Mdbenchmark

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

Features
--------

- Add ability to scan number of MPI ranks and OpenMP threads. (`165 <https://github.com/bio-phys/MDBenchmark/issues/165>`_)
- Add support to run multiple simulations on single nodes (GROMACS-only). (`168 <https://github.com/bio-phys/MDBenchmark/issues/168>`_)

=====

This version was skipped intentionally. Version 3.0.1 is the first release of the major version 3.

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

Features
--------

- Add GPUs to cobra template. (`142 <https://github.com/bio-phys/MDBenchmark/issues/142>`_)
- Lower startup time of the CLI. (`153 <https://github.com/bio-phys/MDBenchmark/issues/153>`_)


Bugfixes
--------

- Already submitted benchmarks are now hidden in the summary of ``mdbenchmark submit``. (`139 <https://github.com/bio-phys/MDBenchmark/issues/139>`_)
- Plotting will now work, even when some benchmarks are unfinished. (`140 <https://github.com/bio-phys/MDBenchmark/issues/140>`_)
- Restarting benchmarks with ``mdbenchmark submit --force`` works again. (`141 <https://github.com/bio-phys/MDBenchmark/issues/141>`_)


Misc
----

- Use ``poetry`` to manage Python dependencies and the project in general. (`155 <https://github.com/bio-phys/MDBenchmark/issues/155>`_)

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

Features
--------

- Updated plotting interface. ``mdbenchmark analyze --plot`` is not deprecated. Use ``mdbenchmark plot`` instead.

The new workflow for plotting data is as follows:

1) Use ``mdbenchmark analyze --save-csv results.csv`` to generate a CSV output file.
2) Use ``mdbenchmark plot --csv results.csv`` to plot the data.

Consult ``mdbenchmark <command> --help`` for options to filter your data accordingly. (`52 <https://github.com/bio-phys/MDBenchmark/issues/52>`_)
- ``mdbenchmark generate`` now accepts ``--cpu`` / ``--no-cpu`` and ``--gpu`` / ``--no-gpu``. The default is ``--cpu`` and ``--no-gpu``. (`69 <https://github.com/bio-phys/MDBenchmark/issues/69>`_)
- Added user prompts to ``mdbenchmark generate`` and ``mdbenchmark submit``. (`90 <https://github.com/bio-phys/MDBenchmark/issues/90>`_)
- Added ``--yes`` flag to ``mdbenchmark generate`` and ``mdbenchmark submit`` to bypass user prompt. (`90 <https://github.com/bio-phys/MDBenchmark/issues/90>`_)
- Added ``-nc`` and ``-ng`` options to ``mdbenchmark generate``. These are short hand for ``--no-cpu`` and ``--no-gpu``, respectively. (`93 <https://github.com/bio-phys/MDBenchmark/issues/93>`_)
- Added template for MPCDF cluster ``cobra``. (`104 <https://github.com/bio-phys/MDBenchmark/issues/104>`_)
- Added ``--template`` and ``-t`` option to ``mdbenchmark generate``, to specify a job template. The ``--host`` option still works. (`106 <https://github.com/bio-phys/MDBenchmark/issues/106>`_)
- Standarize the CLI options across all ``mdbenchmark`` calls. (`107 <https://github.com/bio-phys/MDBenchmark/issues/107>`_)
- Added ``mdbenchmark plot --dpi`` option to change the plot DPI. (`108 <https://github.com/bio-phys/MDBenchmark/issues/108>`_)
- Added ``mdbenchmark plot --font-size`` to change the plot font size. (`108 <https://github.com/bio-phys/MDBenchmark/issues/108>`_)
- Linear scaling fit can now be hidden with ``--no-fit``. (`108 <https://github.com/bio-phys/MDBenchmark/issues/108>`_)
- Updated ``ylim``, ``xtick`` and ``ytick`` defaults. The steps for ``xtick`` can be overwritten with ``mdbenchmark plot --xtick-step``. (`108 <https://github.com/bio-phys/MDBenchmark/issues/108>`_)
- Added a watermark in the top left corner for every plot. Can be easiliy disabled with ``mdbenchmark plot --no-watermark``. (`108 <https://github.com/bio-phys/MDBenchmark/issues/108>`_)
- ``mdbenchmark analyze`` no longer writes CSV files by default. ``--save-csv`` flag added to write csv files. (`119 <https://github.com/bio-phys/MDBenchmark/issues/119>`_)
- Added ``mdbenchmark generate --job-name`` to change the job name submitted to the queuing system. (`125 <https://github.com/bio-phys/MDBenchmark/issues/125>`_)


Bugfixes
--------

- Fixed a bug where benchmark creation with files ending in ``.namd`` did not work. (`124 <https://github.com/bio-phys/MDBenchmark/issues/124>`_)
- Fixed a bug where benchmark creation would fail when the input file was not in the current directory. (`124 <https://github.com/bio-phys/MDBenchmark/issues/124>`_)


Misc
----

- Replaced ``mdsynthesis`` with ``datreant`` and upgraded to the new ``datreant>=1.0`` format. (`110 <https://github.com/bio-phys/MDBenchmark/issues/110>`_)

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

Bugfixes
--------

- Fixed a bug where the user was unable to call ``mdbenchmark analyze --plot``. (`86 <https://github.com/bio-phys/MDBenchmark/issues/86>`_)

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

Bugfixes
--------

- We now print all rows when running ``mdbenchmark analyze``. (`68 <https://github.com/bio-phys/MDBenchmark/issues/68>`_)
- Suppress UserWarning caused by ``MDAnalysis==0.18``. (`71 <https://github.com/bio-phys/MDBenchmark/issues/71>`_)


Misc
----

- Added new error message when running ``mdbenchmark generate [...] --skip-validation`` without providing a supported MD engine. (`74 <https://github.com/bio-phys/MDBenchmark/issues/74>`_)