diff --git a/.github/workflows/notebook-test.yml b/.github/workflows/notebook-test.yml index 06613e6..5c78d51 100644 --- a/.github/workflows/notebook-test.yml +++ b/.github/workflows/notebook-test.yml @@ -11,6 +11,16 @@ jobs: - uses: actions/setup-python@v3 with: python-version: '3.9' + - uses: conda-incubator/setup-miniconda@v2 + with: + python-version: '3.9' + mamba-version: "*" + channels: conda-forge,defaults + channel-priority: true + - name: Install PyImageJ example dependencies + shell: bash -l {0} + run: | + mamba install --yes -c conda-forge pyimagej openjdk=8 pip - name: Install test dependencies run: | python -m pip install --upgrade pip diff --git a/examples/ConvertPyImageJDataset.ipynb b/examples/ConvertPyImageJDataset.ipynb index 8f4c773..7351cf2 100644 --- a/examples/ConvertPyImageJDataset.ipynb +++ b/examples/ConvertPyImageJDataset.ipynb @@ -8,9 +8,9 @@ "outputs": [], "source": [ "import sys, os\n", - "!conda install --yes --prefix {sys.prefix} -c conda-forge pyimagej openjdk=8\n", + "!conda install --yes --prefix {sys.prefix} -c conda-forge openjdk=8\n", "os.environ['JAVA_HOME'] = os.sep.join(sys.executable.split(os.sep)[:-2] + ['jre'])\n", - "!{sys.executable} -m pip install spatial-image-multiscale matplotlib zarr" + "!{sys.executable} -m pip install spatial-image-multiscale matplotlib zarr pyimagej" ] }, {