ENH: Install PyImageJ dependencies in CI

spatial-image · May 5, 2022 · ae28672 · ae28672
1 parent 30151aa
commit ae28672
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git 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
@@ -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"
    ]
   },
   {