choderalab/pymbar issues and pull requests

#432 - Add warning about unstable API

Pull Request - State: closed - Opened by mikemhenry over 2 years ago - 16 comments

#431 - Verify BAR is working with constant energy states

Issue - State: open - Opened by mrshirts over 2 years ago

#430 - Fix #427 : Add BAR compute overlap method

Pull Request - State: closed - Opened by jchodera over 2 years ago - 14 comments

#429 - Add tests for BAR methods

Issue - State: closed - Opened by jchodera over 2 years ago
Labels: tests

#428 - nan uncertainty estimates

Issue - State: open - Opened by proteneer almost 3 years ago - 10 comments

#427 - Add methods to compute overlap and effective sample sizes for BAR?

Issue - State: closed - Opened by jchodera almost 3 years ago - 4 comments

#426 - Removed travis CI config file

Pull Request - State: closed - Opened by mikemhenry about 3 years ago

#425 - Forward maximum_iterations from MBAR constructor

Pull Request - State: closed - Opened by maxentile over 3 years ago - 3 comments
Labels: bug, high priority

#424 - MBAR estimator automatically choosing the usable method

Issue - State: open - Opened by xiki-tempula over 3 years ago - 4 comments

#423 - Remove corrupted lines in xvg files

Issue - State: closed - Opened by hannahbaumann over 3 years ago - 2 comments

#422 - Docs seem to be out of date

Issue - State: open - Opened by mikemhenry over 3 years ago

#421 - How to get the u_kn matrix by reduced potential energy?

Issue - State: closed - Opened by zhybio almost 4 years ago

#420 - Build for Python for 3.9?

Issue - State: closed - Opened by mrshirts almost 4 years ago - 4 comments

#419 - Should have \sum_n W_nk = 1 error with pymbar3.0.5 while analysis is working with pymbar3.0.3

Issue - State: open - Opened by hannahbaumann almost 4 years ago - 30 comments

#418 - Update README installation instructions from -c omnia to -c conda-forge.

Pull Request - State: closed - Opened by bdice almost 4 years ago - 5 comments

#417 - 3.0.6 changelog

Issue - State: closed - Opened by jaimergp about 4 years ago - 2 comments

#416 - Clean branches

Issue - State: open - Opened by jaimergp about 4 years ago

#415 - Deprecate / remove old_mbar

Issue - State: closed - Opened by jaimergp about 4 years ago - 1 comment

#414 - Backport PR 350

Pull Request - State: closed - Opened by jaimergp about 4 years ago - 2 comments

#413 - Modernize setup.py and versioning

Pull Request - State: closed - Opened by jaimergp about 4 years ago - 5 comments

#407 - pymbar.utils.ParameterError encountered with MBAR estimator

Issue - State: open - Opened by xiki-tempula about 4 years ago - 1 comment

#403 - Restrict the number of times that validate_data is called

Issue - State: open - Opened by mrshirts over 4 years ago
Labels: enhancement, pymbar 4

#402 - [WIP] jitted just the inner loop of the adaptive loop

Pull Request - State: open - Opened by mrshirts over 4 years ago
Labels: pymbar 4

#399 - [WIP] pymbar4, with partial jax/jitification

Pull Request - State: open - Opened by mrshirts over 4 years ago
Labels: pymbar 4

#398 - [WIP] just add profiling script

Pull Request - State: open - Opened by mrshirts over 4 years ago - 1 comment
Labels: pymbar 4

#393 - Differences between MBAR and BAR.

Issue - State: open - Opened by AnguseZhang over 4 years ago - 13 comments
Labels: bug

#392 - Apply Black to examples/ too

Pull Request - State: closed - Opened by jaimergp over 4 years ago - 1 comment

#391 - Configure logging with support for verbose flags

Pull Request - State: open - Opened by jaimergp over 4 years ago - 10 comments
Labels: pymbar 4

#390 - Arithmatic -> Arithmetic

Pull Request - State: closed - Opened by jaimergp over 4 years ago - 1 comment

#388 - Should the histogram code automatically correct the PMF for unequal bins?

Issue - State: closed - Opened by mrshirts over 4 years ago - 1 comment
Labels: question

#378 - better KDE bandwidth choice

Issue - State: open - Opened by mrshirts over 4 years ago - 1 comment
Labels: enhancement

#377 - Revisit setup.py and consider versioneer

Issue - State: closed - Opened by jaimergp over 4 years ago - 1 comment
Labels: pymbar 4

#374 - Modernize examples [WIP]

Pull Request - State: closed - Opened by jaimergp over 4 years ago - 16 comments

#364 - List of what to backport to pymbar3 in preparation for pymbar4 release

Issue - State: closed - Opened by mrshirts over 4 years ago - 8 comments

#361 - Black

Pull Request - State: closed - Opened by jaimergp over 4 years ago - 10 comments

#360 - From print to logging

Pull Request - State: closed - Opened by jaimergp over 4 years ago - 9 comments

#340 - Accelerate the code, starting with the inner loops

Issue - State: open - Opened by mrshirts over 4 years ago - 27 comments
Labels: pymbar 4

#338 - Get rid of old_mbar before release of pymbar4

Issue - State: open - Opened by mrshirts over 4 years ago - 2 comments
Labels: pymbar 4

#320 - Should have \sum_n W_nk = 1

Issue - State: open - Opened by bergazin almost 5 years ago - 7 comments

#302 - Bootstrap uncertainties first pass

Pull Request - State: closed - Opened by mrshirts over 6 years ago - 51 comments

#300 - Submit pymbar to Journal of Open Source Software?

Issue - State: closed - Opened by mrshirts over 6 years ago - 1 comment
Labels: question

#283 - Timeseries can be tricked by a couple bad first inputs

Issue - State: open - Opened by Lnaden almost 7 years ago - 15 comments

#281 - Difference in BAR and MBAR uncertainties

Issue - State: closed - Opened by mrshirts almost 7 years ago - 8 comments

#277 - detectEquilibration() fails if first frame is an outlier

Issue - State: open - Opened by ptmerz about 7 years ago - 1 comment

#255 - PyMBAR 4.0 Project planning

Issue - State: open - Opened by Lnaden almost 8 years ago - 4 comments

#239 - Separate out timeseries.py?

Issue - State: open - Opened by mrshirts about 8 years ago - 10 comments
Labels: enhancement

GitHub / choderalab/pymbar issues and pull requests