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docs/source/config_overview.md
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63
docs/source/config_overview.md
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@ -0,0 +1,63 @@
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(configuration-overview)=
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# Configuration Overview
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Beyond the default configuration settings, you can configure a rich array of
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options to suit your workflow. Here are areas that are commonly configured
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when using Jupyter Notebook:
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> - {ref}`Jupyter's common configuration system <configure-common>`
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> - {ref}`Jupyter Server <configure-jupyter-server>`
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> - {ref}`Notebook extensions <configure-nbextensions>`
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Let's look at highlights of each area.
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(configure-common)=
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## Jupyter's Common Configuration system
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Jupyter applications, from the Notebook to JupyterHub to nbgrader, share a
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common configuration system. The process for creating a configuration file
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and editing settings is similar for all the Jupyter applications.
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> - [Jupyter’s Common Configuration Approach](https://jupyter.readthedocs.io/en/latest/use/config.html)
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> - [Common Directories and File Locations](https://jupyter.readthedocs.io/en/latest/use/jupyter-directories.html)
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> - [Language kernels](https://jupyter.readthedocs.io/en/latest/projects/kernels.html)
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> - [traitlets](https://traitlets.readthedocs.io/en/latest/config.html#module-traitlets.config)
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> provide a low-level architecture for configuration.
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(configure-jupyter-server)=
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## Jupyter server
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The Jupyter Server runs the language kernel and communicates with the
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front-end Notebook client (i.e. the familiar notebook interface).
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> - Configuring the Jupyter Server
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>
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> > To create a `jupyter_server_config.py` file in the `.jupyter`
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> > directory, with all the defaults commented out, use the following
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> > command:
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> >
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> > ```
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> > $ jupyter server --generate-config
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> > ```
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>
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> - [Running a Jupyter Server](https://jupyter-server.readthedocs.io/en/stable/operators/public-server.html)
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>
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> - Related: [Configuring a language kernel](https://ipython.readthedocs.io/en/latest/install/kernel_install.html)
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> to run in the Jupyter Server enables your server to run other languages, like R or Julia.
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(configure-nbextensions)=
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## Notebook extensions
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The Notebook frontend can be extending with JupyterLab extensions.
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See the {ref}`Frontend Extension Guide <frontend-extensions>` for more information.
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|
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[Security in Jupyter notebooks:](https://jupyter-server.readthedocs.io/en/stable/operators/security.html)
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Since security policies vary from organization to organization, we encourage you to
|
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consult with your security team on settings that would be best for your use
|
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cases. Our documentation offers some responsible security practices, and we
|
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recommend becoming familiar with the practices.
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@ -1,63 +0,0 @@
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.. _configuration-overview:
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Configuration Overview
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======================
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|
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Beyond the default configuration settings, you can configure a rich array of
|
||||
options to suit your workflow. Here are areas that are commonly configured
|
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when using Jupyter Notebook:
|
||||
|
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- :ref:`Jupyter's common configuration system <configure_common>`
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- :ref:`Jupyter Server <configure_jupyter_server>`
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- :ref:`Notebook extensions <configure_nbextensions>`
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|
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Let's look at highlights of each area.
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.. _configure_common:
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Jupyter's Common Configuration system
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-------------------------------------
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Jupyter applications, from the Notebook to JupyterHub to nbgrader, share a
|
||||
common configuration system. The process for creating a configuration file
|
||||
and editing settings is similar for all the Jupyter applications.
|
||||
|
||||
- `Jupyter’s Common Configuration Approach <https://jupyter.readthedocs.io/en/latest/use/config.html>`_
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- `Common Directories and File Locations <https://jupyter.readthedocs.io/en/latest/use/jupyter-directories.html>`_
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- `Language kernels <https://jupyter.readthedocs.io/en/latest/projects/kernels.html>`_
|
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- `traitlets <https://traitlets.readthedocs.io/en/latest/config.html#module-traitlets.config>`_
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provide a low-level architecture for configuration.
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|
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.. _configure_jupyter_server:
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Jupyter server
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---------------
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|
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The Jupyter Server runs the language kernel and communicates with the
|
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front-end Notebook client (i.e. the familiar notebook interface).
|
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|
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- Configuring the Jupyter Server
|
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|
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To create a ``jupyter_server_config.py`` file in the ``.jupyter``
|
||||
directory, with all the defaults commented out, use the following
|
||||
command::
|
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|
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$ jupyter server --generate-config
|
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|
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- `Running a Jupyter Server <https://jupyter-server.readthedocs.io/en/stable/operators/public-server.html>`_
|
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- Related: `Configuring a language kernel <https://ipython.readthedocs.io/en/latest/install/kernel_install.html>`_
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to run in the Jupyter Server enables your server to run other languages, like R or Julia.
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.. _configure_nbextensions:
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Notebook extensions
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-------------------
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|
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The Notebook frontend can be extending with JupyterLab extensions.
|
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|
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See the :ref:`Frontend Extension Guide <frontend_extensions>` for more information.
|
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|
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`Security in Jupyter notebooks: <https://jupyter-server.readthedocs.io/en/stable/operators/security.html>`_
|
||||
Since security policies vary from organization to organization, we encourage you to
|
||||
consult with your security team on settings that would be best for your use
|
||||
cases. Our documentation offers some responsible security practices, and we
|
||||
recommend becoming familiar with the practices.
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10
docs/source/configuration.md
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10
docs/source/configuration.md
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@ -0,0 +1,10 @@
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# Configuration
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```{toctree}
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:caption: Configuration
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:maxdepth: 1
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config_overview
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Security <https://jupyter-server.readthedocs.io/en/stable/operators/security.html>
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extending/index.rst
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```
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@ -1,11 +0,0 @@
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=============
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Configuration
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=============
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.. toctree::
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:maxdepth: 1
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:caption: Configuration
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|
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config_overview
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Security <https://jupyter-server.readthedocs.io/en/stable/operators/security.html>
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extending/index.rst
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9
docs/source/contributor.md
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9
docs/source/contributor.md
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@ -0,0 +1,9 @@
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# Contributor
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```{toctree}
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:caption: Contributor Documentation
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:maxdepth: 1
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contributing
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development_faq
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```
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@ -1,10 +0,0 @@
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===========
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Contributor
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===========
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.. toctree::
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:maxdepth: 1
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:caption: Contributor Documentation
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|
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contributing
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development_faq
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9
docs/source/development_faq.md
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9
docs/source/development_faq.md
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@ -0,0 +1,9 @@
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(development-faq)=
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# Developer FAQ
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1. How do I install a prerelease version such as a beta or release candidate?
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```bash
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python -m pip install notebook --pre --upgrade
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```
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@ -1,10 +0,0 @@
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.. _development_faq:
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Developer FAQ
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=============
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1. How do I install a prerelease version such as a beta or release candidate?
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|
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.. code-block:: bash
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python -m pip install notebook --pre --upgrade
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@ -1,8 +1,6 @@
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.. _frontend_extensions:
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(frontend-extensions)=
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===========================
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Custom front-end extensions
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===========================
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# Custom front-end extensions
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This describes the basic steps to write a TypeScript extension for the Jupyter
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notebook front-end. This allows you to customize the behaviour of the various
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@ -15,5 +13,5 @@ This means Notebook v7 is able to reuse many of the existing extensions from the
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If you would like to develop a prebuilt extension for Notebook v7, check out:
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|
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- `JupyterLab Extension Tutorial <https://jupyterlab.readthedocs.io/en/latest/extension/extension_tutorial.html>`_: A tutorial to learn how to make a simple JupyterLab extension.
|
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- The `JupyterLab Extension Examples Repository <https://github.com/jupyterlab/extension-examples>`_: A short tutorial series to learn how to develop extensions for JupyterLab by example.
|
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- [JupyterLab Extension Tutorial](https://jupyterlab.readthedocs.io/en/latest/extension/extension_tutorial.html): A tutorial to learn how to make a simple JupyterLab extension.
|
||||
- The [JupyterLab Extension Examples Repository](https://github.com/jupyterlab/extension-examples): A short tutorial series to learn how to develop extensions for JupyterLab by example.
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12
docs/source/extending/index.md
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12
docs/source/extending/index.md
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@ -0,0 +1,12 @@
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# Extending the Notebook
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Certain subsystems of the notebook server are designed to be extended or
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overridden by users. These documents explain these systems, and show how to
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override the notebook's defaults with your own custom behavior.
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|
||||
```{toctree}
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:maxdepth: 2
|
||||
|
||||
Extending the Jupyter Server <https://jupyter-server.readthedocs.io/en/stable/developers/index.html>
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frontend_extensions
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```
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@ -1,13 +0,0 @@
|
||||
======================
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||||
Extending the Notebook
|
||||
======================
|
||||
|
||||
Certain subsystems of the notebook server are designed to be extended or
|
||||
overridden by users. These documents explain these systems, and show how to
|
||||
override the notebook's defaults with your own custom behavior.
