WESTPA commits | Ecosyste.ms: OpenCollective

github.com/westpa/westpa - 22b3e284d4f4c002430e2a76294527c3cfaa565b authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - cf6641006c2e2d5a10777a9cf56279bbea2e9928 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 8c66ac0328fc320fe87bef3e6783d168f3a0063a authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 56a57ad3e47091d53115df0b6c5fef67fcd60527 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - fc1f9e8bf22685132284b104e97d32cbeb08af25 authored over 8 years ago by Adam J. Pratt <[email protected]>

github.com/westpa/westpa - 2408c9ea64cdca59d7f67a9c977c9de53fca9f8d authored over 8 years ago by Adam J. Pratt <[email protected]>

Restored some w_kinavg functionality.

Made the bootstrap optional (!)

github.com/westpa/westpa - 84c6453abb06a38ac4e2219e8ab8b1533990c741 authored over 8 years ago by ajpratt <[email protected]>

Adjusted int index to be long type.

Fixed (likely) infinite loop bug when the number of fluxes became larger
than the max int value.

github.com/westpa/westpa - e947fd331d408cf143fc4a9442eae7d55752310d authored over 8 years ago by ajpratt <[email protected]>

All functions now properly cythoned.

Nothing except for the main function requires the gil.

github.com/westpa/westpa - dedb6693c183e0908c54281b878f7b9d6269e4eb authored over 8 years ago by ajpratt <[email protected]>

Essentially, python free for the main loop.

One last problem with the GIL, however.

github.com/westpa/westpa - eb6ecc8f47251362e2bbdaebeec5f4c9fa610f9e authored over 8 years ago by ajpratt <[email protected]>

Removed more python calls.

calc_state_flux now cython only.

github.com/westpa/westpa - 81f7593c6ea2f2089dfe2d02b31f7c822a15b626 authored over 8 years ago by ajpratt <[email protected]>

Considerable cleanup.

Lots of things moved out of the gil.

github.com/westpa/westpa - c8937eb7bdeaaafffe49d0a4e6865342dba124fc authored over 8 years ago by ajpratt <[email protected]>

Implemented Tarjan's algorithm in cython.

Finds the strongly connected components. This build works, but is slow.
However, it also doubles...

github.com/westpa/westpa - dbf0f483c9802c10804e57c74234bf22a27ba81c authored over 8 years ago by ajpratt <[email protected]>

Moved more things out of the gil.

As efficient as it can be until steadystate_solve can be made gilfree.

github.com/westpa/westpa - d978a1230ca7343205c452206789d23840751ec5 authored over 8 years ago by ajpratt <[email protected]>

Switched from np.linalg.eig to LAPACK function.

Works!

github.com/westpa/westpa - 73ef8c4c6e436e37474adaa39668728b04fe4daf authored over 8 years ago by ajpratt <[email protected]>

Works. Slight optimisations. Fixed segfault.

github.com/westpa/westpa - c4fec4059cc06f8e7e242b317f7cf4a433622b39 authored over 8 years ago by ajpratt <[email protected]>

Everything seems to work correctly.

The code needs massive speed increases, however, as it is likely to take
about a trillion years t...

github.com/westpa/westpa - 446c7442e070ac1bac1646565a2163d323c2898e authored over 8 years ago by ajpratt <[email protected]>

Put in temp measure to restore functionality to w_kinavg.

Need to think of a better fix, but.
More things cythonized and working properly for both analysis...

github.com/westpa/westpa - bd8feea95d20d0347501213061c8b088a1fda0f8 authored over 8 years ago by ajpratt <[email protected]>

More things cythonized!

No longer using scipy to recreate dense matrices.
Still obtaining correct answer. Fewer things w...

github.com/westpa/westpa - f4749515306de82b0d61952a6a4548471d8fd9d5 authored over 8 years ago by ajpratt <[email protected]>

More cython changes.

Still produces correct answers. Slowly trying to turn the gil off in
all core loop functions suc...

github.com/westpa/westpa - a6e5782598df323d6fa62b52826cbdddf9912c99 authored over 8 years ago by ajpratt <[email protected]>

Returns the correct answer!

Forgot to correct for the resolution of the flux matrix.
Still incredibly slow, however. A lot o...

github.com/westpa/westpa - 64a70d9d3f3c47eaeda674c8e4516ba9303ba642 authored over 8 years ago by ajpratt <[email protected]>

Many changes, but nothing is working yet.

