Deprecating JAMS

Release includes all major routines ported from JAMS. It includes the remaining JAMS routines as a subpackage so that JAMS is now officially deprecated.

Major new routines are:

• Reading ASCII and Excel files, for example fsread and xlsxread.
• Meteorological functions such as saturated vapour pressure or conversions between relative, absolute, and specific humidity, for example esat and eair2rhair.
• Simple TKinter GUIs for choosing files and directories (if Tkinter is installed).
• Facilitating handling of netCDF files, for example ncread and module ncio.
• datetime module to handle non-CF-conform calendars such as Excel dates and decimal years., complementing the package cftime.
• Routines to update files in numpy's npz-format.
• Shuffled-Complex-Evolution algorithm for global optimization sce.
• Median absolute deviation test mad.
• Non-parametric kernel regression kernel_regression.

All (appropriate) routines can handle pandas.Series and pandas.Dataframe now.

Documentation moved from ReadTheDocs to Github: https://mcuntz.github.io/pyjams/.

Plotting and date

This release adds:

• date2date, which converts date representations between different regional variants.
• text2plot, routines to put text, signatures, and a), b), c), ... on plots
• int2roman and roman2int, converting integer to and from Roman literals.

It handles linebreaks better in LaTeX mode in Matplotlib. And adds pyjams_color.pdf as reference for all provided color palettes. Docstrings were further cleaned and improved.

Documentation uses now the Alabster scheme with a custom CSS file.

Color module

This release adds:

• color, a collection of color palettes and continuous color maps
• str2tex, converting strings to LaTeX strings
• position, which positions arrays of subplots to be used with Matplotlib's add_axes

It has several bug fixes (see CHANGELOG.rst).
It enhances the tests to have 100% coverage in most modules and functions. Some sections were excluded from coverage such as plotting and MPI sections.
Most docstrings were cleaned for correct presentation with sphinx.
It stills supports Python v3.6 with matplotlib v3.3.4.

New functions and initial commit to conda-forge

This release adds the functions:

• alpha_equ_h2o, isotopic fractionation between liquid water and vapour.
• alpha_kin_h2o, kinetic fractionation factors for molecular diffusion of water isotopologues.
• argmax, argmin and argsort for array_like and Python iterables.
• closest, which searches the closest element in an array.
• division, divides arrays dealing with zero in denominator.
• mcPlot, the standard plotting class of Matthias Cuntz.

The release also added pyjams to conda-forge.

Correct Zenodo metadata format

Yet a minor update fixing JSON format of Zenodo defaults file .zenodo.json again using relation names of https://developers.zenodo.org/.

Correct Zenodo metadata format

Minor update fixing JSON format of Zenodo defaults file .zenodo.json again.

Correct Zenodo metadata format

Minor update fixing JSON format of Zenodo defaults file .zenodo.json.

Automatic versioning and Zenodo update

• This release uses automatic versioning with setuptools_scm. The initial src/pyjams/version.py file was deleted.
• Zenodo defaults were edited to include a full suite of deposit metadata for any new releases.
• The correct DOI was updated in all documentation.
• The __all__ list now implemented in all __init__.py files in pyjams and subpackages. All __init__.py also import explicitly all functions from the individual modules now.

Initial release of pyjams on Github, PyPI, and Zenodo

pyjams is a general Python package offering miscellaneous functions in different categories, such as reading different file formats, Julian date routines, or calculating Elementary Effects. It has several subpackages offering constants or special functions, or objective functions to be used with scipy.optimize.

The package modernises and makes available routines of the JAMS Python library, which was created 2009 by Matthias Cuntz while at the Department of Computational Hydrosystems, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany, and continued while at Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Nancy, France.

The complete documentation of pyjams is available at:
http://pyjams.readthedocs.org/en/latest/