diff --git a/001-Jupyter/.ipynb_checkpoints/Create_JupyterKernel_conda-checkpoint.ipynb b/001-Jupyter/.ipynb_checkpoints/Create_JupyterKernel_conda-checkpoint.ipynb
deleted file mode 100644
index 309c0c8c5cfaee5597aab23be4acd563384bc126..0000000000000000000000000000000000000000
--- a/001-Jupyter/.ipynb_checkpoints/Create_JupyterKernel_conda-checkpoint.ipynb
+++ /dev/null
@@ -1,293 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# - Create your own Jupyter CONDA-Kernel -"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---\n",
- "## Building your own Jupyter CONDA-kernel is a three step process\n",
- "Download Minconda installer\n",
- "1. Download/Install Miniconda\n",
- " * Miniconda3.sh\n",
- "2. Create Conda Environment\n",
- " * conda create\n",
- "2. Create/Edit launch script for the Jupyter kernel\n",
- " * kernel.sh\n",
- "3. Create/Edit Jupyter kernel configuration\n",
- " * kernel.json"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Settings"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Selectable **CONDA_TARGET_DIR** path for the central conda installation, should be in the project filesystem"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "export CONDA_TARGET_DIR=${HOME}/PROJECT_training2005/testdir/miniconda3"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Selectable **CONDA_ENV** name, will be used to specify the environment name"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "export CONDA_ENV=my_env"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---\n",
- "## 1. Download/Install Miniconda"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Start here if you want to run the full installation.\n",
- "If you want to create another environment in an existing conda setup go to **create environment**. If you want to attach yourself to an existing environment go to **create user kernel**."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.1 - Download Minconda installer"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "curl https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -o $HOME/Miniconda3.sh"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.2 - Create target directory"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "mkdir -p ${CONDA_TARGET_DIR}"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.3 - Install Miniconda"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "bash $HOME/Miniconda3.sh -b -u -p ${CONDA_TARGET_DIR}"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "${CONDA_TARGET_DIR}/bin/conda init bash"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.4 - Disable automatic activation"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "${CONDA_TARGET_DIR}/bin/conda config --set auto_activate_base false"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---\n",
- "## 2. Create conda environment"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Create new conda environment. The following steps can be repeated if multiple environments should be created. If the Python version differ towards the external Python version, a mix of Conda modules and external modules will not be possible"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "${CONDA_TARGET_DIR}/bin/conda create -n ${CONDA_ENV} -y python=3.6.8 ipykernel"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---\n",
- "## 3. Create/Edit launch script for the Jupyter kernel"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 3.1 - Create kernel to allow access to the conda environment. Adapte `module purge` and `PYTHONPATH` according to the comments."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "echo '#!/bin/bash\n",
- "\n",
- "# module purge # optional to disable the external environment, necessary, if python version is different\n",
- " \n",
- "# Activate your Python virtual environment\n",
- "source '\"${CONDA_TARGET_DIR}\"'/bin/activate '\"${CONDA_ENV}\"'\n",
- " \n",
- "# Ensure python packages installed in conda are always prefered, not necessary if module purge is used\n",
- "export PYTHONPATH=${CONDA_PREFIX}/lib/python3.6/site-packages:${PYTHONPATH}\n",
- " \n",
- "exec python -m ipykernel $@' > ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "chmod +x ${CONDA_TARGET_DIR}/envs/${CONDA_ENV}/kernel.sh"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---\n",
- "## 4. Create/Edit Jupyter kernel configuration"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 4.1 - Create user kernel, if you want to access the conda environment of a colleague, only these steps are necessary"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "mkdir -p $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 4.2 - Adjust kernel.json file"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "echo '{\n",
- " \"argv\": [\n",
- " \"'\"${CONDA_TARGET_DIR}\"'/envs/'\"${CONDA_ENV}\"'/kernel.sh\",\n",
- " \"-f\",\n",
- " \"{connection_file}\"\n",
- " ],\n",
- " \"display_name\": \"conda_'\"${CONDA_ENV}\"'\",\n",
- " \"language\": \"python\"\n",
- "}' > $HOME/.local/share/jupyter/kernels/conda_${CONDA_ENV}/kernel.json"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "Restart of JupyterLab might be necessary to see the kernel in the kernel selection overview."
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Bash",
- "language": "bash",
- "name": "bash"
- },
- "language_info": {
- "codemirror_mode": "shell",
- "file_extension": ".sh",
- "mimetype": "text/x-sh",
- "name": "bash"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/001-Jupyter/.ipynb_checkpoints/Create_JupyterKernel_general-checkpoint.ipynb b/001-Jupyter/.ipynb_checkpoints/Create_JupyterKernel_general-checkpoint.ipynb
deleted file mode 100644
index 6b106eea6fc7227ef4a847aed12eb69d92da92a6..0000000000000000000000000000000000000000
--- a/001-Jupyter/.ipynb_checkpoints/Create_JupyterKernel_general-checkpoint.ipynb
+++ /dev/null
@@ -1,387 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# - Create your own Jupyter Kernel -"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---\n",
- "## Building your own Jupyter kernel is a three step process\n",
- "1. Create/Pimp new virtual Python environment\n",
- " * venv\n",
- "2. Create/Edit launch script for the Jupyter kernel\n",
- " * kernel.sh\n",
- "3. Create/Edit Jupyter kernel configuration\n",
- " * kernel.json"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "### Settings"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* Set kernel name\n",
- " - change if you like"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# INPUT NEEDED:\n",
- "export KERNEL_NAME=${USER}_kernel\n",
- "\n",
- "echo ${KERNEL_NAME} # double check"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* Set kernel type\n",
- " - private kernel = \"\\${HOME}/.local/\" \n",
- " - project kernel = \"\\${PROJECT}/.local/\" "
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# INPUT NEEDED:\n",
- "export KERNEL_TYPE=private # private or project\n",
- "\n",
- "###################\n",
- "# private kernel\n",
- "if [ \"${KERNEL_TYPE}\" == \"private\" ]; then\n",
- " export KERNEL_SPECS_PREFIX=${HOME}/.local\n",
- " echo \"private kernel\"\n",
- "# project kernel\n",
- "else\n",
- " export KERNEL_SPECS_PREFIX=${PROJECT}/.local\n",
- " echo \"project kernel\"\n",
- "fi\n",
- "export KERNEL_SPECS_DIR=${KERNEL_SPECS_PREFIX}/share/jupyter/kernels\n",
- "\n",
- "# check if kernel name is unique\n",
- "if [ -d \"${KERNEL_SPECS_DIR}/${KERNEL_NAME}\" ]; then\n",
- " echo \"ERROR: Kernel already exists in ${KERNEL_SPECS_DIR}/${KERNEL_NAME}\"\n",
- " echo \" Rename kernel name or remove directory.\"\n",
- "fi\n",
- "\n",
- "echo ${KERNEL_SPECS_DIR}/${KERNEL_NAME} # double check"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* Set directory for kernels virtual environment\n",
- " - change if you like"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# INPUT NEEDED:\n",
- "export KERNEL_VENVS_DIR=${PROJECT}/${USER}/jupyter/kernels\n",
- "\n",
- "###################\n",
- "mkdir -p ${KERNEL_VENVS_DIR}\n",
- "if [ \"${KERNEL_TYPE}\" != \"private\" ]; then\n",
- " echo \"Please check the permissions and ensure your project partners have read/execute permissions:\"\n",
- " namei -l ${KERNEL_VENVS_DIR}\n",
- "fi\n",
- "\n",
- "echo ${KERNEL_VENVS_DIR} # double check"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## 1. Create/Pimp new virual Python environment"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.1 - Load required modules"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "module -q purge\n",
- "module -q use $OTHERSTAGES \n",
- "module -q load Stages/Devel-2019a 2> /dev/null # any stage can be used\n",
- "module -q load GCCcore/.8.3.0 2> /dev/null\n",
- "module -q load Python/3.6.8 # only Python is required\n",
- "module list # double check"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.2 - Load extra modules you need for your kernel"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# module load <module you need>"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.3 - Create and activate a virtual environment for the kernel \n",
- "and ensure python packages installed in the virtual environment are always prefered"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "python -m venv --system-site-packages ${KERNEL_VENVS_DIR}/${KERNEL_NAME}\n",
- "source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate\n",
- "export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.6/site-packages:${PYTHONPATH}\n",