End of day commit. Compiles and runs without segfaulting,
but slow and inaccurate.

github.com/westpa/westpa - f57fc061350d2d74b5cee2c632a9c87d6aae3d62 authored over 8 years ago by ajpratt <[email protected]>

Data structure in place for w_postanalysis.

Need to cythonize functions, now.

github.com/westpa/westpa - 4b023af0a7f1162a7e8dc8fe2d4f7b8b765ccdcc authored over 8 years ago by ajpratt <[email protected]>

Modified data structure.

Seems to be more accurate, oddly enough, suggesting a fixed bug that I
was not aware of.

github.com/westpa/westpa - 1fa7a3988c4c435cc34773b4498f8f6bff858b61 authored over 8 years ago by ajpratt <[email protected]>

Moved w_multi_kin to w_multi_west.

As the old rate constant tool was calculating rates (and error bars)
incorrectly, it made more se...

github.com/westpa/westpa - 975a1104252bc25c727e57f2de502d42b656d474 authored over 8 years ago by ajpratt <[email protected]>

Merge pull request #14 from westpa/kinavg-avg-mod

Kinavg avg mod

github.com/westpa/westpa - 153c6fd6f833c1e71b3a8fdca659256330bec0bf authored over 8 years ago by Adam J. Pratt <[email protected]>

Modified how w_kinetics and the bootstrap work.

This changes the way rates are done; thus far, it seems to produce
better results.
This is prepar...

github.com/westpa/westpa - 9d4e2132fb92d0921d43e59108f47fb3cd6723b6 authored over 8 years ago by ajpratt <[email protected]>

Updated docstrings in w_multi_reweight.py. Also, now supports different estimation schemes for the transition matrix. See --help for options.

github.com/westpa/westpa - 344b0c7c4772eceff10eaa9cab63558309ca10ff authored almost 9 years ago by Alex DeGrave <[email protected]>

Fixed a bug with how bin indices are specified, so that they are now converted to match the indices of the colored matrix.

github.com/westpa/westpa - e97998efaa9e33161c533122e691efb81548ae69 authored almost 9 years ago by Alex DeGrave <[email protected]>

Added options to w_postanalysis_matrix to support observing transitions every timepoint or every iteration. Also commented out check for target states in w_postanalysis_matrix, as I think this tool produces valid results for simulations with target states; this check could perhaps be moved to w_postanalysis_reweight in the future.

github.com/westpa/westpa - 22503ae36d41927e53a8b05bbc6cd3f9da8ed783 authored almost 9 years ago by Alex DeGrave <[email protected]>

Fixed a bug with specifying recycling states.

github.com/westpa/westpa - b10280b71ab5672fc97bc2d7a48cda6185042ddc authored almost 9 years ago by Alex DeGrave <[email protected]>

Merge pull request #13 from ASinanSaglam/yamlBranch

Yaml branch - with limited namespace code execution

github.com/westpa/westpa - 0047ea1b859596aca04dadc88068d9f854d0e4d2 authored almost 9 years ago by Adam J. Pratt <[email protected]>

Fixed some quick syntax errors.

github.com/westpa/westpa - 50ac89979e7e683c2eee7123d4694047f0bbf06a authored almost 9 years ago by Alex DeGrave <[email protected]>

Updated saving of transition matrices and added more help information.

github.com/westpa/westpa - 8de863ea6413f7f68222e0d8f38938224f63c084 authored almost 9 years ago by Alex DeGrave <[email protected]>

Added ability to save transition matrices in w_multi_reweight.py, as well as ability to automatically convert from state indices to bin indices (for denoting bins subject to recycling).

github.com/westpa/westpa - d93dc7178cf2120d714880623f4ef5b87643628d authored almost 9 years ago by Alex DeGrave <[email protected]>

Started adding option for saving transition matrices. This tool is probably broken right now; I will update it again soon.

github.com/westpa/westpa - 6f308f9e46f8ddb4a2d08c225ad3efa9bababd0a authored almost 9 years ago by Alex DeGrave <[email protected]>

Fixed typos and updated TODO notes in w_multi_reweight.py

github.com/westpa/westpa - 5aaf85664df274c5c6f5602370cfa6828072d96c authored almost 9 years ago by Alex DeGrave <[email protected]>

Updated westtools/core.py with a small yaml parsing wrapper function. This is needed to work with w_multi_reweight.py.

github.com/westpa/westpa - ad69a6d0a997ea512940f22eef831f4037817d44 authored almost 9 years ago by Alex DeGrave <[email protected]>

