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WESTPA

Highly scalable software for running extended-timescale simulations with any dynamics engine
Collective - Host: opensource - https://opencollective.com/westpa - Website: https://westpa.github.io/westpa/ - Code: https://github.com/westpa/westpa

converted the rest of test_plothist to mock.patch

github.com/westpa/westpa - 0ef48070744d929c7c027d563312e5c9d412a265 authored about 4 years ago by jml230 <[email protected]>
partial rewrite of test_compare_avg_txt for plothist

github.com/westpa/westpa - e6f1c2c1cb6e83a90fbf2f1bae8e567a4395721d authored about 4 years ago by jml230 <[email protected]>
moved refs up and edited tests accordingly

github.com/westpa/westpa - 646e4b4883ecc46d552ec1ff570fdfef5f3f4917 authored about 4 years ago by jml230 <[email protected]>
Merge pull request #1 from westpa/westpa-2.0-restruct

Westpa 2.0 restruct

github.com/westpa/westpa - 796f532e6e098b0dcfbc8291337e04fa76894ee7 authored over 4 years ago by She Zhang <[email protected]>
forcefully add west_ref.h5 back into branch and did some light cleaning of test_w_pdist.py

github.com/westpa/westpa - 0e9b449fdccfd2881452ae5eb5c8ec2c60e7fa3b authored over 4 years ago by jml230 <[email protected]>
fixed existing tests (assign, direct, ipa) to not interfere with fixtures

github.com/westpa/westpa - 7b8cb7e898033dea2081c21d38f4bb1ed64f9137 authored over 4 years ago by jml230 <[email protected]>
removed unused code in conftest.py and ref folder for easier merging later on

github.com/westpa/westpa - 15fc0f90eb2d28c27e970f0fa831a0364e9177ab authored over 4 years ago by jml230 <[email protected]>
fixed typo in conftest.py

github.com/westpa/westpa - 441104e3e5caebe9e3b5cc67a6e0e5c1c786cbb8 authored over 4 years ago by jml230 <[email protected]>
modified conftest.py for consistency and clarity

github.com/westpa/westpa - 1fe503d2a361ba59a8a039490e8a39cd8c4e9f00 authored over 4 years ago by jml230 <[email protected]>
patchwork implementation of fixtures into test_w_pdist.py

github.com/westpa/westpa - 671cf06ebf93c74f8449bddb10e216dcc95e73a2 authored over 4 years ago by Jeremy Leung <[email protected]>
Merge pull request #132 from jeremyleung521/westpa1.0-pull_templates

Adding Pull requests and Issues templates for WESTPA 1.0.

github.com/westpa/westpa - 870d4f62837ccf3e67d4b4f16eda23c595dcd244 authored over 4 years ago by Jeremy Leung <[email protected]>
removed westpa 2.0 workflows

github.com/westpa/westpa - 42cd32cce8ae33bbc35aacb3913d31cde3ac518f authored over 4 years ago by Jeremy Leung <[email protected]>
added pull templates and issues templates

github.com/westpa/westpa - b0c1d917d8db61705dcab550891cb1e433adab0c authored over 4 years ago by Jeremy Leung <[email protected]>
changed existing tests to remove relative import

github.com/westpa/westpa - 9c6fc44180ff8291e9ce03c1ad3c4c48c9444c94 authored over 4 years ago by Jeremy Leung <[email protected]>
removed __init__.py to fix wemd_current_iteration_error

github.com/westpa/westpa - ea596c68e51594c3c77e7c85ee5c5572735c3d45 authored over 4 years ago by Jeremy Leung <[email protected]>
Merge pull request #131 from jdrusso/add_rc_clearstate

Added function to rc to clear state

github.com/westpa/westpa - c20c9a61d17fa205b40b3b3917b6721ef017dcc4 authored over 4 years ago by Joshua Adelman <[email protected]>
Added function to rc to clear state

github.com/westpa/westpa - 655515a4ef5f7d17ca00c1e3b41f055b2a8cbf92 authored over 4 years ago by John Russo <[email protected]>
Merge pull request #130 from burntyellow/westpa-2.0-restruct-mpi-wm

Incorporate Patrick Pisciuneri's update to the MPI work manager; add …

github.com/westpa/westpa - cc66d2acfaf9db756ff611b0484ae53a467d6896 authored over 4 years ago by Joshua Adelman <[email protected]>
Reverted is_manager back to is_master.

