Mdbenchmark

==================

Bugfixes
--------

- Module name validation is now performed case insensitive. (`61 <https://github.com/bio-phys/MDBenchmark/issues/61>`_)


Misc
----
- Consolidate common functions from ``mdengines.gromacs`` and ``mdengines.namd`` into ``mdengines.utils``, removing code duplication. (`57 <https://github.com/bio-phys/MDBenchmark/issues/57>`_)
- Refactor unit tests. Make everything more concise and use some more pytest functionality. (`58 <https://github.com/bio-phys/MDBenchmark/issues/58>`_)

==================

Features
--------

- Add functionality to perform benchmarks with NAMD. (`29 <https://github.com/bio-phys/MDBenchmark/issues/29>`_)
- Consolidated internal API to output messages to the console. (`42 <https://github.com/bio-phys/MDBenchmark/issues/42>`_)
- Module name is now validated against available modules on host. Can be
skipped with ``--skip-validation``. (`49 <https://github.com/bio-phys/MDBenchmark/issues/49>`_)


Bugfixes
--------

- The option ``--min-nodes`` needs to be bigger than ``--max-nodes``. (`46 <https://github.com/bio-phys/MDBenchmark/issues/46>`_)
- Fixed edge-case in input filename parsing. (`54 <https://github.com/bio-phys/MDBenchmark/issues/54>`_)


Misc
----

- Fixed display of the number of benchmarks to-be generated. (`46 <https://github.com/bio-phys/MDBenchmark/issues/46>`_)

==================

Features
--------

- Added ``Makefile`` to the project. Updated default strings. (`36 <https://github.com/bio-phys/MDBenchmark/issues/36>`_)
- GROMACS .tpr files can now be referenced with and without the file extension. (`32 <https://github.com/bio-phys/MDBenchmark/issues/32>`_)


Bugfixes
--------

- Fixed crash during analyze, if some simulations have not started/finished yet. (`26 <https://github.com/bio-phys/MDBenchmark/issues/26>`_)
- Suppress FutureWarning caused by ``h5py``. (`35 <https://github.com/bio-phys/MDBenchmark/issues/35>`_)

Improved Documentation
----------------------

- Update and add more unit tests. (`36 <https://github.com/bio-phys/MDBenchmark/issues/36>`_)

==================

Misc
----
- Show benchmark png on PyPI.

==================

Features
--------

- Enable to run on macOS. (`10 <https://github.com/bio-phys/MDBenchmark/issues/10>`_)
- Read number of cores from simulation log. (`19 <https://github.com/bio-phys/MDBenchmark/issues/19>`_)


Bugfixes
--------

- Ensure MPI environment is loaded on draco after a purge. (`17 <https://github.com/bio-phys/MDBenchmark/issues/17>`_)


Improved Documentation
----------------------

- Fix readme usage docs for the module argument. (`20 <https://github.com/bio-phys/MDBenchmark/issues/20>`_)

==================

Misc
----

- Fixup ``MANIFEST.in``. (`9 <https://github.com/bio-phys/MDBenchmark/issues/9>`_)