nmraspecds

https://github.com/mirjamschr/nmraspecds

Repository

README.rst

==========
NMRAspecds
==========

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.13293054.svg
   :target: https://doi.org/10.5281/zenodo.13293054
   :align: right

The NMRAspecds package provides tools for handling experimental data obtained using nuclear magnetic resonance (NMR) spectroscopy and is derived from the `ASpecD framework `_,  hence all data generated with the nmraspecds package are completely reproducible and have a complete history.

What is even better: Actual data processing and analysis no longer requires programming skills, but is as simple as writing a text file summarising all the steps you want to have been performed on your dataset(s) in an organised way. Curious? Have a look at the following example::

    format:
      type: ASpecD recipe
      version: '0.2'

    settings:
      default_package: nmraspecds

    datasets:
      - /path/to/first/dataset
      - /path/to/second/dataset

    tasks:
      - kind: processing
        type: Normalisation
        parameters:
          properties:
            kind: scan_number
      - kind: singleplot
        type: SinglePlotter1D
        properties:
          filename:
            - first_dataset.pdf
            - second_dataset.pdf


Interested in more real-live examples? Check out the growing :doc:`list of examples ` providing complete recipes for different needs.


Features
========

A list of features:

* Fully reproducible processing and analysis of NMR data.

* Gap-less record of each processing/analysis step, including explicit and implicit parameters.

* Import of Bruker NMR data

* Generic representation of NMR data, independent of the original format.

* Datasets contain both, numerical data and all crucial metadata, a prerequisite for FAIR data.

* Generic plotting capabilities, easily extendable

* Report generation using pre-defined templates

* Recipe-driven data analysis, allowing tasks to be performed fully unattended in the background


And to make it even more convenient for users and future-proof:

* Open source project written in Python (>= 3.7)

* Developed mostly test-driven

* Extensive user and API documentation



.. info::
  NMRAspecds is currently under active development and still considered in Beta development state. Therefore, expect frequent changes in features and public APIs that may break your own code. Nevertheless, feedback as well as feature requests are highly welcome.


Target audience
===============

The NMRAspecds package addresses scientists working with nuclear magnetic resonance (NMR) data on a daily base and concerned with reproducibility. Due to being based on the `ASpecD framework `_, the NMRAspecds package ensures reproducibility and---as much as possible---replicability of data processing, starting from recording data and ending with their final (graphical) representation, e.g., in a peer-reviewed publication. This is achieved by automatically creating a gap-less record of each operation performed on your data. If you do care about reproducibility and are looking for a system that helps you to achieve this goal, the NMRAspecds package may well be interesting for you.


How to cite
===========

NMRAspecds is free software. However, if you use NMRAspecds for your own research, please cite the software:

  * Mirjam Schröder. NMRAspecds (2024). `doi:10.5281/zenodo.13293054 `_

To make things easier, NMRAspecds has a `DOI `_ provided by `Zenodo `_, and you may click on the badge below to directly access the record associated with it. Note that this DOI refers to the package as such and always forwards to the most current version.

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.13293054.svg
   :target: https://doi.org/10.5281/zenodo.13293054


Installation
============

To install the NMRAspecds package on your computer (sensibly within a Python virtual environment), open a terminal (activate your virtual environment), and type in the following:

.. code-block:: bash

    pip install nmraspecds


License
=======

This program is free software: you can redistribute it and/or modify it under the terms of the **BSD License**. However, if you use NMRAspecds for your own research, please cite it appropriately.


Related projects
================

There is a number of related packages users of the NMRAspecds package may well be interested in, as they have a similar scope, focussing on spectroscopy and reproducible research.

* `ASpecD `_

  A Python framework for the analysis of spectroscopic data focussing on reproducibility and good scientific practice. The framework the NMRAspecds package is based on, developed by T. Biskup.

* `FitPy `_

  Framework for the advanced fitting of models to spectroscopic data focussing on reproducibility, developed by T. Biskup.

Owner

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite both the article from preferred-citation and the software itself."
title: NMRAspecds
abstract: >
    NMRAspecds is a Python package for processing and analysis of nuclear magnetic resonance (NMR) data based on the ASpecD framework and focussing on reproducibility. In short: Each and every processing step applied to your data will be recorded and can be traced back, and additionally, for each representation of your data (e.g., figures, tables) you can easily follow how the data shown have been processed and where they originate from.

    What is even better: Actual data processing and analysis no longer requires programming skills, but is as simple as writing a text file summarising all the steps you want to have been performed on your dataset(s) in an organised way.
authors:
  - family-names: Schröder
    given-names: Mirjam
    orcid: "https://orcid.org/0000-0002-8940-3185"
  - family-names: Taube
    given-names: Florian
    orcid: "https://orcid.org/0009-0001-7269-1782"
  - family-names: Biskup
    given-names: Till
    orcid: "https://orcid.org/0000-0003-2913-0004"
type: software
license: BSD-2-Clause
repository-code: "https://github.com//MirjamSchr/nmraspecds"
keywords:
  - "nuclear magnetic resonance spectroscopy"
  - "NMR spectroscopy"
  - "spectroscopy"
  - "magnetic resonance"
  - "data processing and analysis"
  - "reproducible science"
  - "reproducible research"
  - "good scientific practice"
  - "recipe-driven data analysis"
references:
  - authors:
    - family-names: Biskup
      given-names: Till
      orcid: "https://orcid.org/0000-0003-2913-0004"
    doi: 10.5281/zenodo.4717937
    repository-code: "https://github.com/tillbiskup/aspecd"
    title: ASpecD
    type: software

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