github.com/westpa/westpa - ea0dbaa83f2132cc3d16905e9f08acd61156be86 authored over 4 years ago by Kim F. Wong <[email protected]>
Changed master/slave to manager/worker. Changed mpi4py requirement to extra. Test on CRC HPC cluster.

github.com/westpa/westpa - 43ddb228c40f56ed3e7f05d9488e90cac8268046 authored over 4 years ago by Kim F. Wong <[email protected]>
Incorporate Patrick Pisciuneri's update to the MPI work manager; add in dependency for mpi4py within setup.py. Tested on CRC HPC cluster.

github.com/westpa/westpa - a6b25d4d2b4711f1aff51c3b1eb0dcd4c3e2fe32 authored over 4 years ago by Kim F. Wong <[email protected]>
fixed to remove requirement to search for last itr to prevent error

github.com/westpa/westpa - 8b8a3c46e7cbadd87e19a822498d793f8151286c authored over 4 years ago by Jeremy Leung <[email protected]>
final working test_w_pdist.py using entry_points and mock.patch

github.com/westpa/westpa - 9b1286e1c184919d036a5b9c16ca68b2b013d46a authored over 4 years ago by Jeremy Leung <[email protected]>
Update tests/test_tools/test_w_pdist.py

Co-authored-by: Joshua Adelman <[email protected]>

github.com/westpa/westpa - b20801d6212e2a2568e76a87df4330fcf2836ff9 authored over 4 years ago by Jeremy Leung <[email protected]>
Update tests/test_tools/test_w_pdist.py

Co-authored-by: Joshua Adelman <[email protected]>

github.com/westpa/westpa - e09169546c9ba6a05209d0bf246713ab9f99eece authored over 4 years ago by Jeremy Leung <[email protected]>
changed test_pdist from os.system to entrypoint

github.com/westpa/westpa - d2e70f530d1fa01999409bd558208652c69f06bd authored over 4 years ago by Jeremy Leung <[email protected]>
removed test_w_pdist.py files

github.com/westpa/westpa - 3ab4ade7cfeda7ec47a792d5be4de1454273de4d authored over 4 years ago by Jeremy Leung <[email protected]>
added organization of westpa section in CONTRIBUTING.md

github.com/westpa/westpa - da7e1c4c542920e7f9ca1f984f467d7685c7b7b5 authored over 4 years ago by Jeremy Leung <[email protected]>
added CODE_OF_CONDUCT.md and CONTRIBUTING.md from wiki

github.com/westpa/westpa - 9a6d35d1d7dd2db448884216470ff2f26c339ca1 authored over 4 years ago by Jeremy Leung <[email protected]>
added 2 issues templates and pull request template

Co-authored-by: darianyang <[email protected]>

github.com/westpa/westpa - 82337ec313a4ebb2bb352cc824ff7c44408eee57 authored over 4 years ago by Jeremy Leung <[email protected]>
reordered AUTHORS so it's alphabetical

github.com/westpa/westpa - 4774b1062518290a021e55dbab274f79fa095bbd authored over 4 years ago by Jeremy Leung <[email protected]>
adding test_w_pdist.py functional test and ref files

github.com/westpa/westpa - c041c0d0c76c7e296f25741851a9ee1bb2136238 authored over 4 years ago by Jeremy Leung <[email protected]>
Revert "Added test_w_pdist.py functional test and reference file"

This reverts commit 7474b50443c3ddacf298c6f45ab55687538577bf.

github.com/westpa/westpa - 2f418129d50e34def9947e0a8100278c5b2c1c6d authored over 4 years ago by Jeremy Leung <[email protected]>
Revert "fixed path for w_pdist.py file check"

This reverts commit 9cd9fbfbee35ad3e6d2532208d090fd342615f01.

github.com/westpa/westpa - 5aa97f5e6a35a486012988c81b43d3d1888d33af authored over 4 years ago by Jeremy Leung <[email protected]>
fixed path for w_pdist.py file check

github.com/westpa/westpa - 9cd9fbfbee35ad3e6d2532208d090fd342615f01 authored over 4 years ago by Jeremy Leung <[email protected]>
Added test_w_pdist.py functional test and reference file

github.com/westpa/westpa - 7474b50443c3ddacf298c6f45ab55687538577bf authored over 4 years ago by Jeremy Leung <[email protected]>
Merge pull request #117 from jdrusso/patch-3

Bugfix for states when auxref is None

github.com/westpa/westpa - 4a6080f572ce32f77a4e67d42eca178c4d1dce8c authored over 4 years ago by Joshua Adelman <[email protected]>
Merge pull request #119 from poharrison/westpa-2.0-restruct