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
|
||||
Extending the Jupyter Server <https://jupyter-server.readthedocs.io/en/stable/developers/index.html>
|
||||
frontend_extensions
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||||
17
docs/source/index.md
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17
docs/source/index.md
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@ -0,0 +1,17 @@
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# The Jupyter Notebook
|
||||
|
||||
```{image} ./_static/images/notebook-running-code.png
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||||
|
||||
```
|
||||
|
||||
- [Installation](https://jupyter.readthedocs.io/en/latest/install.html)
|
||||
- [Starting the Notebook](https://jupyter.readthedocs.io/en/latest/running.html)
|
||||
|
||||
```{toctree}
|
||||
:maxdepth: 2
|
||||
|
||||
user-documentation
|
||||
configuration
|
||||
contributor
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||||
migrate_to_notebook7
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```
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@ -1,17 +0,0 @@
|
||||
====================
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||||
The Jupyter Notebook
|
||||
====================
|
||||
|
||||
|
||||
.. image:: ./_static/images/notebook-running-code.png
|
||||
|
||||
* `Installation <https://jupyter.readthedocs.io/en/latest/install.html>`_
|
||||
* `Starting the Notebook <https://jupyter.readthedocs.io/en/latest/running.html>`_
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
|
||||
user-documentation
|
||||
configuration
|
||||
contributor
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||||
migrate_to_notebook7
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@ -1,38 +1,34 @@
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Migrating to Notebook 7
|
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=======================
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# Migrating to Notebook 7
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|
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Build Jupyter Notebook v7 off of JupyterLab components
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
## Build Jupyter Notebook v7 off of JupyterLab components
|
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|
||||
Read more details about the changes currently taking place in the
|
||||
Jupyter Ecosystem in the `JEP 79`_ and `team-compass note`_.
|
||||
Jupyter Ecosystem in the [JEP 79] and [team-compass note].
|
||||
|
||||
Notebook 7 is built on top of JupyterLab components and delivers new features
|
||||
like realtime collaboration, debugger, theming.
|
||||
|
||||
Compatibility with older versions
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
## Compatibility with older versions
|
||||
|
||||
Any extension developed for Notebook < 7 or NbClassic will not be
|
||||
Any extension developed for Notebook \< 7 or NbClassic will not be
|
||||
compatible with Notebook 7 and upwards.
|
||||
|
||||
Some extensions like nbgrader have already been ported. We invite you to
|
||||
check if the extensions you are using have already been ported.
|
||||
|
||||
Simulaneous usage of different versions
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
## Simulaneous usage of different versions
|
||||
|
||||
**NbClassic and Notebook 7**
|
||||
|
||||
You can install NbClassic, Notebook 7 and JupyterLab, all three of
|
||||
which will provide different user interfaces
|
||||
on the same server. When Notebook 7 is available, the NbClassic UI, will
|
||||
be served at the ``/nbclassic/tree`` base path rather than the
|
||||
base path ``/tree`` used otherwise. If you are using Notebook 7 along
|
||||
be served at the `/nbclassic/tree` base path rather than the
|
||||
base path `/tree` used otherwise. If you are using Notebook 7 along
|
||||
with NbClassic, you will also have JupyterLab installed as it is a
|
||||
dependency of Notebook 7, and these front ends will be available
|
||||
through the following base paths: JupyterLab at ``/lab``, Notebook 7 at
|
||||
``/tree``, and NbClassic at ``/nbclassic/tree``.
|
||||
through the following base paths: JupyterLab at `/lab`, Notebook 7 at
|
||||
`/tree`, and NbClassic at `/nbclassic/tree`.
|
||||
|
||||
**NbClassic and Notebook 6.5.x**
|
||||
|
||||
@ -40,46 +36,46 @@ As NbClassic provides the static assets for Notebook 6.5.x, while
|
||||
having both installed should cause no issues, the user interface provided
|
||||
by these two packages will be the same. These UIs will be served by
|
||||
different back end servers. An NbClassic instance will be at a server with the
|
||||
``/tree`` path and opening a Notebook 6.5.x instance will open on a
|
||||
different server with the ``/tree`` path as well, presenting the same
|
||||
`/tree` path and opening a Notebook 6.5.x instance will open on a
|
||||
different server with the `/tree` path as well, presenting the same
|
||||
static assets. When starting an instance of JupyterLab you will be able
|
||||
to access the classic view of Notebook with NbClassic served on the same
|
||||
server at ``/tree``.
|
||||
server at `/tree`.
|
||||
|
||||
**NbClassic and Notebook <= 6.4.x**
|
||||
**NbClassic and Notebook \<= 6.4.x**
|
||||
|
||||
When using NbClassic and Notebook <= 6.4.x you can expect that these UIs
|
||||
When using NbClassic and Notebook \<= 6.4.x you can expect that these UIs
|
||||
will not be only presented at different servers, meaning they will both
|
||||
be available at their respective server under ``/tree`` but they
|
||||
be available at their respective server under `/tree` but they
|
||||
may also differ as potential changes to the NbClassic UI will not be
|
||||
reflected in Notebook versions <= 6.4.x. In this case as well, you would
|
||||
reflected in Notebook versions \<= 6.4.x. In this case as well, you would
|
||||
be able to access the classic view of Notebook with NbClassic served on
|
||||
the same server, at ``/tree``.
|
||||
the same server, at `/tree`.
|
||||
|
||||
**NbClassic and JupyterLab 3.x**
|
||||
|
||||
When only JupyterLab 3.x is installed, then NbClassic does not have to be
|
||||
explicitly installed as JupyterLab 3.x depends on it. They will run on
|
||||
the same server, and are reachable via ``/tree`` for NbClassic and
|
||||
``/lab`` for JupyterLab.
|
||||
the same server, and are reachable via `/tree` for NbClassic and
|
||||
`/lab` for JupyterLab.
|
||||
|
||||
**NbClassic and JupyterLab 4.x**
|
||||
|
||||
When only JupyterLab 4.x is installed, then NbClassic has to be installed
|
||||
explictly. They will run on the same server, and are reachable via
|
||||
``/tree`` for NbClassic, and ``/lab`` for JupyterLab.
|
||||
`/tree` for NbClassic, and `/lab` for JupyterLab.
|
||||
|
||||
**NbClassic Independently**
|
||||
|
||||
When you choose to install only NbClassic via ``pip install nbclassic``,
|
||||
the classic Notebook UI will be presented at the ``/tree`` path. As the
|
||||
When you choose to install only NbClassic via `pip install nbclassic`,
|
||||
the classic Notebook UI will be presented at the `/tree` path. As the
|
||||
other frontends are not installed, attempting to access the other paths
|
||||
will return errors. Note that NbClassic being a Jupyter Server extension,
|
||||
indicated Jupyter Server will be available. This provides an additional
|
||||
way to view the NbClassic frontend. You would be able to manually
|
||||
way to view the NbClassic frontend. You would be able to manually
|
||||
enable the extension when running an instance of Jupyter Server,
|
||||
``> jupyter server --ServerApp.jpserver_extensions="nbclassic=True"``,
|
||||
which will provide the NbClassic frontend at ``/tree`` path when visited.
|
||||
`> jupyter server --ServerApp.jpserver_extensions="nbclassic=True"`,
|
||||
which will provide the NbClassic frontend at `/tree` path when visited.
|
||||
|
||||
.. _JEP 79: https://jupyter.org/enhancement-proposals/79-notebook-v7/notebook-v7.html
|
||||
.. _team-compass note: https://github.com/jupyter/notebook-team-compass/issues/5#issuecomment-1085254000
|
||||
[jep 79]: https://jupyter.org/enhancement-proposals/79-notebook-v7/notebook-v7.html
|
||||
[team-compass note]: https://github.com/jupyter/notebook-team-compass/issues/5#issuecomment-1085254000
|
||||
@ -1,15 +1,13 @@
|
||||
.. _htmlnotebook:
|
||||
(htmlnotebook)=
|
||||
|
||||
The Jupyter Notebook
|
||||
====================
|
||||
# The Jupyter Notebook
|
||||
|
||||
Introduction
|
||||
------------
|
||||
## Introduction
|
||||
|
||||
The notebook extends the console-based approach to interactive computing in
|
||||
a qualitatively new direction, providing a web-based application suitable for
|
||||
capturing the whole computation process: developing, documenting, and
|
||||
executing code, as well as communicating the results. The Jupyter notebook
|
||||
executing code, as well as communicating the results. The Jupyter notebook
|
||||
combines two components:
|
||||
|
||||
**A web application**: a browser-based tool for interactive authoring of
|
||||
@ -20,79 +18,62 @@ rich media output.
|
||||
application, including inputs and outputs of the computations, explanatory
|
||||
text, mathematics, images, and rich media representations of objects.
|
||||
|
||||
.. seealso::
|
||||
:::{seealso}
|
||||
See the {ref}`installation guide <jupyter:install>` on how to install the
|
||||
notebook and its dependencies.
|
||||
:::
|
||||
|
||||
See the :ref:`installation guide <jupyter:install>` on how to install the
|
||||
notebook and its dependencies.
|
||||
### Main features of the web application
|
||||
|
||||
|
||||
Main features of the web application
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
* In-browser editing for code, with automatic syntax highlighting,
|
||||
- In-browser editing for code, with automatic syntax highlighting,
|
||||
indentation, and tab completion/introspection.
|
||||
|
||||
* The ability to execute code from the browser, with the results of
|
||||
- The ability to execute code from the browser, with the results of
|
||||
computations attached to the code which generated them.
|
||||
|
||||
* Displaying the result of computation using rich media representations, such
|
||||
- Displaying the result of computation using rich media representations, such
|
||||
as HTML, LaTeX, PNG, SVG, etc. For example, publication-quality figures
|
||||
rendered by the matplotlib_ library, can be included inline.
