Cytoflow release

Cytoflow release

Fix MANIFEST.in to include logicle.h

• Significant re-work of summary statistics generation and plotting
• Tighten down TASBE calibrated cytometry
• MANY many bug fixes, both in modules and GUI

New in this release:

• A GUI for the calibrated cytometry tools!
  • Bleedthrough compensation (both linear and piecewise-linear)
  • Bead calibration
  • Autofluorescence correction
  • Color mapping
• Keep the same scales on plots in the same x, y facets
• Significant under-the-hood re-wiring
• Other bug-fixes

• Fix some Logicle crashers
• Add error bars to barplot, stats views
• Use FastLogicle -- it's faster!

A public beta!

• The point-and-click GUI is not only functional but useful. Serious restructuring behind the scenes, including a multi-process model to keep the GUI responsive.
• More operations (GMMs) and views (2D histogram, 1 and 2D KDEs, violin plots.)
• Lots (lots) of packaging work. One-click bundles and distribution infrastructure.

A developer's beta!

• Add a public API to Experiment to add conditions and channels.
• Add scaling options to views, data-driven modules
• Add 1D and 2D gaussian mixture models
• Clean up import mess
• Linear bleedthrough module, quad gate

• Drops the isValid() methods from the operations and views, expecting estimate(), plot() and apply() to instead check (early!) if it's valid and throw an exception if not.
• Gave operations an optional defaultView() method, for interactive plots and the like: allows tighter coupling between an interactive plot and the module whose traits it's viewing or changing.
• Unit testing infrastructure. At the moment, mostly smoke tests, not actual functionality testing.
• More examples!
• TASBE workflow fixes. Now they (mostly) match the implementation at synbiotools.bbn.com.

Better packaging, better documentation, better instructions. Now the EasyInstall script should work on Windows!