- "echo ${VIRTUAL_ENV} # double check"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.4 - Install Python libraries required for communication with Jupyter"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "which pip\n",
- "pip install --ignore-installed ipykernel\n",
- "ls ${VIRTUAL_ENV}/lib/python3.6/site-packages/ # double check"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 1.5 - Install whatever else you need in your Python virtual environment (using pip)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "#pip install <python-package you need>"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## 2. Create/Edit launch script for the Jupyter kernel"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 2.1 - Create launch script, which loads your Python virtual environment and starts the ipykernel process inside:"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "echo \"#!/bin/bash\n",
- "\n",
- "# Load required modules\n",
- "module purge\n",
- "module use \"'$OTHERSTAGES'\"\n",
- "module load Stages/Devel-2019a\n",
- "module load GCCcore/.8.3.0\n",
- "module load Python/3.6.8\n",
- "\n",
- "# Load extra modules you need for your kernel (as you did in step 1.2)\n",
- "#module load <module you need>\n",
- " \n",
- "# Activate your Python virtual environment\n",
- "source ${KERNEL_VENVS_DIR}/${KERNEL_NAME}/bin/activate\n",
- " \n",
- "# Ensure python packages installed in the virtual environment are always prefered\n",
- "export PYTHONPATH=${VIRTUAL_ENV}/lib/python3.6/site-packages:\"'${PYTHONPATH}'\"\n",
- " \n",
- "exec python -m ipykernel \"'$@' > ${VIRTUAL_ENV}/kernel.sh\n",
- "chmod +x ${VIRTUAL_ENV}/kernel.sh"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## 3. Create/Edit Jupyter kernel configuration"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 3.1 - Create Jupyter kernel configuration directory and files"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "python -m ipykernel install --name=${KERNEL_NAME} --prefix ${VIRTUAL_ENV}\n",
- "export VIRTUAL_ENV_KERNELS=${VIRTUAL_ENV}/share/jupyter/kernels"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 3.2 - Adjust kernel.json file"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "mv ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json.orig\n",
- "\n",
- "echo '{\n",
- " \"argv\": [\n",
- " \"'${KERNEL_VENVS_DIR}/${KERNEL_NAME}/kernel.sh'\",\n",
- " \"-m\",\n",
- " \"ipykernel_launcher\",\n",
- " \"-f\",\n",
- " \"{connection_file}\"\n",
- " ],\n",
- " \"display_name\": \"'${KERNEL_NAME}'\",\n",
- " \"language\": \"python\"\n",
- "}' > ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME}/kernel.json"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "* 3.3 - Create link to kernel specs"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "cd ${KERNEL_SPECS_DIR}\n",
- "ln -s ${VIRTUAL_ENV_KERNELS}/${KERNEL_NAME} .\n",
- "ls ${KERNEL_SPECS_DIR} # double check"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## 4. Cleanup"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "deactivate"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Bash",
- "language": "bash",
- "name": "bash"
- },
- "language_info": {
- "codemirror_mode": "shell",
- "file_extension": ".sh",
- "mimetype": "text/x-sh",
- "name": "bash"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/001-Jupyter/.ipynb_checkpoints/List_JupyterExtensions-checkpoint.ipynb b/001-Jupyter/.ipynb_checkpoints/List_JupyterExtensions-checkpoint.ipynb
deleted file mode 100644
index e5d1a2240a159f3822d9de4baebb00c7f4c29138..0000000000000000000000000000000000000000
--- a/001-Jupyter/.ipynb_checkpoints/List_JupyterExtensions-checkpoint.ipynb
+++ /dev/null
@@ -1,680 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {
- "toc-hr-collapsed": false
- },
- "source": [
- "# List of Extensions on Jupyter@JSC"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "If you want to use any of these extensions, feel free to use our [examples](https://github.com/kreuzert/Jupyter-JSC) as a starting point."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## AppMode (Classic Notebook only)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[AppMode](https://github.com/oschuett/appmode) is a Jupyter extension that turns notebooks into web applications. \n",
- "To use it click on the menu on \"Help\" -> \"Launch Classic Notebook\"."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![AppMode](https://raw.githubusercontent.com/oschuett/appmode/master/screenshots.png \"AppMode\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Celltags"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The JupyterLab [cell tags](https://github.com/jupyterlab/jupyterlab-celltags) extension enables users to easily add, view, and manipulate descriptive tags for notebook cells. \n",
- "The extension includes the functionality to select all cells with a given tag, supporting the performance of any operation on those cells. \n",
- "Click on the wrench Symbol on the left sidebar to use it. "
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![CellTags](https://camo.githubusercontent.com/ef150fb7721d76e00d95225293662a22504d18ed/687474703a2f2f672e7265636f726469742e636f2f4d78774e365561465a6a2e676966 \"CellTags\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Codefolding (Classic Notebook only)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[CodeFolding](https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tree/master/src/jupyter_contrib_nbextensions/nbextensions/codefolding) adds codefolding functionality from CodeMirror to a codecell. \n",
- "To use it click on the menu on \"Help\" -> \"Launch Classic Notebook\"."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![CodeFolding](https://raw.githubusercontent.com/ipython-contrib/jupyter_contrib_nbextensions/master/src/jupyter_contrib_nbextensions/nbextensions/codefolding/codefolding_indent_unfolded.png \"codefolding\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "toc-hr-collapsed": true
- },
- "source": [
- "## Code Formatter"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[Code Formatter](https://github.com/ryantam626/jupyterlab_code_formatter) allows you to format a Notebook for. \n",
- "You can use it as shown below or you click on \"Format notebook\" at the top of your notebook. "
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![CodeFormatter](https://raw.githubusercontent.com/ryantam626/jupyterlab_code_formatter/master/code-formatter-demo.gif \"CodeFormatter\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Dask (only on HPC Systems)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "An [extension](https://github.com/dask/dask-labextension) to manage Dask clusters, as well as embed Dask's dashboard plots directly into JupyterLab panes. \n",
- "Watch [this](https://www.youtube.com/watch?feature=player_embedded&v=EX_voquHdk0) video until the end to unterstand how to use Dask in JupyterLab. At the moment we only offer to use the panels inside of JupyterLab. \n",
- "We have introduction notebooks for this extensions [here](https://gitlab.version.fz-juelich.de/jupyter4jsc/j4j_notebooks/tree/master/001-Extensions) (or open the gitlab extension on the left sidebar)."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Drawio"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[Drawio](https://github.com/QuantStack/jupyterlab-drawio) is a JupyterLab extension for standalone integration of drawio / mxgraph into jupyterlab."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![Drawio](https://raw.githubusercontent.com/QuantStack/jupyterlab-drawio/master/drawio.gif \"drawio\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Git"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "A JupyterLab [Git](https://github.com/jupyterlab/jupyterlab-git) extension for version control using git."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![Git](https://camo.githubusercontent.com/8e2f2b6abdaff6b180bf6aee95b288a7af0fde4d/687474703a2f2f672e7265636f726469742e636f2f4e39496b7a62796b38502e676966 \"Git\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "toc-hr-collapsed": true
- },
- "source": [
- "## Ipydatawidgets"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[Ipydatawidgets](https://github.com/vidartf/ipydatawidgets) is a set of widgets to help facilitate reuse of large datasets across different widgets, and different packages."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "import numpy as np\n",
- "from ipydatawidgets import DataImage\n",
- "np.random.seed(0)\n",
- "data = np.array(255 * np.random.rand(200, 200, 4), dtype='uint8')\n",
- "DataImage(data=data)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "SIDELEN = 300\n",
- "grad = np.linspace(0, 255, SIDELEN, dtype='uint8')\n",
- "# red and green components:\n",
- "rg = np.dstack(np.meshgrid(grad, grad))\n",
- "# add blue and alpha components (zero and 255):\n",
- "rgba = np.dstack([\n",
- " rg,\n",
- " np.zeros((SIDELEN, SIDELEN), dtype='uint8'),\n",
- " 255 * np.ones((SIDELEN, SIDELEN), dtype='uint8')\n",
- "])\n",
- "DataImage(data=rgba)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "toc-hr-collapsed": true
- },
- "source": [
- "## IPyVolume"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[IPyvolume](https://buildmedia.readthedocs.org/media/pdf/ipyvolume/latest/ipyvolume.pdf) is a Python library to visualize 3d volumes and glyphs."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "import numpy as np\n",
