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Changelog

0.5.0 (2017/12/08)

Fixes

  • Fix syntax problems with the rst files of the documentation
  • Fix docstrings of some python methods
  • Fix version of the dependencies
  • Fix the float index error from the vem_tools.py script
  • Fix the cosine drift problem caused by the latest version of numpy
  • Fix the error caused by trying to compute the log(0) in the entropy function
  • Fix the bug of the free_energy_computation function when the HRF is not estimated.

Enhancements

  • Requirements file (requirements.txt) for developing and installation
  • Improvement of the installation script (setup.py)
    • Auto-install of dependencies using pip and the requirements.txt file.
    • Python version 2.7.x required
    • C extensions are only compiled when PyHRF is built or installed. The same for the installation of the dependencies
    • The outputs of the installation script are colored in order to highlight important information
  • Documentation
    • Improvement readability of the README and CHANGELOG files.
    • Improvement of the documentation with detailed VEM formulas
    • Extension of the documentation with the NeuroElf based visualization tool
    • Extension of the documentation with the installation steps for different GNU/Linux distributions
    • Extension of the documentation with a developer section
    • Deprecated sections of the documentation are hidden

New

  • PyHRF visualization tool based on the NeuroElf tool
  • Creation of a Dockerfile
    • Sharing the docker image on Docker Hub (pyrhf/pyhrf)
    • The CI service (travis) runs the tests and the coveralls using the docker image
    • The releases are now generated using and creating a docker image
  • Documentation
    • Using a responsive, friendly and beautiful Sphinx theme (sphinx_bootstrap_theme)
    • Using readthedocs to build automatically the documentation

Optimizations

  • Optimization of some VEM methods
    • pyhrf.vbjde.vem_tools.create_conditions
    • pyhrf.vbjde.vem_tools.create_neighbours
    • pyhrf.vbjde.vem_tools.poly_drifts_basis
    • pyhrf.vbjde.vem_tools.cosine_drifts_basis
    • pyhrf.vbjde.vem_tools.norm1_constraint
    • pyhrf.vbjde.vem_tools.nrls_expectation
    • pyhrf.vbjde.vem_tools.hrf_entropy
    • pyhrf.vbjde.vem_tools.two_gamma_hrf
    • pyhrf.vbjde.vem_tools.ppms_computation
    • pyhrf.vbjde.vem_tools.computeFit
    • pyhrf.vbjde.vem_tools.contrasts_mean_var_classes
    • pyhrf.vbjde.vem_bold.jde_vem_bold

0.4.3 (2016/07/08)

Fixes

  • Remove non-existing tests in devel mode
  • Correct typo in documentation
  • Correct list display in documentation
  • Fix bug for numpy >= 1.11.1 version
  • Fix bug in contrasts computation
  • Clean tmp folders after some unitary tests
  • Fix VEM script example

0.4.2 (2016/07/07)

Fixes

  • Fix VEM algorithm
    • Fix convergence criteria computation
    • Fix underflow and overflow in labels expectation (set labels to previous value if necessary)
  • Continue to clean setup.py
  • Fix some DeprecationWarning that will become Exceptions in the future
  • Fix detection of parcellation files
  • Fix for scikit-learn version >= 0.17
  • Fix bugs with matplotlib versions >1.4
  • Fix bug with Pillow latest version (see #146)
  • Fix bug with numpy when installing in virtual environment (see commit a971656)
  • Fix the zero constraint on HRF borders

Enhancements

  • Optimize some functions in vem_tools
  • Rewrite and optimize all VEM steps
  • Remove old calls to verbose module and replaced them by logging standard library module
  • Update website documentation

New

  • Updating documentation
    • Updating theme
    • Fixing some reST and display errors
  • Auto-detect CPUs number (mainly to use on cluster and not yet documented)
  • Add covariance regularization matrix
  • Load contrasts from SPM.mat
  • Save contrasts in the same order that the xml configuration file
  • Compute and save PPMs
  • Add multi-session support for VEM BOLD and ASL
  • Add cosine drifts to VEM
  • Add command-line for VEM
  • Add Stanford Willard Parcellation

0.4.1.post1

Fixes

  • Missing function (see #135)
  • nipy version required for installation (see #134)

0.4.1 (2015/08/19)

Fixes

  • Logging level not set by command line (see #113)
  • Error with VEM algorithm (see #115)

Enhancements

  • Clean and update setup.py (see #84)
  • Update travis configuration file (see #123)

0.4 (2015/07/22)

API Changes

  • Deprecate verbose module and implements logging module instead

Fixes

  • Clean up setup.py

No changelog for previous versions