GenePattern Notebook Repository

Release updates for the GenePattern Notebook Repository.

GenePattern Notebook Repository 20.01 (January 7, 2020)

  • Now includes the Globus client. Documentation on how to connect your workspace to Globus is available on the GenePattern Notebook website.
  • Several R packages including Seurat, scater and dyplr are now included by default.
  • Updated to nbtools 20.01 and igv-jupyter 0.9.8, which include several bug fixes.

GenePattern Notebook Repository 19.11 (November 22, 2019)

  • Workshop notebooks now display in their own table inside the Notebook Library tab.
  • Updated to ccal-noir 2.7.1 to fix an incompatibility in that library with the latest version of numpy.
  • Bug fix for notebook sharing emails.

GenePattern Notebook Repository 19.10 (October 28, 2019)

GenePattern Notebook Repository 19.09.2 (October 4, 2019)

GenePattern Notebook Repository 19.09 (September 17, 2019)

GenePattern Notebook Repository 19.08 (August 19, 2019)

  • Update the notebook preview images anytime a public notebook is updated
  • Graceful failure of GenePattern features added for single-user work and non-Python kernels
  • R kernel added to the Docker image
  • Support for MySQL added to the public notebooks service

GenePattern Notebook Repository 19.07 (July 19, 2019)

  • New GenePattern theme added.
  • Public notebooks now sorted by latest by default
  • Added login/register button to preview page.
  • Improved organization of Community notebooks.
  • Added Workshop Notebooks tab.
  • Added optional email notification when a new notebook is published.
  • Added terms of use.
  • Bug fixes.

GenePattern Notebook Repository 19.05 (May 7, 2019)

  • Improved notebook preview functionality.
  • Updated Python 3.7 environment with new Python packages
  • Added repository start and stop scripts.
  • Notebook Library tab will now remember user selection.
  • Improved Dockerized architecture.
  • Added support for SwarmSpawner.
  • Improved theme support.
  • Bug fixes.

GenePattern Notebook Repository 19.04 (April 5, 2019)

  • Added support for user-installed nbextensions.
  • Formalized webtour notebook extension.
  • Formalized repository notebook extension.
  • Added support for newer versions of JupyterHub.
  • Bug fixes.

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 19.09 (September 17, 2019)

  • Added support for HTML in module and parameter descriptions
  • Cell templates moved to "+" origin

GenePattern Notebook 19.08 (August 12, 2019)

  • Cell template improvements
  • Login message fix
  • Graceful failure implemented when operating with a non-Python kernel

GenePattern Notebook 19.07 (July 16, 2019)

  • Build improvements and bug fixes

GenePattern Notebook 19.05 (May 31, 2019)

  • Updated release architecture
  • New versioning scheme

GenePattern Notebook 0.8.6 (April 10, 2019)

  • Bug fix release.

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 1.4.5 (July 31, 2019)

  • Updated release to the latest PIP standards

GenePattern Python 1.4.3 (September 17, 2018)

  • Bug fixes.

GenePattern Python 1.4.2 (August 16, 2018)

  • Lazily call load_params() when a job spec is created from a task. This prevents a common mistake when running jobs.

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 20.01 (January 2, 2020)

  • Bug fixes for the R UI Builder.

Notebook Tool Manager 19.10 (October 28, 2019)

  • Bug fix for the build_ui decorator.

Notebook Tool Manager 19.09.1 (September 26, 2019)

  • Critical bug fix for UI Builder

Notebook Tool Manager 19.09 (September 17, 2019)

  • Added better support for defining and importing UI Builder widgets from a Python module
  • Implemented support for large file uploads in the UI Builder
  • Added support for HTML in widget and parameter descriptions

Notebook Tool Manager 19.07 (July 16, 2019)

  • Adding r_build_ui magic (UI Builder support for R cells)
  • Condensed display for UI Builder widgets with no parameters
  • R support critical fix
  • Origin override option added to UI Builder
  • Dropping support for Python 3.5

Notebook Tool Manager 19.05 (May 31, 2019)

  • Updated release architecture
  • New versioning scheme
  • Added prototype support for R in the UI Builder

Notebook Tool Manager 0.2.6 (April 12, 2019)

  • Bug fix release

Notebook Tool Manager 0.2.5 (April 9, 2019)

  • Allow HTML in UIOutput status
  • Hide custom value option in dropdowns by default
  • Bug fixes

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 19.10 (October 28, 2019)

  • Bug fix for double-clicking erroneously displaying markdown text
  • Bug fix for markdown cells erroneously being changed to code

Rich Text Editor 19.08 (August 25, 2019)

  • Upgraded the rich text widget to TinyMCE 5
  • Added "Rich Text" pseudo-cell type

Rich Text Editor 19.07 (July 31, 2019)

  • Updated PIP deploy to the latest standards

Rich Text Editor 19.05 (May 31, 2019)

  • Updated conda packaging
  • Updated versioning scheme

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.