issues
Tutorial / working Jupyter notebook examples task https://github.com/kassonlab/gmxapi/issues/30
Add test coverage testing with codecov https://github.com/kassonlab/gmxapi/issues/31
Revisit MDHolder gromacs https://github.com/kassonlab/gmxapi/issues/32
checkpoint for data nodes https://github.com/kassonlab/gmxapi/issues/34
workflow-level integration with simulation steps https://github.com/kassonlab/gmxapi/issues/35
more execution graph node types enhancement https://github.com/kassonlab/gmxapi/issues/36
Eigen https://github.com/kassonlab/gmxapi/issues/37
Avoid stdlib and templates at API boundaries https://github.com/kassonlab/gmxapi/issues/38
reusable output node https://github.com/kassonlab/gmxapi/issues/40
Session abstraction in Python module https://github.com/kassonlab/gmxapi/issues/41
resolve protocol for API operation map https://github.com/kassonlab/gmxapi/issues/42
Formalize the external WorkElement interface for plugins https://github.com/kassonlab/gmxapi/issues/43
Formally specify operation Directors for Session builder. enhancement https://github.com/kassonlab/gmxapi/issues/44
Formal AllReduce operation https://github.com/kassonlab/gmxapi/issues/45
WorkSpec parsing to determine Context requirements question https://github.com/kassonlab/gmxapi/issues/46
clean up input parameter specification for plugins task https://github.com/kassonlab/gmxapi/issues/47
clarify plugin development with mixed Python/C++ https://github.com/kassonlab/gmxapi/issues/48
specify pair restraints with selections instead of atom indices https://github.com/kassonlab/gmxapi/issues/49
enable MPI domain decomposition with plugins enhancement https://github.com/kassonlab/gmxapi/issues/50
effective generation of TPR files from MDP data enhancement https://github.com/kassonlab/gmxapi/issues/52
WorkSpec feature: element deletion https://github.com/kassonlab/gmxapi/issues/53
Sample restraint documentation https://github.com/kassonlab/gmxapi/issues/55
Session and client need access to trajectory step https://github.com/kassonlab/gmxapi/issues/56
Allow client management of MPI environment for GROMACS https://github.com/kassonlab/gmxapi/issues/57
GROMACS fatal errors are not handled gracefully https://github.com/kassonlab/gmxapi/issues/58
Stop condition hook enhancement https://github.com/kassonlab/gmxapi/issues/62
schema 0_2 https://github.com/kassonlab/gmxapi/issues/65
Generic data structures for graph edges and state https://github.com/kassonlab/gmxapi/issues/69
Allow Context to inspect GROMACS checkpoint files to determine timestep. https://github.com/kassonlab/gmxapi/issues/70
Allow Context to automatically manipulate simulation input files to restore MD operation to a known state. https://github.com/kassonlab/gmxapi/issues/71
checkpoint interval https://github.com/kassonlab/gmxapi/issues/72
Get a consistent set of checkpoints https://github.com/kassonlab/gmxapi/issues/73
Restore from checkpoint https://github.com/kassonlab/gmxapi/issues/74
Session execution granularity https://github.com/kassonlab/gmxapi/issues/75
Tag artifacts https://github.com/kassonlab/gmxapi/issues/76
Session resources enhancement https://github.com/kassonlab/gmxapi/issues/77
Remove boilerplate for plugin instantiation task https://github.com/kassonlab/gmxapi/issues/78
Safe management of session working files enhancement https://github.com/kassonlab/gmxapi/issues/79
MD stop condition as boolean data flow task https://github.com/kassonlab/gmxapi/issues/83
Callback registration and granularity. https://github.com/kassonlab/gmxapi/issues/84
Clear distinction of Python and C++ domains in plugin environment enhancement https://github.com/kassonlab/gmxapi/issues/87
Reorganize Context and WorkSpec hierarchy enhancement https://github.com/kassonlab/gmxapi/issues/88
Thinner WorkSpec task https://github.com/kassonlab/gmxapi/issues/91
Thinner WorkElements task https://github.com/kassonlab/gmxapi/issues/92
C++ Context for libgromacs task https://github.com/kassonlab/gmxapi/issues/93
Add proxy access to data graph through WorkElement handles task https://github.com/kassonlab/gmxapi/issues/94
Move runner parameters from from_tpr() to gmx.run() https://github.com/kassonlab/gmxapi/issues/95
