Helix/bwVisu/JupyterLab - Revision history

H Schumacher: fix for pip installations in shared envs

2026-03-19T09:33:23Z

fix for pip installations in shared envs

← Older revision		Revision as of 11:33, 19 March 2026
Line 43:		Line 43:
	<syntaxhighlight lang="bash">source <env_parent_dir>/<env_name>/bin/activate</syntaxhighlight></li>		<syntaxhighlight lang="bash">source <env_parent_dir>/<env_name>/bin/activate</syntaxhighlight></li>
	<li>Update pip and install packages:		<li>Update pip and install packages:
	<syntaxhighlight lang="bash">pip install -U pip		<syntaxhighlight lang="bash">pip install -U pip --no-user
			# when the environment is installed in home
⚫	pip install <packagename></syntaxhighlight></li>
			pip install <packagename>
			# when the environment is installed somewhere else and shall not have dependencies in home so that others can access it as well
		⚫	pip install <packagename> --no-user</syntaxhighlight></li>
	<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>		<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>
	</ol>		</ol>

H Schumacher: Added fourth step to the kernel sharing instructions to fix permission issues.

2026-03-02T15:02:00Z

Added fourth step to the kernel sharing instructions to fix permission issues.

← Older revision		Revision as of 17:02, 2 March 2026
Line 20:		Line 20:
	# Use the kernel within JupyterLab		# Use the kernel within JupyterLab
	#* By default new kernels are saved under <code>~/.local/share/jupyter</code> and this location is automatically detected. Therefore, new kernels are directly available.		#* By default new kernels are saved under <code>~/.local/share/jupyter</code> and this location is automatically detected. Therefore, new kernels are directly available.
	[[File:BwVisu JuypterLab KernelPath.png\|In the JupyterLab job configuration form, a custom kernel path can be provided.\|right\|thumb\|x150px]]		#*:[[File:BwVisu JuypterLab KernelPath.png\|In the JupyterLab job configuration form, a custom kernel path can be provided.\|right\|thumb\|x150px]]
	#* If the kernel is saved somewhere else, the path can be provided in the "Kernel path" field when configuring the JupyterLab job (see image). For a kernel placed under <code>path_to_parent_dir/share/jupyter/kernels/my_kernel</code> the needed path would be <code>path_to_parent_dir/share/jupyter</code>.		#* If the kernel is saved somewhere else, the path can be provided in the "Kernel path" field when configuring the JupyterLab job (see image). For a kernel placed under <code>path_to_parent_dir/share/jupyter/kernels/my_kernel</code> the needed "Kernel path" would be <code>path_to_parent_dir/share/jupyter</code>.
			# When the kernel is used the first time, the file <code>notebook_secrets</code> is created automatically. It can be found under "Kernel path". For others to use the kernel, they must have read access to this file. The command <code>chmod 750 notebook_secrets</code> would for example allow the whole SDS@hd SV read access. For the access management in workspaces, please see [[Workspace#Setting_Permissions_for_Sharing_Files\| Wokspace Permissions]].

	<u>Notes regarding the sharing of IPython kernels</u>		<u>Notes regarding the sharing of IPython kernels</u>

H Schumacher: fix typo

2026-01-16T15:34:15Z

fix typo

← Older revision		Revision as of 17:34, 16 January 2026
Line 17:		Line 17:
	#* [[#Add_packages_via_Conda_virtual_environments \| ...conda]] (choose this option if you want to install a different python version) or		#* [[#Add_packages_via_Conda_virtual_environments \| ...conda]] (choose this option if you want to install a different python version) or
	#* ...[https://docs.astral.sh/uv/getting-started/ uv] if you want to install a different python version but don't want to use conda.		#* ...[https://docs.astral.sh/uv/getting-started/ uv] if you want to install a different python version but don't want to use conda.
	# [[#~~Create_an_IPython_kernel~~ \| Create an IPython kernel]] from the virtual environment		# [[#Create_an_IPython_Kernel \| Create an IPython kernel]] from the virtual environment
	# Use the kernel within JupyterLab		# Use the kernel within JupyterLab
	#* By default new kernels are saved under <code>~/.local/share/jupyter</code> and this location is automatically detected. Therefore, new kernels are directly available.		#* By default new kernels are saved under <code>~/.local/share/jupyter</code> and this location is automatically detected. Therefore, new kernels are directly available.
Line 44:		Line 44:
	<syntaxhighlight lang="bash">pip install -U pip		<syntaxhighlight lang="bash">pip install -U pip
	pip install <packagename></syntaxhighlight></li>		pip install <packagename></syntaxhighlight></li>
	<li> [[#~~Create_an_IPython_kernel~~ \| Create an IPython kernel]]</li>		<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>
	</ol>		</ol>

