update CI nightly tests

.github/workflows/nightly.yml

@@ -20,16 +20,12 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-        architecture: 'x64'
-
-    - name: Install dependencies
-      run: |
-        pip install poetry
-        poetry install --extras all --with examples --with dev
+      run: uv python install ${{ matrix.python-version }}
 
     - name: Check if git is dirty
       run: |

_tooling/publish.sh

@@ -14,8 +14,8 @@ for PKG in {cluster_tools,webknossos}/pyproject.toml; do
     echo "__version__ = '$PKG_VERSION'" > ./"$PKG"/version.py
 
     poetry version "$PKG_VERSION"
-    # replace all relative path dependencies with the current version:
-    sed -i 's/\(.*\) = .* path \= \"\.\..*/\1 = "'"$PKG_VERSION"'"/g' pyproject.toml
+    # replace relative path dependencies (i.e. cluster-tools) with the current version:
+    sed -i 's/"cluster-tools"/"cluster-tools=='"${PKG_VERSION}"'"/g' pyproject.toml    
 
     uv build
     uv publish

webknossos/Dockerfile

@@ -1,8 +1,9 @@
-FROM python:3.10
+FROM python:3.12
 
-COPY requirements.txt /
+# Remove once cluster_tools is updated to uv as well
+RUN pip install poetry==1.8 
 
-RUN pip install -r /requirements.txt
+COPY --from=ghcr.io/astral-sh/uv:0.4.20 /uv /bin/uv
 
 RUN mkdir /webknossos
 COPY webknossos/webknossos /webknossos/webknossos
@@ -18,5 +19,6 @@ COPY cluster_tools/README.md /cluster_tools/
 
 WORKDIR /webknossos
 
+RUN uv venv --system-site-packages
 RUN uv sync --all-extras --frozen
 RUN poetry config virtualenvs.create false && poetry install --all-extras