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github.com/westpa/westpa

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

Import functools in westpa.analysis.decorators.

8f6cbf4e56457aa7eb5be1567944d0da5c530b01 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised segment_trajectory() docstring.

2c22398408bebbe45119918591d0a180661f5dd1 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised segment_property() and segment_trajectory() decorators to return the newly created descriptor instead of the undecorated function. Moved trajectory concatenation logic to TrajectoryConcatenator. Combined SegmentTrajectory and TraceTrajectory descriptors into a single Trajectory descriptor.

f3837bbf89c86a0331a984e0b2dcf321ffc4b090 authored over 3 years ago by Jeff Thompson <[email protected]>
fixed a bug in data manager caused by new version of h5py raising TypeError instead of AttributeError when giving wrong types of keys

cd0f85720bc47cddf4b589dc7b0a8d553f9c4be6 authored over 3 years ago by She Zhang <[email protected]>
Merge pull request #11 from westpa/westpa-2.0-restruct

Westpa 2.0 restruct

ee27641326c6f5bbba63df350f8ecccc4c6c989b authored over 3 years ago by She Zhang <[email protected]>
Removed Segment.trajectory and Trace.trajectory.

3787ae385b0ffd5b09d61852e20fdd0e6314e93e authored over 3 years ago by Jeff Thompson <[email protected]>
Made Run a subclass of FileLinkedDSSpec. Fixed typo in Run.__contains__(). Fixed signature of SegmentTrjaectory.__set__().

e5ce9ab78b484c0d1614b48d6371d27f2b3901a6 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README

8c73d0f761cdaabafeb269bececee03171ecec8a authored over 3 years ago by Jeff Thompson <[email protected]>
Added segment_property() and segment_trajectory() decorators.

941c21b8e38f1a82d23b92e0746af54a0e019d47 authored over 3 years ago by Jeff Thompson <[email protected]>
Fixed typo in Run docstring.

e207227552994ee4c132fd32d4f01e706276d4da authored over 3 years ago by Jeff Thompson <[email protected]>
Changed type of Run.iterations from Iterable to Sequence. Modified target state-related properties to gracefully handle equilibrium sampling (no tstates).

044d82c65de86c2d524550f7d755d58a24a6558a authored over 3 years ago by Jeff Thompson <[email protected]>
Cache segment pcoords.

ec142db58f40293edb75dfa3d9bda732287eac96 authored over 3 years ago by Jeff Thompson <[email protected]>
Changed target of final iteration from None to the empty BinUnion. Fixed a bug in Run.successful_segments.

3305eaffae91c1bcec44172e79d14388d1ba5748 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

ff8a042e104dcc2611f7ca28a0274bb9dafde0c6 authored over 3 years ago by Jeff Thompson <[email protected]>
Merge remote-tracking branch 'temp/master' into westpanalysis

Moved westpanalysis into west.analysis, while preserving history.

c8795412dcf2abeb536be38156d9ea296a2b0f48 authored over 3 years ago by Jeff Thompson <[email protected]>
Removed __version__ from __init__.py.

142f3bab1661ee34f0480564079801d40e1ff257 authored over 3 years ago by Jeff Thompson <[email protected]>
Prepared for move to westpa. Deleted unnecessary files.

31adbd2b2ca8cdff3b60bdf2eb6fccafb374ef0c authored over 3 years ago by Jeff Thompson <[email protected]>
Prepared for move to westpa.

e9b267b89265dbfeddc083aa7bf89189fca06ac6 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README to reflect caching of segment and trace trajectories.

4f0a5ec80b14e3758c5916ee2bfc711a5874fd3a authored over 3 years ago by Jeff Thompson <[email protected]>
Added successful_segments() method to Run and Iteration. Made segment/trace trajectories cached proerties.

f606485c1200bc47e8bf1b95393a58ce1d09f7cd authored over 3 years ago by Jeff Thompson <[email protected]>
Import SegmentTrajectoryLoader into the package namespace.

44903f1a54725b995dc0ef4fe24821794a167bf5 authored over 3 years ago by Jeff Thompson <[email protected]>
Temporarily removed license.

05bba8f588c082e8882cd3eda5c67f337b866888 authored over 3 years ago by Jeff Thompson <[email protected]>
Merge pull request #9 from SHZ66/main

update

b45a428250baa21c4749f18365f861279322765e authored over 3 years ago by She Zhang <[email protected]>
Merge pull request #8 from westpa/westpa-2.0-restruct

Westpa 2.0 restruct

3c60ef0448fb05f8f7599f440f427880d5dfa709 authored over 3 years ago by She Zhang <[email protected]>
Removed a couple silly lines.