- "import ipyvolume as ipv\n",
- "V = np.zeros((128,128,128))# our 3d array\n",
- "# outer box\n",
- "V[30:-30,30:-30,30:-30] = 0.75\n",
- "V[35:-35,35:-35,35:-35] = 0.0\n",
- "# inner box\n",
- "V[50:-50,50:-50,50:-50] = 0.25\n",
- "V[55:-55,55:-55,55:-55] = 0.0\n",
- "ipv.quickvolshow(V, level=[0.25, 0.75], opacity=0.03, level_width=0.1, data_min=0, data_max=1)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## JupyterLab LaTeX Extension"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The [LaTeX Extension](https://github.com/jupyterlab/jupyterlab-latex) is an extension for JupyterLab which allows for live-editing of LaTeX documents. \n",
- "[Here](https://annefou.github.io/jupyter_publish/03-latex/index.html) you can find a short example."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "toc-hr-collapsed": true
- },
- "source": [
- "## JupyterLab LMod"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[An extension](https://github.com/cmd-ntrf/jupyter-lmod) that allows user to interact with environment modules before launching kernels. \n",
- "To check the Pythonpath/PATH of your current kernel just run the following command. Remember to restart the kernel after loading other modules. "
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "!echo $PATH # or !echo $PYTHONPATH"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![\"Lmod\"](https://camo.githubusercontent.com/2a1fa198b6b7f35c7b9751664dfe5102fa5aa595/68747470733a2f2f692e696d6775722e636f6d2f3148444837694e2e676966 \"lmod\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## JupyterLab Table of Contents"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "A [Table of Contents extension](https://github.com/jupyterlab/jupyterlab-toc) for JupyterLab. This auto-generates a table of contents in the left area when you have a notebook or markdown document open. \n",
- "The entries are clickable, and scroll the document to the heading in question."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![ToC](https://raw.githubusercontent.com/jupyterlab/jupyterlab-toc/master/toc.gif \"ToC\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Jupyter ThreeJS"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "A Python / [ThreeJS](https://github.com/jupyter-widgets/pythreejs) bridge utilizing the Jupyter widget infrastructure."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![ThreeJS](https://raw.githubusercontent.com/jupyter-widgets/pythreejs/master/screencast.gif \"ThreeJS\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "toc-hr-collapsed": false
- },
- "source": [
- "## Leaflet"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "The [Jupyterlab Leaflet extension](https://github.com/jupyter-widgets/ipyleaflet) enables interactive maps. \n",
- "You can find several example notebooks [here](https://github.com/jupyter-widgets/ipyleaflet/tree/master/examples)."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![Leaflet](https://raw.githubusercontent.com/jupyter-widgets/ipyleaflet/master/basemap.gif \"leaflet\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "toc-hr-collapsed": true
- },
- "source": [
- "## MatplotLib"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[MatplotLib](https://www.github.com/matplotlib/jupyter-matplotlib) enables the interactive features of matplotlib in Jupyterlab. \n",
- "Besides, the figure canvas element is a proper Jupyter interactive widget which can be positioned in interactive widget layouts."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# Enable the matplotlib widget\n",
- "%matplotlib widget"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "import matplotlib.pyplot as plt\n",
- "from mpl_toolkits.mplot3d import axes3d\n",
- "\n",
- "fig = plt.figure()\n",
- "ax = fig.add_subplot(111, projection='3d')\n",
- "\n",
- "# Grab some test data.\n",
- "X, Y, Z = axes3d.get_test_data(0.05)\n",
- "\n",
- "# Plot a basic wireframe.\n",
- "ax.plot_wireframe(X, Y, Z, rstride=10, cstride=10)\n",
- "\n",
- "fig.canvas.layout.max_width = '800px'\n",
- "\n",
- "plt.show()"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# When using the `widget` backend from ipympl,\n",
- "# fig.canvas is a proper Jupyter interactive widget, which can be embedded in\n",
- "# Layout classes like HBox and Vbox.\n",
- "\n",
- "# One can bound figure attributes to other widget values.\n",
- "import numpy as np\n",
- "from ipywidgets import HBox, FloatSlider\n",
- "\n",
- "plt.ioff()\n",
- "plt.clf()\n",
- "\n",
- "slider = FloatSlider(\n",
- " orientation='vertical',\n",
- " value=1.0,\n",
- " min=0.02,\n",
- " max=2.0\n",
- ")\n",
- "\n",
- "fig = plt.figure(3)\n",
- "\n",
- "x = np.linspace(0, 20, 500)\n",
- "\n",
- "lines = plt.plot(x, np.sin(slider.value * x))\n",
- "\n",
- "def update_lines(change):\n",
- " lines[0].set_data(x, np.sin(change.new * x))\n",
- " fig.canvas.draw()\n",
- " fig.canvas.flush_events()\n",
- "\n",
- "slider.observe(update_lines, names='value')\n",
- "\n",
- "HBox([slider, fig.canvas])\n",
- "\n"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## NBDime"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[NBDime](https://github.com/jupyter/nbdime) provides tools for diffing and merging of Jupyter Notebooks."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## NBExtensions Configurator (Classic Notebook only)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "A server extension for jupyter notebook which provides configuration interfaces for notebook extensions (nbextensions). \n",
- "Works only with the classic notebook, not with JupyterLab. \n",
- "To use it click on the menu on \"Help\" -> \"Launch Classic Notebook\". "
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![\"NBExtensions\"](https://raw.githubusercontent.com/Jupyter-contrib/jupyter_nbextensions_configurator/master/src/jupyter_nbextensions_configurator/static/nbextensions_configurator/icon.png \"nbextensions\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "toc-hr-collapsed": true
- },
- "source": [
- "## Plotly"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {
- "slideshow": {
- "slide_type": "slide"
- }
- },
- "source": [
- "A JupyterLab [extension](https://github.com/plotly/plotly.py) for [plotly](https://plot.ly/)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "slideshow": {
- "slide_type": "fragment"
- }
- },
- "outputs": [],
- "source": [
- "import plotly\n",
- "from plotly.offline import init_notebook_mode, iplot\n",
- "init_notebook_mode(connected=True)\n",
- "trace0 = plotly.graph_objs.Scatter(\n",
- " x=[1, 2, 3, 4],\n",
- " y=[10, 15, 13, 17]\n",
- ")\n",
- "trace1 = plotly.graph_objs.Scatter(\n",
- " x=[1, 2, 3, 4],\n",
- " y=[16, 5, 11, 9]\n",
- ")\n",
- "\n",
- "iplot([trace0, trace1])"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Quick Open"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[Quick Open](https://github.com/parente/jupyterlab-quickopen) allows you to quickly open a file in JupyterLab by typing part of its name. Just click on the lens symbol at the left sidebar. \n",
- "<span style=\"color:darkorange\">Takes a long time on HPC systems.</span>"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![QuickOpen](https://raw.githubusercontent.com/parente/jupyterlab-quickopen/master/doc/quickopen.gif \"quickopen\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## RISE (Classic Notebook only)"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "With [RISE](https://rise.readthedocs.io/en/latest), a Jupyter notebook extension, you can instantly turn your jupyter notebook into a live reveal.js-based presentation. \n",
- "To use it click on the menu on \"Help\" -> \"Launch Classic Notebook\"."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![RISE](https://rise.readthedocs.io/en/latest/_images/basic_usage.gif \"rise\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Sidecar"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "A [sidecar](https://github.com/jupyter-widgets/jupyterlab-sidecar) output widget for JupyterLab"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![Sidecar](https://raw.githubusercontent.com/jupyter-widgets/jupyterlab-sidecar/master/sidecar.gif \"Sidecar\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Voilà Preview"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[Voilà](https://github.com/voila-dashboards/voila) turns Jupyter notebooks into standalone web applications.\n",
- "\n",
- "Unlike the usual HTML-converted notebooks, each user connecting to the Voilà tornado application gets a dedicated Jupyter kernel which can execute the callbacks to changes in Jupyter interactive widgets. \n",
- "\n",
- "This extension allows you to render a Notebook with Voilà, so you can see how your Notebook will look with it.\n",
- "\n",
- "You can download a test notebook with the following command: \n",
- "```\n",
- " $ wget --no-check-certificate https://jupyter-jsc.fz-juelich.de/static/files/voila_basics.ipynb\n",
- "``` \n",
- "and get a preview of it with the button at the top of your notebook."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![\"VoilaPreview\"](https://jupyter-jsc.fz-juelich.de/hub/static/images/voila_preview.png \"Voila Preview\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## WebRTC"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "[WebRTC](https://github.com/maartenbreddels/ipywebrtc) allows you to stream video files into Jupyter Notebooks."
