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Redesign installation guide in User Guide
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doc/source/installation.rst

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.. -*- coding: utf-8 -*-
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====================
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Installation
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Installation Guide
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====================
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The latest versions of **MDAnalysis** can be installed using `conda` or `pip`.
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Currently, the conda releases only support serial calculations.
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If you plan to use the parallel OpenMP algorithms, you need to
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install MDAnalysis with pip and have a working OpenMP installation.
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MDAnalysis has a separate :ref:`test suite <mdanalysistests>` **MDAnalysisTests** that is required to run the test cases and examples.
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The test files change less frequently, take up around 90 MB of space,
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and are not needed for daily use of MDAnalysis. However, they are often used in examples,
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including many in this User Guide. If you are not interested in developing
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MDAnalysis or using the example files, you most likely don't need the tests. If you want to
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run examples in the User Guide, install the tests.
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The tests are distributed separately from the main package.
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**MDAnalysis** can be installed using `conda <https://docs.conda.io/projects/conda/en/latest/>`_ (recommended), `pip <https://pip.pypa.io/en/latest/index.html>`_, or from `source <https://github.com/MDAnalysis/mdanalysis/>`_ for development.
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.. note::
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MDAnalysis supports **Linux**, **macOS**, and **Windows** (Python 3.8+).
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If you encounter installation issues, seek help on `GitHub Discussions (Installation) <https://github.com/MDAnalysis/mdanalysis/discussions/categories/installation>`_.
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If you are installing on Windows, you must have
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Microsoft Visual C++ 14.0 installed. If your installation
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fails with the error message:
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error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/
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Try installing Build Tools for Visual Studio from
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https://visualstudio.microsoft.com/downloads/ (scroll
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down to the Tools for Visual Studio section).
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If you encounter any issues following these instructions, please
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ask for help on `GitHub Discussions (Installation)`_.
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.. _`GitHub Discussions (Installation)`: https://github.com/MDAnalysis/mdanalysis/discussions/categories/installation
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conda
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Conda installation
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=====
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If you use ``conda`` to manage your Python environment, we highly recommend creating a new environment for MDAnalysis.
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For most users, `conda <https://docs.conda.io/projects/conda/en/latest/>`_ is the easiest way to install MDAnalysis. We highly recommend creating a new environment for MDAnalysis.
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This will ensure that you have a clean installation of MDAnalysis and its dependencies, and will not interfere with other packages you may have installed.
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We further recommend that you install and use ``mamba``, a faster drop-in replacement for ``conda``.
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.. code-block:: bash
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conda create --name mdanalysis
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conda activate mdanalysis
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conda install -c conda-forge mamba
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conda install -c conda-forge mdanalysis
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To install the latest stable version of MDAnalysis via ``conda``, use the following command. This installs all dependencies needed for full analysis functionality (excluding external programs such as `HOLE`_):
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To upgrade to the latest version:
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.. code-block:: bash
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mamba install -c conda-forge mdanalysis
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conda update mdanalysis
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To upgrade:
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To install the **test suite** (useful for examples and validation):
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.. code-block:: bash
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mamba update mdanalysis
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conda install MDAnalysisTests
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To install the tests:
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.. code-block:: bash
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.. warning::
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Conda installations **do not support OpenMP**.
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If you need **parallel OpenMP calculations**, install MDAnalysis using `pip <https://pip.pypa.io/en/latest/index.html>`_.
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mamba install -c conda-forge MDAnalysisTests
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If you intend to use MDAnalysis in JupyterLab, you will have to install
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an extra package for the progress bar in analysis classes:
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conda install -c conda-forge nodejs
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jupyter labextension install @jupyter-widgets/jupyterlab-manager
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pip
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Pip installation
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=====
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The following command will install or upgrade the latest stable version of MDAnalysis via ``pip``, with core dependencies. This means that some packages required by specific analysis modules will not be installed.
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If you do not use Conda or require **OpenMP support**, install MDAnalysis via `pip <https://pip.pypa.io/en/latest/index.html>`_:
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.. code-block:: bash
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pip install --upgrade MDAnalysis
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If you need to install a fully-featured MDAnalysis, add the ``analysis`` tag. As with ``conda``, this will not install external programs such as `HOLE`_.
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For full functionality with **analysis modules**:
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.. code-block:: bash
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pip install --upgrade MDAnalysis[analysis]
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To install/upgrade tests:
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To install the **test suite**:
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pip install nodejs
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jupyter labextension install @jupyter-widgets/jupyterlab-manager
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.. note::
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If you are installing on **Windows**, and encounter errors related to **Microsoft Visual C++ 14.0**, install **Build Tools for Visual Studio** from `here <https://visualstudio.microsoft.com/downloads/>`_.
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----------------------
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Development versions
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====================

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