Package: mistree
MiSTreeAuthor:         Krishna NaidooVersion:        1.2.2Homepage:https://github.com/knaidoo29/mistreeDocumentation:https://knaidoo29.github.io/mistreedoc/IntroductionTheminimum spanning tree(MST), a graph constructed from a distribution of points, draws lines between pairs of points so that all points are linked in a single skeletal structure that contains no loops and has minimal total edge length. The MST has been used in a broad range of scientific fields such as particle physics, in astronomy and cosmology. Its success in these fields has been driven by its sensitivity to the spatial distribution of points and the patterns within.MiSTree, a publicPythonpackage, allows a user to construct the MST in a variety of coordinates systems, including Celestial coordinates used in astronomy. The package enables the MST to be constructed quickly by initially using ak-nearest neighbour graph (kNN, rather than a matrix of pairwise distances) which is then fed to Kruskal's algorithm to construct the MST.MiSTreeenables a user to measure the statistics of the MST and provides classes for binning the MST statistics (into histograms) and plotting the distributions. Applying the MST will enable the inclusion of high-order statistics information from the cosmic web which can provide additional information to improve cosmological parameter constraints. This information has not been fully exploited due to the computational cost of calculatingN-point statistics.MiSTreewas designed to be used in cosmology but could be used in any field which requires extracting non-Gaussian information from point distributions.DependenciesPython 2.7 or 3.4+numpymatplotlibscipyscikit-learnf2py(should be installed with numpy)For testing you will requirenoseorpytest.InstallationMiSTree can be installed as follows:pip install mistree [--user]The--useris optional and only required if you don’t have write permission. If you
are using a windows machine this may not work, in this case (or as an alternative to pip) clone the repository,git clone https://github.com/knaidoo29/mistree.git
cd mistreeand install by either runningpip install . [--user]orpython setup.py build
python setup.py installSimilarly, if you would like to work and edit mistree you can clone the repository and install an editable version:git clone https://github.com/knaidoo29/mistree.git
cd mistree
pip install -e . [--user]From themistreedirectory you can then test the install usingnose:python setup.py testor usingpytest:python -m pytestYou should now be able to import the module:importmistreeasmistDocumentationIn depth documentation and tutorials are providedhere.TutorialsThe tutorials in the documentation are supplied as ipython notebooks which can be downloaded fromhereor can be run online usingbinder.CitingYou can citeMiSTreeusing the following BibTex:@ARTICLE{Naidoo2019,
       author = {{Naidoo}, Krishna},
        title = "{MiSTree: a Python package for constructing and analysing Minimum Spanning Trees}",
      journal = {The Journal of Open Source Software},
         year = "2019",
        month = "Oct",
       volume = {4},
       number = {42},
          eid = {1721},
        pages = {1721},
          doi = {10.21105/joss.01721},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2019JOSS....4.1721N}
}SupportIf you have any issues with the code or want to suggest ways to improve it please open a new issue (here)
or (if you don't have a github account) emailkrishna.naidoo.11@ucl.ac.uk.