Pygaps

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3.1.0

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New features:

* pyGAPS is now capable of parsing to and from Adsorption Information Files
(AIF). For more info, see *Evans, Jack D., Volodymyr Bon, Irena Senkovska, and
Stefan Kaskel. ‘A Universal Standard Archive File for Adsorption Data’.
Langmuir, 2 April 2021, DOI: 10.1021/acs.langmuir.1c00122.*

3.0.0

------------------

New features:

* The internal Adsorbate list now contains over 170 analytes, 81 of which have a
correspondence in the thermodynamic backend. This includes multiple vapours,
VOCs, and refrigerants.
* Added new mode for pressure as "relative%", which represents relative pressure
as a percentage rather than a fraction (i.e. p/p0 * 100).
* Added two new modes for loading as "fraction" and "percent". This ties the
uptake to the same basis as the adsorbate (i.e. weight%, volume%, mol% or
fractions thereof).
* Conversely, NIST format isotherms based on "wt%" can also be converted.
* Significant improvements to the Horvath-Kawazoe methods of pore size
distribution, including more pore geometries (cylindrical and spherical
through the Saito-Foley and Cheng-Yang modifications) and the inclusion of
extended HK models, with the Cheng-Yang and Rege-Yang corrections.
* Command-line interface: a CLI entry point is automatically added during pyGAPS
installation and can be called with ``pygaps -h`` to perform some simple
commands.
* Isotherm JSON parser (``pygaps.isotherm_to_json``) now passes all extra
parameters to the ``json.dump`` function.
* Perform isotherm branch separation based on maximum pressure, rather than
first derivative. In such way, slight uncertainty in pressures won't lead to a
wrong assignment.
* The reference area for an alpha_s calculation can now be specified as either
"BET" or "Langmuir".
* Convenience function `isotherm.convert()` which combines all isotherm
conversion modes.
* Convenience function `pygaps.model_iso()` which fits a model to a
PointIsotherm, effectively wrapping `ModelIsotherm.from_pointisotherm`.
* Convenience functions for isotherm parsing: `isotherm.to_json()`,
`isotherm.to_csv()` and `isotherm.to_xl()`.
* Parsing from instrument output files now gets more information.
* Plot quality has been overall improved.
* Improved performance for isotherm conversions.
* General refactoring and speed-ups.
* Switched to GitHub actions for CI, now MacOS builds are also tested.

Breaking changes:

* Included Python 3.8 and deprecated Python 3.5.
* All parameters like ``adsorbate_basis`` or ``adsorbate_unit`` have been
changed to ``material_basis`` and ``material_unit`` for consistency. Old
format should still work for some time.
* Some model names have been changed to include only ASCII: ``JensenSeaton``,
``FHVST``, ``WVST``.
* For isotherm pressure/loading, a `limits` tuple is now passed instead of
`min_range` and `max_range`, as for other functions in pyGAPS.
* JSON ModelIsotherms now have ``name`` instead of ``model`` as the model name.
This is now consistent with both CSV and Excel.
* The `isotherm_to_jsonf` and `isotherm_from_jsonf` functions have been removed.
Functionality has been merged with `isotherm_to_json` similarly to the `pandas
model
<https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_json.html>`_.
* Removed the `util_get_file_paths` function.

Fixes:

* Volumetric -> molar conversions were not calculated correctly.
* Isosteric enthalpy could not be calculated if the isotherm was not in mmol/g.
* ModelIsotherm creation could in some cases ignore isotherm branch splitting.
* BET area now attempts to pick at least 3 points if physically consistent.
Should stop failing on some isotherms.
* BET/Langmuir area maximum calculation was offset by one point.
* The "section" returned in tplot/alphas is now consistent for both manual and
automatic limits: a list indices for selected points

2.0.2

------------------

New features:

* Added fluids to database: n-pentane, n-hexane, n-octane, o-xylene, m-xylene,
p-xylene, cyclohexane, hydrogen sulphide and sulphur hexafluoride.

Fixes:

* Converting Adsorbates to a dictionary now correctly outputs the list of
aliases.
* Changed stored critical point molar mass values for some adsorbates.

2.0.1

------------------

* Fixed error in dft kernel acquisition.
* Removed duplicate plot generation from virial initial henry.
* Fixed Appveyor testing.

2.0.0

------------------

Major pyGAPS release following peer review on related manuscript.
Several breaking changes with previous codebase, in particular
with basic isotherm parameters and module structure.
Several function names and parameters have changed as well.

Breaking changes:

* Renamed isotherm parameter `t_iso` to `temperature` for clarity.
* Renamed isotherm parameter `material_name` to `material`.
* Made `material_batch` an optional parameter.
* Renamed the `pytest.calculations` submodule to `pytest.characterisation`.
* Placed all isotherm models in a `pytest.modelling` submodule.

New features:

* The isotherm branches are now saved in the file representation (JSON, CSV,
Excel).
* Not specifying units now raises a warning.
* After attempting a model fit or guess for the creation of a ModelIsotherm, a
fit graph is now plotted alongside the data to be modelled.
* Added a new parameters named logy1 and logy2 to set the plotting vertical axes
to be logarithmic.
* To remove the legend now set the lgd_pos to None

* Pore size distribution improvements:

* Changed names of PSD functions to `psd_microporous`, `psd_mesoporous` and
`psd_dft`, respectively.
* Simplified functions for ease of use and understanding.
* Added cumulative pore volume to the return dictionary of all psd functions.
* Generalized Kelvin methods (psd_mesoporous) to other pore geometries, such
as slit and sphere.
* Added a new Kelvin function, the Kelvin Kruck-Jaroniec-Sayari correction
(use with `kelvin_function='Kelvin-KJS'`
* Corrected a conversion error in the DFT fitting routing.
* Changed HK dictionary name OxideIon(SF) -> 'AlSiOxideIon'
* Added a new HK dictionary 'AlPhOxideIon'

1.6.1

------------------

New features:

* Simplified the slope method for Henry's constant
calculation

Bugfixes:

* Ensured that model initial fitting guess cannot be
outside the bounds of the variables.

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