Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to a form of Semantic Versioning called Realistic (or Practical) Semantic Versioning.

0.0.6 (2025-09-10)

Added

• ccu.adsorption.sites.SiteFinder protocol and built-in implementations ccu.adsorption.sites.HubSpokeFinder and ccu.adsorption.sites.Triangulator

• module-level variables HUB_TAG, SPOKE_TAG, and SITE_TAG for SiteFinder implementations

• ccu.adsorption.orientation.AdsorptionCenter

• ccu.adsorption.orientation.CenterFactory and implementations com_centerer(), special_centerer(), atomic_centerer()

• ccu.adsorption.orientation.OrientationFactory implementations: Transformer and subclasses (OctahedralFactory)

• auto-annotation feature in ccu.fancyplots

• ccu.fancyplots._gui.annotation.auto_annotate()

• ccu.structure.geometry.align()

• ccu.structure.symmetry.Inversion

• ccu.structure.symmetry.Reflection

• ccu.structure.symmetry.Translation

• ccu.workflows: a subpackage containing computational workflows

  • ccu.workflows.infrared: infrared workflow

  • Users can now seed FancyPlots with free energies only using the --data CLI option

  • label keyword argument to ccu.workflows.calculation.run_calculation() function

• enable shell completion with ccu init

• allow users to supply a style file to ccu fed

• DEV: * clean command added to docs hatch environment * testing and test coverage split into separate commands test and test-cov

Changed

• Atoms objects created from ccu.adsorption.complexes.generate_complexes() have metadata describing the adsorbate, site, and orientation in addition to the structure

• Moved generate_figure to ccu.fancyplots.plotting

• bader module renamed to pop

• You can now pass the annotations parameter of ccu.fancyplots.plotting.generate_figure() as a list of appropriately typed tuples

• ccu.adsorption.adsorbatecomplex renamed to ccu.adsorption.complex

• ccu.adsorption.sitefinder renamed to ccu.adsorption.sites

• ccu.adsorption.adsorbateorientation renamed to ccu.adsorption.orientation

• AdsorbateOrientationFactory replaced with protocol, OrientationFactory

• ccu.adsorption.adsorbateorientation.AdsorbateOrientation replaced with ccu.structure.geometry.MolecularOrientation

• ccu.adsorption.adsorbates.ALL renamed to ccu.adsorption.adsorbates.ALL_ADSORBATES

• ccu.adsorption.complexes.AdsorbateComplexFactory:

  • constructor overhauled; see new signature/docstring for details

  • AdsorbateComplexFactory.next_complex replaced with AdsorbateComplexFactory.generate_complexes

  • removed: AdsorbateComplexFactory.adsorbate_orientations, AdsorbateComplexFactory.orient_adsorbate

  • AdsorbateComplexFactory.place_adsorbate no longer accepts the centre argument but instead accepts a site argument and shifts the asdorbate position by site position

  • structure is no longer an attribute but is passed as an argument to .generate_complexes and .place_adsorbate

• generate_complexes():

  • generate_complexes no longer saves the adsorption complexes to files; this can be accomplished using write_complexes(); accordingly, the destination argument was removed

  • a list of Atoms objects is returned instead of a list of tuples

  • special_centres argument removed and replaced with similar argument, centers

  • symmetric argument removed and replaced with similar argument, symmetry

  • The finder argument now accepts adherents to the SiteFinder protocol instead of strings (as a consequence, the vertical argument has been removed since these being returned is controlled by the finder)

  • adsorbate_tag argument has been added

• ccu.adsorption.adsorbates: the special centres key has been changed to special_centres

• documentation refactored (inspired by diataxis)

• expanded development guide to include dedicated sections for documentation and maintenance

• calculate_norm moved to ccu.structure.geometry

• CLI

  • CLI-related modules/packages have been privatized by appending leading underscores

  • ccu adsorb

    • ccu adsorption place-adsorbate command renamed to ccu adsorb

    • added --tag option to ccu adsorb

    • --special-centres option renamed to --centers and changed from flag option to value-accepting option

    • --symmetric option changed to on/off flag --no-symmetry/--symmetry

    • removed --vertical option

    • added --finder option

• ccu.structure.symmetry.SymmetryOperation removed and replaced with ccu.structure.symmetry.Transformation

• only annotations with text are added in FancyPlots

• GUI subpackage is now private ccu.fed._gui

Fixed

• FancyPlots

  • Fixed dashed lines in FED

  • AttributeError when setting title in ccu.fancyplots.plotting.format_primary_axes()

  • The format of the easter egg has been fixed

• Fix plotting transition states in ccu.fancyplots

• saving annotations in FancyPlots

• duplicate annotations are not added in FancyPlots

Removed

• AdsorbateComplex class

• AdsorbateOrientationFactory

• ccu.structure.symmetry.Symmetry and ccu.structure.symmetry.RotationSymmetry

• ccu.hubbard subpackage

0.0.5 (2024-06-11)

Added

• xlim and ylim

Fixed

• xscale and yscale were incorrectly used to set xlim and ylim, respectively

• Saving FancyPlots figures now works

• No more duplicate legend labels

• Tooltips are now visible

• Raised exception when trying to show graph when graph already showing

Removed

• .plotting.plot_solid_lines()

• .plotting.plot_dashed_lines()

