drawnmr

======= drawnmr

What is drawnmr?

drawnmr is a module for viewing NMR data in Python. When used with the nmrglue and bokeh packages, drawnmr provides functions to view and interact with NMR data.

drawnmr is a wrapper around nmrglue capabilities and provide helper functions to show the data in bokeh, which is an interactive visualisation library.

The main purpose is to show NMR data in a Jupyter Notebook. If a Jupyter Notebook installation is not running, bokeh allow the output to be saved to static HTML files.

nmrglue is used for processing nmrdata, and bokeh is used for showing and interacting. The function get_contour_widget() create ipywidgets to easily control contour levels. The function get_peakpick() calls nmrglue peakpick.pick() to find peaks, convert from data point to ppm coordinates, store in a pandas dataframe for easy inspection and add the peaks to the bokeh plot.

Important links

• Source code: https://github.com/tlinnet/drawnmr
• PyPI package: https://pypi.python.org/pypi/drawnmr
• Link to nmrglue: https://www.nmrglue.com and https://github.com/jjhelmus/nmrglue
• Link to bokeh: https://bokeh.pydata.org and https://github.com/bokeh/bokeh

See examples

Use nbviewer.jupyter.org to:

• See default Notebook 15N/13C 2D contour: nmrglue_s4_2d_plotting.ipynb_
• See how to use widgets to alter contour levels: contour_widget.ipynb_
• See how to use nmrglue peak pick, print table and show: contour_find_peaks.ipynb_

.. _nmrglue_s4_2d_plotting.ipynb: http://nbviewer.jupyter.org/github/tlinnet/drawnmr/blob/master/examples/nmrglue_s4_2d_plotting.ipynb .. _contour_widget.ipynb: http://nbviewer.jupyter.org/github/tlinnet/drawnmr/blob/master/examples/contour_widget.ipynb .. _contour_find_peaks.ipynb: http://nbviewer.jupyter.org/github/tlinnet/drawnmr/blob/master/examples/contour_find_peaks.ipynb

Launch interactive Jupyter Notebook mybinder.org_ to try examples:

.. _mybinder.org: https://mybinder.org/v2/gh/tlinnet/drawnmr/master

.. image:: https://mybinder.org/badge.svg :target: https://mybinder.org/v2/gh/tlinnet/drawnmr/master

.. image:: https://raw.githubusercontent.com/tlinnet/drawnmr/master/docs/images/image_2.png .. image:: https://raw.githubusercontent.com/tlinnet/drawnmr/master/docs/images/image_1.png

How to install?

If using conda, these steps will install an environment

.. code-block:: bash

With pip from https://pypi.python.org/pypi/drawnmr

pip install drawnmr

Developer install for local conda environment:

.. code-block:: bash

Create environment

conda env create -f environment.yml

Activate environment

conda env list source activate drawnmr

Enable ipywidgets

jupyter nbextension list jupyter nbextension enable --py widgetsnbextension --sys-prefix

Start jupyter

jupyter notebook

Or manual install in root environment:

.. code-block:: bash

Manually install package

python setup.py install --force

Manually uninstall

python setup.py install --record files.txt PACK=dirname $(head -n 1 files.txt) rm -rf $PACK #cat files.txt | xargs rm -rf

Developer

• Guide for upload: http://peterdowns.com/posts/first-time-with-pypi.html
• Updated info: https://packaging.python.org/guides/migrating-to-pypi-org/#uploading
• PyPI test account: http://testpypi.python.org/pypi?%3Aaction=register_form
• PyPI Live account: http://pypi.python.org/pypi?%3Aaction=register_form

.. code-block:: bash

Modify version in: drawnmr/init.py

Create tag

VERS=python -c "from drawnmr import __version__; print(__version__)"

Adds a tag so that we can put this on PyPI

git tag $VERS -m "" git push --tags origin master

Upload your package to PyPI Test

python setup.py sdist upload -r pypitest open https://testpypi.python.org/pypi/drawnmr

Upload to PyPI Live

Once you've successfully uploaded to PyPI Test, perform the same steps but point to the live PyPI server instead.

python setup.py sdist upload -r pypi open https://pypi.python.org/pypi/drawnmr