GenePattern Notebook Repository

Release updates for the GenePattern Notebook Repository.

GenePattern Notebook Repository 19.02 (February 14, 2019)

  • Improved notebook preview functionality.
  • Added the ability to comment on public notebooks.
  • Added ability to share with collaborators from within a notebook.
  • New repository introductory tour.
  • Loading indicator while generating notebook preview.
  • Bug fixes.

GenePattern Notebook Repository 18.11 (November 13, 2018)

  • Added "My Notebooks" to the notebook library.
  • Renamed Public Notebooks tab to Notebook Library.
  • Added URL to get a copy of the notebook and open it all in a single link click.
  • When opening a public notebook, show the user where it was copied to.
  • Bug fixes.

GenePattern Notebook Repository 18.09 (September 14, 2018)

  • Notify users when others are editing a shared notebook.
  • Added edit sharing button to dialog in public notebooks tab.
  • Restructure notebook sharing to shared by/with me.
  • Add sharing invite badge to public notebooks tab.
  • Added Human Cell Atlas theme.
  • Bug fixes.

GenePattern Notebook Repository 18.07 (July 24, 2018)

  • Added the ability for users to easily share notebooks with others.
  • Improved integration with JupyterHub's Services API.
  • Admins now have an interface for pinning and protecting tags.
  • Improved preview functionality for the public notebooks.
  • Added support for the NDEx2 API

GenePattern Notebook Repository 18.03 (March 23, 2018)

  • Tagging functionality added to the Public Notebooks tab.
  • Public Notebooks tab UI redesign.
  • Preview functionality added to public notebooks.

GenePattern Notebook Repository 18.01 (January 19, 2018)

  • Upgraded repository to JupyterHub 0.8, Jupyter 5.3 and ipywidgets 7.
  • Updated repository containers to include R 3.4.3 and rpy2 package. See R Support documentation for more details.
  • Updated spawner and authenticator plugins to latest JupyterHub API.

GenePattern Notebook Repository 17.12 (December 8, 2017)

  • Improved compute node scaling and performance.
  • Public notebook service port change.

GenePattern Notebook Repository 17.07 (July 27, 2017)

  • Support for Python environment versioning added.
  • Python 3 kernel updated to Python 3.6.
  • GenePattern Notebook extension updated to v0.6.4.
  • GenePattern Python library updated to v1.3.0.
  • Scientific computing libraries updated.
  • Deprecated Python 2 kernel.

GenePattern Notebook Repository 17.05 (May 15, 2017)

  • Notebook sharing functionality.
  • Infrastructure update (AWS hosting).

GenePattern Notebook Extension

Release updates for the GenePattern Notebook nbextension. Install using pip install genepattern-notebook or conda install -c genepattern genepattern-notebook.

GenePattern Notebook 0.8.5 (February 13, 2019)

  • Bug fix release.

GenePattern Notebook 0.8.4 (January 10, 2019)

  • Bug fix release.

GenePattern Notebook 0.8.3 (December 21, 2018)

  • Removed from the list of servers.
  • Added cell templates.
  • Support for output files in subdirectories for GPJob widget.

GenePattern Notebook 0.8.2 (October 31, 2018)

  • Default server changed to GenePattern Cloud.
  • File kinds can include a wildcard character.
  • Compatibility fix for latest version of ipywidgets.
  • Combined the gear menus in analysis/job cells.
  • Warning message added to orphaned analysis cells
  • Jobs that output index.html will display it in an iframe
  • Bug fixes.

GenePattern Notebook 0.8.1 (September 17, 2018)

  • Bug fix release.

GenePattern Notebook 0.8.0 (August 16, 2018)

  • Refactored to support nbtools 0.2.0.
  • Moved UI Builder and UI Output functionality to nbtools package.
  • Support for output files in subdirectories for GPJob widget.

GenePattern Notebook 0.7.3 (July 9, 2018)

  • Added new UI Output widget.
  • Added option to not add UI Builder functions to the Notebook Tool Manager.
  • Updated to latest GenePattern URLs.
  • Better support for multiple widgets in combined cells.
  • Bug fixes.

GenePattern Notebook 0.7.2 (May 30, 2018)

  • Analysis and job widgets will now appear together in the same cell by default.
  • UI Builder cells and outputs will now appear together in the same cell.
  • Added a new widget GPUIOutput intended to visually display programmatic output.
  • An icon has been added to job widgets, indicating their sharing status.
  • Bug fixes.

GenePattern Notebook 0.7.1 (March 21, 2018)

  • UI Builder file upload added.
  • Double-click to edit file parameter functionality added.
  • Added parameter reset to analysis widgets.
  • Bug fixes.

