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@pdp10 pdp10 released this 01 Dec 16:08
· 1058 commits to master since this release
v2.0.0
f01e8d0

This release includes the following features / updates:

  • improved threshold levels for Sampled PLE plots.
  • added 20 tests including wrong configuration file settings.
  • extensive refactory of unit tests.
  • source code uses PEP8 standard
  • source code cleaning and reformatting.
  • improved source code by eliminating some warning highlighted by PyCharm.
  • moved script core functions within sbpipe package.
  • the copasi package is now a dynamically loaded simulator. Users can choose the simulator
    to use in the configuration file.
  • simulators are loaded dynamically. Uncoupling between simulators and pipelines.
  • separation of code for generating data from pipeline package.
  • improved source code modularisation for the whole program.
  • extracted scripts (run_sbpipe and cleanup_sbpipe) from sbpipe/.
  • sbpipe supports execution as a Python module (main.py).
  • all Python imports are now absolute (in agreement with Python 3).
  • improvements to program prints
  • project renamed sbpipe
  • added AIC, AICc, BIC to the parameter estimation summary table.
  • randomisation of initial parameter values for parameter estimation is now only
    performed by Copasi.
  • added plots comparing model simulation vs experimental data in simulate pipeline.
  • improving plot margins for simulate and single parameter scan pipelines.
  • source code refractoring in parameter estimation analysis task.
  • fixed a bug in parameter estimation pipeline related to the filtering of confidence
    intervals from the complete data set.
  • added ratios in parameter estimation summaries to investigate the distance between the
    estimated parameter and its confidence intervals.
  • plot polishing.
  • separated options for plotting 2d correlations within 66%, 95%, or 99% confidence intervals.
  • added 99% confidence intervals parameter estimation plots.
  • added option to plot parameter estimation plots using the scientific notation.
  • improved plots layout (fonts, legends).
  • added option for y axis label to simulate and single parameter scan pipelines.
  • Copasi models are fully consistent.
  • table of estimated parameter and confidence values is in normal scale (not log10).
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