4042e132779662a7e6032c92ba0bfe3766fc638f authored over 3 years ago by Jeff Thompson <[email protected]>
Added __str__() method to Run for prettier printing. Added source parameter to Segment.trace().

0d43edc3f7857e63a2eeced245eda57cd0557e83 authored over 3 years ago by Jeff Thompson <[email protected]>
Modified Run to keep segment weights in memory.

11c9798638561dbb8b0300c7c041389489d73980 authored over 3 years ago by Jeff Thompson <[email protected]>
Run: Added name attribute. Changed __repr__. Added __eq__ comparison. Fixed a bug in basis_state_info.

00c397a4b2894ca8c681386e7bc539780a3809d6 authored over 3 years ago by Jeff Thompson <[email protected]>
Deleted old westdataset.py (previously moved to core.py).

12361928966b7d9d335b7d275878aeb3871071af authored over 3 years ago by Jeff Thompson <[email protected]>
Added num_segments() method to Run.

9f3cac9859946ee521d41095a932523203397d58 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

40e234396274e3de1dd78d201f39009dee0ab7a6 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

3bf047864b6a86471dc38df217c56980576d9d49 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

44b949f255414d9b434ae509eae2a26e626580f4 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

077111e72a11175d30b0375e5fe37348cd28b782 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

8a3521525e8721774dd55167e1e18c5ac3cec3e4 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

c9eacc5b92e2c1c17b09ffb0f1dda634479196a3 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

09d637a5f7edfe840d93b0b61a1b6d7b9ca4415d authored over 3 years ago by Jeff Thompson <[email protected]>
Changed the name of WESTDataset to Run. Made Run and Iteration iterable containers (of Iterations and Segments, respectively).

c0b53db07156be140319900d70fae8d9b4178c6d authored over 3 years ago by Jeff Thompson <[email protected]>
Fixed return type in Iteration.target() docstring.

eacb7de3b615f69bbbf3f5b54733c3a33d4d210f authored over 3 years ago by Jeff Thompson <[email protected]>
Revised docstring for Trace.trajectory().

63083fce0dd35782483185ff8e02e8219d49ec11 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

9d054d74f8a2b9066af72580aa9deea077656a27 authored over 3 years ago by Jeff Thompson <[email protected]>
Revised Target class docstring.

eb084d550d7ee9a47941ebcf5caa96bd7687d32e authored over 3 years ago by Jeff Thompson <[email protected]>
Added basis, initial, and target states.

bcde18f506be78d54aee86f157af7979ec1393e8 authored over 3 years ago by Jeff Thompson <[email protected]>
Small docstring revision.

8fbba10d400cb9ee6c6aa5dc3effe75c403d4703 authored over 3 years ago by Jeff Thompson <[email protected]>
Added Bin and Trace classes. Reordered WESTDataset, Iteration, and Segment classes.

e0f6d1b6f6846bfb8e1c24bd09c6181bcdedd315 authored over 3 years ago by Jeff Thompson <[email protected]>
Docstring revisions

0572035bfc14e6bb02574d74ba43953f1976ef98 authored over 3 years ago by Jeff Thompson <[email protected]>
Docstring revisions

63f67bd8ca3a6744a3f148338711fae11277c73a authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

28df1c060ec7021ea26ae13ed855935fc99c3f9e authored over 3 years ago by Jeff Thompson <[email protected]>
Revised README.

9f11244b14d86d516caf94f73d8e5c41d2cf627b authored over 3 years ago by Jeff Thompson <[email protected]>
Fixed build errors.

de436aff3cd2e1f59b56ccafde236193c59d16de authored over 3 years ago by Jeff Thompson <[email protected]>
Configured a basic setuptools build.

191f940c0f81efe05f0acd1ab2335bb5f4f53388 authored over 3 years ago by Jeff Thompson <[email protected]>
Added LICENSE.

ea366d44a05c34aa797b9ca643e368ac5a2e8a66 authored over 3 years ago by Jeff Thompson <[email protected]>
Added README.

f8f919cb64247dea0e95a0f47eda2c37856c7212 authored over 3 years ago by Jeff Thompson <[email protected]>
Added __init__.py

82869a843cd69a7bc68977329e4631a3f6629cdb authored over 3 years ago by Jeff Thompson <[email protected]>
Moved westpanalysis.py to westpanalysis/westdataset.py.