Line 64:		Line 64:
	<li>Install your packages:		<li>Install your packages:
	<syntaxhighlight lang="bash">conda install <mypackage></syntaxhighlight></li>		<syntaxhighlight lang="bash">conda install <mypackage></syntaxhighlight></li>
	<li> [[#~~Create_an_IPython_kernel~~ \| Create an IPython kernel]]</li>		<li> [[#Create_an_IPython_Kernel \| Create an IPython kernel]]</li>
	</ol>		</ol>

H Schumacher: Added image for kernel path option (based on user feedback)

2025-11-23T17:55:11Z

Added image for kernel path option (based on user feedback)

← Older revision		Revision as of 19:55, 23 November 2025
Line 20:		Line 20:
	# Use the kernel within JupyterLab		# Use the kernel within JupyterLab
	#* By default new kernels are saved under <code>~/.local/share/jupyter</code> and this location is automatically detected. Therefore, new kernels are directly available.		#* By default new kernels are saved under <code>~/.local/share/jupyter</code> and this location is automatically detected. Therefore, new kernels are directly available.
			[[File:BwVisu JuypterLab KernelPath.png\|In the JupyterLab job configuration form, a custom kernel path can be provided.\|right\|thumb\|x150px]]
	#* If the kernel is saved somewhere else, the path can be provided in the "Kernel path" field when ~~submitting~~ the job. For a kernel placed under <code>path_to_parent_dir/share/jupyter/kernels/my_kernel</code> the needed path would be <code>path_to_parent_dir/share/jupyter</code>.		#* If the kernel is saved somewhere else, the path can be provided in the "Kernel path" field when configuring the JupyterLab job (see image). For a kernel placed under <code>path_to_parent_dir/share/jupyter/kernels/my_kernel</code> the needed path would be <code>path_to_parent_dir/share/jupyter</code>.

	<u>Notes regarding the sharing of IPython kernels</u>		<u>Notes regarding the sharing of IPython kernels</u>

H Schumacher: fixed kernel path

2025-09-12T12:49:00Z

fixed kernel path

← Older revision		Revision as of 14:49, 12 September 2025
Line 20:		Line 20:
	# Use the kernel within JupyterLab		# Use the kernel within JupyterLab
	#* By default new kernels are saved under <code>~/.local/share/jupyter</code> and this location is automatically detected. Therefore, new kernels are directly available.		#* By default new kernels are saved under <code>~/.local/share/jupyter</code> and this location is automatically detected. Therefore, new kernels are directly available.
	#* If the kernel is saved somewhere else, the path can be provided in the "Kernel path" field when submitting the job. For a kernel placed under <code>path_to_parent_dir/share/jupyter/kernels/my_kernel</code> the needed path would be <code>path_to_parent_dir</code>.		#* If the kernel is saved somewhere else, the path can be provided in the "Kernel path" field when submitting the job. For a kernel placed under <code>path_to_parent_dir/share/jupyter/kernels/my_kernel</code> the needed path would be <code>path_to_parent_dir/share/jupyter</code>.

	<u>Notes regarding the sharing of IPython kernels</u>		<u>Notes regarding the sharing of IPython kernels</u>

H Schumacher: Restructured page, improved explanation for sharing virtual environments

2025-08-28T18:38:43Z

Restructured page, improved explanation for sharing virtual environments

Show changes

H Schumacher: Splitted into create and use sections

2025-07-08T10:38:47Z

Splitted into create and use sections

← Older revision		Revision as of 12:38, 8 July 2025
Line 66:		Line 66:
	Follow these instructions if you want to share conda environments with your colleagues:		Follow these instructions if you want to share conda environments with your colleagues:

