Upgrading ========= While we try to make upgrades from one version of MDBenchmark to another as easy as possible, we are sometimes forced to break things along the way. This page gives some guidelines on how to migrate to specific versions of MDBenchmark, if you have been using a different version before. To update from a previous MDBenchmark version to a new release, run the following, if you are using ``conda`` and your `conda environment`_ is called ``benchmark``:: conda update -n benchmark mdbenchmark and if you use ``pip``, run:: pip install mdbenchmark --upgrade Refer to our :doc:`installation guide `, if you need help with conda/virtual environments. Migrating to a newer version ---------------------------- Version 2.0.0 ~~~~~~~~~~~~~ .. note:: **TL;DR:** You need to uninstall the unneeded ``datreant.core``, ``datreant.data`` and ``mdsynthesis`` Python packages. Or just get rid of the current environment, e.g., ``conda env remove -n benchmark`` if you are using ``conda``, and :ref:`create it from scratch `. Starting from version 2.0.0, MDBenchmark migrated to a different dependency, than it used before. While the specialized |mdsynthesis|_ package was used in previous version, we migrated to the more general |datreant|_ package. This leads to two things: 1) Previously, every folder representing a specific number of nodes contained a ``Sim..json`` file, where ```` is a `UUID`_. This file contained all information representing a specific benchmark with its parameters. With the newer version of ``datreant``, the format was changed and now each of these folders contains a ``.datreant`` folder instead. 2) ``datreant`` version 1.0 changed its package layout and led to the necessity of uninstalling previous packages. Because we were using a previous ``datreant`` version, you as a user will also need to uninstall those packages. Uninstalling old packages ######################### For proper migration, you need to uninstall the following three packages: 1) ``datreant.core`` 2) ``datreant.data`` 3) ``mdsynthesis`` If you are using ``conda`` and your environment is called ``benchmark``, run the following command:: conda remove -n benchmark datreant.core datreant.data mdsynthesis You can also decide to fully remove the environment (``conda env remove -n benchamrk``) and :ref:`create it from scratch `. If you are using ``pip`` simply run:: pip uninstall datreant.core datreant.data mdsynthesis .. _conda environment: https://conda.io/docs/user-guide/tasks/manage-environments.html .. _instalation guide: .. |mdsynthesis| replace:: ``mdsynthesis`` .. _mdsynthesis: https://mdsynthesis.readthedocs.io/en/master/ .. |datreant| replace:: ``datreant`` .. _datreant: https://datreant.readthedocs.io/en/master/ .. _UUID: https://en.wikipedia.org/wiki/Universally_unique_identifier