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "![WebRTC](https://user-images.githubusercontent.com/1765949/43977008-03dbfac0-9ce3-11e8-9bb9-4a5f8f2cc79a.gif \"WebRTC\")"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.6.8"
- },
- "toc-autonumbering": false,
- "toc-showcode": true,
- "toc-showmarkdowntxt": false
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/001-Jupyter/.ipynb_checkpoints/List_PythonPackages-checkpoint.ipynb b/001-Jupyter/.ipynb_checkpoints/List_PythonPackages-checkpoint.ipynb
deleted file mode 100644
index f774f6919de12fc9eecfb34240873c474a05cd22..0000000000000000000000000000000000000000
--- a/001-Jupyter/.ipynb_checkpoints/List_PythonPackages-checkpoint.ipynb
+++ /dev/null
@@ -1,654 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# List of included Python packages"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "---\n",
- "This lists the python packages available and installed by the install script for Python, SciPy-Stack and Jupyter:\n",
- " - `$EBROOTPYTHON/easybuild/*.eb`\n",
- " - `$EBROOTSCIPYMINSTACK/easybuild/*.eb`\n",
- " - `$EBROOTJUPYTER/easybuild/*.eb`"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 1,
- "metadata": {},
- "outputs": [],
- "source": [
- "pkg_list = [\n",
- " # Python module\n",
- " (\"setuptools\", \"41.6.0\", \"\"),\n",
- " (\"webencodings\", \"0.5.1\", \"\"),\n",
- " (\"six\", \"1.12.0\", \"\"),\n",
- " (\"decorator\", \"4.4.0\", \"\"),\n",
- " (\"MarkupSafe\", \"1.1.1\", \"markupsafe\"),\n",
- " (\"more-itertools\", \"7.2.0\", \"more_itertools\"),\n",
- " (\"pickleshare\", \"0.7.5\", \"\"),\n",
- " (\"jedi\", \"0.15.1\", \"\"),\n",
- " (\"wcwidth\", \"0.1.7\", \"\"),\n",
- " (\"attr\", \"19.3.0\", \"\"),\n",
- " (\"parso\", \"0.5.1\", \"\"),\n",
- " (\"jinja2\", \"2.10.1\", \"\"),\n",
- " (\"pytz\", \"2019.3\", \"\"),\n",
- " (\"pyparsing\", \"2.2.0\", \"\"),\n",
- " (\"packaging\", \"19.2\", \"\"),\n",
- " (\"urllib3\", \"1.25.6\", \"\"),\n",
- " (\"certifi\", \"2019.9.11\", \"\"),\n",
- " (\"requests\", \"2.22.0\", \"\"),\n",
- " (\"python-dateutil\", \"2.8.1\", \"dateutil\"),\n",
- " (\"Pillow\", \"6.2.1\", \"PIL\"),\n",
- " (\"ply\", \"3.11\", \"\"),\n",
- " (\"pyrsistent\", \"0.15.4\", \"\"),\n",
- " (\"lxml\", \"4.4.1\", \"\"),\n",
- " (\"idna\", \"2.8\", \"\"),\n",
- " (\"chardet\", \"3.0.4\", \"\"),\n",
- " (\"pycparser\", \"2.19\", \"\"),\n",
- " (\"cffi\", \"1.13.2\", \"\"),\n",
- " (\"psutil\", \"5.6.3\", \"\"),\n",
- " (\"SQLAlchemy\", \"1.3.10\", \"sqlalchemy\"),\n",
- " (\"certipy\", \"0.1.3\", \"\"),\n",
- " (\"python-editor\", \"1.0.4\", \"editor\"),\n",
- " (\"Mako\", \"1.1.0\", \"mako\"),\n",
- " (\"alembic\", \"1.2.1\", \"\"),\n",
- " (\"click\", \"7.0\", \"\"),\n",
- " (\"appdirs\", \"1.4.3\", \"\"),\n",
- " (\"cloudpickle\", \"1.2.2\", \"\"),\n",
- " (\"toolz\", \"0.10.0\", \"\"),\n",
- " (\"cryptography\", \"2.8\", \"\"),\n",
- " \n",
- " (\"prompt-toolkit\", \"2.0.10\", \"prompt_toolkit\"),\n",
- " (\"oauthlib\", \"3.1.0\", \"\"),\n",
- " (\"async-generator\", \"1.10\", \"async_generator\"),\n",
- " (\"smmap\", \"0.9.0\", \"\"),\n",
- " (\"typed-ast\", \"1.4.0\", \"typed_ast\"),\n",
- "\n",
- " # SciPy-Stack module\n",
- " (\"cycler\", \"0.10.0\", \"\"),\n",
- " (\"numpy\", \"1.15.2\", \"\"),\n",
- " (\"scipy\", \"1.2.1\", \"\"),\n",
- " (\"sympy\", \"1.4\", \"\"),\n",
- " (\"pandas\", \"0.25.3\", \"\"),\n",
- " (\"mpmath\", \"1.1.0\", \"\"),\n",
- " (\"kiwisolver\", \"1.1.0\", \"\"),\n",
- " (\"backports.functools_lru_cache\", \"1.5\", \"\"),\n",
- " (\"matplotlib\", \"3.1.1\", \"\"),\n",
- " (\"xarray\", \"0.11.3\", \"\"),\n",
- " \n",
- " # Jupyter module\n",
- " (\"pyOpenSSL\", \"19.0.0\", \"OpenSSL\"),\n",
- " (\"entrypoints\", \"0.3\", \"\"),\n",
- " (\"async_generator\", \"1.10\", \"\"),\n",
- " (\"absl-py\", \"0.8.1\", \"absl\"),\n",
- " (\"cryptography\", \"2.8\", \"\"),\n",
- " (\"tornado\", \"6.0.3\", \"\"),\n",
- " (\"bokeh\", \"1.3.4\", \"\"),\n",
- " (\"seaborn\", \"0.9.0\", \"\"),\n",
- " (\"nbformat\", \"4.4.0\", \"\"),\n",
- " (\"param\", \"1.9.2\", \"\"),\n",
- " (\"pyviz_comms\", \"0.7.2\", \"\"),\n",
- " (\"holoviews\", \"1.12.6\", \"\"),\n",
- " (\"alabaster\", \"0.7.12\", \"\"),\n",
- " (\"Babel\", \"2.7.0\", \"babel\"),\n",
- " (\"snowballstemmer\", \"2.0.0\", \"\"),\n",
- " (\"docutils\", \"0.15.2\", \"\"),\n",
- " (\"imagesize\", \"1.1.0\", \"\"),\n",
- " (\"sphinxcontrib-websupport\", \"1.1.2\", \"sphinxcontrib.websupport\"),\n",
- " (\"Sphinx\", \"1.8.5\", \"sphinx\"),\n",
- " (\"pexpect\", \"4.7.0\", \"\"),\n",
- " (\"ipython\", \"7.9.0\", \"IPython\"),\n",
- " (\"ipynb\", \"0.5.1\", \"\"),\n",
- " (\"jupyter_core\", \"4.6.1\", \"\"),\n",
- " (\"retrying\", \"1.3.3\", \"\"),\n",
- " (\"plotly\", \"4.2.1\", \"\"),\n",
- " (\"tikzplotlib\", \"0.8.4\", \"\"),\n",
- " (\"jupyter_client\", \"5.3.4\", \"\"),\n",
- " (\"traitlets\", \"4.3.3\", \"\"),\n",
- " (\"pyzmq\", \"18.1.0\", \"zmq\"),\n",
- " (\"singledispatch\", \"3.4.0.3\", \"\"),\n",
- " (\"ipyparallel\", \"6.2.4\", \"\"),\n",
- " (\"ipykernel\", \"5.1.3\", \"\"),\n",
- " (\"terminado\", \"0.8.2\", \"\"),\n",
- " (\"bleach\", \"3.1.0\", \"\"),\n",
- " (\"mistune\", \"0.8.4\", \"\"),\n",
- " (\"pandocfilters\", \"1.4.2\", \"\"),\n",
- " (\"Pygments\", \"2.4.2\", \"pygments\"),\n",
- " (\"testpath\", \"0.4.4\", \"\"),\n",
- " (\"nbconvert\", \"5.6.1\", \"\"),\n",
- " (\"ipython_genutils\",\"0.2.0\", \"\"),\n",
- " (\"Send2Trash\", \"1.5.0\", \"send2trash\"),\n",
- " (\"notebook\", \"6.0.2\", \"\"),\n",
- " (\"version_information\", \"1.0.3\", \"\"),\n",
- " (\"lesscpy\", \"0.13.0\", \"\"),\n",
- " (\"prometheus-client\", \"0.7.1\", \"prometheus_client\"),\n",
- " (\"jupyterthemes\", \"0.20.0\", \"\"),\n",
- " (\"zipp\", \"0.6.0\", \"\"),\n",
- " (\"importlib_metadata\", \"0.23\", \"\"),\n",
- " (\"jsonschema\", \"3.1.1\", \"\"),\n",
- " (\"jupyterlab_launcher\", \"0.13.1\",\"\"),\n",
- " (\"sphinx_rtd_theme\",\"0.4.3\", \"\"),\n",
- " (\"future\", \"0.18.1\", \"\"),\n",
- " (\"commonmark\", \"0.9.1\", \"\"),\n",
- " (\"recommonmark\", \"0.6.0\", \"\"),\n",
- " (\"jupyterlab\", \"1.2.1\", \"\"),\n",
- " (\"json5\", \"0.8.5\", \"\"),\n",
- " (\"jupyterlab_server\", \"1.0.6\", \"\"),\n",
- " (\"ptyprocess\", \"0.6.0\", \"\"),\n",