|
||||
|
||||
* In-browser editing for rich text using the Markdown_ markup language, which
|
||||
rendered by the [matplotlib] library, can be included inline.
|
||||
- In-browser editing for rich text using the [Markdown] markup language, which
|
||||
can provide commentary for the code, is not limited to plain text.
|
||||
- The ability to easily include mathematical notation within markdown cells
|
||||
using LaTeX, and rendered natively by [MathJax].
|
||||
|
||||
* The ability to easily include mathematical notation within markdown cells
|
||||
using LaTeX, and rendered natively by MathJax_.
|
||||
### Notebook documents
|
||||
|
||||
|
||||
|
||||
.. _MathJax: https://www.mathjax.org/
|
||||
|
||||
|
||||
Notebook documents
|
||||
~~~~~~~~~~~~~~~~~~
|
||||
Notebook documents contains the inputs and outputs of a interactive session as
|
||||
well as additional text that accompanies the code but is not meant for
|
||||
execution. In this way, notebook files can serve as a complete computational
|
||||
execution. In this way, notebook files can serve as a complete computational
|
||||
record of a session, interleaving executable code with explanatory text,
|
||||
mathematics, and rich representations of resulting objects. These documents
|
||||
are internally JSON_ files and are saved with the ``.ipynb`` extension. Since
|
||||
are internally [JSON] files and are saved with the `.ipynb` extension. Since
|
||||
JSON is a plain text format, they can be version-controlled and shared with
|
||||
colleagues.
|
||||
|
||||
.. _JSON: https://en.wikipedia.org/wiki/JSON
|
||||
|
||||
Notebooks may be exported to a range of static formats, including HTML (for
|
||||
example, for blog posts), reStructuredText, LaTeX, PDF, and slide shows, via
|
||||
the nbconvert_ command.
|
||||
the [nbconvert] command.
|
||||
|
||||
Furthermore, any ``.ipynb`` notebook document available from a public
|
||||
URL can be shared via the Jupyter Notebook Viewer <nbviewer>.
|
||||
Furthermore, any `.ipynb` notebook document available from a public
|
||||
URL can be shared via the Jupyter Notebook Viewer \<nbviewer>.
|
||||
This service loads the notebook document from the URL and renders it as a
|
||||
static web page. The results may thus be shared with a colleague, or as a
|
||||
static web page. The results may thus be shared with a colleague, or as a
|
||||
public blog post, without other users needing to install the Jupyter notebook
|
||||
themselves. In effect, nbviewer is simply nbconvert_ as
|
||||
themselves. In effect, nbviewer is simply [nbconvert] as
|
||||
a web service, so you can do your own static conversions with nbconvert,
|
||||
without relying on nbviewer.
|
||||
|
||||
:::{seealso}
|
||||
{ref}`Details on the notebook JSON file format <nbformat:notebook_file_format>`
|
||||
:::
|
||||
|
||||
|
||||
.. seealso::
|
||||
|
||||
:ref:`Details on the notebook JSON file format <nbformat:notebook_file_format>`
|
||||
|
||||
|
||||
Notebooks and privacy
|
||||
~~~~~~~~~~~~~~~~~~~~~
|
||||
### Notebooks and privacy
|
||||
|
||||
Because you use Jupyter in a web browser, some people are understandably
|
||||
concerned about using it with sensitive data.
|
||||
However, if you followed the standard
|
||||
`install instructions <https://jupyter.readthedocs.io/en/latest/install.html>`_,
|
||||
[install instructions](https://jupyter.readthedocs.io/en/latest/install.html),
|
||||
Jupyter is actually running on your own computer.
|
||||
If the URL in the address bar starts with ``http://localhost:`` or
|
||||
``http://127.0.0.1:``, it's your computer acting as the server.
|
||||
If the URL in the address bar starts with `http://localhost:` or
|
||||
`http://127.0.0.1:`, it's your computer acting as the server.
|
||||
Jupyter doesn't send your data anywhere else—and as it's open source,
|
||||
other people can check that we're being honest about this.
|
||||
|
||||
@ -102,114 +83,116 @@ If you want to work with sensitive data in those cases,
|
||||
talk to your IT or data protection staff about it.
|
||||
|
||||
We aim to ensure that other pages in your browser or other users on the same
|
||||
computer can't access your notebook server. See the `security documentation <https://jupyter-server.readthedocs.io/en/stable/operators/security.html>`__ for
|
||||
computer can't access your notebook server. See the [security documentation](https://jupyter-server.readthedocs.io/en/stable/operators/security.html) for
|
||||
more about this.
|
||||
|
||||
|
||||
Starting the notebook server
|
||||
----------------------------
|
||||
## Starting the notebook server
|
||||
|
||||
You can start running a notebook server from the command line using the
|
||||
following command::
|
||||
following command:
|
||||
|
||||
jupyter notebook
|
||||
```
|
||||
jupyter notebook
|
||||
```
|
||||
|
||||
This will print some information about the notebook server in your console,
|
||||
and open a web browser to the URL of the web application (by default,
|
||||
``http://127.0.0.1:8888``).
|
||||
`http://127.0.0.1:8888`).
|
||||
|
||||
The landing page of the Jupyter notebook web application, the **dashboard**,
|
||||
shows the notebooks currently available in the notebook directory (by default,
|
||||
the directory from which the notebook server was started).
|
||||
|
||||
You can create new notebooks from the dashboard with the ``New Notebook``
|
||||
button, or open existing ones by clicking on their name. You can also drag
|
||||
and drop ``.ipynb`` notebooks and standard ``.py`` Python source code files
|
||||
You can create new notebooks from the dashboard with the `New Notebook`
|
||||
button, or open existing ones by clicking on their name. You can also drag
|
||||
and drop `.ipynb` notebooks and standard `.py` Python source code files
|
||||
into the notebook list area.
|
||||
|
||||
When starting a notebook server from the command line, you can also open a
|
||||
particular notebook directly, bypassing the dashboard, with ``jupyter notebook
|
||||
my_notebook.ipynb``. The ``.ipynb`` extension is assumed if no extension is
|
||||
particular notebook directly, bypassing the dashboard, with `jupyter notebook my_notebook.ipynb`. The `.ipynb` extension is assumed if no extension is
|
||||
given.
|
||||
|
||||
When you are inside an open notebook, the `File | Open...` menu option will
|
||||
open the dashboard in a new browser tab, to allow you to open another notebook
|
||||
from the notebook directory or to create a new notebook.
|
||||
|
||||
:::{note}
|
||||
You can start more than one notebook server at the same time, if you want
|
||||
to work on notebooks in different directories. By default the first
|
||||
notebook server starts on port 8888, and later notebook servers search for
|
||||
ports near that one. You can also manually specify the port with the
|
||||
`--port` option.
|
||||
:::
|
||||
|
||||
.. note::
|
||||
|
||||
You can start more than one notebook server at the same time, if you want
|
||||
to work on notebooks in different directories. By default the first
|
||||
notebook server starts on port 8888, and later notebook servers search for
|
||||
ports near that one. You can also manually specify the port with the
|
||||
``--port`` option.
|
||||
|
||||
Creating a new notebook document
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
### Creating a new notebook document
|
||||
|
||||
A new notebook may be created at any time, either from the dashboard, or using
|
||||
the :menuselection:`File --> New` menu option from within an active notebook.
|
||||
the {menuselection}`File --> New` menu option from within an active notebook.
|
||||
The new notebook is created within the same directory and will open in a new
|
||||
browser tab. It will also be reflected as a new entry in the notebook list on
|
||||
the dashboard.
|
||||
|
||||
.. image:: _static/images/new-notebook.gif
|
||||
```{image} _static/images/new-notebook.gif
|
||||
|
||||
```
|
||||
|
||||
### Opening notebooks
|
||||
|
||||
Opening notebooks
|
||||
~~~~~~~~~~~~~~~~~
|
||||
An open notebook has **exactly one** interactive session connected to a
|
||||
kernel, which will execute code sent by the user
|
||||
and communicate back results. This kernel remains active if the web browser
|
||||
and communicate back results. This kernel remains active if the web browser
|
||||
window is closed, and reopening the same notebook from the dashboard will
|
||||
reconnect the web application to the same kernel. In the dashboard, notebooks
|
||||
with an active kernel have a ``Shutdown`` button next to them, whereas
|
||||
notebooks without an active kernel have a ``Delete`` button in its place.
|
||||
with an active kernel have a `Shutdown` button next to them, whereas
|
||||
notebooks without an active kernel have a `Delete` button in its place.
|
||||
|
||||
Other clients may connect to the same kernel.
|
||||
When each kernel is started, the notebook server prints to the terminal a
|
||||
message like this::
|
||||
message like this:
|
||||
|
||||
[JupyterNotebookApp] Kernel started: 87f7d2c0-13e3-43df-8bb8-1bd37aaf3373
|
||||
```
|
||||
[JupyterNotebookApp] Kernel started: 87f7d2c0-13e3-43df-8bb8-1bd37aaf3373
|
||||
```
|
||||
|
||||
This long string is the kernel's ID which is sufficient for getting the
|
||||
information necessary to connect to the kernel. If the notebook uses the IPython
|
||||
kernel, you can also see this
|
||||
connection data by running the ``%connect_info`` :ref:`magic
|
||||
<magics_explained>`, which will print the same ID information along with other
|
||||
connection data by running the `%connect_info` {ref}`magic <magics_explained>`, which will print the same ID information along with other
|
||||
details.
