Hi ALl!
opened 02:43AM - 17 Dec 19 UTC
closed 05:23PM - 28 Feb 20 UTC
0/presubmission
Submission Requested
Submitting Author: Morgan J. Williams (@morganjwilliams)
Package Name: pyroli… te
One-Line Description of Package: A set of tools for getting the most from your geochemical data.
Repository Link (if existing): https://github.com/morganjwilliams/pyrolite
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## Description
- Include a brief paragraph describing what your package does:
pyrolite provides tools for munging, transforming and visualising geochemical data from common tabular formats. It enables you to recalculate and rescale whole-rock and mineral compositions, perform compositional statistics and create appropriate visualisations and also includes numerous specific utilities (e.g. a geological timescale).
## Scope
- Please indicate which [category or categories](https://pyopensci.github.io/dev_guide/peer_review/peer_review_proc.html#aims-and-scope) this package falls under:
- [ ] Data retrieval
- [ ] Data extraction
- [x] Data munging
- [ ] Data deposition
- [x] Data visualization
- [x] Reproducibility
- [ ] Geospatial
- [ ] Education
- [x] Unsure/Other (explain below)
- Explain how the and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of:
pyrolite leverages Pandas to enable import, munging and transformation of geochemical data from standard tabular formats, and matplotlib to facilitate common (and some less common) geochemical visualisations. One of the principal project aims is assisting to improve the reproducibility of geochemical research (especially for data-processing steps which often are overlooked or undocumented).
With regards to education, pyrolite is well suited to being incorporated into university-level geochemistry and petrology classes which wish to teach a little Python. The documentation is continually evolving, and more examples and tutorials will gradually be added. It isn't a principal aim of the project, however.
- Who is the target audience and what are scientific applications of this package?
pyrolite is targeted towards geochemists and geoscientists who use geochemical data (chemistry, mineralogy and relevant properties), especially those using lithogeochemistry. pyrolite has been developed principally to enable more reproducible data import, munging, transformation and visualization for geochemical data. In addition to this, pyrolite:
* Encourages better practices throughout these processes, including the use of compositional statistics (i.e. log-transforms).
* Implements some common geochemical models and methods to make these easily accessible and reusable (e.g. lattice strain models, orthogonal polynomial decomposition of Rare Earth Element patterns - 'lambdas').
* Contains a small database of rock forming minerals for normative calculations and looking up mineral formulae.
Extensions beyond the core package are also being developed for specific applications or interfaces (e.g. to alphaMELTS).
- Are there other Python packages that accomplish the same thing? If so, how does yours differ?
There is at least one other Python package which has some minor overlap for visualisations (GeoPyTool, which has a GUI-focused interface), but generally there are few open source Python packages for geochemistry (especially on PyPI). pyrolite provides some broader functionality (for both plotting and handling geochemistry) and is designed to be used from an editor or terminal and encourage geoscientists to further develop transferable Python skills. Where practical, the APIs for the tools on which it is built are exposed (e.g. pandas, matplotlib and sklearn).
- Any other questions or issues we should be aware of?:
**P.S.** *Have feedback/comments about our review process? Leave a comment [here](https://github.com/pyOpenSci/governance/issues/8)*
If anyone is interested in reviewing or serving as editor also please let me know! (assuming morgan will submit it for formal review)