- " (\"defusedxml\", \"0.6.0\", \"\"),\n",
- " (\"widgetsnbextension\", \"3.5.1\", \"\"),\n",
- " (\"ipywidgets\", \"7.5.1\", \"\"),\n",
- " (\"ipydatawidgets\", \"4.0.1\", \"\"),\n",
- " (\"traittypes\", \"0.2.1\", \"\"),\n",
- " (\"bqplot\", \"0.11.9\", \"\"),\n",
- " (\"jupyter_bokeh\", \"1.1.1\", \"\"),\n",
- " (\"pythreejs\", \"2.1.1\", \"\"),\n",
- " (\"PyWavelets\", \"1.1.1\", \"pywt\"),\n",
- " (\"imageio\", \"2.6.1\", \"\"),\n",
- " (\"networkx\", \"2.3\", \"\"),\n",
- " (\"scikit-image\", \"0.16.2\", \"skimage\"),\n",
- " (\"ipywebrtc\", \"0.5.0\", \"\"),\n",
- " (\"ipyvolume\", \"0.5.2\", \"\"),\n",
- " (\"branca\", \"0.3.1\", \"\"),\n",
- " (\"ipyleaflet\", \"0.11.4\", \"\"),\n",
- " (\"ipympl\", \"0.3.3\", \"\"),\n",
- " (\"PyYAML\", \"5.1.2\", \"yaml\"),\n",
- " (\"jupyter_nbextensions_configurator\", \"0.4.1\", \"\"),\n",
- " (\"jupyter_latex_envs\", \"1.4.6\", \"latex_envs\"),\n",
- " (\"jupyter_highlight_selected_word\", \"0.2.0\", \"\"),\n",
- " (\"jupyter_contrib_core\", \"0.3.3\",\"\"),\n",
- " (\"jupyter_contrib_nbextensions\", \"0.5.1\", \"\"),\n",
- " (\"rise\", \"5.5.1\", \"\"),\n",
- " (\"typing-extensions\", \"3.7.4\", \"typing_extensions\"),\n",
- " (\"idna-ssl\", \"1.1.0\", \"idna_ssl\"),\n",
- " (\"multidict\", \"4.5.2\", \"\"),\n",
- " (\"yarl\", \"1.3.0\", \"\"),\n",
- " (\"async-timeout\", \"3.0.1\", \"async_timeout\"),\n",
- " (\"aiohttp\", \"3.6.2\", \"\"),\n",
- " (\"simpervisor\", \"0.3\", \"\"),\n",
- " (\"jupyter_server\", \"0.1.1\", \"\"),\n",
- " (\"jupyter-server-proxy\", \"1.1.0\", \"jupyter_server_proxy\"),\n",
- " (\"jupyterlab_github\", \"1.0.1\", \"\"),\n",
- " (\"jupyterlab-gitlab\", \"0.3.0\", \"jupyterlab_gitlab\"),\n",
- " (\"jupyterlab-quickopen\", \"0.3.0\", \"jupyterlab_quickopen\"),\n",
- " (\"zstandard\", \"0.12.0\", \"\"),\n",
- " (\"itk_core\", \"5.0.1\", \"\"),\n",
- " (\"itk_filtering\", \"5.0.1\", \"\"),\n",
- " (\"itk_segmentation\",\"5.0.1\", \"\"),\n",
- " (\"itk_numerics\", \"5.0.1\", \"\"),\n",
- " (\"itk_registration\",\"5.0.1\", \"\"),\n",
- " (\"itk_io\", \"5.0.1\", \"\"),\n",
- " (\"itk-meshtopolydata\", \"0.5.1\", \"\"),\n",
- " (\"pyct\", \"0.4.6\", \"\"),\n",
- " (\"colorcet\", \"2.0.2\", \"\"),\n",
- " (\"itkwidgets\", \"0.22.0\", \"\"),\n",
- " (\"ujson\", \"1.35\", \"\"),\n",
- " (\"jupyterlab_iframe\", \"0.2.1\", \"\"),\n",
- " (\"python-dotenv\", \"0.10.3\", \"dotenv\"),\n",
- " (\"jupyterlab_latex\",\"1.0.0\", \"\"),\n",
- " (\"jupyterlab_slurm\",\"1.0.5\", \"\"),\n",
- " (\"jupyterlmod\", \"1.7.5\", \"\"),\n",
- " (\"nbresuse\", \"0.3.2\", \"\"),\n",
- " (\"colorama\", \"0.4.1\", \"\"),\n",
- " (\"nbdime\", \"1.1.0\", \"\"),\n",
- " (\"smmap2\", \"2.0.5\", \"smmap\"),\n",
- " (\"gitdb2\", \"2.0.6\", \"gitdb\"),\n",
- " (\"GitPython\", \"3.0.4\", \"git\"),\n",
- " (\"jupyterlab-git\", \"0.8.1\", \"jupyterlab_git\"),\n",
- " (\"sidecar\", \"0.3.0\", \"\"),\n",
- " (\"pycodestyle\", \"2.5.0\", \"\"),\n",
- " (\"autopep8\", \"1.4.4\", \"\"),\n",
- " (\"yapf\", \"0.28.0\", \"\"),\n",
- " (\"toml\", \"0.10.0\", \"\"),\n",
- " (\"pathspec\", \"0.6.0\", \"\"),\n",
- " (\"typed_ast\", \"1.4.0\", \"\"),\n",
- " (\"regex\", \"2019.11.1\",\"\"),\n",
- " (\"black\", \"19.3b0\", \"\"),\n",
- " (\"jupyterlab-code-formatter\", \"0.6.1\", \"jupyterlab_code_formatter\"),\n",
- " (\"pamela\", \"1.0.0\", \"\"),\n",
- " (\"certipy\", \"0.1.3\", \"\"),\n",
- " (\"oauthlib\", \"3.1.0\", \"\"),\n",
- " (\"jupyterhub\", \"1.0.0\", \"\"),\n",
- " (\"appmode\", \"0.6.0\", \"\"),\n",
- " (\"HeapDict\", \"1.0.1\", \"heapdict\"),\n",
- " (\"zict\", \"1.0.0\", \"\"),\n",
- " (\"tblib\", \"1.5.0\", \"\"),\n",
- " (\"sortedcontainers\",\"2.1.0\", \"\"),\n",
- " (\"msgpack\", \"0.6.2\", \"\"),\n",
- " (\"dask\", \"2.6.0\", \"\"),\n",
- " (\"distributed\", \"2.6.0\", \"\"),\n",
- " (\"dask-jobqueue\", \"0.7.0\", \"\"),\n",
- " (\"dask_labextension\", \"1.0.3\", \"\"),\n",
- " (\"Automat\", \"0.8.0\", \"automat\"),\n",
- " (\"PyHamcrest\", \"1.9.0\", \"hamcrest\"),\n",
- " (\"Twisted\", \"19.7.0\", \"twisted\"),\n",
- " (\"autobahn\", \"19.10.1\", \"\"),\n",
- " (\"constantly\", \"15.1.0\", \"\"),\n",
- " (\"hyperlink\", \"19.0.0\", \"\"),\n",
- " (\"incremental\", \"17.5.0\", \"\"),\n",
- " (\"txaio\", \"18.8.1\", \"\"),\n",
- " (\"zope.interface\", \"4.6.0\", \"\"),\n",
- " (\"backcall\", \"0.1.0\", \"\"),\n",
- " (\"wslink\", \"0.1.11\", \"\"),\n",
- " (\"jupyterlab_pygments\", \"0.1.0\",\"\"),\n",
- " (\"ipyvue\", \"1.0.0\", \"\"),\n",
- " (\"ipyvuetify\", \"1.1.1\", \"\"),\n",
- " (\"voila\", \"0.1.14\", \"\"),\n",
- " (\"voila-material\", \"0.2.5\", \"-\"),\n",
- " (\"voila-gridstack\", \"0.0.6\", \"-\"),\n",
- " (\"voila-vuetify\", \"0.1.1\", \"-\"), \n",
- " (\"dicom-upload\", \"v0.1.0\", \"\"),\n",
- " (\"fileupload\", \"master\", \"\"),\n",
- " (\"pvlink\", \"0.1.2\", \"\"),\n",
- " (\"julia\", \"0.5.0\", \"\"),\n",
- " (\"textwrap3\", \"0.9.2\", \"\"),\n",
- " (\"ansiwrap\", \"0.8.4\", \"\"),\n",
- " (\"backports.weakref\",\"1.0.post1\",\"\"),\n",
- " (\"backports.tempfile\",\"1.0\", \"\"),\n",
- " (\"tqdm\", \"4.41.0\", \"\"),\n",
- " (\"tenacity\", \"6.0.0\", \"\"),\n",
- " (\"papermill\", \"1.2.1\", \"\"),\n",
- " \n",
- " # PythonPackages for Tutorials\n",
- " (\"patsy\", \"0.5.1\", \"\"),\n",
- " (\"statsmodels\", \"0.10.2\", \"\"),\n",
- " (\"cftime\", \"1.0.4.2\", \"\"),\n",
- " (\"vega_datasets\", \"0.8.0\", \"\"),\n",
- " (\"arviz\", \"0.5.1\", \"\"),\n",
- " (\"Theano\", \"1.0.4\", \"\"),\n",
- " (\"altair\", \"3.3.0\", \"\"),\n",
- " (\"cssselect\", \"1.1.0\", \"\"),\n",
- " (\"smopy\", \"0.0.7\", \"\"),\n",
- " (\"joblib\", \"0.14.1\", \"\"),\n",
- " (\"scikit-learn\", \"0.22\", \"\"),\n",
- " (\"memory_profiler\", \"0.55.0\", \"\"),\n",
- " (\"h5py\", \"2.10.0\", \"\"),\n",
- " (\"line_profiler\", \"2.1.2\", \"\"),\n",
- " (\"pymc3\", \"3.8\", \"\"),\n",
- " (\"llvmlite\", \"0.30.0\", \"\"),\n",
- " (\"numba\", \"0.46.0\", \"\"),\n",
- " (\"numexpr\", \"2.7.0\", \"\"),\n",
- " (\"ipythonblocks\", \"1.9.0\", \"\"),\n",
- " (\"pydub\", \"0.23.1\", \"\"),\n",
- " (\"multipledispatch\",\"0.6.0\", \"\"),\n",
- " (\"partd\", \"1.1.0\", \"\"),\n",
- " (\"locket\", \"0.2.0\", \"\"),\n",
- " (\"fsspec\", \"0.6.2\", \"\"),\n",
- " (\"datashape\", \"0.5.2\", \"\"),\n",
