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hadimhadim
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Merge pull request #46 from hadim/polyglot
Turn the Scijava kernel into a polyglot kernel
2 parents da112ac + 9068f17 commit a3c34b9

24 files changed

+286
-327
lines changed

‎.ci/test.sh

+13-13
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@@ -26,23 +26,23 @@ export IJ_PATH="$HOME/Fiji.app"
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export IJ_LAUNCHER="$IJ_PATH/ImageJ-linux64"
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JAVA_COMMAND_CLASS="org.scijava.jupyter.commands.InstallScijavaKernel"
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$IJ_LAUNCHER --ij2 --headless --run $JAVA_COMMAND_CLASS "logLevel=\"info\",pythonBinaryPath=\"$(which python)\",installAllKernels=true"
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$IJ_LAUNCHER --ij2 --headless --run $JAVA_COMMAND_CLASS "logLevel=\"info\",pythonBinaryPath=\"$(which python)\""
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jupyter kernelspec list
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# Now run some notebooks
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-python" "$TRAVIS_BUILD_DIR/notebooks/Welcome.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-groovy" "$TRAVIS_BUILD_DIR/notebooks/General.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-python" "$TRAVIS_BUILD_DIR/notebooks/Rich Output.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-python" "$TRAVIS_BUILD_DIR/notebooks/On-The-Fly Grabbing.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-groovy" "$TRAVIS_BUILD_DIR/notebooks/ImageJ.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-groovy" "$TRAVIS_BUILD_DIR/notebooks/Scijava.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-python" "$TRAVIS_BUILD_DIR/notebooks/languages/Python.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-groovy" "$TRAVIS_BUILD_DIR/notebooks/languages/Groovy.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-scala" "$TRAVIS_BUILD_DIR/notebooks/languages/Scala.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-clojure" "$TRAVIS_BUILD_DIR/notebooks/languages/Clojure.ipynb"
46-
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-beanshell" "$TRAVIS_BUILD_DIR/notebooks/languages/Beanshell.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-javascript" "$TRAVIS_BUILD_DIR/notebooks/languages/Javascript.ipynb"
36+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/Welcome.ipynb"
37+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/General.ipynb"
38+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/Rich Output.ipynb"
39+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/On-The-Fly Grabbing.ipynb"
40+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/ImageJ.ipynb"
41+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/Scijava.ipynb"
42+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/languages/Python.ipynb"
43+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/languages/Groovy.ipynb"
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#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/languages/Scala.ipynb"
45+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/languages/Clojure.ipynb"
46+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/languages/Beanshell.ipynb"
47+
#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava" "$TRAVIS_BUILD_DIR/notebooks/languages/Javascript.ipynb"
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‎README.md

+3-4
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@@ -45,7 +45,7 @@ conda create --name java_env scijava-jupyter-kernel
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# Activate the `java_env` environment
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source install java_env
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# Check the kernels have been installed
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# Check the kernel has been installed
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jupyter kernelspec list
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# Launch your favorite Jupyter client
@@ -63,18 +63,17 @@ jupyter lab
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- Drop it in your Fiji plugins directory.
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- Start Fiji and launch `Analyze > Jupyter Kernel > Install Scijava Kernel`.
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- Set the path to your Python binary.
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- Choose a language (for example `jython` or `groovy`) or you can choose to install all the available languages.
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- Choose a log level.
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- Check the kernels have been installed with : `jupyter kernelspec list`.
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- Check the kernel has been installed with : `jupyter kernelspec list`.
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- Launch `jupyter notebook` or `jupyter lab` and **select the kernel you want in the kernel list**.
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![Scijava Jupyter Kernel Installation](teaser.gif)
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## Development
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- [CI with Travis](https://travis-ci.org/hadim/scijava-jupyter-kernel) makes sure the project builds without errors for each new commit.
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- All the [notebook examples](./notebooks) are executed by the kernel during CI with [nbconvert](http://nbconvert.readthedocs.io/en/latest/execute_api.html).
76+
- All the [notebook examples](./notebooks) are executed by the kernel during CI with [nbconvert](http://nbconvert.readthedocs.io/en/latest/execute_api.html) (currently not working).
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- A [Conda package](https://github.com/conda-forge/scijava-jupyter-kernel-feedstock) is built for each new release.
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## License

‎notebooks/General.ipynb

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@@ -17,7 +17,7 @@
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}
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],
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"source": [
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"// TODO"
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"// Highlight here the polyglot features"
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]
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},
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{
@@ -37,13 +37,13 @@
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"name": "scijava-groovy"
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},
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"language_info": {
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"codemirror_mode": "Groovy",
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"file_extension": "[groovy]",
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"mimetype": "[]",
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"name": "Groovy",
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"codemirror_mode": "groovy",
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"file_extension": "",
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"mimetype": "",
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"name": "scijava",
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"nbconverter_exporter": "",
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"pygments_lexer": "Groovy",
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"version": "1.5.6"
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"pygments_lexer": "groovy",
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"version": "1.0"
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}
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},
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"nbformat": 4,

‎notebooks/ImageJ.ipynb

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@@ -17,6 +17,7 @@
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}
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],
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"source": [
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"#!groovy\n",
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"// @ImageJ ij\n",
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"// @NotebookService nb"
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]

