Gmxapi

* Fixes an issue when GROMACS was installed with a buggy version of CMake.
* Update some documentation.

Bug fixes for gmxapi 0.0.7 on GROMACS 2019.

- 232 Invalid attempt to use Context.rank in Context.work setter
- 234 Logic error when checking for operation implementations

Minor bug fix that affected some forms of manipulating MD plugins.

This is the last planned release of the 0.0.7 gmxapi Python package for GROMACS 2019, unless documentation or bug fixes are necessary.

Warning: This release now requires C++ 14. Previous releases only required C++ 11.

Refer to [documentation](https://gmxapi.readthedocs.io/en/release-0_0_7/) and to [tracked issues](https://github.com/kassonlab/gmxapi/projects/5#column-2793836) for change details.

Interface and feature updates

* `gmx.context.Context` is generic (ParallelArrayContext, DefaultContext deprecated)
* `gmx.system.System` deprecated (use `gmx.workflow.from_tpr`)
* Add `end_time` keyword argument to `gmx.workflow.from_tpr()`

Deprecation

* `steps` keyword argument to `gmx.workflow.from_tpr()` is deprecated in accordance with changes planned for GROMACS 2020.

Internal

* substantial updates for compatibility with GROMACS 2019
* various improvements to CI testing
* Context functionality is now composed according to available resources. (Resource tags, such as `ensemble_update` will be specified in workspec version 0.2 before the gmxapi 0.1 release.)

Bug fixes

* `gmx.get_context()` and `gmx.run()` did not behave as expected for all work types.
* substantial documentation updates

Updated `gmx` Python package for gmxapi 0.0.6

Interface and feature updates

- Updates to `gmx.version` module
- Automatically set and restore from MD simulation checkpoints in the session working directory.
- Allow control of whether simulation output is appended or truncated (PR 126).
- Allow plugins to issue a stop signal to MD simulations (reference 62 for gromacs-gmxapi and sample_restraint repos).
- Changes to `gmx.exceptions`
- Allow full CMake-driven install
- Updated example notebooks in sample_restraint repository.

Internal

- Improved CI testing
- 64 Unique work spec identification.

Bug fixes

- 66 Docker does not access current gmxpy version.
- 123 Race condition in session closing.

Also reference [DOI 10.1093/bioinformatics/bty484](https://doi.org/10.1093/bioinformatics/bty484)