Added a bunch of updates to w_multi_reweight.py. It should be ready for some preliminary tests.

github.com/westpa/westpa - e5536697c70c30af45a333097c158f1b542da15a authored almost 9 years ago by Alex DeGrave <[email protected]>

Nearly done with w_multi_reweight.py; it should be ready for bug testing soon.

github.com/westpa/westpa - 40f88f5edc7fdb743443d7fdb533e59d41e332bc authored almost 9 years ago by Alex DeGrave <[email protected]>

Added functionality for averaging together transition matrices to w_multi_reweight.py

github.com/westpa/westpa - ebed58f49294bf4ceebee5893adedbc4f5e4b59e authored almost 9 years ago by Alex DeGrave <[email protected]>

Added in the initial basis of a new tool, which is heavily based on

w_postanalysis_reweight.py

github.com/westpa/westpa - daa6df6ed09fbcb19695be94bf26eaaaf9f47de3 authored almost 9 years ago by Adam P <[email protected]>

Merge branch 'master' into multitool

Forgot to pull in up to date master.

github.com/westpa/westpa - 0710ff24b182f3c790d44c8325c45035dac06406 authored almost 9 years ago by Adam P <[email protected]>

Merge branch 'master' into multitool

Bringing this up to date.

github.com/westpa/westpa - 638a18c7a59e278df42d0541839d68fbfdabd47f authored almost 9 years ago by Adam P <[email protected]>

Significant, albeit incomplete, rewrite.

Relies on new WESTTool type, 'WESTMultiTool', as a base
which handles the file loading and argume...

github.com/westpa/westpa - cd0b3c53e9fa574e67a8776daec2b0080096c5c4 authored almost 9 years ago by Adam P <[email protected]>

Making changes!

github.com/westpa/westpa - 700d3d1a446a8f7510c14c198eae01a081bad289 authored almost 9 years ago by ajpratt <[email protected]>

Removed random print statement from w_kinavg.py

github.com/westpa/westpa - 939326ea1f50fbbc302b8d919831deb63de8ec04 authored almost 9 years ago by Adam P <[email protected]>

Initial commit for porting monte carlo bootstrap function into the reweighting code.

github.com/westpa/westpa - 3f3629821faf662313b5598a2eb6c3ee42c86094 authored almost 9 years ago by Adam P <[email protected]>

Removed a redundant list function call

github.com/westpa/westpa - f24375b42d2df3b593ab3c67cc25ff0bc9af9fb8 authored almost 9 years ago by ASinanSaglam <[email protected]>

Better handling of boundaries

github.com/westpa/westpa - b588d75409ca16ce0807fbf03bbd9cbf0f363999 authored almost 9 years ago by ASinanSaglam <[email protected]>

Merge pull request #11 from westpa/fix-get_typed

fix yamlcfg get_typed()

github.com/westpa/westpa - 6efefc2373250dd10f74e7472dffb9459bc2ae47 authored almost 9 years ago by Matthew Zwier <[email protected]>

fix yamlcfg get_typed()

github.com/westpa/westpa - 3a80ddd97a33adf927bf7ca421172343b8e5c815 authored almost 9 years ago by Joshua L. Adelman <[email protected]>

Merge pull request #20 from ASinanSaglam/master

Small update to the documentation

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github.com/westpa/westpa - 8400b21437a30f1c4c1dda6ad8c096f7d178c589 authored about 9 years ago by Matthew Zwier <[email protected]>

Found a syntax that works

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github.com/westpa/westpa - 0985ad1a4e32b4ecd23f1c8ca2f681ec8773941a authored about 9 years ago by ASinanSaglam <[email protected]>

Well the official one doesn't work

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github.com/westpa/westpa - 32ef6e6529db5f086ff4f949ccdbc7b2886424a1 authored about 9 years ago by ASinanSaglam <[email protected]>

Apparenlty the official markup doesn't work..

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github.com/westpa/westpa - ffaee3e34924644bed20ec2b88c8d892b23b3268 authored about 9 years ago by ASinanSaglam <[email protected]>

Another syntax

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github.com/westpa/westpa - 83dc3f8acafaf3c36ac970258311bcaa3067c761 authored about 9 years ago by ASinanSaglam <[email protected]>

Trying out rst external links

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github.com/westpa/westpa - c2e64f497dd246c6965b1a082d22d395acdac83c authored about 9 years ago by ASinanSaglam <[email protected]>

Fixed a few things in the Makefile

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github.com/westpa/westpa - 3c775bb7a1deb76bc65ff02f3d26e99afb49ff87 authored about 9 years ago by ASinanSaglam <[email protected]>

Fixing the links

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github.com/westpa/westpa - 9234f4b0698751c54d4e91264ccd111d6dd84c21 authored about 9 years ago by ASinanSaglam <[email protected]>

Fixed the make file

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github.com/westpa/westpa - 73acecb1ac29e10b0eae350efc8cb0439ed1376f authored about 9 years ago by ASinanSaglam <[email protected]>

Added links to documentation.

