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github.com/westpa/westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
https://github.com/westpa/westpa

codecov error fix with fetch-depth

9acacc721c56e22cd3c54cb49b3c0bd0dc2a4d7c authored almost 4 years ago by jml230 <[email protected]>
light cleanup to exclude pyproject.toml

4db227dbbd178324cb855a6a0d04f1116ef38644 authored almost 4 years ago by jml230 <[email protected]>
lint issues

0ec40647d3796e278d16f5bda3481947d728f0e7 authored almost 4 years ago by jml230 <[email protected]>
more setup.py fix for pypi

7e886e176ca505f9fb91dddf6d360fbea01b023d authored almost 4 years ago by jml230 <[email protected]>
fixed MANIFEST.in and setup.py for pypi

ddb7d6ee22f777c3f2484f2ffc36e0a86009a719 authored almost 4 years ago by jml230 <[email protected]>
Merge branch 'westpa-2.0-restruct' of ssh://github.com/westpa/westpa into westpa-2.0-restruct

bfdde185e15f3536b3dc13c7a5deb4e1c209c190 authored almost 4 years ago by jml230 <[email protected]>
Merge pull request #136 from jeremyleung521/westpa-2.0-tests

WESTPA 2.0 Tests, Consolidated

a62184885a4a4350f99a4b327757ac9269f68ede authored almost 4 years ago by Jeremy Leung <[email protected]>
removed westpa-2.0-tests reference and fixed codecov error

7d71d597e48d5a97a8d4c22da8f1b3fff8210210 authored almost 4 years ago by jml230 <[email protected]>
moved test_data_manager and fixed test_w_trace

d2f4752a3b6bec8947c304c50404eefecf83d45f authored almost 4 years ago by jml230 <[email protected]>
removed extra comments

fad3541ed759093ac134cf5d83651b28be18488c authored almost 4 years ago by jml230 <[email protected]>
minor fixes

27df7cb08bd6a0248d2cc3a7a20e85b8c3859c36 authored almost 4 years ago by She Zhang <[email protected]>
Changed Numpy version to <=1.18.5 for test_env

5780834920c48be0f823368d5f4d224dab0b2cf0 authored almost 4 years ago by Jeremy Leung <[email protected]>
fixed lint issues

9555525fa76eb91e2c340c25882ef338c56c7cf7 authored almost 4 years ago by jml230 <[email protected]>
rename test_w_init.py back to test_init.py to circumvent error

e7c214e4369028f1895e420a770e012e2a38e743 authored almost 4 years ago by jml230 <[email protected]>
added reason to skipped tests

7c968acba209c4f8f4f4ef34ab79aca467ac465d authored almost 4 years ago by jml230 <[email protected]>
fixed test_sim_manager for lint issues

65458d947151efe7f55476561adea77bc2f24622 authored almost 4 years ago by jml230 <[email protected]>
renamed test_init back to test_w_init

675691b198e1823b39697cd4b4d2abf238ee0f81 authored almost 4 years ago by jml230 <[email protected]>
add pdist_ref.h5 back in to refs

855f0c4d1899fb8132df366f4ff0a8af5a6ad68f authored almost 4 years ago by jml230 <[email protected]>
Merge branch 'westpa-2.0-restruct' of ssh://github.com/westpa/westpa into westpa-2.0-tests

b66542fe1534f02183def0a3a9a11acbc8e6610d authored almost 4 years ago by jml230 <[email protected]>
updated the tests with Josha Adelman's fix to the confests + others

1658502b74ca3a6de987c7a3046a7c9aa23f6060 authored almost 4 years ago by David LeBard <[email protected]>
First draft of the HDF5 framework

d834ce53a8d99f5eab626994a6af62194bf271cc authored almost 4 years ago by She Zhang <[email protected]>
Merge pull request #7 from SHZ66/main

essential fixes

e1fafad75a8fb833151450f268074a514d227afe authored almost 4 years ago by She Zhang <[email protected]>
Merge pull request #6 from westpa/westpa-2.0-restruct

Westpa 2.0 restruct

85de0e0279a06d41ea15fbd597c1fea003a35686 authored almost 4 years ago by She Zhang <[email protected]>
Revert "Merge pull request #2 from westpa/main"

This reverts commit 77c50da8c1ee2e3f7e7ec9cebf638306eb446865, reversing
changes made to 796f532e...

bf45bb594b93c59c3202f3c31b47c2c0b372dbc9 authored almost 4 years ago by She Zhang <[email protected]>
minor change`

