warn_correct(tmp_path):
     atoms = ase.build.molecule("H2O")
 
     # Ensure no warning is issued
-    with pytest.warns(None) as record:
+    # https://docs.pytest.org/en/latest/how-to/capture-warnings.html#additional-use-cases-of-warnings-in-tests
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
         io.append(atoms)
-
-    assert len(record) == 0

tests/test_znh5md.py

@@ -2,7 +2,7 @@
 
 
 def test_version():
-    assert znh5md.__version__ == "0.4.3"
+    assert znh5md.__version__ == "0.4.4"
 
 
 def test_creator(tmp_path):