GenePattern Notebook 0.7.0 (February 16, 2018)

  • GenePattern workflow execution interface added. For more information see the Workflow Execution documentation.
  • Support for job result syntax added to GenePattern analyses. This is a simple syntax for specifying GenePattern analysis inputs based on the output of of upstream jobs. For more information see the Job Result Syntax documentation.
  • Added support for renaming, hiding or overriding the output variable in the UI Builder.
  • Major refactoring of code structure and file names.
  • Updated Javascript code to ES6 standard.
  • New webpack build process added.
  • Bug fixes.

GenePattern Notebook 0.6.8 (December 8, 2017)

  • UI Builder now has type-specific support for file, number, password and bool parameters.
  • Placeholder job cells added.
  • Job cells can now send a browser notification when a job completes.
  • Added the ability to programmatically set the output variable in the UI Builder.
  • Add ability to pass in custom function import path in the UI Builder.
  • Bug fixes.

GenePattern Notebook 0.6.7 (November 8, 2017)

  • Improved UI Builder customization and features.
  • Usability improvements.
  • Bug fixes.

GenePattern Notebook 0.6.6 (October 13, 2017)

  • UI Builder support for choice parameters and dynamic configuration.
  • Support for ipywidgets 7.
  • Bug fixes.

GenePattern Notebook 0.6.5 (September 15, 2017)

  • Beta release of the UI Builder.
  • Package restructuring to better fit Python standards.
  • Bug fixes.

GenePattern Notebook 0.6.4 (July 27, 2017)

  • Added support for parameter groups
  • UI Builder alpha release

GenePattern Notebook 0.6.3 (June 28, 2017)

  • Bug fix release for low-numbered LSIDs

GenePattern Python Library

Release updates for the GenePattern Python Library. Install using pip install genepattern-python or conda install -c genepattern genepattern-python.

GenePattern Python 1.4.2 (September 17, 2018)

  • Bug fixes.

GenePattern Python 1.4.1 (February 16, 2018)

  • CLS file creation function added to package.
  • JSON serialization added to GPFile object.

GenePattern Python 1.4.0 (December 8, 2017)

  • Added write_gct() and write_odf(), which write pandas dataframes to disk in GCT or ODF formats, respectively.
  • ODF() and GCT() now directly create pandas dataframes from the loaded data.
  • Added get_recent_jobs() function to retrieve a list of recently launched jobs.
  • Dropped Python 2 support.

GenePattern Python 1.3.1 (September 15, 2017)

  • Support for local and remote LSID authorities when generating GenePattern modules from Python scripts.

GenePattern Python 1.3.0 (July 27, 2017)

  • Functionality added for creating GenePattern modules from Python (gp.modules)

Notebook Tool Manager

Release updates for the Notebook Tool Manager. Install using pip install nbtools or conda install -c genepattern nbtools.

Notebook Tool Manager 0.2.4 (February 13, 2019)

  • Added ability to send text to UI Builder widgets from markdown cells or upstream output.
  • Added custom status indicator and update call for UIOutput widgets.
  • Added optional/required parameter annotation
  • Fixed bug where some inputs strings would incorrectly be treated as numbers

Notebook Tool Manager 0.2.3 (October 31, 2018)

  • Bug fix release

Notebook Tool Manager 0.2.2 (December 21, 2018)

  • File kinds now support wildcards *
  • Compatibility fix for newer versions of Jupyter
  • Bug fixes

Notebook Tool Manager 0.2.1 (September 17, 2018)

  • Event hooks added to UI Builder
  • Bug fixes

Notebook Tool Manager 0.2.0 (August 16, 2018)

  • Moved UI Builder functionality from the GenePattern Notebook package to nbtools
  • Moved UI Output functionality from the GenePattern Notebook package
  • Added support for output files in subdirectories
  • Added id and events parameters to the UI Builder

Notebook Tool Manager 0.1.7 (April 3, 2018)

  • Changed nbextension installation to match new Jupyter 5.3+ standard.

Notebook Tool Manager 0.1.6 (December 8, 2017)

  • Focus is now automatically given to the search/filter box when the toolbox is opened.

Notebook Tool Manager 0.1.5 (October 19, 2017)

  • Button label for for Jupyter >= 5.1.0.

Rich Text Editor

Release updates for the Rich Text Editor. Install using pip install jupyter-wysiwyg or conda install -c genepattern jupyter-wysiwyg.

Rich Text Editor 0.1.9 (December 4, 2018)

  • Fixed a bug in the install process for Jupyter 5.3.

Rich Text Editor 0.1.8 (May 3, 2018)

  • Added LICENSE.txt file to PyPI source archive.

Rich Text Editor 0.1.7 (April 26, 2018)

  • Fixed an issue that could call installation to fail due to a bug in setuptools.

Rich Text Editor 0.1.6 (April 3, 2018)

  • Changed nbextension installation to match new Jupyter 5.3+ standard.
  • Bug fix for behavior when switching between command and edit modes.

Rich Text Editor 0.1.5 (February 16, 2018)

  • Bootstrap style support added to the editor.