|
||||
|
||||
You can then, for example, manually start a Qt console connected to the *same*
|
||||
kernel from the command line, by passing a portion of the ID::
|
||||
You can then, for example, manually start a Qt console connected to the _same_
|
||||
kernel from the command line, by passing a portion of the ID:
|
||||
|
||||
$ jupyter qtconsole --existing 87f7d2c0
|
||||
```
|
||||
$ jupyter qtconsole --existing 87f7d2c0
|
||||
```
|
||||
|
||||
Without an ID, ``--existing`` will connect to the most recently
|
||||
Without an ID, `--existing` will connect to the most recently
|
||||
started kernel.
|
||||
|
||||
With the IPython kernel, you can also run the ``%qtconsole``
|
||||
:ref:`magic <magics_explained>` in the notebook to open a Qt console connected
|
||||
With the IPython kernel, you can also run the `%qtconsole`
|
||||
{ref}`magic <magics_explained>` in the notebook to open a Qt console connected
|
||||
to the same kernel.
|
||||
|
||||
.. seealso::
|
||||
:::{seealso}
|
||||
{ref}`ipythonzmq`
|
||||
:::
|
||||
|
||||
:ref:`ipythonzmq`
|
||||
|
||||
Notebook user interface
|
||||
-----------------------
|
||||
## Notebook user interface
|
||||
|
||||
When you create a new notebook document, you will be presented with the
|
||||
**notebook name**, a **menu bar**, a **toolbar** and an empty **code cell**.
|
||||
|
||||
.. image:: ./_static/images/blank-notebook-ui.png
|
||||
```{image} ./_static/images/blank-notebook-ui.png
|
||||
|
||||
```
|
||||
|
||||
**Notebook name**: The name displayed at the top of the page,
|
||||
next to the Jupyter logo, reflects the name of the ``.ipynb`` file.
|
||||
next to the Jupyter logo, reflects the name of the `.ipynb` file.
|
||||
Clicking on the notebook name brings up a dialog which allows you to rename it.
|
||||
Thus, renaming a notebook
|
||||
from "Untitled0" to "My first notebook" in the browser, renames the
|
||||
``Untitled0.ipynb`` file to ``My first notebook.ipynb``.
|
||||
`Untitled0.ipynb` file to `My first notebook.ipynb`.
|
||||
|
||||
**Menu bar**: The menu bar presents different options that may be used to
|
||||
manipulate the way the notebook functions.
|
||||
@ -219,52 +202,49 @@ operations within the notebook, by clicking on an icon.
|
||||
|
||||
**Code cell**: the default type of cell; read on for an explanation of cells.
|
||||
|
||||
## Structure of a notebook document
|
||||
|
||||
Structure of a notebook document
|
||||
--------------------------------
|
||||
|
||||
The notebook consists of a sequence of cells. A cell is a multiline text input
|
||||
field, and its contents can be executed by using :kbd:`Shift-Enter`, or by
|
||||
clicking either the "Play" button the toolbar, or :guilabel:`Cell`, :guilabel:`Run` in the menu bar.
|
||||
The execution behavior of a cell is determined by the cell's type. There are three
|
||||
types of cells: **code cells**, **markdown cells**, and **raw cells**. Every
|
||||
The notebook consists of a sequence of cells. A cell is a multiline text input
|
||||
field, and its contents can be executed by using {kbd}`Shift-Enter`, or by
|
||||
clicking either the "Play" button the toolbar, or {guilabel}`Cell`, {guilabel}`Run` in the menu bar.
|
||||
The execution behavior of a cell is determined by the cell's type. There are three
|
||||
types of cells: **code cells**, **markdown cells**, and **raw cells**. Every
|
||||
cell starts off being a **code cell**, but its type can be changed by using a
|
||||
drop-down on the toolbar (which will be "Code", initially), or via
|
||||
:ref:`keyboard shortcuts <keyboard-shortcuts>`.
|
||||
{ref}`keyboard shortcuts <keyboard-shortcuts>`.
|
||||
|
||||
For more information on the different things you can do in a notebook,
|
||||
see the `collection of examples
|
||||
<https://nbviewer.jupyter.org/github/jupyter/notebook/tree/main/docs/source/examples/Notebook/>`_.
|
||||
see the [collection of examples](https://nbviewer.jupyter.org/github/jupyter/notebook/tree/main/docs/source/examples/Notebook/).
|
||||
|
||||
Code cells
|
||||
~~~~~~~~~~
|
||||
A *code cell* allows you to edit and write new code, with full syntax
|
||||
### Code cells
|
||||
|
||||
A _code cell_ allows you to edit and write new code, with full syntax
|
||||
highlighting and tab completion. The programming language you use depends
|
||||
on the *kernel*, and the default kernel (IPython) runs Python code.
|
||||
on the _kernel_, and the default kernel (IPython) runs Python code.
|
||||
|
||||
When a code cell is executed, code that it contains is sent to the kernel
|
||||
associated with the notebook. The results that are returned from this
|
||||
computation are then displayed in the notebook as the cell's *output*. The
|
||||
associated with the notebook. The results that are returned from this
|
||||
computation are then displayed in the notebook as the cell's _output_. The
|
||||
output is not limited to text, with many other possible forms of output are
|
||||
also possible, including ``matplotlib`` figures and HTML tables (as used, for
|
||||
example, in the ``pandas`` data analysis package). This is known as IPython's
|
||||
*rich display* capability.
|
||||
also possible, including `matplotlib` figures and HTML tables (as used, for
|
||||
example, in the `pandas` data analysis package). This is known as IPython's
|
||||
_rich display_ capability.
|
||||
|
||||
.. seealso::
|
||||
:::{seealso}
|
||||
[Rich Output] example notebook
|
||||
:::
|
||||
|
||||
`Rich Output`_ example notebook
|
||||
### Markdown cells
|
||||
|
||||
Markdown cells
|
||||
~~~~~~~~~~~~~~
|
||||
You can document the computational process in a literate way, alternating
|
||||
descriptive text with code, using *rich text*. In IPython this is accomplished
|
||||
descriptive text with code, using _rich text_. In IPython this is accomplished
|
||||
by marking up text with the Markdown language. The corresponding cells are
|
||||
called *Markdown cells*. The Markdown language provides a simple way to
|
||||
called _Markdown cells_. The Markdown language provides a simple way to
|
||||
perform this text markup, that is, to specify which parts of the text should
|
||||
be emphasized (italics), bold, form lists, etc.
|
||||
|
||||
If you want to provide structure for your document, you can use markdown
|
||||
headings. Markdown headings consist of 1 to 6 hash # signs ``#`` followed by a
|
||||
headings. Markdown headings consist of 1 to 6 hash # signs `#` followed by a
|
||||
space and the title of your section. The markdown heading will be converted
|
||||
to a clickable link for a section of the notebook. It is also used as a hint
|
||||
when exporting to other document formats, like PDF.
|
||||
@ -273,44 +253,40 @@ When a Markdown cell is executed, the Markdown code is converted into
|
||||
the corresponding formatted rich text. Markdown allows arbitrary HTML code for
|
||||
formatting.
|
||||
|
||||
Within Markdown cells, you can also include *mathematics* in a straightforward
|
||||
way, using standard LaTeX notation: ``$...$`` for inline mathematics and
|
||||
``$$...$$`` for displayed mathematics. When the Markdown cell is executed,
|
||||
Within Markdown cells, you can also include _mathematics_ in a straightforward
|
||||
way, using standard LaTeX notation: `$...$` for inline mathematics and
|
||||
`$$...$$` for displayed mathematics. When the Markdown cell is executed,
|
||||
the LaTeX portions are automatically rendered in the HTML output as equations
|
||||
with high quality typography. This is made possible by MathJax_, which
|
||||
supports a `large subset <https://docs.mathjax.org/en/latest/input/tex/index.html>`__ of LaTeX functionality
|
||||
with high quality typography. This is made possible by [MathJax], which
|
||||
supports a [large subset](https://docs.mathjax.org/en/latest/input/tex/index.html) of LaTeX functionality
|
||||
|
||||
Standard mathematics environments defined by LaTeX and AMS-LaTeX (the
|
||||
``amsmath`` package) also work, such as
|
||||
``\begin{equation}...\end{equation}``, and ``\begin{align}...\end{align}``.
|
||||
`amsmath` package) also work, such as
|
||||
`\begin{equation}...\end{equation}`, and `\begin{align}...\end{align}`.
|
||||
New LaTeX macros may be defined using standard methods,
|
||||
such as ``\newcommand``, by placing them anywhere *between math delimiters* in
|
||||
such as `\newcommand`, by placing them anywhere _between math delimiters_ in
|
||||
a Markdown cell. These definitions are then available throughout the rest of
|
||||
the IPython session.
|
||||
|
||||
.. seealso::
|
||||
:::{seealso}
|
||||
[Working with Markdown Cells] example notebook
|
||||
:::
|
||||
|
||||
`Working with Markdown Cells`_ example notebook
|
||||
### Raw cells
|
||||
|
||||
Raw cells
|
||||
~~~~~~~~~
|
||||
|
||||
*Raw* cells provide a place in which you can write *output* directly.
