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Installation
============
Preparing for pyUSID
--------------------
`PyUSID <https://github.com/pycroscopy/pyUSID>`_ requires many commonly used scientific and numeric python packages such as numpy, h5py etc.
To simplify the installation process, we recommend the installation of
`Anaconda <https://www.anaconda.com/distribution/>`_ which contains most of the prerequisite packages,
`conda <https://conda.io/docs/>`_ - a package / environment manager,
as well as an `interactive development environment <https://en.wikipedia.org/wiki/Integrated_development_environment>`_ - `Spyder <https://www.coursera.org/learn/python-programming-introduction/lecture/ywcuv/introduction-to-the-spyder-ide>`_.
Do you already have Anaconda installed?
- No? `Download and install Anaconda <https://www.anaconda.com/download/>`_ for Python 3.6
- Yes?
- Is your Anaconda based on python 2.7, 3.4+?
- No?
- Uninstall existing Python / Anaconda distribution(s).
- Restart computer
- Yes?
- Proceed to install pyUSID
Compatibility
~~~~~~~~~~~~~
* pyUSID is compatible with python 2.7, and 3.4 onwards. Please raise an issue if you find a bug.
* We do not support 32 bit architectures
* We only support text that is UTF-8 compliant due to restrictions posed by HDF5
Terminal
--------
Installing, uninstalling, or updating pyUSID (or any other python package for that matter) can be performed using the ``Terminal`` application.
You will need to open the Terminal to type any command shown on this page.
Here is how you can access the Terminal on your computer:
* Windows - Open ``Command Prompt`` by clicking on the Start button on the bottom left and typing ``cmd`` in the search box.
You can either click on the ``Command Prompt`` that appears in the search result or just hit the Enter button on your keyboard.
* Note - be sure to install in a location where you have write access. Do not install as administrator unless you are required to do so.
* MacOS - Click on the ``Launchpad``. You will be presented a screen with a list of all your applications with a search box at the top.
Alternatively, simultaneously hold down the ``Command`` and ``Space`` keys on the keyboard to launch the ``Spotlight search``.
Type ``terminal`` in the search box and click on the ``Terminal`` application.
* Linux (e.g - Ubuntu) - Open the Dash by clicking the Ubuntu (or equivalent) icon in the upper-left, type "terminal".
Select the Terminal application from the results that appear.
Installing pyUSID
-----------------
1. Ensure that a compatible Anaconda distribution has been successfully installed
2. Open a `terminal <#terminal>`_ window.
3. You can now install pyUSID via **either** the ``pip`` or ``conda`` methods shown below.
Type the following commands into the terminal / command prompt and hit the Return / Enter key:
* pip:
.. code:: bash
pip install pyUSID
* conda:
.. code:: bash
conda config --add channels conda-forge
conda install pyusid
Offline installation
~~~~~~~~~~~~~~~~~~~~
In certain cases, you may need your python packages to work on a computer
(typically the computer that controls a scientific instrument) that is not connected to the internet.
In such cases, the aforementioned routes will not work. Please follow these instructions instead:
#. Recall that pyUSID requires python and several other packages. Therefore, you will need to:
#. Download the `Anaconda installer <https://www.anaconda.com/download/>`_ from a computer is online
#. Copy the installer onto the target computer via a USB pen drive
#. Install Anaconda
#. Download the pyUSID repository from GitHub via `this link <https://github.com/pycroscopy/pyUSID/archive/master.zip>`_
#. Copy the resultant zip file to the offline computer via a portable storage device like a USB pen drive
#. Unzip the zip file in the offline computer.
#. Open a `terminal <#terminal>`_ window
#. Navigate to the folder where you unzipped the contents of the zip file via ``cd`` commands
#. Type the following command:
.. code:: bash
python setup.py install
Installing from a specific branch (advanced users **ONLY**)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Note that we do not recommend installing pyUSID this way since branches other than the master branch may contain bugs.
.. note::
Windows users will need to install ``git`` before proceeding. Please type the following command in the Command Prompt:
.. code:: bash
conda install git
Install a specific branch of pyUSID (``usi_dev`` in this case):
.. code:: bash
pip install -U git+https://github.com/pycroscopy/pyUSID@usi_dev
Updating pyUSID
---------------
We recommend periodically updating your conda / anaconda distribution. Please see `these instructions to update anaconda <./external_guides.html#Updating-packages>`_.
If you already have pyUSID installed and want to update to the latest version, use the following command in a terminal window:
* If you originally installed pyUSID via ``pip``:
.. code:: bash
pip install -U --no-deps pyUSID
If it does not work try reinstalling the package:
.. code:: bash
pip uninstall pyUSID
pip install pyUSID
* If you originally installed pyUSID via ``conda``:
.. code:: bash
conda update pyUSID
Other software
--------------
We recommend `HDF View <https://support.hdfgroup.org/products/java/hdfview/>`_ for exploring HDF5 files generated by and used in pyUSID.
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