Context API: place external data object task https://github.com/kassonlab/gmxapi/issues/96
Move docs to GitHub pages https://github.com/kassonlab/gmxapi/issues/99
gmxapi CMake toolchain question https://github.com/kassonlab/gmxapi/issues/101
Capture stdout, stderr during library initialization question https://github.com/kassonlab/gmxapi/issues/105
GIL is not released at any point enhancement https://github.com/kassonlab/gmxapi/issues/113
sample_restraint can't find gromacs_mpi-config.cmake task https://github.com/kassonlab/gmxapi/issues/115
Trajectory continuations need testing https://github.com/kassonlab/gmxapi/issues/131
Need Context-dependent messaging facility enhancement https://github.com/kassonlab/gmxapi/issues/135
ANSI C signal handling for gmxapi enhancement question https://github.com/kassonlab/gmxapi/issues/137
Ambiguous semantics for gmxapi::MDModule::getRestraint() https://github.com/kassonlab/gmxapi/issues/139
restraint potential calculator inputs are confusing enhancement https://github.com/kassonlab/gmxapi/issues/140
Consolidate gmx::restraint::Manager with gmx::Context enhancement gmxapi gromacs https://github.com/kassonlab/gmxapi/issues/145
reconsider gmxapi/version.h scope and usage https://github.com/kassonlab/gmxapi/issues/146
Check for bugs / consistent / expected behavior in specified steps versus trajectory output gromacs https://github.com/kassonlab/gmxapi/issues/147
Links and embedding of C++ docs in Sphinx docs enhancement gmxapi sample_restraint https://github.com/kassonlab/gmxapi/issues/148
Add CMake logic to use FindPython instead of FindPythonInterp and FindPythonLibs https://github.com/kassonlab/gmxapi/issues/150
Name of Python module is not clear enough in sample_restraint docs. https://github.com/kassonlab/gmxapi/issues/161
remove gmx.System gmxapi https://github.com/kassonlab/gmxapi/issues/173
Refine GROMACS integration testing for GROMACS master and client development enhancement gmxapi sample_restraint https://github.com/kassonlab/gmxapi/issues/182
plugin::EnsembleResources has a clumsy protocol bug sample_restraint https://github.com/kassonlab/gmxapi/issues/186
Simulation input tools enhancement gmxapi https://github.com/kassonlab/gmxapi/issues/187
Resolve gmxapi versioning with respect to GROMACS releases and packaging gmxapi gromacs sample_restraint https://github.com/kassonlab/gmxapi/issues/188
General mapping of inputs and outputs for arbitrary tools. enhancement gmxapi https://github.com/kassonlab/gmxapi/issues/190
Simplify / unify Python detection https://github.com/kassonlab/gmxapi/issues/193
Python wrapper for CLI programs gmxapi task https://github.com/kassonlab/gmxapi/issues/198
It is not obvious how to retrieve named plugins from the context or session after launch https://github.com/kassonlab/gmxapi/issues/201
It is not straightforward to set an array of parameters across an array of plugins bug https://github.com/kassonlab/gmxapi/issues/202
InputFile and OutputFile placeholders for Operations gmxapi task https://github.com/kassonlab/gmxapi/issues/203
Make operation inputs and outputs compatible with simulation operation gmxapi task https://github.com/kassonlab/gmxapi/issues/204
Looping operations and subgraph management enhancement gmxapi https://github.com/kassonlab/gmxapi/issues/205
Prescribe, proscribe dependencies gmxapi https://github.com/kassonlab/gmxapi/issues/206
support find_program(gmx) gromacs https://github.com/kassonlab/gmxapi/issues/207
Conventions and utilities for Python Operations enhancement https://github.com/kassonlab/gmxapi/issues/208
allow subgraph to be used as an operation https://github.com/kassonlab/gmxapi/issues/209
Context still thinks it has an active session after Session.close() bug gromacs https://github.com/kassonlab/gmxapi/issues/214
Do more to check for unexpected mpiexec bug https://github.com/kassonlab/gmxapi/issues/215
Provide more support for GROMACS Jenkins testing. gmxapi sample_restraint https://github.com/kassonlab/gmxapi/issues/216
Avoid race conditions from unsynchronized ensembles enhancement gmxapi https://github.com/kassonlab/gmxapi/issues/231
Specifications for referencing external data sources in serialized work https://github.com/kassonlab/gmxapi/issues/237