westpa - v2022.12 - Bug Fixes and Compatibility Release

Bug fixes for WESTPA 2.0 (v2022.XX).

See previous release notes for the new features in WESTPA 2.0.

What's Changed

• Python 3.8 is no longer supported (https://github.com/westpa/westpa/pull/449)
• Added Numpy 2 and Python 3.13 Support (https://github.com/westpa/westpa/pull/450, https://github.com/westpa/westpa/pull/442)
• Fix MAB 86 Reporting by @jeremyleung521 in https://github.com/westpa/westpa/pull/435
• remove w_fluxanl deprecation warning by @jeremyleung521 in https://github.com/westpa/westpa/pull/443
• Fixing the MAB skip function in 2+ dimensions. by @HScheiber in https://github.com/westpa/westpa/pull/436
• Allow WESS and WEED to detect when a simulation has been truncated by @gma57 in https://github.com/westpa/westpa/pull/452
• Fix w_init when using hdf5 framework with processes work manager by @jeremyleung521 in https://github.com/westpa/westpa/pull/457
• Misc. backend update/cleanups (Sphinx, CI, tests)

Full Changelog: https://github.com/westpa/westpa/compare/v2022.11...v2022.12

sha256 checksum:

westpa-2022.12.zip ba8bd0e71a9b757f4ca830d9c1a676ae9823e4839c037b094b7e7a9df852abb8

westpa-2022.12.tar.gz c5b77bf9ee0c046d50665aa739d29b4a16176b320e8742ed39dc90870e3f8ca0

- Python
Published by jeremyleung521 about 1 year ago

westpa - v2022.11 - Bugfix + Matplotlib hotfix

Bug fixes for WESTPA 2.0 (v2022.XX).

See previous release notes for the new features in WESTPA 2.0.

What's Changed

• Support Matplotlib 3.9
• wtruncate will no longer take -n > max current iteration; wtruncate without -n will delete the last iteration
• Bugfix for when west.executable.dataset is defined in west.cfg but empty
• Misc. backend update/cleanups (Sphinx, CI, tests)

Full Changelog: https://github.com/westpa/westpa/compare/v2022.10...v2022.11

sha256 checksum:

westpa-2022.11.zip ed310174a8af9649f8310c4398989d9031442652acb0cc7619d05693093f2a03

westpa-2022.11.tar.gz fb9984634c9c937b3b0c98bb36cd6febdbea0344fae5ff83d6028e3938634137

- Python
Published by jeremyleung521 over 1 year ago

westpa - v2022.10 - MDTraj dependency hot fix

Bug fixes for WESTPA 2.0 (v2022.XX).

See previous release notes for the new features in WESTPA 2.0.

What's Changed

• Support MDTraj v1.10.0
• Wheels for Python 3.12

Full Changelog: https://github.com/westpa/westpa/compare/v2022.09...v2022.10

sha256 checksum:

westpa-2022.10.zip 168d1e64d0509fdb3589cb137e116575978c05e187c03c940f9b93365f692141

westpa-2022.10.tar.gz 8d9f627c9d7fbdd62c2ba952c00c27e3bcee7c97c7a91476f1fe6c4b27926a38

- Python
Published by jeremyleung521 almost 2 years ago

westpa - v2022.09 - QOL/Feature Release

Bug fixes for WESTPA 2.0 (v2022.XX).

See release notes for v2022.01 for the new features in WESTPA 2.0.