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github.com/westpa/westpa - 36dd88fe3092c11567bda13563023c47aa819e49 authored about 9 years ago by ASinanSaglam <[email protected]>

Minor modifications.

github.com/westpa/westpa - a327b2a79d5c4cb89122b2f740c38a5dfad696a0 authored about 9 years ago by ajpratt <[email protected]>

Added in color functionality and the ability to directly pull from it from the west.cfg file.

github.com/westpa/westpa - b87a4f52c2e113cc332896ee000153aedd3ed871 authored about 9 years ago by Adam Pratt <[email protected]>

Modified _rc.py in westpa such that more driver options are available (for the grouping function).

github.com/westpa/westpa - 7d9c5330ceb04554b8d9c04ddbe8f97f7b8e464e authored about 9 years ago by Adam Pratt <[email protected]>

Merge pull request #18 from ASinanSaglam/master

Documentation update for the gh-pages branch

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github.com/westpa/westpa - 8eece1bd50bef17b0bc614539da670318e50f6ba authored about 9 years ago by Lillian Chong <[email protected]>

No need to change the templates folder name

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github.com/westpa/westpa - d3e29391a2c91607e02ab0042d72b6dca6c4e770 authored about 9 years ago by ASinanSaglam <[email protected]>

Easier workaround is here, fix the file naming in sphinx

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github.com/westpa/westpa - 38f59e27b07c1db6086ac18f6267165f5f7562d0 authored about 9 years ago by ASinanSaglam <[email protected]>

A crude way to protect some html names

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github.com/westpa/westpa - c0cedf3498abe2279cae6814e6e2851160757858 authored about 9 years ago by ASinanSaglam <[email protected]>

Fixing the make file so the sed commands work properly

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github.com/westpa/westpa - 60e504b99b936a7045181c1b3c6e36d224662694 authored about 9 years ago by ASinanSaglam <[email protected]>

Almost there this makefile

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github.com/westpa/westpa - ed0359c2feee257171f43821457dd1e53fb64c81 authored about 9 years ago by ASinanSaglam <[email protected]>

Makefile almost ready

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github.com/westpa/westpa - 0ac35d759505948a27c4bcbf2f94eafb739239cd authored about 9 years ago by ASinanSaglam <[email protected]>

Testing out different workarounds

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github.com/westpa/westpa - 567d6e8d723e08163b427a4ff73ba2bfc00949ea authored about 9 years ago by ASinanSaglam <[email protected]>

Fixing around the makefile still

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github.com/westpa/westpa - 134a0978d205c6132849e19b3ab94e0cfabeaf8c authored about 9 years ago by ASinanSaglam <[email protected]>

Have to move up a folder in makefile

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github.com/westpa/westpa - 18b6c2cbc2e6effb7d9814541c5a0b532344d8c4 authored about 9 years ago by ASinanSaglam <[email protected]>

maving around the images

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github.com/westpa/westpa - 59f4ebb77bea5e5f40ed11df33e5d60dbfb23f80 authored about 9 years ago by ASinanSaglam <[email protected]>

Current makefile in testing

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github.com/westpa/westpa - 335354103eae1560e1859c69e9c61b9b8b3ed784 authored about 9 years ago by ASinanSaglam <[email protected]>

Moved the images out of build folder

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github.com/westpa/westpa - 750a818182ed0a8416f592d9de552cd4567d750c authored about 9 years ago by ASinanSaglam <[email protected]>

First attempt at auto-generating the documentation

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github.com/westpa/westpa - fb3bc345781a41ff5e76dbbd33ba0accdded14b4 authored about 9 years ago by ASinanSaglam <[email protected]>

Merge pull request #3 from KarlTDebiec/sphinx-wip

Converted Alex's style guide to sphinx

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github.com/westpa/westpa - 8c790811392040a7bb7e20b6aa4e99bf852b8d28 authored about 9 years ago by Ali Sinan Saglam <[email protected]>

