Preparing files for version 2.2

CHANGELOG.md

@@ -1,6 +1,22 @@
 # Changelog
 
-All notable changes to this project will be documented in this file.
+All notable changes to this project are documented in this file.
+
+## [2.2] 20-Dec-2024
+
+### Added
+- **Stiffness coefficients parsing**: added to ability to parse stiffness coefficient information from `general_output.txt` using `zacrostools.parse_general_output_file`.
+- **Examples:**  
+  - **`DRM_on_PtHfC`**: Demonstrates how to analyze hundreds of output files to generate heatmaps.
+  - **`custom_lattice_models`**: Illustrates how to create custom lattice models for Zacros simulations..
+
+### Changed
+- **Analysis of output files:**  
+  - Renamed `window_percent` to `analysis_range` 
+  - Renamed `window_type` to `range_type`
+
+### Improved
+- **Documentation**: Improved the [ZacrosTools Documentation](https://zacrostools.readthedocs.io/en/latest/).
 
 ## [2.1] 27-Nov-2024
 
@@ -25,8 +41,6 @@ All notable changes to this project will be documented in this file.
 - **Docstrings**: updated all docstrings to adhere to the NumPy format for better clarity and consistency.
 - **Documentation**: Improved the [ZacrosTools Documentation](https://zacrostools.readthedocs.io/en/latest/).
 
-Full details are available in the [ZacrosTools CHANGELOG](https://github.com/hprats/ZacrosTools/blob/main/CHANGELOG.md).
-
 ## [1.3] 07-Nov-2024
 
 ### Added

docs/source/index.md

@@ -74,27 +74,20 @@ The ZacrosTools documentation is organized into the following sections:
 
 ## Recent changes
 
-### [2.1] 27-Nov-2024
-
-#### Added
-- **New classes and methods**: introduced the following classes, which can be instantiated from a Python dictionary, a Pandas DataFrame, or a `.csv` file:
-  - `GasModel`: information about gas-phase species. Methods available: `add_species` and `remove_species`. 
-  - `EnergeticsModel`: information about each cluster in the cluster expansion. Methods available: `add_cluster`, `remove_cluster` and `write_energetics_input`.
-  - `ReactionModel`: information about each elementary step. Methods available: `add_step`, `remove_steps` and `write_mechanism_input`.
-- **Automatic neighboring structure generation**: use a distance criteria between site to automatically create the neighboring structure for a custom lattice model. 
-- **Total pressure in heatmap axes**: the `total_pressure` parameter can now be selected for either the `x` or `y` axis in heatmap plots, enabling the creation of pressure vs temperature heatmaps.
-- **Continuous integration tests**: added a new test for GitHub Actions that generates all input files and compares them against reference files to ensure consistency.
-- **New parameters**: 
-  - `sig_figs_lattice`: added to `KMCModel.create_job_dir` to control the number of significant figures used when writing coordinates in `lattice_input.dat`.
-  - `show_max`: added to `plot_heatmap` to display a green 'x' marker at the point with the highest TOF. 
-
-#### Changed
-- **Building a `KMCModel`**: the `KMCModel` construction process now requires a `GasModel`, an `EnergeticsModel`, a `ReactionModel`, and a `LatticeModel`.
-
-#### Improved
-- **Output file parsing**: enhanced `parse_general_output` to support parsing `general_output.txt` files generated by Zacros version 2.x. 
-- **Parameter validation**: improved the parsing and validation of selected parameters across all modules to prevent errors. 
-- **Docstrings**: updated all docstrings to adhere to the NumPy format for better clarity and consistency.
+## [2.2] 20-Dec-2024
+
+### Added
+- **Stiffness coefficients parsing**: added to ability to parse stiffness coefficient information from `general_output.txt` using `zacrostools.parse_general_output_file`.
+- **Examples:**  
+  - **`DRM_on_PtHfC`**: Demonstrates how to analyze hundreds of output files to generate heatmaps.
+  - **`custom_lattice_models`**: Illustrates how to create custom lattice models for Zacros simulations..
+
+### Changed
+- **Analysis of output files:**  
+  - Renamed `window_percent` to `analysis_range` 
+  - Renamed `window_type` to `range_type`
+
+### Improved
 - **Documentation**: Improved the [ZacrosTools Documentation](https://zacrostools.readthedocs.io/en/latest/).
 
 Full details are available in the [ZacrosTools CHANGELOG](https://github.com/hprats/ZacrosTools/blob/main/CHANGELOG.md).

zacrostools/version.py

@@ -1 +1 @@
-__version__ = "2.1"
+__version__ = "2.2"