What's Changed

• MacOS Wheels now available for both x86-64 (Intel) and arm64 (Apple Silicon) (#402, #405)
• Data manager should now process deprecated numpy dtypes (like int vs np.int) (#399)
• MAB Lite/ direction: 86: An MAB option to not put leading/trailing walkers into separate bins (#403)
• A fallback mode where users can specify executable config under westpa.data.datasets (#408)
• Custom binning can be passed to msm_we through haMSM restarting Plugin (#382)
• west.cfg will now accept more formats for maxrunwallclock (#413)
• w_pdist will now take care of negative max values (#414)
• Debug Mode now works for w_ipa (#401)
• Segfault that occasionally occur during process work manager shutdown is fixed (#412)
• Errors fixed when multiple callbacks/multiple plugins are used simultaneously (#410)
• NaturalNameWarning from HDF5 Framework is now suppressed (#416)
• westpa.analysis summary tables will now display properly (#418)
• w_states --replace will report properly (#421 )
• Other backend/README updates.

Full Changelog: https://github.com/westpa/westpa/compare/v2022.08...v2022.09

sha256 checksum:

westpa-2022.09.zip fd038ec4eb64987d24f93631d5e7a87e37ebe0628a867917915d27173c6ae6df

westpa-2022.09.tar.gz 66211eb7686f9b485d0f89a2b35a39e6538623e46113edc84dfbf2e55353070f

- Python
Published by jeremyleung521 almost 2 years ago

westpa - v2020.07 - Bug Fix (LEGACY)

WESTPA 1.0 Bug Fix. Note this is a back-port of a fix for WESTPA 1.0.

New users should download v2022.04 or later instead! This is for legacy users.

What's Changed

• Callback bug fix

Full Changelog: https://github.com/westpa/westpa/compare/v2020.06...v2020.07

sha256 checksum:

westpa-2020.07.zip 788954371d36a8fb9f1437df5956925a4dc3960d48173f4de90ed53cf3dddd03

westpa-2020.07.tar.gz 09d1521345eaf9a2894261d7f42407ced694d9b07dc8a6e163ec0d3b4104439a

- Python
Published by jeremyleung521 almost 2 years ago

westpa - v2022.08 - Hot Fix

Bug fixes for WESTPA 2.0 (v2022.XX).

See release notes for v2022.01 for the new features in WESTPA 2.0.

What's Changed

• w_succ will now respect the -W argument
• Hot fix for unintended error during initialization (w_init)
• Fix where the wrong loader is chosen for HDF5 Framework if you have another aux dataset

Full Changelog: https://github.com/westpa/westpa/compare/v2022.07...v2022.08

sha256 checksum:

westpa-2022.08.zip 37f97d7880ff0184dfefc4acb81f1a14164809c107368c2438fe3c444511cb68

westpa-2022.08.tar.gz 40fcb7d16747eb6c55cbba56b3167bae849dc4192d8cce754b055012519f2a1a

- Python
Published by jeremyleung521 almost 2 years ago

westpa - v2022.07 - QOL/Bug Fixes Release

Bug fixes for WESTPA 2.0 (v2022.XX).

See release notes for v2022.01 for the new features in WESTPA 2.0.

What's Changed

• WESTPA will require numpy < 2. We plan to allow numpy>=2 in v2022.08 once the we've reasonably vetted.
• Bug fixes and QOL improvements for w_multi_west
• Bug fixes for w_states (edge cases where the order the bins are added affects the bin label output)
• Bug fixe for nested YAMLConfigs
• QOL Improvements for tstate files (allow empty lines and comments)
• Better Error Messages (segment numbers included in pcoord length error, errors marked as HDF5 Framework related)
• Better GitHub Forms
• More Tests for ibstates

Full Changelog: https://github.com/westpa/westpa/compare/v2022.06...v2022.07

sha256 checksum:

westpa-2022.07.zip 6973e19842631639a68956a6a853393cb138f76f9b3637d1084d751f20f2e750

westpa-2022.07.tar.gz 8f25f1256269ea74b55d409b9979e846aa29f699b8752bc554a1d10f9ecb6bbb

- Python
Published by jeremyleung521 almost 2 years ago

westpa - v2022.06 - Bug Fixes Release

Bug fixes for WESTPA 2.0 (v2022.XX).

See release notes for v2022.01 for the new features in WESTPA 2.0.

