Legacy release notes

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v.0.2.2 Titanium (6 Feb 2014)

• Export/Import workflow template in .json format

• Improved Runs Graph: (expand/collapse, small nodes, tooltips and keep positions)

• Get working the Relion polishing

• Review and update of the tutorials (specially the introdocutory one)

• Updated Spider protocols and tools

• Last fixes after Initial Volume WebTool

• MPI steps parallelization improved (95%)

v.0.1.4 Sillicon (6 Jun 2014)

• Improved handling of large logs files (preview, refresh, colors…​for web and tk)

• Fixed the use of MPI process in Parallel Protocols.

• Stored protocol steps in a separated .sqlite file (for performance)

• Stored objects creation time.

• Allowed selection of individual items from a set.

• Completion of the MDA workflow with all protocols and updated the Spider script parsing (Tapu visit) and Custom mask wizard

• More processing tests with ribo tutorial, and PcV viruses.

• Showj visualization now directly from the .sqlite files…​Improved the Creation of subsets

v.0.1.3 Aluminium (9 May 2014)

• Managing multiple runs selection (in Tk and Web): Copy and Delete

• Re-factored the Visualizers to use "Views", now more centralized between Tk and Web

• Re-factored the wizards in Web

• Improved read of big log files.

• Test files are centralized in DataSets and their are automatically downloaded.

• Added Groups and Lines for more compact parameters in Protocol Form (also working with Expert Level and Condition)

• Improved developer documentation (architecture and welcome guide)

v.0.1.2 Magnesium (10 Apr 2014)

• Relion protocols completed (2D, 3D refine and classify, wizards, viewer…​and web)

• Frealign 9.07 update (refine, wizards, viewers…​and web)

• Protocols to import/export EMX format

• Created Protocol steps view

• Created Data view (and checked Relations inheritance, such as CTF)

• Improved tests datasets and classes.

• Improved way to create Materials & Methods, citations and summary (added bibtex parsing)

• Centralized execution under scipion entry script (also generation of stats)

• More protocols added from Scipion week

v.0.1.1 Sodium (10 Mar 2014)

• Missing release, due SAB visit.

v.0.1.0 Neon (10 Feb 2014)

• Missing release, due Scipion week for Xmipp protocols porting.

v.0.0.9 Fluor (10 Jan 2014)

• Mainly documentation and bug fixing.

v.0.0.8 Oxygen (18 Dic 2013)

• Changes:

  • BIG re-design, in both Web and Tk interfaces (automatic refresh also)

  • Wizards and Analyze results refined.

  • Added Twiki small subset of hypertext tags for Helps and Summaries

  • Scipion Day and several starting protocols.

• Known issues:

  • Memory leak (when the Tkinter GUI is open for long time, the RAM is consumed)

  • Performance issues with big datasets (Laura issues and RM complaints)

  • Need to handle multiple plots from Analyze results in Web (example ML3D)

v.0.0.7 Nitrogen (11 Nov 2013)

• Added relations (For CTF, Aligment is missing)

• Developed first SPIDER protocols (align, filter, dimension reduction and classification) MDA workflow

• Included protocol viewer with Forms( ProtocolViewer) in Tkinter and Web

• More wizards for Tkinter and Web (adapted for SPIDER protocols)

• Improved protocols main interface.

v.0.0.6 Carbon (4 Oct 2013)

• Data classes are not sub-classes per packages, now they have a common Scipion representation and storage (sqlite). Added related convert.py modules for conversion.

• Web: fix styles, wizards.

v.0.0.5 Boron (5 Sept 2013)

• Missed release due vacations of team members

v.0.0.4 Beryllium (6 Aug 2013)

• Design changes:

  • All elements in a Set should contains an unique ID inside the set, that should be maintained in transformations of the set.

  • Eman version have been changed to 2.1, carrying different access using hdf and json

• Xmipp protocols:

  • OnlyAlignCL2D

  • RotSpectra

  • KerdenSOM

  • ML3D

  • Filters, Mask

• Eman protocols:

  • Boxing

  • Initial model

• GUI

  • Graph tree is working on Web

  • Wizards on Tkinter

  • Form improved, now using Tabs, include summary and parameters validations.

  • Basic analyze results of some protocols.

  • First try with web visualization of volumes with Astex and Chimera-WebGL

• Tests

  • Update new tests for protocols.

  • Running Buildbot for continuous integration.

v.0.0.3 Lithium (5 Jul 2013)

• Protocol execution:

  • Basic launch and update of protocols.

• Some Xmipp protocols, starting with Eman boxing, CTFFIND included

• GUI

  • Graph tree is working on Tkinter

  • Basic way of editing execution hosts and Host view in projects.

• Tests

  • Setup of the general organization of the tests and creation of several ones.

  • First try with Buildbot