|
||||
_Raw_ cells provide a place in which you can write _output_ directly.
|
||||
Raw cells are not evaluated by the notebook.
|
||||
When passed through nbconvert_, raw cells arrive in the
|
||||
When passed through [nbconvert], raw cells arrive in the
|
||||
destination format unmodified. For example, you can type full LaTeX
|
||||
into a raw cell, which will only be rendered by LaTeX after conversion by
|
||||
nbconvert.
|
||||
|
||||
|
||||
Basic workflow
|
||||
--------------
|
||||
## Basic workflow
|
||||
|
||||
The normal workflow in a notebook is, then, quite similar to a standard
|
||||
IPython session, with the difference that you can edit cells in-place multiple
|
||||
times until you obtain the desired results, rather than having to
|
||||
rerun separate scripts with the ``%run`` magic command.
|
||||
|
||||
rerun separate scripts with the `%run` magic command.
|
||||
|
||||
Typically, you will work on a computational problem in pieces, organizing
|
||||
related ideas into cells and moving forward once previous parts work
|
||||
@ -318,67 +294,61 @@ correctly. This is much more convenient for interactive exploration than
|
||||
breaking up a computation into scripts that must be executed together, as was
|
||||
previously necessary, especially if parts of them take a long time to run.
|
||||
|
||||
To interrupt a calculation which is taking too long, use the :guilabel:`Kernel`,
|
||||
:guilabel:`Interrupt` menu option, or the :kbd:`i,i` keyboard shortcut.
|
||||
To interrupt a calculation which is taking too long, use the {guilabel}`Kernel`,
|
||||
{guilabel}`Interrupt` menu option, or the {kbd}`i,i` keyboard shortcut.
|
||||
Similarly, to restart the whole computational process,
|
||||
use the :guilabel:`Kernel`, :guilabel:`Restart` menu option or :kbd:`0,0`
|
||||
use the {guilabel}`Kernel`, {guilabel}`Restart` menu option or {kbd}`0,0`
|
||||
shortcut.
|
||||
|
||||
A notebook may be downloaded as a ``.ipynb`` file or converted to a number of
|
||||
other formats using the menu option :guilabel:`File`, :guilabel:`Download as`.
|
||||
A notebook may be downloaded as a `.ipynb` file or converted to a number of
|
||||
other formats using the menu option {guilabel}`File`, {guilabel}`Download as`.
|
||||
|
||||
.. seealso::
|
||||
:::{seealso}
|
||||
[Running Code in the Jupyter Notebook] example notebook
|
||||
|
||||
`Running Code in the Jupyter Notebook`_ example notebook
|
||||
[Notebook Basics] example notebook
|
||||
:::
|
||||
|
||||
`Notebook Basics`_ example notebook
|
||||
(keyboard-shortcuts)=
|
||||
|
||||
.. _keyboard-shortcuts:
|
||||
### Keyboard shortcuts
|
||||
|
||||
Keyboard shortcuts
|
||||
~~~~~~~~~~~~~~~~~~
|
||||
All actions in the notebook can be performed with the mouse, but keyboard
|
||||
shortcuts are also available for the most common ones. The essential shortcuts
|
||||
to remember are the following:
|
||||
|
||||
* :kbd:`Shift-Enter`: run cell
|
||||
Execute the current cell, show any output, and jump to the next cell below.
|
||||
If :kbd:`Shift-Enter` is invoked on the last cell, it makes a new cell below.
|
||||
This is equivalent to clicking the :guilabel:`Cell`, :guilabel:`Run` menu
|
||||
item, or the Play button in the toolbar.
|
||||
- {kbd}`Shift-Enter`: run cell
|
||||
: Execute the current cell, show any output, and jump to the next cell below.
|
||||
If {kbd}`Shift-Enter` is invoked on the last cell, it makes a new cell below.
|
||||
This is equivalent to clicking the {guilabel}`Cell`, {guilabel}`Run` menu
|
||||
item, or the Play button in the toolbar.
|
||||
- {kbd}`Esc`: Command mode
|
||||
: In command mode, you can navigate around the notebook using keyboard shortcuts.
|
||||
- {kbd}`Enter`: Edit mode
|
||||
: In edit mode, you can edit text in cells.
|
||||
|
||||
* :kbd:`Esc`: Command mode
|
||||
In command mode, you can navigate around the notebook using keyboard shortcuts.
|
||||
For the full list of available shortcuts, click {guilabel}`Help`,
|
||||
{guilabel}`Keyboard Shortcuts` in the notebook menus.
|
||||
|
||||
* :kbd:`Enter`: Edit mode
|
||||
In edit mode, you can edit text in cells.
|
||||
## Plotting
|
||||
|
||||
For the full list of available shortcuts, click :guilabel:`Help`,
|
||||
:guilabel:`Keyboard Shortcuts` in the notebook menus.
|
||||
|
||||
Plotting
|
||||
--------
|
||||
One major feature of the Jupyter notebook is the ability to display plots that
|
||||
are the output of running code cells. The IPython kernel is designed to work
|
||||
seamlessly with the matplotlib_ plotting library to provide this functionality.
|
||||
seamlessly with the [matplotlib] plotting library to provide this functionality.
|
||||
Specific plotting library integration is a feature of the kernel.
|
||||
|
||||
Installing kernels
|
||||
------------------
|
||||
## Installing kernels
|
||||
|
||||
For information on how to install a Python kernel, refer to the
|
||||
`IPython install page <https://ipython.org/install.html>`__.
|
||||
[IPython install page](https://ipython.org/install.html).
|
||||
|
||||
The Jupyter wiki has a long list of `Kernels for other languages
|
||||
<https://github.com/jupyter/jupyter/wiki/Jupyter-kernels>`_.
|
||||
The Jupyter wiki has a long list of [Kernels for other languages](https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).
|
||||
They usually come with instructions on how to make the kernel available
|
||||
in the notebook.
|
||||
|
||||
(signing-notebooks)=
|
||||
|
||||
.. _signing_notebooks:
|
||||
|
||||
Trusting Notebooks
|
||||
------------------
|
||||
## Trusting Notebooks
|
||||
|
||||
To prevent untrusted code from executing on users' behalf when notebooks open,
|
||||
we store a signature of each trusted notebook.
|
||||
@ -393,22 +363,21 @@ load.
|
||||
|
||||
If you need to see HTML or Javascript output without re-executing,
|
||||
and you are sure the notebook is not malicious, you can tell Jupyter to trust it
|
||||
at the command-line with::
|
||||
at the command-line with:
|
||||
|
||||
$ jupyter trust mynotebook.ipynb
|
||||
```
|
||||
$ jupyter trust mynotebook.ipynb
|
||||
```
|
||||
|
||||
See the `security documentation <https://jupyter-server.readthedocs.io/en/stable/operators/security.html>`__ for more details about the trust mechanism.
|
||||
See the [security documentation](https://jupyter-server.readthedocs.io/en/stable/operators/security.html) for more details about the trust mechanism.
|
||||
|
||||
|
||||
|
||||
Browser Compatibility
|
||||
---------------------
|
||||
## Browser Compatibility
|
||||
|
||||
The Jupyter Notebook aims to support the latest versions of these browsers:
|
||||
|
||||
* Chrome
|
||||
* Safari
|
||||
* Firefox
|
||||
- Chrome
|
||||
- Safari
|
||||
- Firefox
|
||||
|
||||
Up to date versions of Opera and Edge may also work, but if they don't, please
|
||||
use one of the supported browsers.
|
||||
@ -416,4 +385,9 @@ use one of the supported browsers.
|
||||
Using Safari with HTTPS and an untrusted certificate is known to not work
|
||||
(websockets will fail).
|
||||
|
||||
```{eval-rst}
|
||||
.. include:: links.txt
|
||||
```
|
||||
|
||||
[json]: https://en.wikipedia.org/wiki/JSON
|
||||
[mathjax]: https://www.mathjax.org/
|
||||
243
docs/source/troubleshooting.md
Normal file
243
docs/source/troubleshooting.md
Normal file
@ -0,0 +1,243 @@
|
||||
# What to do when things go wrong
|
||||
|
||||
First, have a look at the common problems listed below. If you can figure it out
|
||||
from these notes, it will be quicker than asking for help.
|
||||
|
||||
Check that you have the latest version of any packages that look relevant.
|
||||
Unfortunately it's not always easy to figure out what packages are relevant,
|
||||
but if there was a bug that's already been fixed,
|
||||
it's easy to upgrade and get on with what you wanted to do.
|
||||
|
||||
## Jupyter fails to start
|
||||
|
||||
- Have you [installed it](https://jupyter.org/install.html)? ;-)
|
||||
- If you're using a menu shortcut or Anaconda launcher to start it, try
|
||||
opening a terminal or command prompt and running the command `jupyter notebook`.
|
||||
- If it can't find `jupyter`,
|
||||
you may need to configure your `PATH` environment variable.
|
||||
If you don't know what that means, and don't want to find out,
|
||||
just (re)install Anaconda with the default settings,
|
||||
and it should set up PATH correctly.
|
||||
- If Jupyter gives an error that it can't find `notebook`,
|
||||
check with pip or conda that the `notebook` package is installed.
