* squashing w_multi_west bugs.

* update tests for w_multi_west and removing unused code.

*...

Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from...

updates:
- [github.com/psf/black-pre-commit-mirror: 23.10.1 → 23.11.0](https://github.com/psf/b...

* fix gh actions badge

* fix broken link in hamsm documentation

updates:
- [github.com/psf/black-pre-commit-mirror: 23.10.0 → 23.10.1](https://github.com/psf/b...

updates:
- [github.com/psf/black-pre-commit-mirror: 23.9.1 → 23.10.0](https://github.com/psf/bla...

* Add bin_log functionality

* include py3.12 in testing (but not building)

* Bump pypa/cibuildwheel from 2.15.0 to 2.16.1 (#346)

Bumps [pypa/cibuildwheel](https://githu...

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-com...

* make pyproject.toml version pinning more readable

* pin pytables to < 3.9 for python <= 3.8...

* pin cython to certain versions for <py3.9

* looser pinning at cython<3.0.3

Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4.
- [Release notes](ht...

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.15.0 to 2.16.1.
- [Relea...

Pushing Develop changes into westpa2

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](h...

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.14.1 to 2.15.0.
- [Relea...

Pushing recent `develop` changes to `westpa2`

* pre-commit autoupdate

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more in...

* added a while block for mab_manager and binless_manager to wait for istates_futures

* add i...

Update westpa2 branch with newest changes

* add in pytest-rerunfailures and remove nose

* test on macOS too!

* reverse github action...

v2022.05 release

* add py3.11 to wheel building

Prep for v2022.05 release

* force smallest allowed weight to 1e-320 instead of 1e-323

* 1e-310 threshold instead. Rough...

* update gh-actions tests to run weekly

* update verify dev-env to py3.11

* tests update t...

* force cython < 3 for now

* bug fix... apparently it's an import order thing

Merging develop changes into westpa2

* allow npy_loader to load pickled npy files

* added loader tests

* lint for test_loaders
...

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.13.0 to 2.13.1.
- [Relea...

* -W option for w_truncate

* lint

* w_truncate test update

* rc fixes

* minor fix

---------

Co-authored-by: She Zhang <shz620@DESKTOP-CIELO>

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.12.3 to 2.13.0.
- [Relea...

Pushing CI build fixes to westpa2

* fix CI-build workflow

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.12.1 to 2.12.3.
- [Relea...

Pushing develop changes to westpa2

* fix ibstates option to account for mismatch dtype

* turn into basis_auxref into empty bytes...

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.12.0 to 2.12.1.
- [Relea...

Co-authored-by: She Zhang <shz620@DESKTOP-CIELO>

* bug fix in the MAB scheme code

* changed the default value from False to 0 in MAB code

-...

Co-authored-by: She Zhang <[email protected]>

Push develop to westpa2 (versioneer version update)

* update versioneer to v0.28

* remove redundant get_versions

Bump pypa/cibuildwheel from 2.11.4 to 2.12.0 (#297)

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.11.4 to 2.12.0.
- [Relea...

Merging develop changes to westpa2

fixes #115

* change to mambaforge for CI tests

* test on py3.11 but don't build wheels yet due to MDTraj

* Adding tarfile member sanitization to extractall()

* lint

* Create codeql.yml

* move ...

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.11.2 to 2.11.4.
- [Relea...

* remove licensing info in w_multi_west

* initial working that saves the ibstates if and only...

Merging develop into westpa2

PR to fix merge conflict issues (#282).

* Bump pypa/cibuildwheel from 2.11.1 to 2.11.2

Bumps [pypa/cibuildwheel](https://github.com/p...

* update codecov to v2

* Documentation Fix (#257)

* update logo and some little config fix...

Resolving develop/westpa2 merge conflict

Resolving merge conflicts between westpa2 and develop branches.

* update test.yaml actions versions

* new GH Actions workflow for making wheels and publishin...

* add square brackets around nw.weights in sim_manager line 700

* add longer timeout to zmq t...

* deprecate w_fluxanl

* make it clear that target state uses entire bin in w_init

* change...

* update codecov to v2

* Documentation Fix (#257)

* update logo and some little config fix...

Co-authored-by: Lillian Chong <[email protected]>

* update versioneer to 0.23 to work with PEP660

* lint

* w_assign fix for newest pyyaml version load() function deprecation

* changed yaml.safe_load...

* update codecov to v2

* Documentation Fix (#257)

* update logo and some little config fix...

* new implementation of thresholds

* moved threshold checks to their own functions

* initi...

* fixes for mab split and mab_log reporting

* removed dependence on splitting for mab_log

...

* Set 'istate_status_names' and 'istate_type_names' class attributes.

* Add 'ISTATE_xxxx_' pr...

* update logo and some little config fixes

* trim down white space in logo

* trim wiki_images

* readthedocs title page fix

* modify readme so it's clear what is recommended

* add in WE...

* added mab_log option

* mab.py lint

* refine mab_log to output only at end of iteration
...

* initial try to fix bin reporting

* fixed init bin reporting and mab bin reporting

* move...

* change it so processes will run with 'fork' on macs

* Added commentary on multiprocessing s...

Co-authored-by: Anthony Bogetti <[email protected]>

* added logging details to binless manager and driver

* update to west file version 9 and fix...

* port of w_pdist custom weights

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

* f...