uv upgrade (#779)

* migrate to uv

* remove TODO (won't work)

* update tests

* bump znh5md

.github/workflows/publish.yaml

@@ -10,9 +10,6 @@
 name: Publish Docker image
 
 on:
-  # push:
-  #     branches:
-  #         - dev
   release:
     types: [published]
 
@@ -49,11 +46,8 @@ 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
@@ -62,5 +56,5 @@ jobs:
         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/test.yaml

@@ -14,6 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
+          - "3.13"
           - "3.12"
           - "3.11"
           - "3.10"
@@ -37,29 +38,18 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      # - uses: oven-sh/setup-bun@v1
-      - 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: bun build install
-      #   run: |
-      #     cd app
-      #     bun install
-      #     bun vite build
       - name: Install package
         run: |
-          poetry install --no-interaction
+           uv sync --all-extras --dev
       - name: Pytest
         run: |
-          poetry run python --version
-          poetry run coverage run -m pytest -vv
-          poetry run coverage xml
+          uv run python --version
+          uv run coverage run -m pytest -vv
+          uv run coverage xml
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         env:

.python-version

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

pyproject.toml

@@ -1,65 +1,52 @@
-[tool.poetry]
+[project]
 name = "zndraw"
-version = "0.5.8"
+version = "0.5.8a1"
 description = "Display and Edit Molecular Structures and Trajectories in the Browser."
-authors = ["zincwarecode <[email protected]>"]
-license = "License :: OSI Approved :: Eclipse Public License 2.0 (EPL-2.0)"
+authors = [
+    { name = "Fabian Zills", email = "[email protected]" },
+]
+classifiers = ["License :: OSI Approved :: Eclipse Public License 2.0 (EPL-2.0)"]
 readme = "README.md"
-include = ["zndraw/templates/**/*", "zndraw_app/**/*"]
-
-[tool.poetry.dependencies]
-python = "^3.10"
-ase = "^3"
-typer = {extras = ["all"], version = "^0.13"}
-flask = "^3"
-tqdm = "^4"
-flask-socketio = "^5"
-networkx = "^3"
-pydantic = "^2"
-python-socketio = {extras = ["client"], version = "^5.11"}
-plotly = "^5"
-pandas = "^2"
-celery = "^5"
-sqlalchemy = "^2"
-redis = "^5"
-splines = "^0.3"
-znsocket = "^0.2.7"
-znjson = "^0.2.4"
-eventlet = "^0.38"
-
-
-[tool.poetry.group.dev.dependencies]
-eventlet = "^0"
-pre-commit = "^3"
-pytest = "^7"
-coverage = "^7"
-ruff = "^0.1"
-ipykernel = "^6.29.4"
-mdanalysis = {version = "^2"}
-tidynamics = {version = "^1"}
-rdkit2ase = {version = "^0.1"}
-zntrack = {version = "^0.8"}
-znh5md = {version = "^0.4"}
+requires-python = ">=3.10"
+dependencies = [
+    "ase>=3.24.0",
+    "celery>=5.4.0",
+    "eventlet>=0.39.0",
+    "flask>=3.1.0",
+    "flask-socketio>=5.5.1",
+    "networkx>=3.4.2",
+    "pandas>=2.2.3",
+    "plotly>=6.0.0",
+    "pydantic>=2.10.6",
+    "python-socketio[client]>=5.12.1",
+    "redis>=5.2.1",
+    "splines>=0.3.2",
+    "sqlalchemy>=2.0.38",
+    "tqdm>=4.67.1",
+    "typer>=0.15.1",
+    "znjson>=0.2.6",
+    "znsocket>=0.2.8",
+]
 
+[project.urls]
+Repository = "https://github.com/zincware/ZnDraw"
+Releases = "https://github.com/zincware/ZnDraw/releases"
+Discord = "https://discord.gg/7ncfwhsnm4"
+Documentation = "https://zndraw.readthedocs.io/"
 
 
+[project.scripts]
+zndraw = 'zndraw_app.cli:cli'
 
-[tool.poetry.group.docs.dependencies]
-sphinx = "^8.1.3"
-furo = "^2024.8.6"
-nbsphinx = "^0.9.5"
-sphinx-copybutton = "^0.5.2"
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.poetry.scripts]
-zndraw = 'zndraw_app.cli:cli'
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
-
-[tool.poetry.urls]
-repository = "https://github.com/zincware/ZnDraw"
+[tool.hatch.build.targets.sdist]
+exclude = [
+  "/app",
+]
 
 [tool.ruff]
 line-length = 90
@@ -73,3 +60,20 @@ addopts = "-m 'not chrome'"
 
 [tool.codespell]
 skip = "*.svg,*.lock"
+
+[dependency-groups]
+dev = [
+    "coverage>=7.6.10",
+    "mdanalysis>=2.8.0",
+    "pytest>=8.3.4",
+    "rdkit2ase>=0.1.4",
+    "tidynamics>=1.1.2",
+    "znh5md>=0.4.4",
+    "zntrack>=0.8.2",
+]
+docs = [
+    "furo>=2024.8.6",
+    "nbsphinx>=0.9.6",
+    "sphinx>=8.1.3",
+    "sphinx-copybutton>=0.5.2",
+]