ADicksonLab/wepy issues and pull requests

#131 - Bugfix/test system builder na cl

Pull Request - State: open - Opened by berkatik 2 months ago

#130 - fixed the subscripts in slurm tutorial

Pull Request - State: open - Opened by berkatik 5 months ago

#129 - General update of the documentation

Pull Request - State: closed - Opened by berkatik 5 months ago

#128 - Docs update

Pull Request - State: closed - Opened by berkatik 5 months ago - 6 comments
Labels: documentation

#127 - np.float -> float

Pull Request - State: closed - Opened by alexrd 6 months ago

#126 - Atom pair distance

Pull Request - State: closed - Opened by alexrd 10 months ago - 1 comment

#125 - Updated install instructions

Pull Request - State: closed - Opened by alexrd 10 months ago

#123 - Reading weights from the HDF5 is slow

Issue - State: open - Opened by alexrd about 1 year ago - 3 comments
Labels: bug, enhancement

#122 - Support multiple progress fields in BCDashboardSection

Issue - State: open - Opened by salotz about 1 year ago

#121 - Mechanism to calculate ensemble based progress

Issue - State: open - Opened by salotz about 1 year ago

#120 - Default BoundaryCondition `DISCONTINUITY_TARGET_IDXS`

Issue - State: open - Opened by salotz about 1 year ago
Labels: enhancement

#119 - Appropriately handle omm_states that don't have parameter derivatives

Pull Request - State: closed - Opened by alexrd about 1 year ago - 2 comments

#117 - Refactor and consistent handling of OpenMMState fields

Issue - State: open - Opened by salotz about 1 year ago - 2 comments

#116 - Try to detect dynamics errors post-segment

Issue - State: open - Opened by salotz about 1 year ago - 2 comments
Labels: enhancement