What's Changed

• Tighter dependencies to fix bugs introduced in Cython 3
• Dropped wheel support for Python 3.7 (EOL: 2023-06-27)
• Fixed bug where MAB/Binless Managers would not wait for istates futures
• 'bin_log' option to output MAB bin boundaries. Documentation
• Documentation Update
• HDF5 Framework bug fixes
• Misc code cleanups and CI updates.

Full Changelog: https://github.com/westpa/westpa/compare/v2022.05...v2022.06

sha256 checksum:

westpa-2022.06.zip 23fc9819e3ad9a9d65f62e8566a72dc15060e03417a6c74ee0bef51f51aa6fd9

westpa-2022.06.tar.gz 02b4ebdaef21b1011322da03fbe2c6c487bd3403ae592112cce5c5d0c0fb6cd5

- Python
Published by jeremyleung521 over 2 years ago

westpa - v2022.05 - More Bug fixes

Bug fixes for WESTPA 2.0 (v2022.XX).

See release notes for v2022.01 for the new features in WESTPA 2.0.

What's Changed

• Bug fixes to MAB's "skip" function, Data Manager
• w_multi_west will now combine files made before and after PR #235 / March 31st, 2022.
• w_truncate will now accept H5 files names directly from the command line (Defaults to what's in west.cfg)
• npy_loader will now accept pickled objects.
• Misc code cleanups and CI updates.

Full Changelog: https://github.com/westpa/westpa/compare/v2022.04...v2022.05

sha256 checksum:

westpa-2022.05.zip c784a08043015b7b056070841e73ffcdcf9d0071e922c87ec45a2ae950c50a15

westpa-2022.05.tar.gz 7e313c514da0cdf9b291025b7af59b6a5bd0b318e38facebaa1011613f154578

- Python
Published by jeremyleung521 over 2 years ago

westpa - v2022.04 - Bug fixes

Bug fixes for WESTPA 2.0 (v2022.XX).

See release notes for v2022.01 for the new features in WESTPA 2.0.

What's Changed

• More robust w_multi_west which allows for compatibility with westpa.analysis when files are combined with --ibstates flag
• Bug fixes for w_multi_west's istate combining logic
• Updated versioneer to 0.28
• Support numpy 1.24+
• Misc code cleanups.

Full Changelog: https://github.com/westpa/westpa/compare/v2022.03...v2022.04

sha256 checksum:

westpa-2022.04.zip 5e7e50a572357c479c209765f47027e5fa35f42bd337c008747c0c4a6a287525

westpa-2022.04.tar.gz ee5f8221359bbc2ab81151ead2130edfb5977c61560ce3ab30e866bebeebcf6c

- Python
Published by jeremyleung521 about 3 years ago

westpa - v2020.06 - Misc bug fixes (LEGACY)

WESTPA 1.0 Python 3. Miscellaneous fixes, including that for w_multi_west. Note this is a back-port of fixes for WESTPA 1.0. Equivalent changes for WESTPA 2.0 are available as part of v2022.04.

New users should download v2022.04 or later instead! This is for legacy users.

What's Changed

• Fix of w_multi_west
• plothist changes
• Misc Code Cleanup

Full Changelog: https://github.com/westpa/westpa/compare/v2020.05...v2020.06

sha256 checksum:

westpa-2020.06.zip 34c62c108eb22090b33b382009c61fcdc7af354b7b7d252d1074ff9598a62a59

westpa-2020.06.tar.gz 55b8f0d0dfca3f3886df0afc000e9f8db72f5590add7ff4b225a470931ef5d51

- Python
Published by jeremyleung521 about 3 years ago

westpa - v2022.03 - Bug fixes

Bug fixes for WESTPA 2.0 (v2022.XX).

See release notes for v2022.01 for the new features in WESTPA 2.0.

What's Changed

• Better Documentation
• Recycled segment counts are now reported correctly all the time
• New built-in data loaders can be specified for each dataset (npy_data_loader and pickle_data_loader)
• w_fluxanl is currently deprecated
• Misc code cleanups.