71a053ed4b9431197b0f20416bf0c627b0914979 authored almost 4 years ago by She Zhang <[email protected]>
documentation changes

cb3fe5a0c4a6327b05d2071895859a5e2fa31669 authored almost 4 years ago by She Zhang <[email protected]>
Added west_version to west.h5

5c90e4f2f615f95a2084c324386c950f96167488 authored almost 4 years ago by She Zhang <[email protected]>
Merge pull request #4 from westpa/westpa-2.0-restruct

Westpa 2.0 restruct

07f0eb456bd4be25ab7b0dedf8daf5a40e494637 authored almost 4 years ago by She Zhang <[email protected]>
Revert "Merge pull request #3 from westpa/main"

This reverts commit 725784650250e79606a6559a046ab8a5b06969b6, reversing
changes made to b13b32ad...

d2ec670b223d0135e4d96981c4f2fbeb245b169f authored almost 4 years ago by She Zhang <[email protected]>
Fixed a bug caused by bytestring when reading the basis state filename from west.h5

f88ea8593dcec6ca85722bad25ed3aee90c55959 authored almost 4 years ago by She Zhang <[email protected]>
Merge pull request #3 from westpa/main

Update README.rst

725784650250e79606a6559a046ab8a5b06969b6 authored almost 4 years ago by She Zhang <[email protected]>
Merge pull request #2 from westpa/main

Update README.rst

77c50da8c1ee2e3f7e7ec9cebf638306eb446865 authored almost 4 years ago by She Zhang <[email protected]>
fixed GH Action settings to account for master->main branch name change

12c82ad39186a8db935b07a5772d6fc33555db52 authored almost 4 years ago by Jeremy Leung <[email protected]>
Merge pull request #145 from jeremyleung521/westpa-2.0-restruct

Documentation Update and Github Action CI Updates to run on Ubunutu 20.04 and Python 3.9

2774279fdc54f127925635b486a9d0ebc7ca03f9 authored almost 4 years ago by Lillian Chong <[email protected]>
Switched from GPL3 to MIT License

2b747ca830ca20a9472c8f9d628badf1407fcdea authored almost 4 years ago by Jeremy Leung <[email protected]>
Update README.rst

9dc62478fcef0001b9c038cd56a40b6be1b9d64a authored almost 4 years ago by Lillian Chong <[email protected]>
Fix string method hash to check as bytes

49806718c7966863a2c9f0aba15b3013c0e17d9f authored almost 4 years ago by Joshua L. Adelman <[email protected]>
a few broken tests remain (fixtures issue?)

de95d61d431fd6222c9c74bf0f3c85a50dd1df90 authored almost 4 years ago by David LeBard <[email protected]>
begin converting string method plugin to westpa 2.0

7935932b04c0a40ed138e7c80ae809054c4938ea authored almost 4 years ago by Joshua L. Adelman <[email protected]>
test dev env in python 3.8 so it's quicker

cf6fb945806dde92ea7d8443205dbe5b64abf9c6 authored almost 4 years ago by jml230 <[email protected]>
testing python 3.9 on ubuntu-latest

cb4aec83dccd55ef2d5712976e894638fd84febf authored almost 4 years ago by jml230 <[email protected]>
Merge pull request #140 from jeremyleung521/westpa-2.0-restruct

Updated Github Action Settings

38db2d91895dcf0e46b8d19efb932fd26f3f2b63 authored almost 4 years ago by Lillian Chong <[email protected]>
updated github action settings

9b3b72a7738e8afcaef5c14dd7ea899d490062e7 authored almost 4 years ago by jml230 <[email protected]>
Merge branch 'westpa-2.0-restruct' of ssh://github.com/westpa/westpa into westpa-2.0-restruct

68756b084afcf40bf33eef9ebbfcecc68bda1780 authored almost 4 years ago by jml230 <[email protected]>
Merge pull request #128 from jeremyleung521/westpa2-pull_templates

Github pull/issues templates for WESTPA 2.0

e64ed7c853fcbb01b220bb7f4aa91f269c9701af authored almost 4 years ago by Lillian Chong <[email protected]>
Update README.rst

cf0edc18147e1a376330fe17fe5b7bffeac2a7a2 authored about 4 years ago by Lillian Chong <[email protected]>
updated data manager test

4b1805482150c0d27efb890292a209841b605acf authored about 4 years ago by jml230 <[email protected]>
Revert "added test_sim_manager.py"

This reverts commit 48b470f0003ef096cce3af6b6f2f926fc54075bb.

