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Commits on Aug 15, 2019

• Merge branch 'issue-50'

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• Replaced all the itertools cycle.next() calls with next(cycle) built-in calls.

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Commits on Jul 31, 2019

• Merge branch 'issue-51'

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• Updated the portion of the notebook relevant for issue 51.

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• Added some extra int casting in the COMTraj parallelized MSD function. Added a new update_rcparams function to the plot_generation_functions module.

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• Merge branch 'block_average_BSEvLength'

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• Fixed some bugs.

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• Fixed some bugs in the tests.

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Commits on Jul 29, 2019

• Commented out some conditional print blocks used for debugging in MSDProtocol, as well as removed the block that resets the time origin after 50000.0 ps used for custom analysis.

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• Addition of the block_average_bse_v_size function.

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• Fixed a _last_frame reset bug in the reset of the iterator.

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• Added the use_gaussian_filter input arg setting and application of gaussian_filter to the surface.

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Commits on Feb 25, 2019

• Update Landscape Badge for switch to Lolab-VU

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• Updated the parse_args in the MassWeightedStdDistProtocol to look for selection_string setting keyword instead of selection.

  blakeaw

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• Updated the parse_args in the PeakToPeakProtocol to look for selection_string setting keyword instead of selection.

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• Update Landscape Badge for switch to Lolab-VU

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• Merge branch 'update_rtd_environment_file'

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• Updated the activate code lines in the readme to conda activate (for updated conda version) instead the older source activate calls.

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• Updated the RTD conda environment file. Now uses python 3.6 and corresponding updated packages.

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• Merge branch 'analysis_protocol/leaflet_to_leaflet_distance'

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• Updated the rst and md files for the ba_analyses doc pages.

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• Updated the rst and md files for the ba_analyses doc pages.

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• Miscelllaneous fixes picked up when generating new docpages.

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• Double checked the assignemnts fot the analaysis keys of the new thickness protocols and updated there docstrings.

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• Added 3 more estimators for bilayer thickness to the protocols for the BilayerAnalyzer. Also some corresponding changes and fixes.

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Commits on Feb 22, 2019

• Merge branch 'lipid_grid_fixed_area_per_bin'

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• Made some updates to the docstring for the BilayerAnalyzer to include new rep settings.

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• Added the option to set a fixed area per bin when constructing the lipid_grid reps. Includes other accomapnying and miscellaneous changes.

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Commits on Jan 26, 2019

• Added the average_per_lipid_type function to the LipidGrid2d class.

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Commits on Jan 17, 2019

• Made a few changes to the docstring for the nnf protocol.'

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Commits on Jan 16, 2019

• Merge branch 'vectorize_unwrap'

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• Merge branch 'run_bilayer_analyzer_command_line'

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• Updated the run script to use argparse for input arguments.

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• Updated the run script to now take the second command line argument as the file path to dump the output after the analyzer is finished running.

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• Removed leftover print calls used in debugging.

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