- " (\"datashader\", \"0.9.0\", \"\"),\n",
- " (\"selenium\", \"3.141.0\", \"\"),\n",
- " (\"graphviz\", \"0.13.2\", \"\"),\n",
- " (\"vincent\", \"0.4.4\", \"\"),\n",
- " (\"Shapely\", \"1.6.4.post2\",\"\"),\n",
- " (\"pyshp\", \"2.1.0\", \"\"),\n",
- " (\"Cartopy\", \"0.17.0\", \"\"),\n",
- " (\"pandas-datareader\",\"0.8.1\", \"\"),\n",
- "]\n",
- "\n",
- "from pip._vendor import pkg_resources\n",
- "def get_version(package):\n",
- " package = package.lower()\n",
- " return next((p.version for p in pkg_resources.working_set if p.project_name.lower() == package), f\"{Fore.RED}NO MATCH{Style.RESET_ALL}\")"
- ]
- },
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Run a Sanity Check\n",
- "A test of the Python packages follows here. \n",
- "\n",
- "Attention:\n",
- " - Slight changes in the version numbers are due to compatibility problems we encountered and therefore had to make adjustments.\n",
- " - \"NO MATCH\" - Not all package versions can be automatically found by this script\n",
- " - \"IMPORT FAILED\" - Import failures are possible if python packages are not ment to be importable by the developer."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 2,
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "PYPI NAME : IMPORT NAME REQ.VERS.|INST.VERS. IMPORT TIME\n",
- "=================================================================================\n",
- "setuptools : setuptools 41.6.0 0.385978s\n",
- "webencodings : webencodings 0.5.1 0.016903s\n",
- "six : six 1.12.0 0.000052s\n",
- "decorator : decorator 4.4.0 0.000052s\n",
- "MarkupSafe : markupsafe 1.1.1 0.006108s\n",
- "more-itertools : more_itertools 7.2.0 != \u001b[31m7.0.0 \u001b[0m 0.030407s\n",
- "pickleshare : pickleshare 0.7.5 0.000044s\n",
- "jedi : jedi 0.15.1 != \u001b[31m0.13.3 \u001b[0m 0.000032s\n",
- "wcwidth : wcwidth 0.1.7 0.000029s\n",
- "attr : attr 19.3.0 != \u001b[31m19.1.0 \u001b[0m 0.017762s\n",
- "parso : parso 0.5.1 != \u001b[31m0.3.4 \u001b[0m 0.000041s\n",
- "jinja2 : jinja2 2.10.1 != \u001b[31m2.10 \u001b[0m 0.028386s\n",
- "pytz : pytz 2019.3 != \u001b[31m2019.1 \u001b[0m 0.093399s\n",
- "pyparsing : pyparsing 2.2.0 != \u001b[31m2.3.1 \u001b[0m 0.049335s\n",
- "packaging : packaging 19.2 != \u001b[31m19.0 \u001b[0m 0.027138s\n",
- "urllib3 : urllib3 1.25.6 != \u001b[31m1.24.1 \u001b[0m 0.019931s\n",
- "certifi : certifi 2019.9.11 != \u001b[31m2019.03.09\u001b[0m 0.002952s\n",
- "requests : requests 2.22.0 != \u001b[31m2.21.0 \u001b[0m 0.288162s\n",
- "python-dateutil : dateutil 2.8.1 != \u001b[31m2.8.0 \u001b[0m 0.000026s\n",
- "Pillow : PIL 6.2.1 != \u001b[31m6.0.0 \u001b[0m 0.007693s\n",
- "ply : ply 3.11 0.019242s\n",
- "pyrsistent : pyrsistent 0.15.4 != \u001b[31m0.14.11 \u001b[0m 0.013004s\n",
- "lxml : lxml 4.4.1 != \u001b[31m4.3.3 \u001b[0m 0.055928s\n",
- "idna : idna 2.8 0.000051s\n",
- "chardet : chardet 3.0.4 0.000036s\n",
- "pycparser : pycparser 2.19 0.207475s\n",
- "cffi : cffi 1.13.2 != \u001b[31m1.12.2 \u001b[0m 0.015289s\n",
- "psutil : psutil 5.6.3 != \u001b[31m5.6.1 \u001b[0m 0.046984s\n",
- "SQLAlchemy : sqlalchemy 1.3.10 != \u001b[31m1.3.1 \u001b[0m 0.994233s\n",
- "certipy : certipy 0.1.3 0.037884s\n",
- "python-editor : editor 1.0.4 0.007516s\n",
- "Mako : mako 1.1.0 != \u001b[31m1.0.8 \u001b[0m 0.053407s\n",
- "alembic : alembic 1.2.1 != \u001b[31m1.0.8 \u001b[0m 1.590335s\n",
- "click : click 7.0 0.018214s\n",
- "appdirs : appdirs 1.4.3 0.012561s\n",
- "cloudpickle : cloudpickle 1.2.2 != \u001b[31m0.8.1 \u001b[0m 0.006038s\n",
- "toolz : toolz 0.10.0 != \u001b[31m0.9.0 \u001b[0m 0.020046s\n",
- "cryptography : cryptography 2.8 0.000043s\n",
- "prompt-toolkit : prompt_toolkit 2.0.10 != \u001b[31m2.0.9 \u001b[0m 0.000035s\n",
- "oauthlib : oauthlib 3.1.0 0.009413s\n",
- "async-generator : async_generator 1.10 0.009577s\n",
- "smmap : smmap 0.9.0 != \u001b[31m2.0.5 \u001b[0m 0.005029s\n",
- "typed-ast : typed_ast 1.4.0 0.007294s\n",
- "cycler : cycler 0.10.0 0.007537s\n",
- "numpy : numpy 1.15.2 0.509992s\n",
- "scipy : scipy 1.2.1 0.028397s\n",
- "sympy : sympy 1.4 != \u001b[31m1.3 \u001b[0m 7.210424s\n",
- "pandas : pandas 0.25.3 != \u001b[31m0.24.2 \u001b[0m 1.315975s\n",
- "mpmath : mpmath 1.1.0 0.000075s\n",
- "kiwisolver : kiwisolver 1.1.0 != \u001b[31m1.0.1 \u001b[0m 0.033678s\n",
- "backports.functools_lru_cache : backports.functools_lru_cache \u001b[31mIMPORT FAILED\u001b[0m\n",
- "matplotlib : matplotlib 3.1.1 != \u001b[31m3.0.3 \u001b[0m 0.000086s\n",
- "xarray : xarray 0.11.3 != \u001b[31m0.12.1 \u001b[0m 1.172104s\n",
- "pyOpenSSL : OpenSSL 19.0.0 0.000034s\n",
- "entrypoints : entrypoints 0.3 0.002844s\n",
- "async_generator : async_generator 1.10 0.000047s\n",
- "absl-py : absl 0.8.1 0.012326s\n",
- "cryptography : cryptography 2.8 0.000051s\n",
- "tornado : tornado 6.0.3 0.000029s\n",
- "bokeh : bokeh 1.3.4 0.089318s\n",
- "seaborn : seaborn 0.9.0 11.679716s\n",
- "nbformat : nbformat 4.4.0 0.195660s\n",
- "param : param 1.9.2 0.209250s\n",
- "pyviz_comms : pyviz_comms 0.7.2 0.092592s\n",
- "holoviews : holoviews 1.12.6 1.424016s\n",
- "alabaster : alabaster 0.7.12 0.014988s\n",
- "Babel : babel 2.7.0 0.081024s\n",
- "snowballstemmer : snowballstemmer 2.0.0 0.351891s\n",
- "docutils : docutils 0.15.2 0.027402s\n",
- "imagesize : imagesize 1.1.0 0.004413s\n",
- "sphinxcontrib-websupport : sphinxcontrib.websupport 1.1.2 0.889744s\n",
- "Sphinx : sphinx 1.8.5 0.000060s\n",
- "pexpect : pexpect 4.7.0 0.000043s\n",
- "ipython : IPython 7.9.0 0.000038s\n",
- "ipynb : ipynb 0.5.1 0.014553s\n",
- "jupyter_core : jupyter_core 4.6.1 0.000053s\n",
- "retrying : retrying 1.3.3 0.020777s\n",
- "plotly : plotly 4.2.1 6.939769s\n",
- "tikzplotlib : tikzplotlib 0.8.4 0.114980s\n",
- "jupyter_client : jupyter_client 5.3.4 0.000043s\n",
- "traitlets : traitlets 4.3.3 0.000031s\n",
- "pyzmq : zmq 18.1.0 0.000028s\n",
- "singledispatch : singledispatch 3.4.0.3 0.062908s\n",
- "ipyparallel : ipyparallel 6.2.4 0.000068s\n",
- "ipykernel : ipykernel 5.1.3 0.000048s\n",
- "terminado : terminado 0.8.2 0.047164s\n",
- "bleach : bleach 3.1.0 0.469373s\n",
- "mistune : mistune 0.8.4 0.023354s\n",
- "pandocfilters : pandocfilters 1.4.2 0.001329s\n",
- "Pygments : pygments 2.4.2 0.000043s\n",