Update test_w_trace

github.com/westpa/westpa - 543144cb793e19f93247d0cf04dfffdf8050706f authored over 4 years ago by Page Harrison <[email protected]>
Fix h5diff.py to conform to black formatting

github.com/westpa/westpa - 6cc5b589c18fcd04108438f04bf3f89e347320f5 authored over 4 years ago by Page Harrison <[email protected]>
Formatted h5diff to comply with black

github.com/westpa/westpa - d4e6f824dbedca4062ff447d16146d3047e0da93 authored over 4 years ago by Anthony Bogetti <[email protected]>
Merge branch 'westpa-2.0-restruct' into westpa-2.0-restruct

github.com/westpa/westpa - 50b8d0eb29c67d8ad2f1b5c0f3ee851756a75d8a authored over 4 years ago by Anthony Bogetti <[email protected]>
Update h5diff.py

Removed unnecessary import and sys.bitecode line.

github.com/westpa/westpa - a7948ef0f6c37e020ddff74ca264b0bccdb22f3f authored over 4 years ago by Anthony Bogetti <[email protected]>
Added functional tests for w_assign,direct and ipa. (#118)

* Added functional tests for w_assign,direct and ipa.

* fixed h5diff import

* fixed black ...

github.com/westpa/westpa - 9c4971594d8479d1b4576bdfef803f807d6ff8af authored over 4 years ago by Anthony Bogetti <[email protected]>
Update h5diff.py with fix to conform to black formatting.

github.com/westpa/westpa - 6dff27c267206da39c45e627652298150da3475a authored over 4 years ago by Page Harrison <[email protected]>
Update w_trace_tests file to compare h5 data using H5diff module

github.com/westpa/westpa - 39d3eb5d6ce01059bdaebdfafa3c413d0dc3fd6a authored over 4 years ago by Page Harrison <[email protected]>
Add h5diff.py file to test_tools.

github.com/westpa/westpa - 2095ba70f8b09498b626497de2847cc10ffdaca0 authored over 4 years ago by Page Harrison <[email protected]>
Fix reference h5 files for w_trace_tests to work with both arg combos.

github.com/westpa/westpa - 3dd269f9de2e2b8baea305871d702bfe75419948 authored over 4 years ago by Page Harrison <[email protected]>
Add reference files for w_trace tests to refs folder.

github.com/westpa/westpa - 3178d62307551fe227d7f0d3029eaa2c475ea661 authored over 4 years ago by Page Harrison <[email protected]>
Bugfix for states when auxref is None

If no auxref is provided for a state (it's an optional parameter) then `state.auxref` will be se...

github.com/westpa/westpa - da7bdbcfc21952bdb60ed1a7fc812a886db249c4 authored over 4 years ago by JD Russo <[email protected]>
Merge pull request #116 from jdrusso/patch-2

Fix: clear westpa.rc state on teardown

github.com/westpa/westpa - 37d7904b61abe1bf3ac5d5ca19a66d90ae611ce1 authored over 4 years ago by Joshua Adelman <[email protected]>
Fix: clear westpa.rc state on teardown

Previously, the _sim_manager attribute of westpa.rc was cleared, but the _system was not. This r...

github.com/westpa/westpa - 753053fc7147c0066cb185ba9d7909cada697abd authored over 4 years ago by JD Russo <[email protected]>
Fix uninitialized propagator in w_init

github.com/westpa/westpa - 671369d92f49804d22a7cf518467f49925777618 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Fix circular import in atools for AnalysisMixin

github.com/westpa/westpa - 39ef04e07fffe4362d215f1e4fde20354ee1cca9 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Merge pull request #112 from synapticarbors/fb-more-infrastructure

More infrastructure

github.com/westpa/westpa - 3d66ad365b5bf15e6043ebc4815e733d746d6559 authored over 4 years ago by Joshua Adelman <[email protected]>
Add install_requires and extras_require to setup.py

Also add workflow to test `pip install` editable
in bare environment using pip only (no conda).

github.com/westpa/westpa - 32965a6be01bb42e593d79fd1d3a1ff96dc8d66a authored over 4 years ago by Joshua L. Adelman <[email protected]>
Merge pull request #110 from synapticarbors/fb-make-proper-pkg2