5856255071940505d42929359502bcb2ab917520 authored about 4 years ago by jml230 <[email protected]>
Revert "moved sim_manager so it runs later"

This reverts commit 20d449e4465eea03764d7aab74a9deef76f9649a.

fbf1adea4dcb4d2ed79f7f08f920fc82aece0ea4 authored about 4 years ago by jml230 <[email protected]>
moved sim_manager so it runs later

20d449e4465eea03764d7aab74a9deef76f9649a authored about 4 years ago by jml230 <[email protected]>
Revert "renamed test_sim_manger.py so it runs later"

This reverts commit de11c2e02ba1523639ab94c67748d148f4129c7d.

461cf46b8cc230121ad2b15fe127d466fae1010d authored about 4 years ago by jml230 <[email protected]>
renamed test_sim_manger.py so it runs later

de11c2e02ba1523639ab94c67748d148f4129c7d authored about 4 years ago by jml230 <[email protected]>
added test_sim_manager.py

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

48b470f0003ef096cce3af6b6f2f926fc54075bb authored about 4 years ago by jml230 <[email protected]>
small fix to a potential bug in kinetics_tool

b13b32ad6d2df2c32a78668140c889b2d1a7b340 authored about 4 years ago by She Zhang <[email protected]>
reenabled w_states test

8f23b8b903108ea57e5d3417f243d031b3288cba authored about 4 years ago by jml230 <[email protected]>
fixes to states.py when label and auxref are bytestrings

d16b27d27de4c5413c30dff820102c6bc948b898 authored about 4 years ago by jml230 <[email protected]>
Merge branch 'westpa-2.0-tests' of ssh://github.com/jeremyleung521/westpa into westpa-2.0-tests

9f22b2fcdb2eb327341b1443b78692fd3004a773 authored about 4 years ago by jml230 <[email protected]>
restrict numpy to v1.18.4 in CI

b4985294c276367c00dc11aba631cc1cc8188f54 authored about 4 years ago by jml230 <[email protected]>
swap CI from ubuntu-latest to ubuntu-18.04

ubuntu-latest will automatically swap to 20.04 soon. This is to prevent CI from any unintended b...

a1a3c420ce442762a6bdd9322b55ebd79b5e1524 authored about 4 years ago by Jeremy Leung <[email protected]>
Revert "attempt to re-enable test_w_states.py"

This reverts commit a63b86c15e8affefa232cd88d92f3c7b18fbdb4e.

838b58897991c9dbcaf14c89b05026c6872a9d94 authored about 4 years ago by jml230 <[email protected]>
attempt to re-enable test_w_states.py

a63b86c15e8affefa232cd88d92f3c7b18fbdb4e authored about 4 years ago by jml230 <[email protected]>
lint

976379b412c3a82ff25507c15dbe4365ccf78478 authored about 4 years ago by jml230 <[email protected]>
skip w_state test

314a1e008529a86fc86005c3c016c06b87213893 authored about 4 years ago by jml230 <[email protected]>
attempt to clear settings to make w_states run properly

0b17b25e0b563792b950e1201f872b0b630663d6 authored about 4 years ago by jml230 <[email protected]>
changed to setup-python@v2 for CI

32e2dd52dc33df5ca25234913a336ef08f3f4a51 authored about 4 years ago by jml230 <[email protected]>
removed test_data_manager.py

b0af5b3b871d1b0bf24556eea15ca48dc07149a2 authored about 4 years ago by jml230 <[email protected]>
re-add test_w_states.py

62361146a94feb8d2730e0ded919dba1632f1de5 authored about 4 years ago by jml230 <[email protected]>
re-add test_data_manager.py

120de42a8d6420b918f301dc1bd587c44a74dd8d authored about 4 years ago by jml230 <[email protected]>
removed test_w_states.py

1fb2d335e5e4a481573e07f0c0bdcc6d5d038d75 authored about 4 years ago by jml230 <[email protected]>
changed to conda-incubator/setup-miniconda@v2 for CI

f0599df4dfd74a28bb1319aea91d6752d2f829cd authored about 4 years ago by jml230 <[email protected]>
Revert "added data manager test"

This reverts commit b5a75293d0bd28f9ba1022e0fba6d04c1e1758cf.

