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Legacy release notes

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