0.3.0

0.3.0 Changelog

• New Contributor: Lucy Mathieson
• Continuous Integration has been migrated from Travis to GitHub Actions.
• Added an environment.yml file for development environment consistency.
• Removed some tests dependent on xlrd due to external issues with reading .xls and .xlsx files with some OS-Python version combinations.
• Fixed some broken documentation links.
• Added psutil to requirements.

pyrolite.plot

• Bugfix: Fixed a bug where there scatter and line arguments would conflict for spider (#46). To address this, spider and related functions will now accept the keyword arguments line_kw and scatter_kw to explicitly configure the scatter and line aspects of the spider plot - enabling finer customization. An extra example has been added to the docs to illustrate the use of these parameters. Thanks go to Lucy Mathieson for raising this one!
• Added the set_ticks keyword argument to spider and associated functions, allowing ticks to be optionally set (set_ticks=False if you don't want to set the x-ticks).
• Updated pyrolite.plot.color.process_color to better handle colour mapping and added examples illustrating this. You can also now use RGBA colours when using the color_mappings keyword argument.
• Updated automated pyrolite matplotlib style export to be more reliable.* Changed the default shading for density to suppress error about upcoming matplotlib depreciation.
• Ordering for contours, contour names and contour styles is now preserved for density and related functions.
• Updated pyrolite.plot.templates.pearce to use ratios from Sun & McDonough (1989), as in the Pearce (2008) paper.

pyrolite.geochem

• Bugfix: Fixed a bug where Eu was unnecessarily excluded from the lambda_lnREE fit in all cases.
• Bugfix: Fixed a bug where ratio-based normalisation was not implemented for get_ratio and related functions (#34).
• Added a local variable to pyrolite.geochem.ind to allow referencing of indexing functions (e.g. by_incompatibility) by name, allowing easier integration with :func:~pyrolite.plot.pyroplot.spider.
• Added by_number for indexing a set of elements by atomic number.

pyrolite.comp

• Updated the docstring for pyrolite.comp.impute.EMCOMP.
• Minor updates for pyrolite.comp.codata labelling, and reflected changes in pyrolite.util.skl.transform. Issues were identified where the column name 'S' appears, and a workaround has been put in place for now.

pyrolite.util

• Expanded pyrolite.util.lambdas to allow fitting of tetrad functions, anomalies and estimation of parameter uncertainties for all three algorithms.
• Added pyrolite.util.resampling for weighted spatiotemporal bootstrap resampling and estimation, together with added a number of updates to pyrolite.util.spatial to provide required spatial-similarity functionality.
• Updated the geological timescale in pyrolite.util.time to use the 2020/03 version of the International Chronostratigraphic Chart (#45).
• Added alphalabel_subplots for automatic alphabetic labelling of subplots (e.g. for a manuscript figure).
• Fixed an low-precision integer rollover issue in a combinatorial calculation for pyrolite.util.missing by increasing precision to 64-bit integers.
• Added example_patterns_from_parameters to work with pyrolite.util.lambdas and generate synthetic REE patterns based on
  lambda and/or tetrad-parameterised curves.
• Moved get_centroid from pyrolite.util.classification to pyrolite.util.plot.helpers
• Made a small change to density to allow passing contour labels as a list.
• mappable_from_values will not accept a norm keyword argument, allowing use of colormap normalisers like matplotlib.colors.Normalize. This function was also updated to better handle Series objects.
• Fixed a small bug for TAS instantiation which didn't allow passing the variables to be used from a pandas.DataFrame. If you have different variable names, you can now pass them as a list with the axes keyword argument (e.g. TAS(axes=['sio2', 'alkali'])).
• Homogenised logging throughout the package - now all managed through pyrolite.util.log. The debugging and logging streaming function
  stream_log can now also be accessed here (pyrolite.util.log.stream_log).