0.0.4 (2024-06-06)

Added

• logging via a rotating file handler

Fixed

• fixed bug where the legend wasn’t rendered

• fixed bug in FancyPlots when incrementing number of pathways after defining the number of steps (see commit c188153d)

0.0.3 (2024-06-03)

Added

• ccu.fancyplots.validation: classes and functions for validating user input

• tooltip.Tooltip: a robust tooltip class

• .gui.root.Windows: TypedDict containing all FancyPlots subwindows

• .gui.root.Sections: TypedDict containing the immediate subframes of a FancyPlots appliction

• ccu.fancyplots.data: data models for importing/exporting FancyPlots data

  • ccu.fancyplots.data.FancyCache: simplified interface for importing data into and exporting data from FancyPlots

• ccu.fancyplots.gui.annotation: GUI elements for the annotation section

• ccu.fancyplots.gui.energy: GUI elements for the free energy declaration window

• ccu.fancyplots.gui.formatting: GUI elements for the formatting parameters section

• ccu.fancyplots.gui.frames: custom GUI elements with built-in validation and custom event generation (<<Validation>>)

• ccu.fancyplots.gui.instructions: GUI elements for displaying instructions

• ccu.fancyplots.gui.mechanism: GUI elements for defining reaction mechanisms

• ccu.fancyplots.gui.palette: GUI elements for displaying the matplotlib colour palette

• ccu.fancyplots.styles: custom Tkinter styles for themed widgets

• ccu.fancyplots.gui.utils.open_image(): open Tkinter-compatible image

• ccu.fancyplots.gui.utils.print_easter_egg(): print Easter egg

• ccu.fancyplots.validation: lightweight, Pydantic-like validation from type-hints

• ccu adsorption place-adsorbate: --list CLI option

• ccu.thermo.chempot.ChemPotDatabase: database of chemical potential parametrization data

• ccu.thermo.chempot.ChemPotCalculator: class encapsulating chemical potential calculation logic

• logging and terminal printing control for all CLI commands via ccu --log-level, ccu-thermo-gibbs --log-file, ccu --verbose, and ccu --quiet CLI options that can be passed alongside any subcommand options

• ccu.cli.utils: utilities for CLI commands

Changed

• FancyPlots re-written with ttk

• .root.FancyPlotsGUI replaces Root

• ~ccu.fancyplots.gui.root.FancyPlotsGUI refactored to encompass all GUI elements as children

• redefined as ~tkinter.ttk.LabelFrame or ~tkinter.Frame subclasses

  • ccu.fancyplots.gui.annotation.AnnotationSection

  • ccu.fancyplots.gui.footer.FooterSection

• redefined as ~tkinter.Toplevel subclasses

  • ccu.fancyplots.gui.energy.EnergyWindow

  • ccu.fancyplots.gui.fed.FreeEnergyDiagram

• ccu.fancyplots.gui.menu.make_textmenu() renamed to ccu.fancyplots.gui.menu.create_edit_menu()

• ccu.fancyplots.gui.menu.show_textmenu() renamed to ccu.fancyplots.gui.menu.show_edit_menu() and re-written as factory

• ccu.fancyplots.gui.fancyplots renamed to ccu.fancyplots.gui.plotting

  • functions no longer depend on global variables

  • main function (init) renamed to ccu.fancyplots.gui.plotting.generate_figure()

• ccu.fancyplots.gui.utils.mouse_coordinates moved to instance method ccu.fancyplots.gui.fed.FreeEnergyDiagram.mouse_coordinates()

• ccu thermo chempot-calculator refactored and renamed to ccu thermo chempot; parametrized data moved to resource; CLI options added for molecule, temperature and pressure

Removed

• .tooltip.ToolTip: use ccu.fancyplots.gui.tooltip.Tooltip

• ccu.fancyplots.gui.defaults: use ccu.fancyplots.data instead

• ccu.fancyplots.gui.utils

  • .add_path

  • .add_text_converter

  • .convert_path_to_list

  • .get_path

  • .obtain_boxsizes

• ccu-thermo-gibbs --verbose and ccu-bader-sum --verbose (use ccu --verbose instead; e.g., ccu --verbose thermo gibbs)

• Reordering steps in FancyPlots is temporarily removed until further notice

0.0.2 (2024-05-23)

Added

• Changelog descriptions for release 0.0.1.

• ccu structure permute: create permutations of atoms within a structure

• ccu fed: a GUI utility for creating free energy diagrams

• ccu adsorption place-adsorbate now includes additional intermediates

• ccu bader: CLI utility for Bader charge analysis

• ccu.hubbard: calculation of Hubbard U parameter by the linear response method of M. Cococcioni and S. de Gironcoli, Phys. Rev. B 71, 035105 (2005).

• ccu.relaxation: standard function for running DFT calculation with ASE

• ccu.thermo: CLI utility and Python API for thermochemistry

Changed

• Format changelog in Keep a Changelog style.

• Testing with Tox to Nox

• Drop pylint for Ruff + Mypy

• .sitefinder.MOFSiteFinder no longer includes between-linker sites by default, pass between_linkers=True to obtain previous behaviour

0.0.1 (2023-06-22)

Added

• First release on PyPI.

• Created ccu.adsorption and ccu.structure subpackages and unit tests