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morganjwilliams/pyrolite: 0.2.7

Morgan Williams; Louise Schoneveld

Note that this is the version of pyrolite offically peer-reviewed by pyOpenSci.

0.2.7 Changelog

  • Bugfix to include radii data in MANIFEST.in

0.2.6 Changelog

  • New Contributors: Kaarel Mand and Laura Miller
  • PR Merged: Louise Schonevel submitted a pull request to fill out the newly-added Formatting and Cleaning Up Plots tutorial. This tutorial aims to provide some basic guidance for common figure and axis formatting tasks as relevant to pyrolite.
  • Added codacy for code quality checking, and implemented numerous clean-ups and a few new tests across the package.
  • Performance upgrades, largely for the documentation page. The docs page should build and load faster, and have less memory hang-ups - due to smaller default image sizes/DPI.
  • Removed dependency on fancyimpute, instead using functions from scikit-learn

pyrolite.geochem

  • Bugfix: pyrolite lambdas differ slightly from O'Neill's 2016 paper<sup><a href='#ONeill2016'>[1]</a></sup> (#39). Differences between the lambda coefficients of the original and pyrolite implementations of the lambdas calculation were identified (thanks to Laura Miller for this one). With further investigation, it's likely the cost function passed to scipy.optimize.least_squares contained an error. This has been remedied, and the relevant pyrolite functions now by default should give values comparable to O'Neill (2016). As part of this, the reference composition ChondriteREE_ON was added to the reference database with the REE abundances presented in that paper..
  • Bugfix: Upgrades for pyrolite.geochem.transform.convert_chemistry to improve performance (#29). This bug appears to have resulted from caching the function calls to pyrolite.geochem.ind.simple_oxides, which is addressed with 18fede0.
  • Feature: Added the Whittaker and Muntus (1970)<sup><a href='#Whittaker'>[2]</a></sup> ionic radii for use in silicate geochemistry (#41), which can optionally be used with pyrolite.geochem.ind.get_ionic_radii using the source keyword argument (source='Whittaker'). Thanks to Charles Le Losq for the suggestion!
  • Bugfix: Removed an erroneous zero from the GLOSS reference composition (GLOSS_P2014 value for Pr).
  • Updated pyrolite.geochem.ind.REE to default to dropPm=True
  • Moved pyrolite.mineral.ions to pyrolite.geochem.ions

<sup>

<p> <a id="oneill2016">[1]</a>: O'Neill, H.S.C., 2016. The Smoothness and Shapes of Chondrite-normalized Rare Earth Element Patterns in Basalts. J Petrology 57, 1463–1508. doi: <a href="https://doi.org/10.1093/petrology/egw04">10.1093/petrology/egw047</a> </p>

<p> <a id="Whittaker">[2]</a>: Whittaker, E.J.W., Muntus, R., 1970. Ionic radii for use in geochemistry. Geochimica et Cosmochimica Acta 34, 945–956. doi: <a href="https://doi.org/10.1016/0016-7037(70)90077-3">10.1016/0016-7037(70)90077-3</a> </p> </sup>

pyrolite.mineral

  • Bugfix: Added the mineral database to MANIFEST.in to allow this to be installed with pyrolite (fixing a bug where this isn't present, identified by Kaarel Mand).

pyrolite.plot

  • Bugfix: Updated pyrolite.plot to use pandas.DataFrame.reindex over pandas.DataFrame.loc where indexes could include missing values to deal with #31.
  • Updated pyrolite.plot.spider.spider to accept logy keyword argument, defaulting to True

pyrolite.util

  • Broke down pyrolite.util.plot into submodules, and updated relevant imports. This will result in minimal changes to API usage where functions are imported explicitly.
  • Split out pyrolite.util.lambdas from pyrolite.util.math
  • Added a minimum figure dimension to pyrolite.util.plot.axes.init_axes to avoid having null-dimensions during automatic figure generation from empty datasets.
  • Added pyrolite.util.synthetic.example_spider_data to generate an example dataset for demonstrating spider diagrams and associated functions. This allowed detailed synthetic data generation for pyrolite.plot.pyroplot.spider and pyrolite.plot.pyroplot.REE plotting examples to be cut down significantly.
  • Removed unused submodule pyrolite.util.wfs

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