#115 - Errorless cleanup of un-initialized HDF5 files

Issue - State: open - Opened by salotz about 1 year ago
Labels: bug, enhancement

#112 - Runtime error in WepyHDF5

Issue - State: open - Opened by SamikBose over 1 year ago - 3 comments

#111 - work

Issue - State: closed - Opened by SamikBose over 1 year ago

#110 - fixes pandas deprecation warning

Pull Request - State: closed - Opened by salotz over 1 year ago

#109 - Remove deprecated np.int & np.float usage

Pull Request - State: closed - Opened by salotz over 1 year ago

#108 - Clean up the boundar_conditions.boundary module

Pull Request - State: closed - Opened by salotz over 1 year ago

#107 - Move dashboard progress summary to BC section

Pull Request - State: closed - Opened by salotz over 1 year ago

#106 - Fixes #103: Probing for OpenMMState before getting

Pull Request - State: closed - Opened by salotz over 1 year ago - 1 comment

#105 - removes revo image dtype instrospection completely

Pull Request - State: closed - Opened by salotz over 1 year ago

#104 - Handle saving of OpenMM IntegratorParameters State data type

Issue - State: open - Opened by salotz over 1 year ago
Labels: enhancement

#103 - Gracefully handle missing velocities in initial states

Issue - State: closed - Opened by salotz over 1 year ago - 1 comment
Labels: bug

#102 - Proper error handling for missing OpenMM state variables

Issue - State: open - Opened by salotz over 1 year ago
Labels: bug

#101 - remove eliot start_action calls

Pull Request - State: closed - Opened by salotz over 1 year ago

#100 - Change `simtk.unit` to `openmm.unit`

Issue - State: open - Opened by salotz over 1 year ago
Labels: enhancement

#99 - removes eliot logging

Pull Request - State: closed - Opened by salotz over 1 year ago - 1 comment

#98 - Get wepy_test_drive working again

Issue - State: open - Opened by salotz over 1 year ago
Labels: bug

#97 - Get Examples working again

Issue - State: open - Opened by salotz over 1 year ago
Labels: documentation

#96 - removes imports of simtk.openmm

Pull Request - State: closed - Opened by salotz over 1 year ago

#95 - Fix logging

Pull Request - State: closed - Opened by salotz over 1 year ago - 1 comment

#93 - formatting codebase

Pull Request - State: closed - Opened by salotz over 1 year ago - 1 comment

#92 - adds 'graphics' extras, fixes pillow version

Pull Request - State: closed - Opened by salotz over 1 year ago - 1 comment

#91 - Support for distributed work mappers

Issue - State: open - Opened by alexrd over 1 year ago
Labels: enhancement

#90 - Add support for GROMACS

Issue - State: open - Opened by alexrd over 1 year ago
Labels: enhancement

#89 - Replace simtk.openmm with openmm

Issue - State: closed - Opened by salotz over 1 year ago
Labels: bug

#88 - Handle logging properly

Issue - State: closed - Opened by salotz over 1 year ago
Labels: bug, enhancement

#87 - Bump pillow from 9.5.0 to 10.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#86 - Various contributions

Pull Request - State: open - Opened by salotz over 1 year ago
Labels: invalid

#85 - Format codebase

Pull Request - State: closed - Opened by salotz over 1 year ago
Labels: enhancement, devex

#84 - Clean lint

Issue - State: open - Opened by salotz over 1 year ago - 1 comment
Labels: enhancement, devex

#83 - Format Codebase

Issue - State: closed - Opened by salotz over 1 year ago - 1 comment
Labels: enhancement, devex

#82 - Conda package

Issue - State: open - Opened by salotz over 1 year ago
Labels: enhancement, distribution

#81 - Remove networkx version limitation

Issue - State: open - Opened by salotz over 1 year ago
Labels: enhancement, dependencies

#80 - docs: adds FAQ entry for clearing HDF5 locks

Pull Request - State: closed - Opened by salotz over 1 year ago

#79 - Working build and deployment of documentation

Issue - State: open - Opened by salotz over 1 year ago
Labels: documentation

#78 - h5py > v3 support

Issue - State: open - Opened by salotz over 1 year ago
Labels: bug, dependencies

#76 - Fixes instance of string access as bytes

Pull Request - State: closed - Opened by salotz over 1 year ago

#75 - set_nodes_field in MacroStateNetwork

Issue - State: open - Opened by BK33333 over 1 year ago - 1 comment
Labels: documentation

#74 - Incorrect output from parent_table_discontinuities function

Issue - State: open - Opened by kilince over 1 year ago
Labels: bug

#73 - multiple GPU

Issue - State: closed - Opened by BK33333 over 1 year ago - 2 comments

#72 - Simplifying the test suite

Pull Request - State: closed - Opened by alexrd almost 2 years ago - 1 comment

#71 - Totally clean slate

Pull Request - State: closed - Opened by salotz almost 2 years ago

#70 - Clean slate implementation with extra developer helpers

Pull Request - State: closed - Opened by salotz almost 2 years ago - 4 comments

#69 - Efficient hdf5 read/write/analysis tests

Pull Request - State: closed - Opened by alexrd almost 2 years ago - 1 comment

#68 - Bump ipython from 7.21.0 to 8.10.0 in /envs/dev

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#67 - walker pkl reporter for easier restarts

Pull Request - State: closed - Opened by alexrd almost 2 years ago

#66 - Bump cryptography from 3.4.6 to 39.0.1 in /envs/dev

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#65 - Bump cryptography from 2.9.2 to 39.0.1 in /.jubeo

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#64 - Bump cryptography from 2.9 to 39.0.1 in /envs/simultaneous_dev

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies, python

#63 - Bump wheel from 0.36.2 to 0.38.1 in /envs/dev

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#62 - Bump certifi from 2020.4.5.1 to 2022.12.7 in /envs/simultaneous_dev

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#61 - Bump certifi from 2020.4.5.1 to 2022.12.7 in /.jubeo

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#60 - Bump certifi from 2020.12.5 to 2022.12.7 in /envs/dev

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#59 - fix bugs in the dashboard reporter

Pull Request - State: closed - Opened by ndonyapour about 2 years ago

#58 - fix a bug in the dashboard reporter

Pull Request - State: closed - Opened by ndonyapour about 2 years ago - 1 comment

