Changelog#

4.5.0 (2023-06-20)

  • Added a new function that calculates the enthalpy of adsorption using a method proposed by Whittaker et al in pygaps.characterisation.enth_sorp_whittaker. Thanks to L Scott Blankenship for contribution!

  • Updated AIF parser to latest version. Thanks to Jack Evans for contribution.

  • Refactored DR/DA calculations.

  • Docs updating to fix issue #42

  • Added data types to excel output parsing to fix edge cases where these were not correctly parsed.

  • Testing correctly on Python 3.11.

  • Fixed various accumulating issues and bugs and deprecations.

4.4.0 (2022-09-03)#

4.3.0 (2022-08-27)#

  • AIF can read/write all isotherm types (models/points). Also further improved parsing of units and metadata.

  • Quantachrome txt files are now fully parseable

  • Isotherm data can now be other things beside numbers.

  • Added two standard isotherms (silica+carbon black). Can be used in thickness calculations.

4.2.0 (2022-06-29)#

  • Better error handling of nonphysical mesoporous PSD models

  • CLI now prints package version with --version argument

4.1.1 (2022-03-10)#

Fixes:

  • AIF file export now more reliable with custom properties

  • Isotherm models correctly instantiate their variables (parameters would otherwise be shared between instances)

4.1.0 (2022-03-02)#

New features:

  • 🐍 Minimum python reduced to 3.6 to increase compatibility.

  • 🎆 pyGAPS is now (actually) on conda-forge.

4.0.0 (2022-02-23)#

New features:

  • ⚠️ To reduce import bloat pyGAPS is now modular. Previously global functions must be accessed through submodules. For example: pygaps.area_BET now must be imported from pygaps.characterisation.area_BET.

  • 🎆 pyGAPS is now on conda-forge

  • Volumetric adsorbed amount is now given in either volume_gas or volume_liquid basis, corresponding to the volume amount the adsorbate would occupy in the bulk gas phase, or the volume of an ideal liquid phase of adsorbate (at isotherm temperature). The old loading_basis of volume is deprecated and automatically converted to volume_gas while emitting a warning.

  • Manufacturer parsing is streamlined with the introduction of the pygaps.parsing.isotherm_from_commercial function.

  • Drastically improved reliability and modularity of code in preparation for the release of the pyGAPS-gui interface.

  • Added a "zero" thickness model that assumes no mono/multilayer sorption. Useful in the case of condensation in hydrophobic materials.

  • Better documentation.

Changes:

  • ⚠️ Minimum python is now 3.7, maximum increased to 3.10.

  • Removed the need to pass DataFrame column names with the other_keys syntax. PointIsotherms, now save all passed DataFrame columns.

  • Smart assigning of isotherm metadata caused confusion and was removed. Metadata assigned like isotherm.myparam is now no longer serialized to dictionaries, parsers etc. Instead, isotherms have a isotherm.properties dictionary which contains all metadata.

  • Adsorption/desorption branches are internally represented as 0 and 1 instead of False/True. This allows the possibility for further cycles to be introduced in a future release.

  • Isotherm material and adsorbate are now always instantiated as pygaps.Material and pygaps.Adsorbate classes.

Plus many small and large bugs fixed.

3.1.0 (2021-04-22)#

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 (2021-03-14)#

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.

  • 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 (2019-12-18)#

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 (2019-07-08)#

  • Fixed error in dft kernel acquisition.

  • Removed duplicate plot generation from virial initial henry.

  • Fixed Appveyor testing.

2.0.0 (2019-07-08)#

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 (2019-05-09)#

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.

1.6.0 (2019-05-08)#

New features:

  • Added a function to get isotherms from the NIST ISODB, pygaps.load_nist_isotherm which takes the ISODB filename as an argument.

  • Added hexane as an adsorbate in the database.

  • Isotherm adsorbate is now a pygaps.Adsorbate object and can be accessed directly for all attributes (only when available in the internal database, otherwise still a string).

  • ModelIsotherms can now be saved and imported from JSON, CSV and Excel.

  • Added a marker option to the plot_iso function which acts similar to the color parameter and allows simple selection of the marker style.

  • Added three new isotherm models: Freundlich, Dubinin-Radushkevich and Dubinin-Astakov. They can be used for fitting by specifying Freundlich, DR or DA as the model, respectively.

  • Faster performance of some models due to analytical calculations, as well as more thorough testing

  • Isotherm modelling backend is now more robust.

  • Added an isotherm plot function to plot an individual isotherm.

  • Added functions to import and export JSON files directly from a file: isotherm_from_jsonf and isotherm_to_jsonf.

  • Added github issue templates.

  • Removed some plotting styles.

Breaking changes:

  • Deprecated and removed the MADIREL excel format.

  • Renamed isosteric_heat functions as isosteric_enthalpy for more correct nomenclature.

  • Some model parameters have been renamed for consistency.

Bugfixes:

  • REFPROP backend now correctly accessible (it was previously impossible to activate).

  • Fixed issue in excel import which could lead to incorrect import.

  • Some of the adsorbate values in the database were incorrect. They have been now updated.

  • Fixed secondary data not being automatically plotted when print_info called.

1.5.0 (2019-03-12)#

New features:

  • Increased number of adsorbates available in pyGAPS to 40.

  • New material characterisation functions: Dubinin-Radushkevich (dr_plot) and Dubinin-Astakov (da_plot) plots.

  • Added a new way to create an isotherm, from an two arrays of pressure and loading (the old DataFrame method is still valid but changed: check breaking changes).

