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V0.4.x#8

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rtrhd wants to merge 74 commits intomaartenmennes:mastermaartenmennes/ICA-AROMA:masterfrom rtrhd:v0.4.xrtrhd/ICA-AROMA:v0.4.xCopy head branch name to clipboard

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Commits on Jan 26, 2017

• Merge fuctions module into main script to simplify installation, add rng seed option to allow regression testing.

  

  rtrhd

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  Ronald Hartley-Davies

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• Added refactored implementation and regressions tests to example output from original

  

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• Patched subprocess for missing check_output in python2.6; fixed some wrong file paths

  

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• Added version and tidied up some comments

  

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• Fixed typo in logging; fixed dubious var name; white space and comment changes

  

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• Add .gitignore

  

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• Handle argument validation earlier with argparse

  

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• Supress stderr chatter from argparse

  

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• Move source directory to start rather than end of sys.path for testing

  

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• remove superflous check of outdir (handled by argparse now)

  

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• Remove non-ascii chars

  

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• change shebang to allow testing with different pythons

  

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• move more parameter validation into argparser

  

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• Add tests for is_valid_feat_dir

  

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• refactor zsums to reduce calls to fsl commands

  

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• Conversion of Manual.pdf to markdown

  

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• clean up code blocks and suppress dubious highlighting

  

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• mv manual to subdir

  

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• Use nibabel for nifti image access, determine AROMADIR dynamically, minor changes to argument checking

  

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• clean up markdown formatting of README

  

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• Replace fsl_filt with an internal routine and require nibabel for header and image access

  

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• fix some typos etc in main and cosmetic changes for better pep8

  

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• add .spyderproject to .gitignore

  

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• update manual for new invocation

  

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• Move old version into test area

  

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• Remove old pdf manual

  

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• move aroma.py into package (icaaroma)

  

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• Add setup.py and a link in bin to install script without .py extension

  

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• install mask files inside package directory

  

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• Handle aroma mask files as package data if installed as python package; Use setuptools to install executable script; Add manual install with Makefile

  

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• Fix paths to aromadir for tests

  

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• Fix typos in cmdline parser

  

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• Fix typo in command line arg handling; update docs for installation and changed argument handling

  

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• Add clean clause to Makefile

  

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• Small tidy up of cmdline args, tests, Makefile and docs

  

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• Create LICENSE.md

  

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• Add -T as alias for --tr

  

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• Drafting changes to manual

  

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• Fix authors etc in setup.py

  

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• Further memory optimisation in reg_filter(), modify data in-place

  

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• Add build artefacts to .gitignore

  

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• Tweaks to setup.py

  

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• Tweaks to test_aroma.py and Makefile

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• Jupyter notebooks from refactoring experiments.

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• Add more details to Regfilt notebook.

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• Tweaks to Makefiles and install instructions.

  

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• Simplify README

  

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• remove large test datasets

  

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• Add Makefile in tests dir

  

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• Fix Makefiles to download test data from separate repo

  

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• Use standard three digit version numbers

  

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• change name of test dir

  

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• Use unbzip2 explicitly with tar for compatibility

  

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• Tweak .gitignore

  

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• Add Dockerfile for testing on neurodebian

  

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• Tweaks to manual.

  

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• Tweaks to docs and licence.

  

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• Add .travis.yml file for CI

  

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• Add requirements.txt

  

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• Add fsl to travis build

  

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• Fix LD_LIBRARY_PATH for fsl in travis

  

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• Source fsl.sh in travis config. Skip some tests in python 3.

  

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• reapply simpler licence file

  

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• fixed case of LICENSE.md

  

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Commits on Jan 31, 2017

• removed obsolete sanitizing wrapper script

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Commits on Feb 1, 2017

• fix error when copying existing mask

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• use check_call() instead if call() and handle exceptions explicitly

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Commits on Oct 18, 2017

• tracking fix for minor upstream issue with propagating nans

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• fix inconsistent header information in mask files

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Commits on Mar 12, 2018

• Fix error in accessing previous melodic run

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Commits on Apr 5, 2018

• Reduce bloat in Docker image

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• Update .travis.yml

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Commits on Apr 6, 2018

• Update .travis.yml

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• Update .travis.yml

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