Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / Becksteinlab/MDPOW issues and pull requests

#293 - test data not included in installable package

Issue - State: closed - Opened by orbeckst 4 months ago - 3 comments
Labels: testing

#292 - auto-deploy GHA workflow

Pull Request - State: closed - Opened by orbeckst 4 months ago - 1 comment

#291 - [CI] automatically deploy to PyPi

Issue - State: closed - Opened by orbeckst 4 months ago - 2 comments
Labels: release, CI

#290 - change Python support to 3.10 - 3.12

Pull Request - State: closed - Opened by orbeckst 4 months ago - 1 comment

#288 - [CI] no GROMACS 2023.1 package for macOS with Python 3.10

Issue - State: closed - Opened by orbeckst 4 months ago - 1 comment
Labels: CI

#287 - update versioneer

Pull Request - State: closed - Opened by orbeckst 4 months ago - 2 comments

#286 - Python 3.9 test fails due jax not properly declaring its python compatibility

Issue - State: closed - Opened by orbeckst 4 months ago - 2 comments
Labels: bug, installation, Python 3, CI

#285 - update versioneer

Issue - State: closed - Opened by orbeckst 4 months ago
Labels: bug, installation, CI

#284 - Update .readthedocs.yaml

Pull Request - State: closed - Opened by orbeckst 4 months ago - 2 comments

#283 - enable Python 3.11 and 3.12

Issue - State: closed - Opened by orbeckst 4 months ago
Labels: installation, CI

#282 - replace scipy.integrate.simps with simpson

Pull Request - State: closed - Opened by orbeckst 4 months ago - 2 comments

#281 - update how simpson integration is called

Issue - State: closed - Opened by orbeckst 4 months ago
Labels: bug

#280 - readthedocs build fails

Issue - State: closed - Opened by orbeckst 4 months ago
Labels: bug, docs, CI

#278 - Fix stage checking

Pull Request - State: closed - Opened by a-ws-m about 1 year ago - 3 comments

#276 - remove logger for SI in mdpow.fep

Pull Request - State: closed - Opened by VOD555 over 1 year ago - 1 comment
Labels: bug

#273 - Obscure TypeError when supplying unused kwargs to `Gsolv`

Issue - State: open - Opened by a-ws-m over 1 year ago - 1 comment

#272 - Simulation stages cannot be restarted in case of an error

Issue - State: closed - Opened by a-ws-m over 1 year ago - 1 comment
Labels: bug, scripts

#271 - use black for unified formatting

Issue - State: closed - Opened by orbeckst over 1 year ago
Labels: refactoring

#269 - Black formatting

Pull Request - State: closed - Opened by a-ws-m over 1 year ago - 5 comments

#268 - initial dihedrals

Pull Request - State: closed - Opened by cadeduckworth over 1 year ago - 2 comments

#267 - Use OOP forcefields

Pull Request - State: closed - Opened by a-ws-m over 1 year ago - 20 comments

#266 - setting different temperature in MDP files leads to incorrect free energies

Issue - State: open - Opened by orbeckst over 1 year ago - 2 comments
Labels: bug, help wanted, configuration, analysis

#264 - initialize guess_atoms function PR

Pull Request - State: closed - Opened by cadeduckworth over 1 year ago - 4 comments

#263 - Review all kwargs and consistency in top-level function calls

Pull Request - State: closed - Opened by cadeduckworth over 1 year ago - 2 comments

#262 - add solvents kwarg to build_universe in mdpow.workflows.dihedrals

Issue - State: closed - Opened by cadeduckworth over 1 year ago - 1 comment

#261 - Correct/Modify intersphinx mapping for workflows module docs

Issue - State: closed - Opened by cadeduckworth over 1 year ago - 1 comment

#259 - dihedrals workflow violin plot hue order

Issue - State: open - Opened by cadeduckworth over 1 year ago

#258 - update to mamba-org/setup-micromamba

Pull Request - State: closed - Opened by orbeckst over 1 year ago - 3 comments

#257 - use relative imports inside MDPOW

Pull Request - State: closed - Opened by orbeckst over 1 year ago - 2 comments

#256 - support GROMACS 2022 and 2023

Issue - State: closed - Opened by orbeckst over 1 year ago
Labels: enhancement, docs, testing, installation