75dbedcb5c89cd6b95d5827317b41b73d862f85b authored over 3 years ago by Jeff Thompson <[email protected]>
Docstrings.

4837bed277d4963c2d3b033dfb7e0ac11090643e authored over 3 years ago by Jeff Thompson <[email protected]>
Added support for loading segment trajectories via a user-provided function.

f3bde23817501580ade34aa4cff73df265d988a2 authored over 3 years ago by Jeff Thompson <[email protected]>
Added previous/next links to iterations. Some additional reorganization.

06114750abe17cd39f57591f0e76f59591c16a8c authored over 3 years ago by Jeff Thompson <[email protected]>
First commit

83c2d46a3d4f985df09e9149b2629f9967968162 authored over 3 years ago by Jeff Thompson <[email protected]>
TEMP Fix for CI (#173)

* minimum setuptools version to support pyproject.toml

* try with __legacy__ tag

* Typo: C...

4002a5b328521690fb89740216a97b4da025ae12 authored over 3 years ago by Jeremy Leung <[email protected]>
Merge pull request #149 from jeremyleung521/westpa-2.0-restruct

Creating a PIP Install

66cb6678edb561f5f88528e9755721a8a49b8750 authored over 3 years ago by Jeremy Leung <[email protected]>
Merge pull request #153 from jeremyleung521/2.0-error-messages

3943d3a054b9399a153f224f9907e2bdef585763 authored over 3 years ago by Jeremy Leung <[email protected]>
Merge pull request #160 from jeremyleung521/westpa-2.0-div

fixed div and rdiv in wipi.py

0b758d9b5c3d1323e48131b80192d5e933b5ca70 authored over 3 years ago by Jeremy Leung <[email protected]>
Merge pull request #171 from jeremyleung521/westpa-2.0-hashfix

Binhash error fix (WESTPA 2.0)

ac942f27ec7fec58fe67379b0a181c5b93d4d5fb authored over 3 years ago by Jeremy Leung <[email protected]>
fixed so bytes version of hashval is checked for binhash

9f658df17245335075d1da6804e2ec9e3e99c9f9 authored over 3 years ago by jml230 <[email protected]>
Merge pull request #169 from jeremyleung521/westpa-2.0-revcmap

Removed revcmap in oldtools/aframe/plotting.py

a0990ee8495204b3036d424c46abb2fe353e73f9 authored over 3 years ago by Jeremy Leung <[email protected]>
fixed revcmap in aframe/plotting.py

17fa4f86c2cb818e2fa4211a69276db73eaa724d authored over 3 years ago by Jeremy Leung <[email protected]>
Merge branch 'main' into hdf5

e19850d0ae3570c0fb3064988723bf3b09b15f24 authored almost 4 years ago by She Zhang <[email protected]>
more edits to README.rst

cd3acbc2fc324902cc72d2b419cf558a1c5f0314 authored almost 4 years ago by Jeremy Leung <[email protected]>
removed references to 1.0 variables in README.rst

7b52e98fdfbaeb8fc9d2c8beb8d5c0a9edbcff12 authored almost 4 years ago by Jeremy Leung <[email protected]>
Fixes for w_ipa run_calculation and reading filenames from h5 file (#147)

* added pull templates and issues templates

* removed westpa 2.0 workflows

* small fix to ...

f1df2b5b9720889078c9e24cdcfb215c2b9f3ac4 authored almost 4 years ago by She Zhang <[email protected]>
Removed unnecessary arguments

bcfaec6d1d0b4a6fc4605a6cbf3d97f58346536c authored almost 4 years ago by John Russo <[email protected]>
Refactored w_succ to remove mock.patch usage

261a0a12791080109ae2ae6401aa77d398be5559 authored almost 4 years ago by John Russo <[email protected]>
Refactored MockArgs class into common.py

bfaeb36b1aa3e6e206cfc58c9581deccacea50a0 authored almost 4 years ago by John Russo <[email protected]>
Refactored w_states test to remove mock.patch usage

3ae2c01acba9fbd0ef2e5767f29a12ae42deb753 authored almost 4 years ago by John Russo <[email protected]>
Refactored initialization logic out of w_states entry_point

ad3d16b1cfc824dee8d3c2cb21530a8b08ee4d9d authored almost 4 years ago by John Russo <[email protected]>
fixed div and rdiv in wipi.py

93b4a4e808cb251b6d64420dc61789042337e42c authored almost 4 years ago by Jeremy Leung <[email protected]>
Merge pull request #158 from Poruthoor/westpa-2.0-restruct

westpa-2.0-restruct : Minor tweak in weed plugin to make it python 3.x compatible

96f2dc80680329b1caecdb070bf1e40ab427ee6c authored almost 4 years ago by Jeremy Leung <[email protected]>
Modifications to enable binless strategies using an external function. (#151)

* Modifications to enable binless strategies using an external function.