WESTPA Restructuring

github.com/westpa/westpa - dbafb2b0d7823e24aaf0e0684c86a9718bd12d13 authored over 4 years ago by Joshua Adelman <[email protected]>
Add github actions to run CI

github.com/westpa/westpa - 347433e12f68e27298a7fac46f5d9afd6e25ea28 authored over 4 years ago by Joshua L. Adelman <[email protected]>
more cleanup

github.com/westpa/westpa - 1ef40215bd7aeb6b084835a0b9d57cbc1062f334 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Port extloader to use importlib instead of deprecated imp module

github.com/westpa/westpa - cfa0c77e4befcc3d38dbd2b5f6a1cf668ce709de authored over 4 years ago by Joshua L. Adelman <[email protected]>
Fix test for test module organization

github.com/westpa/westpa - 064993f381e643760da60b93838b206c9fd465b2 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Get tests to work with coverage.py

github.com/westpa/westpa - 0da5761e58fffa9ae9ea584ce287731c33357fc1 authored over 4 years ago by Joshua L. Adelman <[email protected]>
apply black and flake8; setup pre-commit

github.com/westpa/westpa - ad553cd4ceab92f1109657131c2d8891951697d5 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Fix traceback isinstance type

github.com/westpa/westpa - 35e8833410b6ef24c4be4a6ae599ae467196e050 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Allow tests to be run with pytest

github.com/westpa/westpa - 5360561ebb91f0637c462e1d33aa398b00b18157 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Remove inheritance from

github.com/westpa/westpa - dc06e7f29c899ed870e6f17279c3a000ea2ac63c authored over 4 years ago by Joshua L. Adelman <[email protected]>
no bare excepts

github.com/westpa/westpa - c2208f27d27138efcef366833d803bc32be7bf62 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Change all ==/!= comparisons to True, False and None to is/is not

github.com/westpa/westpa - 48e1d28b653ee2f6d48927d7153942995e56fe35 authored over 4 years ago by Joshua L. Adelman <[email protected]>
change to python3-style super()

github.com/westpa/westpa - a7dd597cf69d26598a1cba377048a3673be4205f authored over 4 years ago by Joshua L. Adelman <[email protected]>
Fixes from running test_kinetics

github.com/westpa/westpa - f8f77478fe42edb47f592773538435dda006f442 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Fix mpi wm import and add basic test

github.com/westpa/westpa - a6d316b9e335935c063c90fd8b8d4670bf2a5b9a authored over 4 years ago by Joshua L. Adelman <[email protected]>
Fix executable propogator

github.com/westpa/westpa - 0f52d863c163b66b0f8a2a69670bf66f2a7cce41 authored over 4 years ago by Joshua L. Adelman <[email protected]>
More cleanup

github.com/westpa/westpa - bed69ec0c3df3d7fbbad1f8fa65b91c500ee6c7a authored over 4 years ago by Joshua L. Adelman <[email protected]>
more import fixes

github.com/westpa/westpa - 51b5f71bde873562da86b6a8919e3e3491cb7e2e authored over 4 years ago by Joshua L. Adelman <[email protected]>
fix missing import in executable propagator

github.com/westpa/westpa - d63215fa0e7306608988519a5c4724f239570586 authored over 4 years ago by Joshua L. Adelman <[email protected]>
More work on tests

github.com/westpa/westpa - d12d1e94af804433ecad1ac7422c76a32ec00ee8 authored over 4 years ago by Joshua L. Adelman <[email protected]>
work on tests

github.com/westpa/westpa - 21bd08d72814d0a6a12c75e5f1d60341b6488b18 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Fix imports so all console scripts can run with -h flag

github.com/westpa/westpa - b93ad56196d649461e98ab455863b690d979ecd2 authored over 4 years ago by Joshua L. Adelman <[email protected]>
More working tests

github.com/westpa/westpa - 846915ea12d1d8de5a841f32e4aabac2a57c5f59 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Working commit

github.com/westpa/westpa - a921d15476e76013197ba5e2dd16532731a1b177 authored over 4 years ago by Joshua L. Adelman <[email protected]>
working commit

github.com/westpa/westpa - 4d254af430e6d1d0296d3d0c5dc6f5bdae8a3f46 authored over 4 years ago by Joshua L. Adelman <[email protected]>
fixes to zmq work manager tests

github.com/westpa/westpa - 898c97e480def28500abb74c57c0ba147f8fc962 authored over 4 years ago by Joshua L. Adelman <[email protected]>
remove hg legacy files and westpa_gen.py

github.com/westpa/westpa - 4175b2548629a60f7648a9e1597f622bddd032a0 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Begin restructuring repo

github.com/westpa/westpa - 43811c490509534a0856cebfd293374901fce6b0 authored over 4 years ago by Joshua L. Adelman <[email protected]>
trigger git gc

github.com/westpa/westpa - 8618ab598f9bb38a7bc1479932f5332b137dfcbc authored over 4 years ago by Joshua L. Adelman <[email protected]>
Revert "Merge branch 'master' into master"