Converted Alex's style guide to sphinx

ReStructuredText unfortunately does not support nested inline markup, so
generic classes and var...

github.com/westpa/westpa - 145d81564b10d8b1eb800513707ed3a7d74d04f0 authored about 9 years ago by Karl Debiec <[email protected]>

Merge pull request #2 from KarlTDebiec/sphinx-wip

Ported simulation checklist from wiki

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github.com/westpa/westpa - 1aab903b1299fda7e2c5be33c090f8a0d1f68743 authored about 9 years ago by Ali Sinan Saglam <[email protected]>

Removed comment about installing napoleon

Sphinx 1.3 is now released and manual upgrade is not necessary

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github.com/westpa/westpa - b9506294c458c0309dd961e315f6a03558a3ded1 authored about 9 years ago by Karl Debiec <[email protected]>

missed index.rst

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github.com/westpa/westpa - c1b6b60fde0f74225bc681d74e4ac08d850f80ac authored about 9 years ago by Karl Debiec <[email protected]>

cleaned up checklist

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github.com/westpa/westpa - 051f7202fe3b07a9cb522a1c4f9a95603502f22b authored about 9 years ago by Karl Debiec <[email protected]>

ported checklist from wiki

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github.com/westpa/westpa - 4423f92be464ea26a987d559bebcaac40e3138a5 authored about 9 years ago by Karl Debiec <[email protected]>

removed outdated development stumps

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github.com/westpa/westpa - 191dfd3b472ae5bef042877ce347854225036f76 authored about 9 years ago by Karl Debiec <[email protected]>

Merge pull request #1 from KarlTDebiec/sphinx-wip

integrated most remaining wiki pages into sphinx

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github.com/westpa/westpa - 61dc86db1c9c8549b1f42a3a86f3e2e5d717015e authored about 9 years ago by Ali Sinan Saglam <[email protected]>

Merge pull request #3 from westpa/post-analysis-reweighting

post-analysis reweighting tools

github.com/westpa/westpa - 357536cfeecf353a73cac68ca11ffff04b247ba2 authored about 9 years ago by Adam J. Pratt <[email protected]>

Merge pull request #10 from westpa/post-analysis-reweighting-resolution

Post analysis reweighting resolution

github.com/westpa/westpa - aa6b60ef476ea8c53bce9a70953dc318c6197203 authored about 9 years ago by Adam J. Pratt <[email protected]>

Fully working complete with the proper test.

github.com/westpa/westpa - b829d8fe03de7e208d2570d91590f09ed05cc9a7 authored about 9 years ago by ASinanSaglam <[email protected]>

Forget about that syntax, it doesn't work, rewrote it back and added test

github.com/westpa/westpa - 2d7975ba381a6addda760dfd3f421a10b4962baf authored about 9 years ago by ASinanSaglam <[email protected]>

Commented and changed class checking style to be clearer

github.com/westpa/westpa - c6000ed4582bfe788e9df4cd3cd47e6712dd7103 authored about 9 years ago by ASinanSaglam <[email protected]>

Added the capability to parse list comprehensions/numpy functions

github.com/westpa/westpa - 3f3200122ae4ae75994d2d0803270f2a388bfdc9 authored over 9 years ago by ASinanSaglam <[email protected]>

fixed some logic errors with parameters and timeouts

github.com/westpa/westpa - eb67ff80feb9ee57e1f495284ecd34c6e524611f authored over 9 years ago by Matthew Zwier <[email protected]>

Deleted old version

github.com/westpa/westpa - e3125b2cae407a1dbb0143e9db54d6f0bd675397 authored over 9 years ago by Matthew Zwier <[email protected]>

Added support for WM_PROCESS_INDEX and cleanup of host info files

github.com/westpa/westpa - f4667f9115839fe3fe323d5c766feb76c3cdfc07 authored over 9 years ago by Matthew Zwier <[email protected]>

fixed boneheaded indent error; node works as expected

github.com/westpa/westpa - 18aa44bd3c8f4b1c3f694554808ebf89e6019447 authored over 9 years ago by Matthew Zwier <[email protected]>

ZMQ work manager can run the ODLD example and exit on signals

github.com/westpa/westpa - 9b76a629b3f195f59a580d82d2053cf1d5f82a72 authored over 9 years ago by Matthew Zwier <[email protected]>

wip for construction from the environment

github.com/westpa/westpa - af248d51f401f2b82fd55c7bfad5bfd81c226898 authored over 9 years ago by Matthew Zwier <[email protected]>