3e17bf16b9e817207921765f3db25e15509bc06a authored about 4 years ago by jml230 <[email protected]>
:Revert "temporary removed test_data_manager due to incompatibility on CI server-side"

This reverts commit 73a917b07eae723082846730a0864e02a0d4aefc.

ed92e9ecd1537ad145108f8f83669e1c5fe76089 authored about 4 years ago by jml230 <[email protected]>
temporary removed test_data_manager due to incompatibility on CI server-side

73a917b07eae723082846730a0864e02a0d4aefc authored about 4 years ago by jml230 <[email protected]>
added data manager test

b5a75293d0bd28f9ba1022e0fba6d04c1e1758cf authored about 4 years ago by jml230 <[email protected]>
fixed lint error

24e4c45c531fb7ad6d13f65bd018e46b385754f8 authored about 4 years ago by jml230 <[email protected]>
renamed tests so init test runs before assign test. Circumvents incompatibility problem

f3943067d06d0a1d4a7626de78d398413a3d2ce9 authored about 4 years ago by jml230 <[email protected]>
Includes all changes from Pull Request #123

9577313fb1d5ebb650c6d1be69025b29e292a7e0 authored about 4 years ago by jml230 <[email protected]>
modified test_w_trace.py

fa215c02745a69d4bdb83e2f94ba6f4972ca1eae authored about 4 years ago by jml230 <[email protected]>
removed unused lines in w_init.py

1b20f58f9b921751520b7fb9b0de916b0c389e2a authored about 4 years ago by jml230 <[email protected]>
sim manager test changes

3e8d2b0c5f0f248a77b91ebae78d4d780dd6cb1d authored about 4 years ago by jml230 <[email protected]>
Revert "removed pull templates/issues templates"

This reverts commit b19a140461ba6032cb83fb06efd9f85db606dc45.

fc1e786ed02ffc0814e3891ae0a8651a468f8855 authored about 4 years ago by Jeremy Leung <[email protected]>
removed pull templates/issues templates

b19a140461ba6032cb83fb06efd9f85db606dc45 authored about 4 years ago by Jeremy Leung <[email protected]>
added w_run, w_init, w_states and w_truncate. w_assign interferes so skipped for now

742cc33972cc224760b54e0f52df096006b7c814 authored about 4 years ago by jml230 <[email protected]>
added execute permission to tests and files

4a3899490d8264a6a36a6424836b411b21e2cef8 authored about 4 years ago by jml230 <[email protected]>
replaced h5diff with John's updated version

eefcc4ddb9f8456c94dcfb90d6b699f29beea65b authored about 4 years ago by jml230 <[email protected]>
added John's reference files and fixtures

b2b4496bd2a7851be8b3d469d71bf60551ef29bf authored about 4 years ago by jml230 <[email protected]>
ran pre-commit

a595df846cc8672d992bfe03846e2941cd063314 authored about 4 years ago by jml230 <[email protected]>
restored old w_ipa test

a9224b216ef5582d3d3541d829730473d073def5 authored about 4 years ago by jml230 <[email protected]>
fixed w_direct test names

d9d63081405938ec9a50d573c61ea40a9a82c156 authored about 4 years ago by jml230 <[email protected]>
added the old w_direct test back in

c886586cb258dc00ed4a95fed42688641106385e authored about 4 years ago by jml230 <[email protected]>
ran pre-commit and fixed unused imports

4b3c17c92cdd1bc2da1da727cd3f609a80ab7ff9 authored about 4 years ago by jml230 <[email protected]>
Merge branch 'westpa-2.0-tests' of ssh://github.com/jeremyleung521/westpa into westpa-2.0-tests

a3591a48d6a2905fc019e80242147f19d154a1ba authored about 4 years ago by jml230 <[email protected]>
changed tests to debug mode

809c1e083c8dc0fbaa71fb23167df50cafb956dd authored about 4 years ago by jml230 <[email protected]>
added and simplified test_w_assign.py

d410d0124b8da48fb5e98cdcf775c20dbf5ca189 authored about 4 years ago by jml230 <[email protected]>
removed Python 3.9 Tests

Takes too long, will wait for packages to update

97caf3d9293e6888c7efcdd8b62114138946c669 authored about 4 years ago by Jeremy Leung <[email protected]>
changed MacOS/Linux installation check back to Python 3.8

917a343491a8b8b46c91724f5f08bdb09aad683e authored about 4 years ago by jml230 <[email protected]>
added python 3.9 to CI integration

458fc0238dafa93dea2f7ec1e6068c5e604c8f52 authored about 4 years ago by jml230 <[email protected]>
fixed test_w_succ.py

57256807a7b065a8a84dd57cbd8992bfa01909fb authored about 4 years ago by jml230 <[email protected]>
run workflow for this branch

0de19f077a8d64c063878820c7c371c5a6ff5c72 authored about 4 years ago by jml230 <[email protected]>
small changes in plothist and w_pdist test and h5diff test for plot_hist evol

7c5010a94e3f3f34526f6be8ec641fc5204e92cd authored about 4 years ago by jml230 <[email protected]>