This reverts commit 4f38b334cfadbe47d69179d3583d7bf9ee78d982 [formerly 28bb11b20fbe693f0b00f7865...

github.com/westpa/westpa - a205e137cf9c4ca47da023e3385f77561a1d4128 authored over 4 years ago by Kim F. Wong <[email protected]>
Merge branch 'master' into master

Former-commit-id: 28bb11b20fbe693f0b00f78658756d86bb250359

github.com/westpa/westpa - 4f38b334cfadbe47d69179d3583d7bf9ee78d982 authored over 4 years ago by burntyellow <[email protected]>
Update README.rst

Former-commit-id: b9e1be96deb588d88d69be531e7966164e16a16e

github.com/westpa/westpa - 49206982cf5e6364797bd9c0fff3e1fb78ef9c80 authored over 4 years ago by Page Harrison <[email protected]>
Updated links and added powerpoint

Former-commit-id: f7b672bd3fceffba2da06f59094d9fed0697e006

github.com/westpa/westpa - 2062c5e5f4791d9bee64ecb07fd17635d28be841 authored over 4 years ago by Anthony Bogetti <[email protected]>
trigger git gc

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github.com/westpa/westpa - ed56dc8f0757d4f57f3afa10bb85517e15f3d052 authored over 4 years ago by Joshua L. Adelman <[email protected]>
Merge pull request #102 from burntyellow/install

Updated miniconda_install_westpa.sh to use release 2020.03.

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github.com/westpa/westpa - 6b3a057742580d5a465e5ca34a9cc4f1af659ca5 authored over 4 years ago by burntyellow <[email protected]>
Updated miniconda_install_westpa.sh to use release 2020.03.

Former-commit-id: 2ba3636e72be09da85c11c5311ebbdf0b09beb5d [formerly bf0430c3a0aa0834dd376558fd...

github.com/westpa/westpa - 1585027614e88621a31eb4f000cb2a59d56a346e authored over 4 years ago by Kim F. Wong <[email protected]>
Changed formatting of westpa-devel link.

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github.com/westpa/westpa - 58a7fda653feeeb1af6c537e305c0702a638e7bd authored over 4 years ago by Anthony Bogetti <[email protected]>
Added a link to westpa-developers google group.

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github.com/westpa/westpa - 4b0cb54fe3eab1048f48eee80f7cf694b940ac65 authored over 4 years ago by Anthony Bogetti <[email protected]>
Moved tutorials to westpa_tutorials.

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github.com/westpa/westpa - 904cfd1ad2654b82aa5419a2211148ac5ee276e5 authored over 4 years ago by atbogetti <[email protected]>
Added old tutorials to lib

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github.com/westpa/westpa - 4ccdd5c236828c3ecec0eadbb552e51503c502f7 authored over 4 years ago by Anthony Bogetti <[email protected]>
Merge pull request #100 from burntyellow/install

Updated miniconda_install_westpa.sh to use release 2020.02.

Former-commit-id: 73702787a66df247e...

github.com/westpa/westpa - 8e9d464210fd824892832f8ec9767308512266d6 authored over 4 years ago by burntyellow <[email protected]>
Updated miniconda_install_westpa.sh to use release 2020.02.

Former-commit-id: d9d825198d902705e0c1a77952326a32ddaf5905 [formerly 75811796d60d9d3a2be2648e04...

github.com/westpa/westpa - b99921b10189ccce645a13cca75d9f2d778d8308 authored over 4 years ago by Kim F. Wong <[email protected]>
Merge pull request #99 from burntyellow/install

Install

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github.com/westpa/westpa - fcfc51d0f9783da44c4e70a8b4bf14d0d3643c72 authored over 4 years ago by Lillian Chong <[email protected]>
Fixed environment name to be consistent with documentation.

Former-commit-id: 0a9c32b0f8cb1bc52e023837883b396242e4ded4 [formerly 0d754783946cbd4884d95e76e9...

github.com/westpa/westpa - 31e091a068a27b199f5dba54dd96f15820308eaf authored over 4 years ago by Kim F. Wong <[email protected]>
Updated miniconda install script.

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github.com/westpa/westpa - 0633e04e46d76c7da29cdad38b69b11ce691c98d authored over 4 years ago by Kim F. Wong <[email protected]>