#57 - fix a bug in the REVO dashboard

Pull Request - State: closed - Opened by ndonyapour about 2 years ago - 1 comment

#56 - HDF5 file reading error

Issue - State: open - Opened by ndonyapour over 2 years ago - 5 comments
Labels: bug

#55 - Bump py from 1.8.1 to 1.10.0 in /envs/simultaneous_dev

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#54 - Bump py from 1.8.1 to 1.10.0 in /envs/test

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#53 - Bump urllib3 from 1.26.4 to 1.26.5 in /envs/dev

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#52 - Bump nbconvert from 5.6.1 to 6.5.1 in /envs/simultaneous_dev

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#51 - Bump nbconvert from 6.0.7 to 6.5.1 in /envs/dev

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#50 - Bump nbconvert from 5.6.1 to 6.3.0 in /envs/simultaneous_dev

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#49 - Bump nbconvert from 6.0.7 to 6.3.0 in /envs/dev

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#48 - Revo merge algorithms

Pull Request - State: closed - Opened by alexrd over 2 years ago - 3 comments

#47 - Add `h5clear` commands to FAQ

Issue - State: closed - Opened by salotz-sitx almost 3 years ago
Labels: documentation

#46 - Bump paramiko from 2.7.1 to 2.10.1 in /.jubeo

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies, python

#45 - Fix WExplore image bug

Pull Request - State: closed - Opened by salotz-sitx almost 3 years ago - 1 comment

#44 - Fix merge bug

Pull Request - State: closed - Opened by dixonth1 about 3 years ago - 2 comments

#43 - traj_fields_to_mdtraj gets topology incorrectly

Issue - State: closed - Opened by salotz-sitx about 3 years ago - 1 comment

#42 - Fix.gh.16

Pull Request - State: closed - Opened by salotz-sitx about 3 years ago - 1 comment
Labels: bug, enhancement, need-repro

#41 - add/fix the progress section #27 #32 RDAS-37

Pull Request - State: closed - Opened by salotz-sitx about 3 years ago - 1 comment
Labels: bug, enhancement

#40 - improved error handling of hdf5 field data shapes

Pull Request - State: closed - Opened by alexrd over 3 years ago - 1 comment

#39 - Saving Pressure in reporter

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

#38 - changed westpa's python version to 3 and mentioned ability to run on …

Pull Request - State: closed - Opened by atbogetti over 3 years ago

#37 - Optimized cycle slicing routines

Issue - State: open - Opened by salotz-sitx over 3 years ago
Labels: enhancement

#36 - No buffer space available error in `TaskMapper`

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

#35 - Add githook for deploying documentation

Issue - State: closed - Opened by salotz-sitx over 3 years ago

#34 - Support for variable number of walkers in `WepyHDF5`

Issue - State: open - Opened by salotz-sitx over 3 years ago - 1 comment
Labels: enhancement

#33 - Remove Eliot Logging

Issue - State: closed - Opened by salotz-sitx over 3 years ago
Labels: enhancement, dependencies

#32 - UnbindingBCDashboardSection not reporting warps correctly

Issue - State: open - Opened by alexrd over 3 years ago - 3 comments
Labels: bug, need-repro

#31 - added fast minimum_distance calculation to UnbindingBC.

Pull Request - State: closed - Opened by alexrd over 3 years ago - 4 comments

#30 - Update the OpenMM installation instructions

Issue - State: closed - Opened by salotz-sitx over 3 years ago - 1 comment

#29 - parallel distance calculations in REVO

Pull Request - State: closed - Opened by alexrd over 3 years ago

#28 - Adding box vector argument to gen_sim_state()

Pull Request - State: closed - Opened by alexrd over 3 years ago - 1 comment

#27 - BC and REVO Resampler dashboard section not reporting correct information.

Issue - State: closed - Opened by dixonth1silicon over 3 years ago - 3 comments
Labels: enhancement

#26 - Add public method for `progress` for all boundary conditions

Issue - State: open - Opened by salotz-sitx over 3 years ago
Labels: enhancement

GitHub / ADicksonLab/wepy issues and pull requests