‎notebooks/On-The-Fly Grabbing.ipynb

+7-6
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@@ -8,6 +8,7 @@
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},
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"outputs": [],
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"source": [
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"#!python\n",
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"# TODO"
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]
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},
@@ -28,13 +29,13 @@
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"name": "scijava-python"
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},
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"language_info": {
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"codemirror_mode": "Python",
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"file_extension": "[py]",
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"mimetype": "[text/python, application/python, text/x-python, application/x-python]",
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"name": "Python",
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"codemirror_mode": "groovy",
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"file_extension": "",
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"mimetype": "",
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"name": "scijava",
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"nbconverter_exporter": "",
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"pygments_lexer": "Python",
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"version": "2.7"
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"pygments_lexer": "groovy",
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"version": "1.0"
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}
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},
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"nbformat": 4,

‎notebooks/Rich Output.ipynb

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@@ -17,6 +17,7 @@
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}
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],
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"source": [
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"#!python\n",
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"# @NotebookService nb"
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]
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},
@@ -282,13 +283,13 @@
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"name": "scijava-python"
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},
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"language_info": {
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"codemirror_mode": "Python",
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"file_extension": "[py]",
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"mimetype": "[text/python, application/python, text/x-python, application/x-python]",
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"name": "Python",
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"codemirror_mode": "groovy",
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"file_extension": "",
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"mimetype": "",
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"name": "scijava",
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"nbconverter_exporter": "",
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"pygments_lexer": "Python",
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"version": "2.7"
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"pygments_lexer": "groovy",
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"version": "1.0"
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}
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},
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"nbformat": 4,

‎notebooks/Scijava.ipynb

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@@ -26,6 +26,7 @@
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}
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],
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"source": [
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"#!groovy\n",
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"// @ImageJ ij\n",
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"\n",
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"// The plugin service manages the available plugins (see \"Plugins\" below).\n",
@@ -52,7 +53,7 @@
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{
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"data": {
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"text/plain": [
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"java.util.concurrent.FutureTask@2915ef5b"
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"java.util.concurrent.FutureTask@cae6b0b"
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]
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},
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"execution_count": 2,
@@ -105,7 +106,7 @@
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{
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"data": {
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"text/plain": [
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"java.util.concurrent.FutureTask@72e027c6"
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"java.util.concurrent.FutureTask@abe9271"
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]
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},
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"execution_count": 3,
@@ -161,7 +162,7 @@
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"Module count: 1102\n",
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"Service count: 96\n",
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"SciJava version: 2.62.1\n",
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"Where is SciJava? file:/home/hadim/local/Fiji.app/jars/scijava-common-2.62.1.jar\n"
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"Where is SciJava? file:/opt/local/Fiji.app/jars/scijava-common-2.62.1.jar\n"
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]
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},
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{
@@ -200,13 +201,13 @@
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"name": "scijava-groovy"
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},
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"language_info": {
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"codemirror_mode": "Groovy",
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"file_extension": "[groovy]",
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"mimetype": "[]",
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"name": "Groovy",
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"codemirror_mode": "groovy",
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"file_extension": "",
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"mimetype": "",
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"name": "scijava",
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"nbconverter_exporter": "",
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"pygments_lexer": "Groovy",
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"version": "1.5.6"
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"pygments_lexer": "groovy",
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"version": "1.0"
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}
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},
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"nbformat": 4,

‎notebooks/Welcome.ipynb

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"name": "scijava-python"
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},
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"language_info": {
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"codemirror_mode": "Python",
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"file_extension": "[py]",
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"mimetype": "[text/python, application/python, text/x-python, application/x-python]",
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"name": "Python",
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"codemirror_mode": "groovy",
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"file_extension": "",
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"mimetype": "",
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"name": "scijava",
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"nbconverter_exporter": "",
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"pygments_lexer": "Python",
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"version": "2.7"
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"pygments_lexer": "groovy",
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"version": "1.0"
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}
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},
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"nbformat": 4,

‎notebooks/languages/Beanshell.ipynb

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"cells": [
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{
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"cell_type": "code",
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"execution_count": 2,
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"execution_count": 1,
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"metadata": {},
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"outputs": [
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{
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"null"
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]
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},
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"execution_count": 2,
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"execution_count": 1,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"#!Beanshell\n",
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"printBanner();"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"1493250700406\n",
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"1493774310652\n",
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"0\n",
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"1\n",
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"2\n",
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"null"
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]
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},
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"execution_count": 5,
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"execution_count": 2,
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"metadata": {},
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"output_type": "execute_result"
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}
@@ -67,22 +68,31 @@
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"for (int i=0; i<5; i++)\n",
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" print(i);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"collapsed": true
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},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Scijava - BeanShell",
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"language": "BeanShell",
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"name": "scijava-beanshell"
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"display_name": "Scijava",
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"language": "groovy",
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"name": "scijava"
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},
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"language_info": {
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"codemirror_mode": "BeanShell",
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"file_extension": "[bsh, bs]",
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"mimetype": "[]",
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"name": "BeanShell",
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"codemirror_mode": "groovy",
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"file_extension": "",
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"mimetype": "",
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"name": "scijava",
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"nbconverter_exporter": "",
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"pygments_lexer": "BeanShell",
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"version": "0.3.1"
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"pygments_lexer": "groovy",
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"version": "1.0"
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}
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},
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"nbformat": 4,

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