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| 1 | +#!/bin/bash |
| 2 | +set -ex |
| 3 | + |
| 4 | + |
| 5 | +# Install python |
| 6 | + |
| 7 | +cd $HOME/ |
| 8 | +wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh |
| 9 | +bash miniconda.sh -b -p "$HOME/conda" |
| 10 | +export PATH="$HOME/conda/bin:$PATH" |
| 11 | + |
| 12 | +conda config --set always_yes yes --set changeps1 no |
| 13 | +conda config --add channels conda-forge |
| 14 | +conda update --yes conda |
| 15 | +conda update --yes --all |
| 16 | +conda info -a |
| 17 | + |
| 18 | +conda create --yes -n scijava python jupyter nbconvert |
| 19 | + |
| 20 | +source activate scijava |
| 21 | + |
| 22 | + |
| 23 | +# Install a kernel with Java in the Fiji folder |
| 24 | + |
| 25 | +export IJ_PATH="$HOME/Fiji.app" |
| 26 | +export IJ_LAUNCHER="$IJ_PATH/ImageJ-linux64" |
| 27 | + |
| 28 | +JAVA_COMMAND_CLASS="org.scijava.jupyter.commands.InstallScijavaKernel" |
| 29 | +$IJ_LAUNCHER --ij2 --headless --run $JAVA_COMMAND_CLASS "logLevel=\"info\",pythonBinaryPath=\"$(which python)\",installAllKernels=true" |
| 30 | + |
| 31 | +jupyter kernelspec list |
| 32 | + |
| 33 | + |
| 34 | +# Now run some notebooks |
| 35 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-python" "$TRAVIS_BUILD_DIR/notebooks/Welcome.ipynb" |
| 36 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-groovy" "$TRAVIS_BUILD_DIR/notebooks/General.ipynb" |
| 37 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-python" "$TRAVIS_BUILD_DIR/notebooks/Rich Output.ipynb" |
| 38 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-python" "$TRAVIS_BUILD_DIR/notebooks/On-The-Fly Grabbing.ipynb" |
| 39 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-groovy" "$TRAVIS_BUILD_DIR/notebooks/ImageJ.ipynb" |
| 40 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-groovy" "$TRAVIS_BUILD_DIR/notebooks/Scijava.ipynb" |
| 41 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-python" "$TRAVIS_BUILD_DIR/notebooks/languages/Python.ipynb" |
| 42 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-groovy" "$TRAVIS_BUILD_DIR/notebooks/languages/Groovy.ipynb" |
| 43 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-scala" "$TRAVIS_BUILD_DIR/notebooks/languages/Scala.ipynb" |
| 44 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-clojure" "$TRAVIS_BUILD_DIR/notebooks/languages/Clojure.ipynb" |
| 45 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-beanshell" "$TRAVIS_BUILD_DIR/notebooks/languages/Beanshell.ipynb" |
| 46 | +#jupyter nbconvert --execute --ExecutePreprocessor.timeout="60" --ExecutePreprocessor.kernel_name="scijava-javascript" "$TRAVIS_BUILD_DIR/notebooks/languages/Javascript.ipynb" |
| 47 | + |
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