- "testpath : testpath 0.4.4 0.003176s\n",
- "nbconvert : nbconvert 5.6.1 0.042023s\n",
- "ipython_genutils : ipython_genutils 0.2.0 0.000036s\n",
- "Send2Trash : send2trash 1.5.0 0.010062s\n",
- "notebook : notebook 6.0.2 0.000031s\n",
- "version_information : version_information 1.0.3 0.047597s\n",
- "lesscpy : lesscpy 0.13.0 0.005995s\n",
- "prometheus-client : prometheus_client 0.7.1 0.025599s\n",
- "jupyterthemes : jupyterthemes 0.20.0 0.052266s\n",
- "zipp : zipp 0.6.0 0.000048s\n",
- "importlib_metadata : importlib_metadata 0.23 0.000036s\n",
- "jsonschema : jsonschema 3.1.1 0.000030s\n",
- "jupyterlab_launcher : jupyterlab_launcher 0.13.1 0.109656s\n",
- "sphinx_rtd_theme : sphinx_rtd_theme 0.4.3 0.008458s\n",
- "future : future 0.18.1 0.006830s\n",
- "commonmark : commonmark 0.9.1 0.095996s\n",
- "recommonmark : recommonmark 0.6.0 0.002422s\n",
- "jupyterlab : jupyterlab 1.2.1 0.002643s\n",
- "json5 : json5 0.8.5 0.003840s\n",
- "jupyterlab_server : jupyterlab_server 1.0.6 0.004840s\n",
- "ptyprocess : ptyprocess 0.6.0 0.000037s\n",
- "defusedxml : defusedxml 0.6.0 0.000027s\n",
- "widgetsnbextension : widgetsnbextension 3.5.1 0.016441s\n",
- "ipywidgets : ipywidgets 7.5.1 0.000042s\n",
- "ipydatawidgets : ipydatawidgets 4.0.1 0.134411s\n",
- "traittypes : traittypes 0.2.1 0.000048s\n",
- "bqplot : bqplot 0.11.9 0.271027s\n",
- "jupyter_bokeh : jupyter_bokeh 1.1.1 != \u001b[31m\u001b[31mNO MATCH\u001b[0m\u001b[0m 1.545438s\n",
- "pythreejs : pythreejs 2.1.1 1.858083s\n",
- "PyWavelets : pywt 1.1.1 0.377231s\n",
- "imageio : imageio 2.6.1 0.387762s\n",
- "networkx : networkx 2.3 3.447984s\n",
- "scikit-image : skimage 0.16.2 0.284224s\n",
- "ipywebrtc : ipywebrtc 0.5.0 0.040460s\n",
- "ipyvolume : ipyvolume 0.5.2 0.409094s\n",
- "branca : branca 0.3.1 0.226449s\n",
- "ipyleaflet : ipyleaflet 0.11.4 0.070324s\n",
- "ipympl : ipympl 0.3.3 0.123354s\n",
- "PyYAML : yaml 5.1.2 0.000082s\n",
- "jupyter_nbextensions_configurator : jupyter_nbextensions_configurator 0.4.1 0.003318s\n",
- "jupyter_latex_envs : latex_envs 1.4.6 != \u001b[31m1.4.0 \u001b[0m 0.005721s\n",
- "jupyter_highlight_selected_word : jupyter_highlight_selected_word 0.2.0 0.020243s\n",
- "jupyter_contrib_core : jupyter_contrib_core 0.3.3 0.002995s\n",
- "jupyter_contrib_nbextensions : jupyter_contrib_nbextensions 0.5.1 0.002769s\n",
- "rise : rise 5.5.1 0.188142s\n",
- "typing-extensions : typing_extensions 3.7.4 0.037277s\n",
- "idna-ssl : idna_ssl 1.1.0 0.002152s\n",
- "multidict : multidict 4.5.2 0.004443s\n",
- "yarl : yarl 1.3.0 0.003127s\n",
- "async-timeout : async_timeout 3.0.1 0.003045s\n",
- "aiohttp : aiohttp 3.6.2 0.077788s\n",
- "simpervisor : simpervisor 0.3 0.003966s\n",
- "jupyter_server : jupyter_server 0.1.1 0.001706s\n",
- "jupyter-server-proxy : jupyter_server_proxy 1.1.0 != \u001b[31m1.2.0 \u001b[0m 0.004240s\n",
- "jupyterlab_github : jupyterlab_github 1.0.1 != \u001b[31m1.0.0 \u001b[0m 0.000919s\n",
- "jupyterlab-gitlab : jupyterlab_gitlab 0.3.0 != \u001b[31m0.2.0 \u001b[0m 0.001144s\n",
- "jupyterlab-quickopen : jupyterlab_quickopen 0.3.0 0.002939s\n",
- "zstandard : zstandard 0.12.0 0.000029s\n",
- "itk_core : itk_core \u001b[31mIMPORT FAILED\u001b[0m\n",
- "itk_filtering : itk_filtering \u001b[31mIMPORT FAILED\u001b[0m\n",
- "itk_segmentation : itk_segmentation \u001b[31mIMPORT FAILED\u001b[0m\n",
- "itk_numerics : itk_numerics \u001b[31mIMPORT FAILED\u001b[0m\n",
- "itk_registration : itk_registration \u001b[31mIMPORT FAILED\u001b[0m\n",
- "itk_io : itk_io \u001b[31mIMPORT FAILED\u001b[0m\n",
- "itk-meshtopolydata : itk-meshtopolydata \u001b[31mIMPORT FAILED\u001b[0m\n",
- "pyct : pyct 0.4.6 0.076661s\n",
- "colorcet : colorcet 2.0.2 != \u001b[31m1.0.0 \u001b[0m 1.035480s\n",
- "itkwidgets : itkwidgets 0.22.0 13.082362s\n",
- "ujson : ujson 1.35 0.037301s\n",
- "jupyterlab_iframe : jupyterlab_iframe 0.2.1 0.004151s\n",
- "python-dotenv : dotenv 0.10.3 0.056290s\n",
- "jupyterlab_latex : jupyterlab_latex 1.0.0 0.004882s\n",
- "jupyterlab_slurm : jupyterlab_slurm 1.0.5 0.002469s\n",
- "jupyterlmod : jupyterlmod 1.7.5 0.003136s\n",
- "nbresuse : nbresuse 0.3.2 0.001697s\n",
- "colorama : colorama 0.4.1 0.000065s\n",
- "nbdime : nbdime 1.1.0 0.020851s\n",
- "smmap2 : smmap 2.0.5 0.000058s\n",
- "gitdb2 : gitdb 2.0.6 0.025730s\n",
- "GitPython : git 3.0.4 0.099233s\n",
- "jupyterlab-git : jupyterlab_git 0.8.1 0.016555s\n",
- "sidecar : sidecar 0.3.0 0.018072s\n",
- "pycodestyle : pycodestyle 2.5.0 0.007567s\n",
- "autopep8 : autopep8 1.4.4 0.004303s\n",
- "yapf : yapf 0.28.0 0.025461s\n",
- "toml : toml 0.10.0 0.003055s\n",
- "pathspec : pathspec 0.6.0 0.077891s\n",
- "typed_ast : typed_ast 1.4.0 0.000055s\n",
- "regex : regex 2019.11.1 != \u001b[31m2.5.65 \u001b[0m 0.087107s\n",
- "black : black 19.3b0 0.265862s\n",
- "jupyterlab-code-formatter : jupyterlab_code_formatter 0.6.1 0.001970s\n",
- "pamela : pamela 1.0.0 0.081929s\n",
- "certipy : certipy 0.1.3 0.000066s\n",
- "oauthlib : oauthlib 3.1.0 0.000042s\n",
- "jupyterhub : jupyterhub 1.0.0 0.003949s\n",
- "appmode : appmode 0.6.0 0.001285s\n",
- "HeapDict : heapdict 1.0.1 0.000043s\n",
- "zict : zict 1.0.0 0.000043s\n",
- "tblib : tblib 1.5.0 0.000032s\n",
- "sortedcontainers : sortedcontainers 2.1.0 0.000033s\n",
- "msgpack : msgpack 0.6.2 0.000029s\n",
- "dask : dask 2.6.0 0.000039s\n",
- "distributed : distributed 2.6.0 0.000030s\n",
- "dask-jobqueue : dask-jobqueue \u001b[31mIMPORT FAILED\u001b[0m\n",
- "dask_labextension : dask_labextension 1.0.3 0.012876s\n",
- "Automat : automat 0.8.0 0.056752s\n",
- "PyHamcrest : hamcrest 1.9.0 0.317690s\n",
- "Twisted : twisted 19.7.0 0.044753s\n",
- "autobahn : autobahn 19.10.1 0.006888s\n",
- "constantly : constantly 15.1.0 0.039913s\n",
- "hyperlink : hyperlink 19.0.0 0.074022s\n",
- "incremental : incremental 17.5.0 0.000064s\n",
- "txaio : txaio 18.8.1 0.038220s\n",
- "zope.interface : zope.interface 4.6.0 0.138110s\n",
- "backcall : backcall 0.1.0 0.000064s\n",
- "wslink : wslink 0.1.11 0.007843s\n",
- "jupyterlab_pygments : jupyterlab_pygments 0.1.0 0.009341s\n",
- "ipyvue : ipyvue 1.0.0 0.025899s\n",
- "ipyvuetify : ipyvuetify 1.1.1 0.414047s\n",
- "voila : voila 0.1.14 0.010617s\n",
- "voila-material : - 0.2.5 0.000001s\n",
