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 introductory one)
Updated Spider protocols and tools
Last fixes after Initial Volume WebTool
MPI steps parallelization improved (95%)

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

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)

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

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)

Added relations (For CTF, Alignment 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.

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.

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.

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