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Further minor edits to the documentation #122

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -14,7 +14,7 @@ The early versions of DeerLab (up to version 0.9.2) are written in MATLAB. The o

### Requirements

DeerLab is available for Windows, Mac and Linux systems and requires **Python 3.6**, **3.7**, or **3.8**.
DeerLab is available for Windows, Mac and Linux systems and requires **Python 3.6**, **3.7**, **3.8**, or **3.9**.

All additional dependencies are automatically downloaded and installed during the setup.

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15 changes: 8 additions & 7 deletions docsrc/source/beginners_guide.rst
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Expand Up @@ -123,21 +123,22 @@ DeerLab provides a wide range of functionality to analyze experimental dipolar E
Picking the right model
***********************

DeerLab provides a very flexible framework to model dipolar signals originating from many different dipolar EPR spectroscopy experiments. Choosing a model that properly describes your sample and experiment is of paramount importance. In ``fitmodel`` the main structure of the model is already defined, with the following components:
* **Distance range**: Also called the distance-axis, is the range of distances where the distribution is defined.
* **Distribution model**: Describes the intra-molecular distance distribution in either a parametric (e.g. a Gaussian distribution) or a non-parametric way.
* **Background model**: Describes the dipolar background signal arising from the inter-molecular contributions.
* **Experiment model**: Describes the experiment-specific shape of the dipolar signal.
DeerLab provides a very flexible framework to model dipolar signals originating from many different dipolar EPR spectroscopy experiments. Choosing a model that properly describes your sample and experiment is of paramount importance. In ``fitmodel`` the main structure of the model is already defined, with the following components:

* **Distance range**: Also called the distance-axis, is the range of distances where the distribution is defined.
* **Distribution model**: Describes the intra-molecular distance distribution in either a parametric (e.g. a Gaussian distribution) or a non-parametric way.
* **Background model**: Describes the dipolar background signal arising from the inter-molecular contributions.
* **Experiment model**: Describes the experiment-specific shape of the dipolar signal.

For each of these four components, a choice needs to be made:

(1) **Choosa a distance range**
(1) **Choose a distance range**

The distance range :math:`[r_\mathrm{min},r_\mathrm{max}]` is an important choice, as any distance distribution is truncated to this range, i.e. :math:`P(r)=0` for:math:`r<r_\mathrm{min}` and :math:`r>r_\mathrm{max}`. The lower limit of the distance range is determined by the bandwidth of the pulses, and also by the time increment. Typically, 1.5 nm is a reasonable choice. The upper limit depends on the length of the experimental time trace and on the distances in your sample. The number of points in ``r`` is usually set equal to the number of time points. Such a distance-axis is usually defined as ``r`` is most easily defined using the ``linspace`` function from NumPy: ::

r = np.linspace(1.5,6,len(t)) # define distance range form 1.5nm to 6nm with the same amount of points as t

(2) **Choosa a distribution model**
(2) **Choose a distribution model**

A non-parametric distribution is specified using the string ``'P'`` in ``fitmodel``. In a non-parametric distribution, each element :math:`P_i` of the distribution is a parameter. Non-parametric distributions are obtained via methods such as Tikhonov regularization. If there are reasons to believe that the distance distribution has a specific shape (e.g. Gaussian, Rice, random-coil, etc.), or if there is very little information in the data, use a parametric distance distribution model from the :ref:`list of available models<modelsref_dd>`. If a sample does not have a intra-molecular distance distribution (if there are no doubly labelled molecules), set the distribution model to ``'None'``.

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4 changes: 3 additions & 1 deletion docsrc/source/installation.rst
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Expand Up @@ -6,7 +6,9 @@ Installation
Requirements
------------

To install DeerLab, first install Python on your computer. Python can be downloaded from the `official Python distribution <https://www.python.org/>`_. There are many online tutorials to guide you through the installation and setup (see `here <https://realpython.com/installing-python/>`_ for example). Make sure you install one of the Python versions compatible with DeerLab, as listed :ref:`here <installation>`.
To install DeerLab, first install Python on your computer. Python can be downloaded from the `official Python distribution <https://www.python.org/>`_. There are
many online tutorials to guide you through the installation and setup (see `here <https://realpython.com/installing-python/>`_ for example). Make sure you install
one of the Python versions compatible with DeerLab, either **Python 3.6**, **3.7**, **3.8**, or **3.9**

For Windows systems it is important to ensure that the **Install launcher for all users (recommended)** and the **Add Python 3.x to PATH** checkboxes at the bottom are checked. To test if python has been successfully installed, open a terminal window and run the command::

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1 change: 1 addition & 0 deletions setup.py
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Expand Up @@ -99,6 +99,7 @@ def run(self):
'Programming Language :: Python :: 3.6',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Topic :: Scientific/Engineering',
]
)