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
#237 - Specifications for referencing external data sources in serialized work
Issue -
State: open - 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
#201 - It is not obvious how to retrieve named plugins from the context or session after launch
Issue -
State: open - Opened by eirrgang over 5 years ago
- 1 comment
#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
#71 - Allow Context to automatically manipulate simulation input files to restore MD operation to a known state.
Issue -
State: open - Opened by eirrgang about 6 years ago
#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