|
||||
- Try running `jupyter-notebook` (with a hyphen). This should normally be the
|
||||
same as `jupyter notebook` (with a space), but if there's any difference,
|
||||
the version with the hyphen is the 'real' launcher, and the other one wraps
|
||||
that.
|
||||
|
||||
## Jupyter doesn't load or doesn't work in the browser
|
||||
|
||||
- Try in another browser (e.g. if you normally use Firefox, try with Chrome).
|
||||
This helps pin down where the problem is.
|
||||
- Try disabling any browser extensions and/or any Jupyter extensions you have
|
||||
installed.
|
||||
- Some internet security software can interfere with Jupyter.
|
||||
If you have security software, try turning it off temporarily,
|
||||
and look in the settings for a more long-term solution.
|
||||
- In the address bar, try changing between `localhost` and `127.0.0.1`.
|
||||
They should be the same, but in some cases it makes a difference.
|
||||
|
||||
## Jupyter can't start a kernel
|
||||
|
||||
Files called _kernel specs_ tell Jupyter how to start different kinds of kernels.
|
||||
To see where these are on your system, run `jupyter kernelspec list`:
|
||||
|
||||
```
|
||||
$ jupyter kernelspec list
|
||||
Available kernels:
|
||||
python3 /home/takluyver/.local/lib/python3.6/site-packages/ipykernel/resources
|
||||
bash /home/takluyver/.local/share/jupyter/kernels/bash
|
||||
ir /home/takluyver/.local/share/jupyter/kernels/ir
|
||||
```
|
||||
|
||||
There's a special fallback for the Python kernel:
|
||||
if it doesn't find a real kernelspec, but it can import the `ipykernel` package,
|
||||
it provides a kernel which will run in the same Python environment as the notebook server.
|
||||
A path ending in `ipykernel/resources`, like in the example above,
|
||||
is this default kernel.
|
||||
The default often does what you want,
|
||||
so if the `python3` kernelspec points somewhere else
|
||||
and you can't start a Python kernel,
|
||||
try deleting or renaming that kernelspec folder to expose the default.
|
||||
|
||||
If your problem is with another kernel, not the Python one we maintain,
|
||||
you may need to look for support about that kernel.
|
||||
|
||||
## Python Environments
|
||||
|
||||
Multiple python environments, whether based on Anaconda or Python Virtual environments,
|
||||
are often the source of reported issues. In many cases, these issues stem from the
|
||||
Notebook server running in one environment, while the kernel and/or its resources,
|
||||
derive from another environment. Indicators of this scenario include:
|
||||
|
||||
- `import` statements within code cells producing `ImportError` or `ModuleNotFound` exceptions.
|
||||
- General kernel startup failures exhibited by nothing happening when attempting
|
||||
to execute a cell.
|
||||
|
||||
In these situations, take a close look at your environment structure and ensure all
|
||||
packages required by your notebook's code are installed in the correct environment.
|
||||
If you need to run the kernel from different environments than your Notebook
|
||||
server, check out [IPython's documentation](https://ipython.readthedocs.io/en/stable/install/kernel_install.html#kernels-for-different-environments)
|
||||
for using kernels from different environments as this is the recommended approach.
|
||||
Anaconda's [nb_conda_kernels](https://github.com/Anaconda-Platform/nb_conda_kernels)
|
||||
package might also be an option for you in these scenarios.
|
||||
|
||||
Another thing to check is the `kernel.json` file that will be located in the
|
||||
aforementioned _kernel specs_ directory identified by running `jupyter kernelspec list`.
|
||||
This file will contain an `argv` stanza that includes the actual command to run
|
||||
when launching the kernel. Oftentimes, when reinstalling python environments, a previous
|
||||
`kernel.json` will reference an python executable from an old or non-existent location.
|
||||
As a result, it's always a good idea when encountering kernel startup issues to validate
|
||||
the `argv` stanza to ensure all file references exist and are appropriate.
|
||||
|
||||
## Windows Systems
|
||||
|
||||
Although Jupyter Notebook is primarily developed on the various flavors of the Unix
|
||||
operating system it also supports Microsoft
|
||||
Windows - which introduces its own set of commonly encountered issues,
|
||||
particularly in the areas of security, process management and lower-level libraries.
|
||||
|
||||
### pywin32 Issues
|
||||
|
||||
The primary package for interacting with Windows' primitives is `pywin32`.
|
||||
|
||||
- Issues surrounding the creation of the kernel's communication file utilize
|
||||
`jupyter_core`'s `secure_write()` function. This function ensures a file is
|
||||
created in which only the owner of the file has access. If libraries like `pywin32`
|
||||
are not properly installed, issues can arise when it's necessary to use the native
|
||||
Windows libraries.
|
||||
|
||||
Here's a portion of such a traceback:
|
||||
|
||||
```
|
||||
File "c:\users\jovyan\python\myenv.venv\lib\site-packages\jupyter_core\paths.py", line 424, in secure_write
|
||||
win32_restrict_file_to_user(fname)
|
||||
File "c:\users\jovyan\python\myenv.venv\lib\site-packages\jupyter_core\paths.py", line 359, in win32_restrict_file_to_user
|
||||
import win32api
|
||||
ImportError: DLL load failed: The specified module could not be found.
|
||||
```
|
||||
|
||||
- As noted earlier, the installation of `pywin32` can be problematic on Windows
|
||||
configurations. When such an issue occurs, you may need to revisit how the environment
|
||||
was setup. Pay careful attention to whether you're running the 32 or 64 bit versions
|
||||
of Windows and be sure to install appropriate packages for that environment.
|
||||
|
||||
Here's a portion of such a traceback:
|
||||
|
||||
```
|
||||
File "C:\Users\jovyan\AppData\Roaming\Python\Python37\site-packages\jupyter_core\paths.py", line 435, in secure_write
|
||||
win32_restrict_file_to_user(fname)
|
||||
File "C:\Users\jovyan\AppData\Roaming\Python\Python37\site-packages\jupyter_core\paths.py", line 361, in win32_restrict_file_to_user
|
||||
import win32api
|
||||
ImportError: DLL load failed: %1 is not a valid Win32 application
|
||||
```
|
||||
|
||||
#### Resolving pywin32 Issues
|
||||
|
||||
> In this case, your `pywin32` module may not be installed correctly and the following
|
||||
> should be attempted:
|
||||
>
|
||||
> ```
|
||||
> pip install --upgrade pywin32
|
||||
> ```
|
||||
>
|
||||
> or:
|
||||
>
|
||||
> ```
|
||||
> conda install --force-reinstall pywin32
|
||||
> ```
|
||||
>
|
||||
> followed by:
|
||||
>
|
||||
> ```
|
||||
> python.exe Scripts/pywin32_postinstall.py -install
|
||||
> ```
|
||||
>
|
||||
> where `Scripts` is located in the active Python's installation location.
|
||||
|
||||
- Another common failure specific to Windows environments is the location of various
|
||||
python commands. On `*nix` systems, these typically reside in the `bin` directory
|
||||
of the active Python environment. However, on Windows, these tend to reside in the
|
||||
`Scripts` folder - which is a sibling to `bin`. As a result, when encountering
|
||||
kernel startup issues, again, check the `argv` stanza and verify it's pointing to a
|
||||
valid file. You may find that it's pointing in `bin` when `Scripts` is correct, or
|
||||
the referenced file does not include its `.exe` extension - typically resulting in
|
||||
`FileNotFoundError` exceptions.
|
||||
|
||||
## This Worked An Hour Ago
|
||||
|
||||
The Jupyter stack is very complex and rightfully so, there's a lot going on. On occasion
|
||||
you might find the system working perfectly well, then, suddenly, you can't get past a
|
||||
certain cell due to `import` failures. In these situations, it's best to ask yourself
|
||||
if any new python files were added to your notebook development area.
|
||||
|
||||
These issues are usually evident by carefully analyzing the traceback produced in
|
||||
the notebook error or the Notebook server's command window. In these cases, you'll typically
|
||||
find the Python kernel code (from `IPython` and `ipykernel`) performing _its_ imports
|
||||
and notice a file from your Notebook development error included in that traceback followed
|
||||
by an `AttributeError`:
|
||||
|
||||
```
|
||||
File "C:\Users\jovyan\anaconda3\lib\site-packages\ipykernel\connect.py", line 13, in
|
||||
from IPython.core.profiledir import ProfileDir
|
||||
File "C:\Users\jovyan\anaconda3\lib\site-packages\IPython_init.py", line 55, in
|
||||
from .core.application import Application
|
||||
...
|
||||
File "C:\Users\jovyan\anaconda3\lib\site-packages\ipython_genutils\path.py", line 13, in
|
||||
import random
|
||||
File "C:\Users\jovyan\Desktop\Notebooks\random.py", line 4, in
|
||||
rand_set = random.sample(english_words_lower_set, 12)
|
||||
AttributeError: module 'random' has no attribute 'sample'
|
||||
```
|
||||
|
||||
What has happened is that you have named a file that conflicts with an installed package
|
||||
that is used by the kernel software and now introduces a conflict preventing the
|
||||
kernel's startup.
|
||||
|
||||
**Resolution**: You'll need to rename your file. A best practice would be to prefix or
|
||||
_namespace_ your files so as not to conflict with any python package.
|
||||
|
||||
## Asking for help
|
||||
|
||||
As with any problem, try searching to see if someone has already found an answer.