Full Changelog: https://github.com/westpa/westpa/compare/v2022.02...v2022.03

sha256 checksum:

westpa-2022.03.zip 54361202c9821518f0b99830dc3a3e46f4737050f66e2e905f11c642feb0c811

westpa-2022.03.tar.gz 2cd6fb1bdb76e6c83f3b3b82a458f1e5a54aedbd4fb7790b37537412696d8aa7

- Python
Published by jeremyleung521 over 3 years ago

westpa - v2022.02 - Bug fixes

Bug fixes for WESTPA 2.0 (v2022.XX).

See release notes for v2022.01 for the new features in WESTPA 2.0.

What's Changed

• MAB "skip" option now works
• Max/min weight thresholds code is rewritten
• Misc code cleanups.

Full Changelog: https://github.com/westpa/westpa/compare/v2022.01...v2022.02

sha256 checksum:

westpa-2022.02.zip 6478a48ebd8511badb6254d58c71727cae45d0312fdc059701671e461e598a53

westpa-2022.02.tar.gz a40a4110031e1bc5b0d336f39886cdf6c617e19c52a7914ef6f2e3fd2731ebf0

- Python
Published by jeremyleung521 over 3 years ago

westpa - Stable Release: WESTPA v2022.01

This is a stable release of WESTPA 2.0, called v2022.01. WESTPA v2022.01 is incompatible with previous versions (v2020.XX) and will not work with simulations generated using previous versions.

This build introduces major upgrades and restructuring to the previous WESTPA software package. In order to use this build concurrently with older WESTPA releases on the same computer, we suggest updating your current WESTPA v1.0 build (v2020.XX) to v2020.05 (or later). See the wiki for more information.

Key features of the new WESTPA 2.0 software include features critical to efficiency and ease of use: - Installation as a standard Python package using pip or conda install - A generalized resampler module for implementing both binned and “binless” WE strategies, including the minimal, adaptive binning (MAB) scheme - Streamlined handling of large simulation datasets using the HDF5 framework - More efficient rate-constant estimates using the RED scheme and history augmented Markov State Model (haMSM) restarting plugin - Developer-friendly tools for creating new WE methods including automated CI tests - Improved ease-of-use as with a Python API

For instructions and other options on how to install WESTPA v2022.01, see this wiki page.

**Please note that if you used the HDF5 Framework with v2.0dev1, there were breaking changes since then. It is recommended that you keep a separate v2.0dev1 install to continue analyzing files generated with that version.

sha256 checksum:

westpa-2022.01.zip 5e625adb0fa7a08b125bdd29b7b7d2bffd089d8f0192e370938275d31f14c6fe

westpa-2022.01.tar.gz 0fae9ba2a21b0e44d158e945370133f3a664874ac8de4c41ce6da089ae1021b0

- Python
Published by jeremyleung521 over 3 years ago

westpa - Beta Release: WESTPA v2.0dev1

This is a pre-release (beta) build of WESTPA 2.0, called v2.0dev1. WESTPA v2.0dev1 is incompatible with previous versions (v2020.XX) and will not work with simulations generated using previous versions.

This build introduces major upgrades and restructuring to the previous WESTPA software package. In order to use this build concurrently with older WESTPA releases on the same computer, we suggest updating your current WESTPA v1.0 build (v2020.XX) to v2020.05 (or later). See the wiki for more information.

