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Beyond the Kuiper Belt

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@pdp10 pdp10 released this 26 Jun 15:13
v4.21.0
fe74ce2
  • added support for Copasi Optimisation task. This also uses the -e option.
  • bugfix: added is_package_installed.r to MANIFEST.ini.
  • SBpipe v4.18.0, sbpiper v1.8.0, sbpipe_snake v1.0.0 and above are released under MIT License.
    Previous versions of these packages were released under GNU GPL v3.
  • Improved project consistency and added warnings.
  • Snakemake files moved to a separate repository (https://github.com/pdp10/sbpipe_snake.git).
  • Added script for moving data sets and update indexes.
  • Project and documentation clean-up.
  • SBpipe is now available on pypi.org.
  • Improved setup.py file for python packaging
  • SBpipe tests no longer require CopasiSE.
  • Documentation update.
  • Added generate_tarball option to all the remaining pipelines in native SBpipe.
  • Improved output messages.
  • Added progress information for native SBpipe.
  • Added PCA analysis for the best parameter estimates. Replaced conda channel "r" with "conda-forge".
  • Improved data analysis scalability for parameter estimation (using Snakemake).
  • Added checks whether a COPASI model can be loaded and executed correctly. This is based on Python bindings for COPASI.
  • Optimisation of snakemake pipelines. Improved efficiency of rules for analyses.
  • Bugfix - SGE and LSF job names now include a random string, avoiding potential interactions among multiple
    SBpipe executions. Whilst this does not affect the results, it was still a performance-related bug.
  • SBpipe R code is now an independent R package called sbpiper. This is imported by SBpipe as
    an external dependency. Users can invoke SBpipe functions for data analysis directly from their R code.
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