* Initialize group_f...

707eb0c74464dc76605409e1376e68955f6d9fef authored almost 4 years ago by burntyellow <[email protected]>
Update src/westpa/core/h5io.py

Changed based on review.

Co-authored-by: Jeremy Leung <[email protected]...

424c48f1c57c1549b8346fdfc25a94f05bbb25a1 authored almost 4 years ago by She Zhang <[email protected]>
w_multi_west (Multitool) Ported to WESTPA2.0 (#152)

* ported w_multi_west to westpa2.0

* lint fixes

* fixed some westpa.binning in deprecated ...

762ef586dc407a121fbb46254560bf2265a889b1 authored almost 4 years ago by Jeremy Leung <[email protected]>
Added parent_id to WESTTrajectory

94c4d04f936d292b25d38472a96d7c4a3bf5fdea authored almost 4 years ago by She Zhang <[email protected]>
Updated TestArgs object to auto-populate attributes from kwargs

81ab51ca9359b1dd670e92beecfea1416ae8c297 authored almost 4 years ago by John Russo <[email protected]>
Updated test_w_assign to not use mock.patch

cf44ab9b7855b893ee02ae323b324e649ca684ab authored almost 4 years ago by John Russo <[email protected]>
Refactored simulation logic out of w_run.entry_point() and updated test

c92921ea8b45354feaab74b6130d0983b1853759 authored almost 4 years ago by John Russo <[email protected]>
Moved initialization functionality out of w_init entry_point, and removed mock.patch usage from test.

0d12a7e19f67dd2b5f5a53fd20ca96a0ea37fff4 authored almost 4 years ago by John Russo <[email protected]>
Updating division operator to make it python3.x compatible

cebd21475cf0b3e00e09a1f99d0568ac6f364af8 authored almost 4 years ago by Ashlin James Poruthoor <[email protected]>
formatting changes

fd8975808ab2e8f2d0c9780d1c88430e590066cb authored almost 4 years ago by She Zhang <[email protected]>
format changes

6fb8f8d810e2e7316155053625c134d62b8d69c7 authored almost 4 years ago by She Zhang <[email protected]>
Removed an unused function

9839802d14c87a726c44264b20a25e67e564bad6 authored almost 4 years ago by She Zhang <[email protected]>
Merge pull request #150 from jeremyleung521/sphinx2

Sphinx Documentation

6df148c742876c4edbdac632039d01bd04b87ad3 authored almost 4 years ago by Lillian Chong <[email protected]>
modified propagator executable to present better pccord error message

30b92d3331b5f4e191bd52b765e1f07af4bb7e99 authored almost 4 years ago by Jeremy Leung <[email protected]>
added in min files to create sphinx doc

c516e594d795ee394d266a99d5e22dd6b5ab0750 authored almost 4 years ago by Jeremy Leung <[email protected]>
lint

646c8656c244501b2b158b3e88da482265b24b30 authored almost 4 years ago by jml230 <[email protected]>
Changed install process to pyproject.toml

cddfa6306a1fd58c3801b72515500d72ce708a8d authored almost 4 years ago by jml230 <[email protected]>
Revert "testing 20.04"

This reverts commit d236df691222f7066dbb8d4fea3ea672158fcb3a.

7151b27d9484e28c529a743a585ea3d2ca8054c0 authored almost 4 years ago by jml230 <[email protected]>
testing 20.04

d236df691222f7066dbb8d4fea3ea672158fcb3a authored almost 4 years ago by jml230 <[email protected]>
trying out ubuntu-latest

11356a641e3ca66cceeb75895ddae0c92bd24083 authored almost 4 years ago by jml230 <[email protected]>
HDF5 implement w. restart

25700f951e62a9371ede735ab2688bda2fade242 authored almost 4 years ago by She Zhang <[email protected]>
HDF5 implementation

f5cf727067325ef71782475c34ecd4d07d40cf79 authored almost 4 years ago by She Zhang <[email protected]>