#255 - test on GROMACS 2022 and 2023

Pull Request - State: closed - Opened by orbeckst over 1 year ago - 5 comments

#254 - update tests that follow old nose style

Issue - State: closed - Opened by orbeckst over 1 year ago
Labels: testing, refactoring

#253 - replace AutoMBAR with MBAR

Issue - State: closed - Opened by orbeckst over 1 year ago - 1 comment

#252 - [CI] GROMACS installation uninstalls mdanalysis

Issue - State: closed - Opened by orbeckst over 1 year ago - 3 comments
Labels: bug, testing

#251 - [CI] update micromamba set up

Issue - State: closed - Opened by orbeckst over 1 year ago
Labels: testing

#249 - drop python 3.7 and testing improvements

Pull Request - State: closed - Opened by orbeckst over 1 year ago - 17 comments

#248 - remove support for Python 3.7

Issue - State: closed - Opened by orbeckst over 1 year ago
Labels: installation

#247 - update banner logging

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

#246 - update to use pymbar >= 4.0

Issue - State: closed - Opened by orbeckst over 1 year ago - 1 comment
Labels: bug, installation

#245 - Fix import error in workflows base module (develop branch)

Issue - State: closed - Opened by cadeduckworth almost 2 years ago - 2 comments

#244 - Create MDPOW Project Analysis Output Manifest DataFrame/CSV

Issue - State: open - Opened by cadeduckworth almost 2 years ago
Labels: workflows

#243 - Dihedral Plots: RDKit Mol Object

Pull Request - State: closed - Opened by cadeduckworth almost 2 years ago - 42 comments

#242 - Periodic Angle Padding

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

#240 - Revisit method for parsing solvent input for plots in MDPOW.mdpow.workflows.dihedrals

Issue - State: closed - Opened by cadeduckworth almost 2 years ago
Labels: workflows

#239 - Determine if scipy or pytest responsible for version-specific failure

Issue - State: closed - Opened by cadeduckworth about 2 years ago - 3 comments
Labels: testing

#235 - change pytest fixture scopes to 'session' and add tmpdir methods if required

Issue - State: open - Opened by cadeduckworth about 2 years ago - 3 comments
Labels: testing, refactoring

#234 - Use AutoMBAR instead of MBAR

Pull Request - State: closed - Opened by VOD555 about 2 years ago - 1 comment

#233 - Use AutoMBAR instead of MBAR

Issue - State: closed - Opened by VOD555 about 2 years ago - 3 comments

#232 - Finish documentation for workflows/dihedrals automation tutorial notebook (ipynb)

Issue - State: open - Opened by cadeduckworth about 2 years ago - 1 comment
Labels: docs, workflows

#230 - Fix setup and support toluene in `mdpow-solvationenergy`

Pull Request - State: closed - Opened by VOD555 about 2 years ago - 2 comments

#229 - Workflows Base Module

Pull Request - State: closed - Opened by cadeduckworth about 2 years ago - 13 comments

#228 - Support cgenff toluene

Pull Request - State: closed - Opened by VOD555 about 2 years ago - 1 comment

#227 - Automated Solvation Shell Analysis

Pull Request - State: open - Opened by cadeduckworth about 2 years ago - 15 comments

#226 - Automated Solvation Shell Analysis

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

#225 - HydrogenBondAnalysis, and automation (linked to issue #197)

Pull Request - State: open - Opened by cadeduckworth about 2 years ago - 2 comments

#224 - Support toluene solvent

Pull Request - State: closed - Opened by VOD555 about 2 years ago - 6 comments

#223 - add toluene as solvent

Pull Request - State: closed - Opened by VOD555 about 2 years ago

#222 - add toluene as solvent

Issue - State: closed - Opened by orbeckst about 2 years ago - 7 comments
Labels: enhancement, forcefield

