From 2516d26339ea6c7185157b97dd508497c9232ccb Mon Sep 17 00:00:00 2001 From: Luis Fabregas Date: Fri, 26 Mar 2021 13:27:33 +0100 Subject: [PATCH 1/2] docs: fix typos and formatting in beginners guide --- docsrc/source/beginners_guide.rst | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/docsrc/source/beginners_guide.rst b/docsrc/source/beginners_guide.rst index bb2bd3529..3eb51c220 100644 --- a/docsrc/source/beginners_guide.rst +++ b/docsrc/source/beginners_guide.rst @@ -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:`rr_\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`. If a sample does not have a intra-molecular distance distribution (if there are no doubly labelled molecules), set the distribution model to ``'None'``. From 425d84a425749739c2b1e4ca1c095f0058db0ee2 Mon Sep 17 00:00:00 2001 From: Luis Fabregas Date: Mon, 29 Mar 2021 09:52:12 +0200 Subject: [PATCH 2/2] add Python 3.9 to list of supported interpreter versions --- README.md | 2 +- docsrc/source/installation.rst | 4 +++- setup.py | 1 + 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 386c9e0a3..ea007e877 100644 --- a/README.md +++ b/README.md @@ -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. diff --git a/docsrc/source/installation.rst b/docsrc/source/installation.rst index 75a873146..965be69c5 100644 --- a/docsrc/source/installation.rst +++ b/docsrc/source/installation.rst @@ -6,7 +6,9 @@ Installation Requirements ------------ -To install DeerLab, first install Python on your computer. Python can be downloaded from the `official Python distribution `_. There are many online tutorials to guide you through the installation and setup (see `here `_ for example). Make sure you install one of the Python versions compatible with DeerLab, as listed :ref:`here `. +To install DeerLab, first install Python on your computer. Python can be downloaded from the `official Python distribution `_. There are +many online tutorials to guide you through the installation and setup (see `here `_ 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:: diff --git a/setup.py b/setup.py index 60add0ce6..c4c650bf9 100644 --- a/setup.py +++ b/setup.py @@ -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', ] ) \ No newline at end of file