- "voila-gridstack : - 0.0.6 0.000000s\n",
- "voila-vuetify : - 0.1.1 0.000000s\n",
- "dicom-upload : dicom-upload \u001b[31mIMPORT FAILED\u001b[0m\n",
- "fileupload : fileupload master != \u001b[31m0.1.0.dev \u001b[0m 0.014791s\n",
- "pvlink : pvlink 0.1.2 0.012866s\n",
- "julia : julia 0.5.0 0.102546s\n",
- "textwrap3 : textwrap3 0.9.2 0.023105s\n",
- "ansiwrap : ansiwrap 0.8.4 0.039140s\n",
- "backports.weakref : backports.weakref 1.0.post1 0.020673s\n",
- "backports.tempfile : backports.tempfile 1.0 0.006095s\n",
- "tqdm : tqdm 4.41.0 0.101886s\n",
- "tenacity : tenacity 6.0.0 0.093667s\n",
- "papermill : papermill 1.2.1 0.417333s\n",
- "patsy : patsy 0.5.1 0.281202s\n",
- "statsmodels : statsmodels 0.10.2 0.000063s\n",
- "cftime : cftime 1.0.4.2 0.000048s\n",
- "vega_datasets : vega_datasets 0.8.0 0.124947s\n",
- "arviz : arviz 0.5.1 8.192571s\n",
- "Theano : Theano \u001b[31mIMPORT FAILED\u001b[0m\n",
- "altair : altair 3.3.0 0.572322s\n",
- "cssselect : cssselect 1.1.0 0.074927s\n",
- "smopy : smopy 0.0.7 != \u001b[31m0.0.6 \u001b[0m 0.005187s\n",
- "joblib : joblib 0.14.1 0.000062s\n",
- "scikit-learn : scikit-learn \u001b[31mIMPORT FAILED\u001b[0m\n",
- "memory_profiler : memory_profiler 0.55.0 0.048130s\n",
- "h5py : h5py 2.10.0 1.163224s\n",
- "line_profiler : line_profiler 2.1.2 != \u001b[31m\u001b[31mNO MATCH\u001b[0m\u001b[0m 0.041151s\n",
- "pymc3 : pymc3 3.8 6.798788s\n",
- "llvmlite : llvmlite 0.30.0 0.000073s\n",
- "numba : numba 0.46.0 0.000051s\n",
- "numexpr : numexpr 2.7.0 0.101310s\n",
- "ipythonblocks : ipythonblocks 1.9.0 0.023981s\n",
- "pydub : pydub 0.23.1 0.209780s\n",
- "multipledispatch : multipledispatch 0.6.0 0.062537s\n",
- "partd : partd 1.1.0 0.168488s\n",
- "locket : locket 0.2.0 0.000052s\n",
- "fsspec : fsspec 0.6.2 0.136985s\n",
- "datashape : datashape 0.5.2 0.177264s\n",
- "datashader : datashader 0.9.0 13.161141s\n",
- "selenium : selenium 3.141.0 0.009461s\n",
- "graphviz : graphviz 0.13.2 0.088085s\n",
- "vincent : vincent 0.4.4 0.167066s\n",
- "Shapely : Shapely \u001b[31mIMPORT FAILED\u001b[0m\n",
- "pyshp : pyshp \u001b[31mIMPORT FAILED\u001b[0m\n",
- "Cartopy : Cartopy \u001b[31mIMPORT FAILED\u001b[0m\n",
- "pandas-datareader : pandas-datareader \u001b[31mIMPORT FAILED\u001b[0m\n"
- ]
- }
- ],
- "source": [
- "import importlib\n",
- "from colorama import Fore, Style\n",
- "from timeit import default_timer as timer\n",
- "\n",
- "print(\"PYPI NAME\".ljust(20), \": \", \"IMPORT NAME\".ljust(20) + \"REQ.VERS.|INST.VERS.\".ljust(25) + \"IMPORT TIME\")\n",
- "print(\"=================================================================================\")\n",
- "for pkg_name, pkg_version, pkg_importname in pkg_list:\n",
- " if not pkg_importname:\n",
- " pkg_importname = pkg_name\n",
- " pkg = None\n",
- " \n",
- " try:\n",
- " # import package\n",
- " start_time = timer()\n",
- " if pkg_importname != \"-\":\n",
- " pkg = importlib.import_module(pkg_importname)\n",
- " import_time = timer() - start_time\n",
- " \n",
- " # get version\n",
- " try:\n",
- " version = pkg.__version__\n",
- " if not isinstance(pkg.__version__, str):\n",
- " raise\n",
- " except:\n",
- " version = get_version(pkg_name)\n",
- " \n",
- " if version != pkg_version:\n",
- " version = pkg_version.ljust(10) + \" != \" + f\"{Fore.RED}\" + version.ljust(10) + f\"{Style.RESET_ALL}\"\n",
- "\n",
- " print(pkg_name.ljust(20), \": \", pkg_importname.ljust(20), version.ljust(24), f\"{import_time:.6f}\"+\"s\")\n",
- " except:\n",
- " print(pkg_name.ljust(20), \": \", pkg_importname.ljust(20), f\"{Fore.RED}IMPORT FAILED{Style.RESET_ALL}\") \n",
- " \n",
- " #try:\n",
- " # print(\"\".ljust(24), pkg.__file__)\n",
- " #except:\n",
- " # print(\"\".ljust(24), f\"{Fore.RED}UNKNOWN{Style.RESET_ALL}\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.6.8"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}
diff --git a/001-Jupyter/002-JupyterExtensions/.ipynb_checkpoints/CodeFormatter-checkpoint.ipynb b/001-Jupyter/002-JupyterExtensions/.ipynb_checkpoints/CodeFormatter-checkpoint.ipynb
deleted file mode 100644
index e88a7dcf474f20d8d73544fd4a2efb1a5c1eb27f..0000000000000000000000000000000000000000
--- a/001-Jupyter/002-JupyterExtensions/.ipynb_checkpoints/CodeFormatter-checkpoint.ipynb
+++ /dev/null
@@ -1,80 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- " # Press \"Format notebook\" or in the menu \"Edit -> Apply ... Formatter\"\n",
- " # useless comment\n",
- "import requests # useless comment\n",
- "\n",
- "headers = {\n",
- " 'Referer': 'https://www.transtats.bts.gov/DL_SelectFields.asp?Table_ID=236&DB_Short_Name=On-Time',\n",
- " 'Origin': 'https://www.transtats.bts.gov',\n",
- " 'Content-Type': 'application/x-www-form-urlencoded',\n",
- "}\n",
- "\n",
- "params = (\n",
- " ('Table_ID', '236'),\n",
- " ('Has_Group', '3'), ('Is_Zipped', '0'),\n",
- ")\n",
- "\n",
- "with open('modern-1-url.txt', encoding='utf-8') as f:\n",
- " data = f.read().strip()\n",
- "\n",
- "os.makedirs('data', exist_ok=True)\n",
- "\n",
- "\n",
- "import pandas as pd\n",
- "\n",
- "\n",
- "\n",
- "\n",
- "\n",
- "\n",
- "def read(fp):\n",
- " df = (pd.read_csv(fp)\n",
- " .rename(columns=str.lower) .drop('unnamed: 36', axis=1) .pipe(extract_city_name) .pipe(time_to_datetime, ['dep_time', 'arr_time', 'crs_arr_time', 'crs_dep_time'])\n",
- " .assign(fl_date=lambda x: pd.to_datetime(x['fl_date']),\n",
- " dest=lambda x: pd.Categorical(x['dest']),\n",
- " origin=lambda x: pd.Categorical(x['origin']), tail_num=lambda x: pd.Categorical(x['tail_num']), unique_carrier=lambda x: pd.Categorical(x['unique_carrier']),\n",
- " cancellation_code=lambda x: pd.Categorical(x['cancellation_code'])))\n",
- " return df\n",
- "\n",
- "\n",
- "def extract_city_name(df:pd.DataFrame) -> pd.DataFrame:\n",
- " '''\n",
- " Chicago, IL -> Chicago for origin_city_name and dest_city_name\n",
- " '''\n",
- " cols = ['origin_city_name', 'dest_city_name']\n",
- " city = df[cols].apply(lambda x: x.str.extract(\"(.*), \\w{2}\", expand=False))\n",
- " df = df.copy()\n",
- " df[['origin_city_name', 'dest_city_name']] = city\n",
- " return df\n"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.6.8"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 4
-}