|
||||
If you can't find an existing answer, you can ask questions at:
|
||||
|
||||
- The [Jupyter Discourse Forum](https://discourse.jupyter.org/)
|
||||
|
||||
- The [jupyter-notebook tag on Stackoverflow](https://stackoverflow.com/questions/tagged/jupyter-notebook)
|
||||
|
||||
- Peruse the [jupyter/help repository on Github](https://github.com/jupyter/help) (read-only)
|
||||
|
||||
- Or in an issue on another repository, if it's clear which component is
|
||||
responsible. Typical repositories include:
|
||||
|
||||
> - [jupyter_core](https://github.com/jupyter/jupyter_core) - `secure_write()`
|
||||
> and file path issues
|
||||
> - [jupyter_client](https://github.com/jupyter/jupyter_core) - kernel management
|
||||
> issues found in Notebook server's command window.
|
||||
> - [IPython](https://github.com/ipython/ipython) and
|
||||
> [ipykernel](https://github.com/ipython/ipykernel) - kernel runtime issues
|
||||
> typically found in Notebook server's command window and/or Notebook cell execution.
|
||||
|
||||
### Gathering Information
|
||||
|
||||
Should you find that your problem warrants that an issue be opened in
|
||||
[notebook](https://github.com/jupyter/notebook) please don't forget to provide details
|
||||
like the following:
|
||||
|
||||
- What error messages do you see (within your notebook and, more importantly, in
|
||||
the Notebook server's command window)?
|
||||
- What platform are you on?
|
||||
- How did you install Jupyter?
|
||||
- What have you tried already?
|
||||
|
||||
The `jupyter troubleshoot` command collects a lot of information
|
||||
about your installation, which can also be useful.
|
||||
|
||||
When providing textual information, it's most helpful if you can _scrape_ the contents
|
||||
into the issue rather than providing a screenshot. This enables others to select
|
||||
pieces of that content so they can search more efficiently and try to help.
|
||||
|
||||
Remember that it's not anyone's job to help you.
|
||||
We want Jupyter to work for you,
|
||||
but we can't always help everyone individually.
|
||||
@ -1,233 +0,0 @@
|
||||
What to do when things go wrong
|
||||
===============================
|
||||
|
||||
First, have a look at the common problems listed below. If you can figure it out
|
||||
from these notes, it will be quicker than asking for help.
|
||||
|
||||
Check that you have the latest version of any packages that look relevant.
|
||||
Unfortunately it's not always easy to figure out what packages are relevant,
|
||||
but if there was a bug that's already been fixed,
|
||||
it's easy to upgrade and get on with what you wanted to do.
|
||||
|
||||
Jupyter fails to start
|
||||
----------------------
|
||||
|
||||
* Have you `installed it <https://jupyter.org/install.html>`__? ;-)
|
||||
* If you're using a menu shortcut or Anaconda launcher to start it, try
|
||||
opening a terminal or command prompt and running the command ``jupyter notebook``.
|
||||
* If it can't find ``jupyter``,
|
||||
you may need to configure your ``PATH`` environment variable.
|
||||
If you don't know what that means, and don't want to find out,
|
||||
just (re)install Anaconda with the default settings,
|
||||
and it should set up PATH correctly.
|
||||
* If Jupyter gives an error that it can't find ``notebook``,
|
||||
check with pip or conda that the ``notebook`` package is installed.
|
||||
* Try running ``jupyter-notebook`` (with a hyphen). This should normally be the
|
||||
same as ``jupyter notebook`` (with a space), but if there's any difference,
|
||||
the version with the hyphen is the 'real' launcher, and the other one wraps
|
||||
that.
|
||||
|
||||
Jupyter doesn't load or doesn't work in the browser
|
||||
---------------------------------------------------
|
||||
|
||||
* Try in another browser (e.g. if you normally use Firefox, try with Chrome).
|
||||
This helps pin down where the problem is.
|
||||
* Try disabling any browser extensions and/or any Jupyter extensions you have
|
||||
installed.
|
||||
* Some internet security software can interfere with Jupyter.
|
||||
If you have security software, try turning it off temporarily,
|
||||
and look in the settings for a more long-term solution.
|
||||
* In the address bar, try changing between ``localhost`` and ``127.0.0.1``.
|
||||
They should be the same, but in some cases it makes a difference.
|
||||
|
||||
Jupyter can't start a kernel
|
||||
----------------------------
|
||||
|
||||
Files called *kernel specs* tell Jupyter how to start different kinds of kernels.
|
||||
To see where these are on your system, run ``jupyter kernelspec list``::
|
||||
|
||||
$ jupyter kernelspec list
|
||||
Available kernels:
|
||||
python3 /home/takluyver/.local/lib/python3.6/site-packages/ipykernel/resources
|
||||
bash /home/takluyver/.local/share/jupyter/kernels/bash
|
||||
ir /home/takluyver/.local/share/jupyter/kernels/ir
|
||||
|
||||
There's a special fallback for the Python kernel:
|
||||
if it doesn't find a real kernelspec, but it can import the ``ipykernel`` package,
|
||||
it provides a kernel which will run in the same Python environment as the notebook server.
|
||||
A path ending in ``ipykernel/resources``, like in the example above,
|
||||
is this default kernel.
|
||||
The default often does what you want,
|
||||
so if the ``python3`` kernelspec points somewhere else
|
||||
and you can't start a Python kernel,
|
||||
try deleting or renaming that kernelspec folder to expose the default.
|
||||
|
||||
If your problem is with another kernel, not the Python one we maintain,
|
||||
you may need to look for support about that kernel.
|
||||
|
||||
Python Environments
|
||||
-------------------
|
||||
Multiple python environments, whether based on Anaconda or Python Virtual environments,
|
||||
are often the source of reported issues. In many cases, these issues stem from the
|
||||
Notebook server running in one environment, while the kernel and/or its resources,
|
||||
derive from another environment. Indicators of this scenario include:
|
||||
|
||||
* ``import`` statements within code cells producing ``ImportError`` or ``ModuleNotFound`` exceptions.
|
||||
* General kernel startup failures exhibited by nothing happening when attempting
|
||||
to execute a cell.
|
||||
|
||||
In these situations, take a close look at your environment structure and ensure all
|
||||
packages required by your notebook's code are installed in the correct environment.
|
||||
If you need to run the kernel from different environments than your Notebook
|
||||
server, check out `IPython's documentation <https://ipython.readthedocs.io/en/stable/install/kernel_install.html#kernels-for-different-environments>`_
|
||||
for using kernels from different environments as this is the recommended approach.
|
||||
Anaconda's `nb_conda_kernels <https://github.com/Anaconda-Platform/nb_conda_kernels>`_
|
||||
package might also be an option for you in these scenarios.
|
||||
|
||||
Another thing to check is the ``kernel.json`` file that will be located in the
|
||||
aforementioned *kernel specs* directory identified by running ``jupyter kernelspec list``.
|
||||
This file will contain an ``argv`` stanza that includes the actual command to run
|
||||
when launching the kernel. Oftentimes, when reinstalling python environments, a previous
|
||||
``kernel.json`` will reference an python executable from an old or non-existent location.
|
||||
As a result, it's always a good idea when encountering kernel startup issues to validate
|
||||
the ``argv`` stanza to ensure all file references exist and are appropriate.
|
||||
|
||||
Windows Systems
|
||||
---------------
|
||||
Although Jupyter Notebook is primarily developed on the various flavors of the Unix
|
||||
operating system it also supports Microsoft
|
||||
Windows - which introduces its own set of commonly encountered issues,
|
||||
particularly in the areas of security, process management and lower-level libraries.
|
||||
|
||||
pywin32 Issues
|
||||
^^^^^^^^^^^^^^^^^^
|
||||
The primary package for interacting with Windows' primitives is ``pywin32``.
|
||||
|
||||
* Issues surrounding the creation of the kernel's communication file utilize
|
||||
``jupyter_core``'s ``secure_write()`` function. This function ensures a file is
|
||||
created in which only the owner of the file has access. If libraries like ``pywin32``
|
||||
are not properly installed, issues can arise when it's necessary to use the native
|
||||
Windows libraries.
|
||||
|
||||
Here's a portion of such a traceback::
|
||||
|
||||
File "c:\users\jovyan\python\myenv.venv\lib\site-packages\jupyter_core\paths.py", line 424, in secure_write
|
||||
win32_restrict_file_to_user(fname)
|
||||
File "c:\users\jovyan\python\myenv.venv\lib\site-packages\jupyter_core\paths.py", line 359, in win32_restrict_file_to_user
|
||||
import win32api
|
||||
ImportError: DLL load failed: The specified module could not be found.
|
||||
|
||||
* As noted earlier, the installation of ``pywin32`` can be problematic on Windows
|
||||
configurations. When such an issue occurs, you may need to revisit how the environment
|
||||
was setup. Pay careful attention to whether you're running the 32 or 64 bit versions
|
||||
of Windows and be sure to install appropriate packages for that environment.
