Ecosyste.ms: Issues

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

GitHub / kassonlab/gmxapi issues and pull requests

#274 - `gmxapi.commandline_operation` seems to have memory leaks

Issue - State: open - Opened by wehs7661 about 1 year ago - 3 comments

#273 - How to control the operation of MD by output conformation

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

#272 - Patch to work around CMake bug

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

#271 - How to replace coordinates in the simulation input

Issue - State: closed - Opened by ghost almost 2 years ago - 1 comment

#270 - Using interactive gmx commands such as trjconv within gmxapi

Issue - State: closed - Opened by patriciabrandl about 2 years ago - 1 comment

#269 - Neural Net potential and py interface

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

#268 - How to implement trjcat?

Issue - State: open - Opened by sperezconesa over 3 years ago - 3 comments

#267 - TypeError when importing gmxapi 0.0.8

Issue - State: closed - Opened by sperezconesa over 3 years ago - 9 comments

#265 - Gromacs2021b1

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

#264 - Gmxapi02rc1

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

#263 - Update master from upstream

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

#262 - Accesing commandline output.

Issue - State: open - Opened by sperezconesa about 4 years ago - 5 comments

#261 - Validity checks for WorkSpec updates are not applied consistently.

Issue - State: open - Opened by eirrgang about 4 years ago
Labels: bug

#260 - Update master branch

Pull Request - State: closed - Opened by eirrgang about 4 years ago

#259 - G16160

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#258 - Merge GROMACS master branch

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#257 - [wip] Update commandline_operation with features and error checking.

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

#256 - Merge from upstream.

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#255 - commandline_operation should be able to read from STDIN

Issue - State: closed - Opened by sperezconesa over 4 years ago - 10 comments

#254 - Further clarify versioning.

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#253 - gmxapi-252: make gmxapi 0.0.7 install docs less confusing.

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#252 - reposority reorganization makes gmxapi 0.0.7 install docs confusing

Issue - State: closed - Opened by eirrgang over 4 years ago
Labels: bug, gmxapi

#251 - Provide long description for gmxapi package

Issue - State: open - Opened by eirrgang over 4 years ago

#250 - Enable readthedocs build for >= 0.2a

Issue - State: open - Opened by eirrgang over 4 years ago
Labels: task, gmxapi

#249 - Enable readthedocs build for 0.1.0.1

Issue - State: open - Opened by eirrgang over 4 years ago
Labels: task, gmxapi

#248 - G14804

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#247 - Merge upstream GROMACS master branch

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#246 - 2020 rc 1

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#245 - Beta3

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#244 - Prepare GROMACS 2020 beta 3

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

#243 - Beta2

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#242 - Use latest tagged release of mpi4py in CI tests.

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#241 - GROMACS 2020 beta 2

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#240 - Pybind and setup.py updates

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#239 - Merge upstream changes in advance of GROMACS 2020 beta 2

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#238 - Update Travis-CI config.

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#236 - Convert CI configuration back to bash scripts

Pull Request - State: closed - Opened by eirrgang over 4 years ago

#235 - Handle automatic operation registration in more cases.

Pull Request - State: closed - Opened by eirrgang almost 5 years ago
Labels: gmxapi

#234 - Logic error when checking for operation implementations

Issue - State: closed - Opened by eirrgang almost 5 years ago
Labels: bug, gmxapi

#233 - Update context.py

Pull Request - State: closed - Opened by eirrgang almost 5 years ago
Labels: gmxapi

#232 - Invalid attempt to use Context.rank in Context.work setter.

Issue - State: closed - Opened by eirrgang almost 5 years ago
Labels: bug, gmxapi

#231 - Avoid race conditions from unsynchronized ensembles

Issue - State: open - Opened by eirrgang almost 5 years ago - 3 comments
Labels: enhancement, gmxapi

#230 - docker images for 0.0.7

Issue - State: closed - Opened by eirrgang almost 5 years ago - 2 comments
Labels: task, gromacs, sample_restraint, gmxapi

#229 - Make WorkElement attributes explicitly native str type.

Pull Request - State: closed - Opened by eirrgang almost 5 years ago

#228 - Inconsistent type for WorkElement.namespace and WorkElement.operation

Issue - State: closed - Opened by eirrgang almost 5 years ago
Labels: sample_restraint, gmxapi

#227 - Merge development to master for 0.0.7 release finalization.

Pull Request - State: closed - Opened by eirrgang almost 5 years ago

#226 - uninitialized use of py::object

Issue - State: closed - Opened by eirrgang about 5 years ago
Labels: bug, sample_restraint, gmxapi

#225 - Tie gmxapi 0.0.7 to GROMACS 2019

Pull Request - State: closed - Opened by eirrgang about 5 years ago

#224 - Gmxapi 221

Pull Request - State: closed - Opened by eirrgang about 5 years ago - 3 comments
Labels: gmxapi

#223 - gmxapi-222 Update Travis-CI configuration.

Pull Request - State: closed - Opened by eirrgang about 5 years ago

#222 - Travis-CI configuration is out of date.

Issue - State: closed - Opened by eirrgang about 5 years ago
Labels: bug

#221 - Allow an array of plugins to be assigned to an array of ensemble members

Issue - State: closed - Opened by jmhays about 5 years ago - 6 comments
Labels: enhancement, sample_restraint, gmxapi

#220 - Update installation instructions w.r.t. GROMACS 2019.

Pull Request - State: closed - Opened by eirrgang about 5 years ago

#219 - Update installation instructions w.r.t. GROMACS 2019.

Pull Request - State: closed - Opened by eirrgang about 5 years ago

#218 - update documentation for GROMACS 2019 install

Issue - State: closed - Opened by jmhays about 5 years ago

#217 - Make sure Context does not contain an active session when it shouldn't.