			# Create the environment:
	# Create a shared directory (optimally on SDS@hd) into wich the ipython kernels are installed, for example "conda_kernels". Never share your home directory.		#* Create a shared directory (optimally on SDS@hd) into wich the ipython kernels are installed, for example "conda_kernels". Never share your home directory.
	# [[#Add_packages_via_conda_environments \| Create a conda environment and register it as kernel]].		#* [[#Add_packages_via_conda_environments \| Create a conda environment and register it as kernel]].
	#* Optional: You can add another shared directory, for example "conda_envs", to share not just the kernels but also the underlying conda environments. A conda environment can be [[Development/Conda#Reproducible_Conda_Environments \| saved as a yml file]].		#* Optional: You can add another shared directory, for example "conda_envs", to share not just the kernels but also the underlying conda environments. A conda environment can be [[Development/Conda#Reproducible_Conda_Environments \| saved as a yml file]].
			# Use the shared environment:
	# Add the new data directory to the jupyter paths:
			#* After having the conda environment installed as a jupyter kernel, JupyterLab needs be able to detect the kernel. Therefore, the path to the kernel must be added to the list of juypter data directories. This can be done by setting a specific environment variable in your .bashrc file. The file can be edited via a terminal or with the bwVisu file viewer.
	#:<syntaxhighlight lang="bash">		#*:<syntaxhighlight lang="bash">
	# Check the current paths
⚫	jupyter --paths
	# Add the following line to your .bashrc file
	export JUPYTER_DATA_DIR=<path_to_shared_directory>		export JUPYTER_DATA_DIR=<path_to_shared_directory>
	</syntaxhighlight>		</syntaxhighlight>
			#* Optional: You can check the jupyter paths by running the following line in a terminal within JupyterLab or on Helix. The latter needs Jupyter to be installed.
	# Start bwVisu JupyterLab Job
			#*:<syntaxhighlight lang="bash">
		⚫	jupyter --paths
			</syntaxhighlight>
			#* Start a bwVisu JupyterLab Job. You can find the new environment under "Kernels".

	=== Multi-Language Support ===		=== Multi-Language Support ===

H Schumacher: Added instructions to create shared conda environments / kernels

2025-06-30T18:41:15Z

Added instructions to create shared conda environments / kernels

@@ Line 47: / Line 47: @@
 <syntaxhighlight lang="bash">python3 -m ipykernel install --user --name=<myKernel></syntaxhighlight></li></ol>
-=== Multi-Language Support ===
+=== Interactive Widgets ===
 ==== R Kernel ====
@@ Line 84: / Line 113: @@
 After that, Julia is available as a kernel.
 == FAQ ==

H Schumacher: Changed Miniconda to Miniforge

2025-06-13T12:41:57Z

Changed Miniconda to Miniforge

← Older revision		Revision as of 14:41, 13 June 2025
Line 32:		Line 32:
	<syntaxhighlight lang="bash">python3 -m ipykernel install --user --name=<myKernel></syntaxhighlight></li></ol>		<syntaxhighlight lang="bash">python3 -m ipykernel install --user --name=<myKernel></syntaxhighlight></li></ol>

	=== Add packages via ~~miniconda~~ ===		=== Add packages via conda environments ===

	<ol style="list-style-type: decimal;">		<ol style="list-style-type: decimal;">
	<li>Load the ~~miniconda~~ module by clicking first on the blue hexagon icon on the left-hand side of Jupyter's start page and then on the "load" ~~Button~~ right of the entry for ~~miniconda~~ in the software module menu.		<li>Load the miniforge module by clicking first on the blue hexagon icon on the left-hand side of Jupyter's start page and then on the "load" button right of the entry for miniforge in the software module menu.
	Open a terminal and complete the miniconda setup with:
	<pre>source $MINICONDA_HOME/etc/profile.d/conda.sh </pre></li>
	<li>Open a terminal and create a conda environment:		<li>Open a terminal and create a conda environment:
	<syntaxhighlight lang="bash">conda create --name <myenv></syntaxhighlight></li>		<syntaxhighlight lang="bash">conda create --name <myenv></syntaxhighlight></li>

H Winkhardt: /* Multi-Language Support */

2025-04-24T11:19:38Z

Multi-Language Support

← Older revision		Revision as of 13:19, 24 April 2025
Line 52:		Line 52:

	JupyterLab supports over 40 programming languages including Python, R, Julia, and Scala. This is achieved through the use of different kernels, which are implementations of the Jupyter notebook environment for each language. You can switch between kernels easily, allowing you to use the best tool for a specific task.		JupyterLab supports over 40 programming languages including Python, R, Julia, and Scala. This is achieved through the use of different kernels, which are implementations of the Jupyter notebook environment for each language. You can switch between kernels easily, allowing you to use the best tool for a specific task.

			By default, custom kernels are installed to ~/.local/share/jupyter/kernels/

	==== R Kernel ====		==== R Kernel ====