|
||||
|
||||
Here's a portion of such a traceback::
|
||||
|
||||
File "C:\Users\jovyan\AppData\Roaming\Python\Python37\site-packages\jupyter_core\paths.py", line 435, in secure_write
|
||||
win32_restrict_file_to_user(fname)
|
||||
File "C:\Users\jovyan\AppData\Roaming\Python\Python37\site-packages\jupyter_core\paths.py", line 361, in win32_restrict_file_to_user
|
||||
import win32api
|
||||
ImportError: DLL load failed: %1 is not a valid Win32 application
|
||||
|
||||
Resolving pywin32 Issues
|
||||
""""""""""""""""""""""""""""
|
||||
In this case, your ``pywin32`` module may not be installed correctly and the following
|
||||
should be attempted:
|
||||
::
|
||||
|
||||
pip install --upgrade pywin32
|
||||
|
||||
or::
|
||||
|
||||
conda install --force-reinstall pywin32
|
||||
|
||||
followed by::
|
||||
|
||||
python.exe Scripts/pywin32_postinstall.py -install
|
||||
|
||||
where ``Scripts`` is located in the active Python's installation location.
|
||||
|
||||
* Another common failure specific to Windows environments is the location of various
|
||||
python commands. On ``*nix`` systems, these typically reside in the ``bin`` directory
|
||||
of the active Python environment. However, on Windows, these tend to reside in the
|
||||
``Scripts`` folder - which is a sibling to ``bin``. As a result, when encountering
|
||||
kernel startup issues, again, check the ``argv`` stanza and verify it's pointing to a
|
||||
valid file. You may find that it's pointing in ``bin`` when ``Scripts`` is correct, or
|
||||
the referenced file does not include its ``.exe`` extension - typically resulting in
|
||||
``FileNotFoundError`` exceptions.
|
||||
|
||||
This Worked An Hour Ago
|
||||
-----------------------
|
||||
The Jupyter stack is very complex and rightfully so, there's a lot going on. On occasion
|
||||
you might find the system working perfectly well, then, suddenly, you can't get past a
|
||||
certain cell due to ``import`` failures. In these situations, it's best to ask yourself
|
||||
if any new python files were added to your notebook development area.
|
||||
|
||||
These issues are usually evident by carefully analyzing the traceback produced in
|
||||
the notebook error or the Notebook server's command window. In these cases, you'll typically
|
||||
find the Python kernel code (from ``IPython`` and ``ipykernel``) performing *its* imports
|
||||
and notice a file from your Notebook development error included in that traceback followed
|
||||
by an ``AttributeError``::
|
||||
|
||||
File "C:\Users\jovyan\anaconda3\lib\site-packages\ipykernel\connect.py", line 13, in
|
||||
from IPython.core.profiledir import ProfileDir
|
||||
File "C:\Users\jovyan\anaconda3\lib\site-packages\IPython_init.py", line 55, in
|
||||
from .core.application import Application
|
||||
...
|
||||
File "C:\Users\jovyan\anaconda3\lib\site-packages\ipython_genutils\path.py", line 13, in
|
||||
import random
|
||||
File "C:\Users\jovyan\Desktop\Notebooks\random.py", line 4, in
|
||||
rand_set = random.sample(english_words_lower_set, 12)
|
||||
AttributeError: module 'random' has no attribute 'sample'
|
||||
|
||||
What has happened is that you have named a file that conflicts with an installed package
|
||||
that is used by the kernel software and now introduces a conflict preventing the
|
||||
kernel's startup.
|
||||
|
||||
**Resolution**: You'll need to rename your file. A best practice would be to prefix or
|
||||
*namespace* your files so as not to conflict with any python package.
|
||||
|
||||
|
||||
Asking for help
|
||||
---------------
|
||||
|
||||
As with any problem, try searching to see if someone has already found an answer.
|
||||
If you can't find an existing answer, you can ask questions at:
|
||||
|
||||
* The `Jupyter Discourse Forum <https://discourse.jupyter.org/>`_
|
||||
* The `jupyter-notebook tag on Stackoverflow <https://stackoverflow.com/questions/tagged/jupyter-notebook>`_
|
||||
* Peruse the `jupyter/help repository on Github <https://github.com/jupyter/help>`_ (read-only)
|
||||
* Or in an issue on another repository, if it's clear which component is
|
||||
responsible. Typical repositories include:
|
||||
|
||||
* `jupyter_core <https://github.com/jupyter/jupyter_core>`_ - ``secure_write()``
|
||||
and file path issues
|
||||
* `jupyter_client <https://github.com/jupyter/jupyter_core>`_ - kernel management
|
||||
issues found in Notebook server's command window.
|
||||
* `IPython <https://github.com/ipython/ipython>`_ and
|
||||
`ipykernel <https://github.com/ipython/ipykernel>`_ - kernel runtime issues
|
||||
typically found in Notebook server's command window and/or Notebook cell execution.
|
||||
|
||||
Gathering Information
|
||||
^^^^^^^^^^^^^^^^^^^^^
|
||||
Should you find that your problem warrants that an issue be opened in
|
||||
`notebook <https://github.com/jupyter/notebook>`_ please don't forget to provide details
|
||||
like the following:
|
||||
|
||||
* What error messages do you see (within your notebook and, more importantly, in
|
||||
the Notebook server's command window)?
|
||||
* What platform are you on?
|
||||
* How did you install Jupyter?
|
||||
* What have you tried already?
|
||||
|
||||
The ``jupyter troubleshoot`` command collects a lot of information
|
||||
about your installation, which can also be useful.
|
||||
|
||||
When providing textual information, it's most helpful if you can *scrape* the contents
|
||||
into the issue rather than providing a screenshot. This enables others to select
|
||||
pieces of that content so they can search more efficiently and try to help.
|
||||
|
||||
Remember that it's not anyone's job to help you.
|
||||
We want Jupyter to work for you,
|
||||
but we can't always help everyone individually.
|
||||
@ -1,5 +1,4 @@
|
||||
User interface components
|
||||
=========================
|
||||
# User interface components
|
||||
|
||||
When opening bug reports or sending emails to the Jupyter mailing list, it is
|
||||
useful to know the names of different UI components so that other developers
|
||||
@ -7,44 +6,47 @@ and users have an easier time helping you diagnose your problems. This section
|
||||
will familiarize you with the names of UI elements within the Notebook and the
|
||||
different Notebook modes.
|
||||
|
||||
Notebook Dashboard
|
||||
-------------------
|
||||
## Notebook Dashboard
|
||||
|
||||
When you launch ``jupyter notebook`` the first page that you encounter is the
|
||||
When you launch `jupyter notebook` the first page that you encounter is the
|
||||
Notebook Dashboard.
|
||||
|
||||
.. image:: ./_static/images/jupyter-notebook-dashboard.png
|
||||
```{image} ./_static/images/jupyter-notebook-dashboard.png
|
||||
|
||||
Notebook Editor
|
||||
---------------
|
||||
```
|
||||
|
||||
## Notebook Editor
|
||||
|
||||
Once you've selected a Notebook to edit, the Notebook will open in the Notebook
|
||||
Editor.
|
||||
|
||||
.. image:: ./_static/images/jupyter-notebook-default.png
|
||||
```{image} ./_static/images/jupyter-notebook-default.png
|
||||
|
||||
Interactive User Interface Tour of the Notebook
|
||||
-----------------------------------------------
|
||||
```
|
||||
|
||||
## Interactive User Interface Tour of the Notebook
|
||||
|
||||
If you would like to learn more about the specific elements within the Notebook
|
||||
Editor, you can go through the user interface tour by selecting *Help* in the
|
||||
menubar then selecting *User Interface Tour*.
|
||||
Editor, you can go through the user interface tour by selecting _Help_ in the
|
||||
menubar then selecting _User Interface Tour_.
|
||||
|
||||
Edit Mode and Notebook Editor
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
### Edit Mode and Notebook Editor
|
||||
|
||||
When a cell is in edit mode, the Cell Mode Indicator will change to reflect
|
||||
the cell's state. This state is indicated by a small pencil icon on the
|
||||
top right of the interface. When the cell is in command mode, there is no
|
||||
icon in that location.
|
||||
|
||||
.. image:: ./_static/images/jupyter-notebook-edit.png
|
||||
```{image} ./_static/images/jupyter-notebook-edit.png
|
||||
|
||||
File Editor
|
||||
-----------
|
||||
```
|
||||
|
||||
## File Editor
|
||||
|
||||
Now let's say that you've chosen to open a Markdown file instead of a Notebook
|
||||
file whilst in the Notebook Dashboard. If so, the file will be opened in the
|
||||
File Editor.
|
||||
|
||||
.. image:: ./_static/images/jupyter-file-editor.png
|
||||
```{image} ./_static/images/jupyter-file-editor.png
|
||||
|
||||
```
|
||||
11
docs/source/user-documentation.md
Normal file
11
docs/source/user-documentation.md
Normal file
@ -0,0 +1,11 @@
|
||||
# User Documentation
|
||||
|
||||
```{toctree}
|
||||
:maxdepth: 2
|
||||
|
||||
notebook
|
||||
ui_components
|
||||
examples/Notebook/examples_index.rst
|
||||
troubleshooting
|
||||
changelog
|
||||
```
|
||||
@ -1,12 +0,0 @@
|
||||
==================
|
||||
User Documentation
|
||||
==================
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 2
|
||||
|
||||
notebook
|
||||
ui_components
|
||||
examples/Notebook/examples_index.rst
|
||||
troubleshooting
|
||||
changelog
|
||||
Loading…
Reference in New Issue
Block a user