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Installation
============
Released versions of NeXpy are available on `PyPI
<https://pypi.python.org/pypi/NeXpy/>`__ and `conda-forge
<https://anaconda.org/conda-forge/nexpy>`__.
You can therefore install using 'pip'::
$ pip install nexpy
or 'conda'::
$ conda install -c conda-forge nexpy
.. note:: You can add conda-forge to your default channels so that it is
automatically searched when installing. Just type
``conda config --add channels conda-forge``.
If you have the `Python Setup Tools
<https://pypi.python.org/pypi/setuptools>`__, you can install the
package from the source code either by downloading one of the `Github
releases <https://github.com/nexpy/nexpy/releases>`__ or by cloning the
latest development version in the `NeXpy Git repository
<https://github.com/nexpy/nexpy>`__::
$ git clone https://github.com/nexpy/nexpy.git
Then use standard Python tools to build and/or install a distribution
from within the source directory::
$ python -m build # build a distribution
$ python -m pip install . # install the package
The Python API for reading and writing NeXus files is in a separate
package, `nexusformat <https://github.com/nexpy/nexusformat>`__, which
is also available on `PyPI <https://pypi.python.org/pypi/nexusformat>`__
and `conda-forge <https://anaconda.org/conda-forge/nexusformat>`__.
If the NeXpy GUI is not required, the package may be used in any Python
shell. It may be installed using::
$ pip install nexusformat
or::
$ conda install -c conda-forge nexusformat
The package can also be installed from the source code either by
downloading one of the `Github releases
<https://github.com/nexpy/nexusformat/releases>`__ or by cloning the
latest development version in the `NeXpy Git repository
<https://github.com/nexpy/nexusformat>`__::
$ git clone https://github.com/nexpy/nexusformat.git
Required Libraries
==================
Python Command-Line API
-----------------------
NeXpy provides a GUI interface to the `nexusformat API
<https://github.com/nexpy/nexusformat>`__, which uses `h5py
<http://h5py.org>`__ to read and write HDF5 files that implement the
`NeXus data format standard <https://www.nexusformat.org>`__. It does
not use the NeXus C API, which means that the current version cannot
read and write legacy HDF4 or XML NeXus files. One of the `NeXus
conversion utilities <https://manual.nexusformat.org/utilities.html>`__
should be used to convert such files to HDF5.
If you only intend to utilize the Python API from the command-line, the
only other required libraries are `NumPy <https://numpy.org>`__ and
`SciPy <http://scipy.org>`__. Autocompletion of group and field paths
within an open file is available if `IPython <https://ipython.org/>`__
is installed.
================= =================================================
Library URL
================= =================================================
nexusformat https://github.com/nexpy/nexusformat/
h5py https://www.h5py.org
numpy https://numpy.org/
scipy https://scipy.org/
packaging https://packaging.pypa.io/
dateutil https://dateutil.readthedocs.io/
colored https://dslackw.gitlab.io/colored/
pygments https://pygments.org/
================= =================================================
NeXpy GUI
---------
The GUI is built using the PyQt. The `qtpy package
<https://github.com/spyder-ide/qtpy>`__ is used to import whatever PyQt
library is installed, whether PyQt5, PyQt6, PySide2, or PySide6.
NeXpy embeds an `IPython shell <http://ipython.org/>`__ and `Matplotlib
plotting pane <http://matplotlib.sourceforge.net>`__, within a Qt GUI
based on the Jupyter QtConsole with an in-process kernel.
Least-squares fitting of 1D data uses the `LMFIT package
<https://lmfit.github.io/lmfit-py/>`__.
================= =================================================
Library URL
================= =================================================
IPython https://ipython.org/
qtconsole https://qtconsole.readthedocs.io/
qtpy https://github.com/spyder-ide/qtpy
matplotlib https://matplotlib.org/
lmfit https://lmfit.github.io/lmfit-py/
fabio https://github.com/silx-kit/fabio
pillow https://pillow.readthedocs.io/
pylatexenc https://pylatexenc.readthedocs.io/
ansi2html https://pypi.python.org/pypi/ansi2html/
mplcursors https://mplcursors.readthedocs.io/
================= =================================================
Additional Packages
-------------------
Importers may require additional libraries to read the imported files in
their native format, *e.g.*, `spec2nexus
<http://spec2nexus.readthedocs.org/>`__ for reading SPEC files.
From v0.9.1, a new 2D smoothing option is available in the list of
interpolations in the signal tab if `astropy <http://www.astropy.org>`__
is installed. It is labelled 'convolve' and provides, by default, a
2-pixel Gaussian smoothing of the data. The number of pixels can be
changed in the shell by setting ``plotview.smooth``.
================= =================================================
Library URL
================= =================================================
spec2nexus http://spec2nexus.readthedocs.org/
astropy http://www.astropy.org/
================= =================================================
.. note:: NeXpy should still run without these additional packages, but
invoking the relevant menu items may trigger a warning.
Running the GUI
---------------
To run from the installed location, add the $prefix/bin directory to
your path if you installed outside the python installation, and then
run::
$ nexpy [-r]
The -r option restores all files loaded in the previous session.
Semantic Versioning
-------------------
NeXpy uses `Semantic Versioning <http://semver.org/spec/v2.0.0.html>`__.
User Support
------------
Consult the `NeXpy documentation <http://nexpy.github.io/nexpy/>`__ for
details of both the Python command-line API and how to use the NeXpy
GUI. If you have any general questions concerning the use of NeXpy,
please address them to the `NeXus Mailing List
<http://download.nexusformat.org/doc/html/mailinglist.html>`__. If you
discover any bugs, please submit a `Github issue
<https://github.com/nexpy/nexpy/issues>`__, preferably with relevant
tracebacks.
Acknowledgements
----------------
The `NeXus format <http://www.nexusformat.org>`__ for neutron, x-ray and
muon data is developed by an international collaboration under the
supervision of the `NeXus International Advisory Committee
<https://www.nexusformat.org/NIAC.html>`__. The Python tree API used in
NeXpy was originally developed by Paul Kienzle, who also wrote the
standard Python interface to the NeXus C-API. The original version of
NeXpy was initially developed by Boyana Norris, Jason Sarich, and Daniel
Lowell, and Ray Osborn using wxPython, and formed the inspiration for
the current PyQt version. Validation of NeXus files was developed by
Kaitlyn Marlor and Justin Wozniak. I am grateful to Tom Schoonjans for
installing the packages on conda-forge.
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