Key features of the new WESTPA 2.0 software include features critical to efficiency and ease of use: - Installation as a standard Python package using pip or conda install - A generalized resampler module for implementing both binned and “binless” WE strategies, including the minimal, adaptive binning (MAB) scheme - Streamlined handling of large simulation datasets using the HDF5 framework - More efficient rate-constant estimates using the RED scheme and history augmented Markov State Model (haMSM) restarting plugin - Developer-friendly tools for creating new WE methods including automated CI tests - Improved ease-of-use as with a Python API

For instructions and other options on how to install WESTPA 2.0dev1, see this wiki page.

sha256 checksum:

westpa-2.0dev1.zip d231674db62ca3ed4ba1ae78f7a339321f49b73e465eb1857a1fbeb2705c0d7c

westpa-2.0dev1.tar.gz 23f2a4c3ea67cc3fe2beba34bb61706d8668ccf8bae28d81ceef5df91dc73aa6

- Python
Published by jeremyleung521 over 4 years ago

westpa - v2020.05 - Misc bug fixes

WESTPA Python 3. Miscellaneous fixes and other changes made in conjunction with new conda recipe updates.

sha256 checksum:

westpa-2020.05.zip 572fe3ea1ab13dc635c8a895ca36b3b7c5eb72c78287783152a640c23db1f89c

westpa-2020.05.tar.gz e93755babb0db4138f3a5da24f5a3a33885a655920352e803b5d84b1861a569f

- Python
Published by jeremyleung521 over 4 years ago

westpa - v2020.04 - Bug fixes for binhash and addition of w_multi_west

WESTPA Python 3.

sha256 checksum:

westpa-2020.04.zip 8e262de6f8b99cdfa559c9beb8d9b31180bfea3f2538c27d4e934a3e6a8398ff

westpa-2020.04.tar.gz 48576bf29ebbc8bed3d6c97c9104f503d5d9781ecccc72366340db2589ae89fe

- Python
Published by jeremyleung521 almost 5 years ago

westpa - v2020.03: Cleanup and migration of examples in /lib to westpa_tutorials.

WESTPA Python 3.

sha256 checksum:

v2020.03.zip 0377c5bfe646815f2a5738affee076632962bd6fa4986f9cb295d86a68c1c592

v2020.03.tar.gz 0a1f7b30f405a0f3ca1d9808adbf10fb93451cfd2b79c4ce992ff5cedcb65c3d

- Python
Published by burntyellow almost 6 years ago

westpa - v2020.02: bugfixes & update to miniconda install script

WESTPA Python 3.

sha256 checksum:

v2020.02.zip 52e6d1fc46e4950bce4023e8f4b584a9ddd313d627486b1522784a03097dc492

v2020.02.tar.gz b7b057ee61368713dd3de0338d1ce0e8ffddfb5004d725df707ea9f81ce840bd

- Python
Published by burntyellow almost 6 years ago

westpa - WESTPA Python 3

The release tag is v{YYYY}.{MAJOR}, where YYYY is the year and MAJOR is 0-padded major-release index.

sha256 checksum:

v2020.01.zip aa1ffb27d7e8c91f6df470fd0cf5e00138ffaf25009fcb887b7b67ecb3f77e1a

v2020.01.tar.gz 11e39a76af081dfd6b3472a9bb68579d55aac66d08ea6eff6a6cbaee9386e72d

- Python
Published by burntyellow almost 6 years ago

westpa - v2017.10 Updated Analysis Tools

westpav2017.10.zip

Pushed fix to rate handling. Please download the zip file above.

- Python
Published by astatide over 8 years ago

westpa - v2017.07: Fixes for h5py Anaconda 2-4.4.0

Recently, h5py has changed some of the arguments to open a file. WESTPA has been updated to support this.

- Python
Published by astatide over 8 years ago

westpa - v2017.06: w_ipa release

WESTPA now supports automated analysis and analysis profiles via a new tool, wipa. In addition, a wjupyter tool has been created which eases the creation of ipython notebooks (an example exists in the odld propagator example: https://github.com/westpa/westpa/blob/master/lib/examples/odld/analysis.ipynb

- Python
Published by astatide almost 9 years ago

westpa - v2017.05 May Release

A significant update to the analysis routines has been made; see changelog.

- Python
Published by astatide almost 9 years ago

westpa -

- Python
Published by mczwier over 11 years ago