  • Made adsorbates searchable by a list of aliases rather than a single name.

  • Exposed the CoolProp backend on adsorbate objects for convenience, it is accessible through the adsorbate.backend property.

  • Streamlined the internal database functions.

  • Updated NIST json import to new format. Cannot import multicomponent isotherms.

  • Functions which generate matplotlib graphs now can take an Ax as parameter (similar to behaviour of pandas) to plot on existing figures.

  • Changed behaviour of ModelIsotherm.guess function to accept a list of models to attempt to guess for.

  • Added b-spline smoothing to output of dft fitting.

Breaking changes:

  • The Sample class is now renamed as Material.

  • Isotherm creation parameters have changed from 'sample_name', 'sample_batch' and 't_exp' to 'material_name', 'material_batch' and 't_iso'.

  • Backend database has been simplified. Many required fields are no longer present and left to the discretion of the user.

  • Several database functions have been renamed. All functions switched: 'sample' -> 'material' and 'experiment' -> 'isotherm'.

  • When passing a DataFrame for isotherm creation, it now has to be specified as the parameter 'isotherm_data'.

  • Isotherm unique ID is now generated on the fly (previously generated at each isotherm modification). It also now takes into account only the required parameters for each isotherm ( 'sample_name', 'sample_batch', 't_exp' and 'adsorbate') as well as the model name, if the isotherm is a ModelIsotherm.

  • Renamed Adsorbate.from_list() method to Adsorbate.find()

Bugfixes:

  • Fixed issue in CSV import which read all values as strings (instead of floats/bools)

  • Fixed an issue with Excel import of bools, as they were previously read as 1/0

  • Fixed a bug where the automatic branch detection was not working when the DataFrame passed had a non-standard index.

  • Fixed not being able to call _repr_ on an isotherm.

1.4.0 (2018-11-10)#

New features:

  • Added the GAB isotherm model

Bugfixes:

  • Improved pore size distribution calculations to display cumulative pore volume when called.

  • Fixed the "all-nol" selection parameter for legend display in isotherm graphs.

1.3.0 (2018-08-13)#

New features:

  • Added an excel import which can take Micromeritics or Belsorp report (.xls) files. Micromeritics code was taken from the official python repo.

  • Added an import option which can read and import Belsorp data (.DAT) files.

  • Improved plotting functions to allow for more customisation over how the graph looks.

  • The extra arguments to print_info() are now passed to the plotting function allowing for styles such as #8.

Breaking changes:

  • The unique isotherm ID is now generated only on a small subset of properties instead of all isotherm properties.

  • The isotherm 'other_properties' subdictionary has been removed. Instead, all isotherm properties are now direct members of the class.

  • When plotting, isotherm branches are now defined as 'ads', 'des' 'all' (both branches) and 'all-nol' (both branches without legend entry) instead of a list of branches.

  • Plot types are now universal. Any property can be plotted against any other property by specifying the x_data, y1_data and y2_data.

Bugfixes:

  • Fixed 'source' not being recognised as an isotherm field

  • Re-worked plot_iso color selection to avoid errors (#10)

  • Re-worked plot_isp legend placement to ensure no overlap

  • Added correct common name for ethylene, propylene, methanol and ethanol in the database

  • Renamed some model parameters for consistency

  • A lot of typo fixes

1.2.0 (2018-02-19)#

New features:

  • The plotting legend now works with any isotherm attribute specified

  • Changed model parent class to print out model name when displayed

  • Added Toth and Jensen-Seaton models to the IAST calculation (spreading pressure is computed numerically using scipy.integrate.quad, #7)

Bugfixes:

  • Fixed an issue where the returned IAST selectivity v pressure data would not include all pressures

  • Changed sqlite retrieval order to improve performance (#2)

  • Fixed an error where IAST vle data was plotted opposite to the graph axes

  • Fixed a mistake in the Jensen-Seaton equation

  • Fixed a mistake in the FH-VST equation

1.1.1 (2018-02-11)#

New features:

  • Allowed for branch selection for isosteric heat and fixed an error where this was an issue (#3)

Bugfixes:

  • Fixed an issue when plotting isotherms with and without secondary data simultaneously

  • Fixed error with magnitude of polarizability of adsorbate from database in microporous PSD

1.1.0 (2018-01-24)#

  • Automatic travis deployment to PyPI

  • Improved enthalpy modelling for initial enthalpy determination

  • Improved documentation

1.0.1 (2018-01-08)#

  • Fixed wrong value of polarizability for nitrogen in database

  • Added a check for initial enthalpy when the isotherm is measured in supercritical mode

1.0.0 (2018-01-01)#

  • Improved unit management by adding a unit/basis for both the adsorbent (ex: amount adsorbed per g, kg or cm3 of material are all valid) and loading (ex: mmol, g, kg of gas adsorbed per amount of material are all valid)

  • Separated isotherm models so that they can now be easily created by the used.

  • Added new isotherm models: Toth, Jensen-Seaton, W-VST, FH-VST.

  • Made creation of classes (Adsorbate/Sample/Isotherms) more intuitive.

  • Many small fixes and improvements

0.9.3 (2017-10-24)#

  • Added unit_adsorbate and basis_loading as parameters for an isotherm, although they currently do not have any influence on data processing

0.9.2 (2017-10-24)#

  • Slightly changed json format for efficiency

0.9.1 (2017-10-23)#

  • Better examples

  • Small fixes and improvements

0.9.0 (2017-10-20)#

  • Code is now in mostly working state.

  • Manual and reference are built.

0.1.0 (2017-07-27)#

  • First release on PyPI.