#221 - use new micro mamba action

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

#220 - CI updates

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

#219 - improve codecov upload reliability

Issue - State: closed - Opened by orbeckst about 2 years ago

#218 - changed dihedral atom group selection strings in test_dihedral.py

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

#217 - Automated Dihedral Analysis

Pull Request - State: closed - Opened by cadeduckworth over 2 years ago - 31 comments

#216 - developing back end run methods

Pull Request - State: closed - Opened by cadeduckworth over 2 years ago - 4 comments

#215 - Does Dihedral analysis use dimensions from separate universes?

Issue - State: closed - Opened by orbeckst over 2 years ago - 3 comments
Labels: question, analysis

#214 - DihedralAnalysis test_results_recursive2 fails most of the time

Issue - State: closed - Opened by orbeckst over 2 years ago - 7 comments
Labels: testing

#213 - Fix ensemble.EnsembleAnalysis.check_groups_from_common_ensemble

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

#212 - Ensemble Group Identity Verification Issue

Issue - State: closed - Opened by cadeduckworth over 2 years ago

#210 - Update em_charmm.mdp

Pull Request - State: closed - Opened by VOD555 over 2 years ago - 2 comments

#209 - Add documentation for settings in the yml file

Issue - State: open - Opened by VOD555 over 2 years ago
Labels: docs

#206 - update example runinput.yml file from docs

Issue - State: open - Opened by orbeckst almost 3 years ago - 1 comment
Labels: docs

#205 - update docs and README to use GitHub Discussions for questions

Issue - State: open - Opened by orbeckst almost 3 years ago
Labels: docs

#204 - merge master and develop into main

Issue - State: open - Opened by orbeckst about 3 years ago - 1 comment
Labels: refactoring

#202 - support Python 3.10

Issue - State: closed - Opened by orbeckst about 3 years ago - 1 comment
Labels: Python 3

#201 - prep release 0.8.0

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

#200 - release 0.8.0 with EnsembleAnalysis and Python 3 only

Issue - State: closed - Opened by orbeckst about 3 years ago - 3 comments
Labels: release

#199 - Add ensemble_wrapper decorator function

Pull Request - State: open - Opened by ALescoulie over 3 years ago - 6 comments
Labels: enhancement, work in progress, analysis

#198 - Fix Dihedral box

Pull Request - State: closed - Opened by ALescoulie over 3 years ago - 2 comments
Labels: bug, analysis

#197 - Hydrogen Bonding Analysis

Issue - State: open - Opened by ALescoulie over 3 years ago - 10 comments
Labels: analysis

#196 - Solvation Shell

Pull Request - State: closed - Opened by ALescoulie over 3 years ago - 3 comments
Labels: analysis

#195 - Solvation Shell Tool

Issue - State: closed - Opened by ALescoulie over 3 years ago
Labels: analysis

#194 - replace bundled tempdir with pytest tmpdir fixture

Issue - State: open - Opened by orbeckst over 3 years ago - 2 comments
Labels: testing, refactoring

#193 - Dihedral Analysis

Pull Request - State: closed - Opened by ALescoulie over 3 years ago - 5 comments

#192 - Make EnsembleAtomGroup.ensemble() return original

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

#191 - removed deprecated mdpow-gyhd script

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

#190 - Adding Dihedral Analysis

Issue - State: closed - Opened by ALescoulie over 3 years ago - 4 comments
Labels: analysis

#189 - Fix Ensemble Docs

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

#188 - fix ensemble docs for add_system() example

Issue - State: closed - Opened by orbeckst over 3 years ago
Labels: bug, docs, analysis

#187 - config.POWConfigParser fixes and enhancements

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

#186 - finalize 0.7.1

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

#185 - fix mdpow solvationenergy and p_transfer()

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

#184 - mdpow-solvation fails for benzene example

Issue - State: closed - Opened by orbeckst over 3 years ago - 1 comment
Labels: bug, scripts