fix run test-notebooks

Author: melonora

examples/ConvertPyImageJDataset.ipynb

@@ -9,7 +9,9 @@
    "source": [
     "import sys, os\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",
+    "# In case of being already installed through pixi it should not be set to this path.\n",
+    "if 'JAVA_HOME' not in os.environ:\n",
+    "    os.environ['JAVA_HOME'] = os.sep.join(sys.executable.split(os.sep)[:-2] + ['jre'])\n",
     "!{sys.executable} -m pip install multiscale-spatial-image matplotlib zarr pyimagej"
    ]
   },

pixi.lock

@@ -105,9 +105,10 @@ openjdk = "8.*"
 maven = ">=3.9.8,<3.10"
 jupyterlab = ">=4.2.4,<4.3"
 python = "3.10.*"
+jpype1 = ">=1.4.0,<1.5.0"
 
 [tool.pixi.feature.notebooks.tasks]
-init-imagej = { cmd = "python3 -c \"import imagej; ij = imagej.init('2.15.0'); print(ij.getVersion())\"", description = "Initialize the python imagej installation" }
+init-imagej = { cmd = "python -c \"import imagej; ij = imagej.init('2.15.0'); print(ij.getVersion())\"", description = "Initialize the python imagej installation" }
 test-notebooks = { cmd = "pytest --nbmake --nbmake-timeout=3000 examples/ConvertImageioImageResource.ipynb examples/ConvertITKImage.ipynb examples/ConvertPyImageJDataset.ipynb examples/ConvertTiffFile.ipynb examples/HelloMultiscaleSpatialImageWorld.ipynb", depends-on = ["init-imagej"], description = "Test the notebooks" }
 dev-notebooks = { cmd = "jupyter lab examples", description = "Start Jupyter Lab" }