Pull Request - State: closed - Opened by eirrgang over 5 years ago

#216 - Provide more support for GROMACS Jenkins testing.

Issue - State: open - Opened by eirrgang over 5 years ago
Labels: sample_restraint, gmxapi

#215 - Do more to check for unexpected mpiexec

Issue - State: open - Opened by eirrgang over 5 years ago
Labels: bug

#214 - Context still thinks it has an active session after Session.close()

Issue - State: open - Opened by eirrgang over 5 years ago - 5 comments
Labels: bug, gromacs

#213 - Update CMake options required for GROMACS 2019 install

Issue - State: closed - Opened by eirrgang over 5 years ago - 2 comments
Labels: bug, sample_restraint, gmxapi

#212 - Improve ccache handling in CI tests

Issue - State: closed - Opened by eirrgang over 5 years ago - 1 comment

#211 - Doc layout update

Pull Request - State: closed - Opened by eirrgang over 5 years ago

#210 - Remove deprecated exceptions.

Pull Request - State: closed - Opened by eirrgang over 5 years ago

#209 - allow subgraph to be used as an operation

Issue - State: open - Opened by eirrgang over 5 years ago

#208 - Conventions and utilities for Python Operations

Issue - State: open - Opened by eirrgang over 5 years ago
Labels: enhancement

#207 - support find_program(gmx)

Issue - State: open - Opened by eirrgang over 5 years ago
Labels: gromacs

#206 - Prescribe, proscribe dependencies

Issue - State: open - Opened by eirrgang over 5 years ago
Labels: gmxapi

#205 - Looping operations and subgraph management

Issue - State: open - Opened by eirrgang over 5 years ago - 11 comments
Labels: enhancement, gmxapi

#204 - Make operation inputs and outputs compatible with simulation operation

Issue - State: open - Opened by eirrgang over 5 years ago - 2 comments
Labels: task, gmxapi

#203 - InputFile and OutputFile placeholders for Operations

Issue - State: open - Opened by eirrgang over 5 years ago - 7 comments
Labels: task, gmxapi

#202 - It is not straightforward to set an array of parameters across an array of plugins

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

#200 - Python wrapper for CLI programs

Pull Request - State: closed - Opened by eirrgang over 5 years ago - 1 comment

#199 - Minor clean-up.

Pull Request - State: closed - Opened by eirrgang over 5 years ago

#198 - Python wrapper for CLI programs

Issue - State: open - Opened by eirrgang over 5 years ago - 1 comment
Labels: task, gmxapi

#197 - Issue deprecation warning for DefaultContext.

Pull Request - State: closed - Opened by eirrgang over 5 years ago

#196 - Clean up test_pymd.py

Pull Request - State: closed - Opened by eirrgang over 5 years ago

#195 - Rewrite TPR file with updated parameters

Pull Request - State: closed - Opened by eirrgang over 5 years ago

#194 - Basic TPR reader

Pull Request - State: closed - Opened by eirrgang over 5 years ago

#192 - TPR file reader

Issue - State: closed - Opened by eirrgang over 5 years ago
Labels: task, gmxapi

#190 - General mapping of inputs and outputs for arbitrary tools.

Issue - State: open - Opened by eirrgang over 5 years ago - 2 comments
Labels: enhancement, gmxapi

#188 - Resolve gmxapi versioning with respect to GROMACS releases and packaging

Issue - State: open - Opened by eirrgang over 5 years ago - 2 comments
Labels: gromacs, sample_restraint, gmxapi

#187 - Simulation input tools

Issue - State: open - Opened by eirrgang over 5 years ago
Labels: enhancement, gmxapi

#182 - Refine GROMACS integration testing for GROMACS master and client development

Issue - State: open - Opened by eirrgang over 5 years ago
Labels: enhancement, sample_restraint, gmxapi

#153 - comment on GROMACS source code retrieval for readthedocs and BUILDGROMACS builds.

Issue - State: closed - Opened by eirrgang almost 6 years ago - 2 comments
Labels: question, task

#152 - Need to manage src/gmx/version.in `release` attribute

Issue - State: closed - Opened by eirrgang almost 6 years ago - 1 comment

#141 - build MPI for continuous integration testing

Issue - State: closed - Opened by eirrgang almost 6 years ago - 1 comment

#125 - map gmxapi C++ exceptions to Python gmx.exceptions

Issue - State: closed - Opened by eirrgang about 6 years ago - 8 comments

#121 - inconsistent gmx.Status and gmx.core.Status

Issue - State: closed - Opened by eirrgang about 6 years ago - 8 comments
Labels: bug, question

#99 - Move docs to GitHub pages

Issue - State: open - Opened by eirrgang about 6 years ago - 3 comments

#90 - Implicit context stored in Python module variable

Issue - State: closed - Opened by eirrgang about 6 years ago - 2 comments
Labels: task

#86 - Tool to update TPR

Issue - State: closed - Opened by eirrgang about 6 years ago - 3 comments
Labels: task

#85 - Modify simulation parameter

Issue - State: closed - Opened by eirrgang about 6 years ago
Labels: task

#79 - Safe management of session working files

Issue - State: open - Opened by eirrgang about 6 years ago - 1 comment
Labels: enhancement

#39 - multiple MD elements in a single workflow

Issue - State: closed - Opened by eirrgang about 6 years ago - 3 comments

#33 - Use Travis-CI with docker images

Issue - State: closed - Opened by eirrgang about 6 years ago - 1 comment

#32 - Revisit MDHolder

Issue - State: open - Opened by eirrgang about 6 years ago
Labels: gromacs

#30 - Tutorial / working Jupyter notebook examples

Issue - State: open - Opened by eirrgang about 6 years ago - 2 comments
Labels: task