Version_fixes_and_updates_list.txt

=====Version 1.5 Full canine atrial code added
    22/01/2024  - Canine atrial model with integrated 0D ca handling has been implemented
                - Preparation for Zenodo and Gtihub release package
                - Documentation updated and publication-specific documentation added, including scripts for the most recent papers

=====Version 1.4 SRF read for reproducibility added, canine atrial model, and Auckland-humana atrial and fibrosis models
    24/11/2023  - Variables added for 1/dt as double and integer explicitly, to solve the incorrect iterations issue that occured in Windows (but not Linux and Mac). This should now be resolved. Please confirm if you are a Windows user.
                - Citations for network model and human atrial geometries from Auckland have been added to end-of-simulation outputs

    02/11/2023  - csv file format added for main outputs -> unncessary?? Are there softwares that actually need it? -> leave functions in outputs, but not implemented; users are welcome to implement if they wish. Simply change the function call where it outputs

    08/09/2023  - Arrays dependent on number of celltypes increased from size 20 to size 50

    07/09/2023  - Minimal model CCS variants for Whole heart basic simulations

    30/06/2023  - Auckland geos updated
                - new rat vent DTI geo Benson added for network model sims
    
    27/06/2023  - Tidy of tissue IF selection statements to avoid else if
                    - t->Tissue_settings_set  flag added
                - Maximum duration of SRF updated from 1000ms to 1500ms (this would be slowest wave allowed)
                    - if (srf->duration > 1500)   srf->duration = 1500; in Spontaneous_release_functions.cpp
                - Also minimum updated to assign to max, so that we don't get over-representation of short waves, as would happen if assigned to smallest
                    -  if (srf->duration < 20)     srf->duration = 1500

    20/06/2023  - Functionality to uncouple (electrically) physically-connected regions
                    - Add settings if wanted:
                        t->disconnect_regions_flag         = true;
                        t->Ndisconnected_regions           = 2; // region junctions really, as it is N pairs of regions to disconnect
                        t->disconnect_regions[0][0]        = x; // pair 1 region x to be uncoupled from region y
                        t->disconnect_regions[0][1]        = y; // pair 1 region y to be uncoupled from region x
                    - Function "Modify_neighbours_region_disconnect" added to lib/Tissue.cpp and called in both FDM tissue mains
                    - Additional clause added to network model create junctions function to make false if disconnected regions
                    - This functionality has been added to canine atria models to ensure PV and RA do not directly couple electrically

    19/06/2023  - AF remodelling for minimal RA model added
                - minimal RA model also updated to have a higher resting potential

    12/06/2023  - Functilnality to read in SRF from file added -> "SRF_Mode Read" now controls this
                    - Argument to set filename to read in "SRF_read_filename"
                    - Note: SRF properties output when read in may be slighlty different due to t_init, but none of those that affect the read will be different (all actual waveform parameters are the same)
                    - Default ARG value for SRF mode set, as main files use Arg rather that SRF mode to determine whether to read in
                - Tissue model "basic_small" added; tissue dimensions added to screen and file settings outputs
                - Default spatial outputs changed: now 1 ms for binary and 5 ms for vtk


=====Version 1.3 Canine atria full 3D model added
    01/04/2023  - Change to the way network model handles nodes without fibres
                    - now assigns all directions as fibre, so that it does not intoduce an artificial region of less coupling (assuming less coupling more arrhythmic than over coupling)
                    - fibreflag and output to screen that this has been done

    01/02/2023  - Tissue model for canine atria added
                - 0D canine atrial models added
                - Network connections for fibrosis in canine atria map added
                - Bug with Ca_cellular_het argument fixed


=====Version 1.2 Network model included, conduction velocity calculation improved, OS Compatability issues addressed
    18/10/2022 - Network model of tissue excitation included, associated with Tissue_native_network and Tissue_integrated_network
                    - New tissue state read/write functions added for network
                    - CV calculation has been improved based on curvature arguments
                    - New tissue models have been added - fibre vector field in 2D and 3D sheets 
                                                         - rat DTI three eigenvector 3D ventricle
                    - New arguments associated with the network model
                        - network connection maps
                        - symmetry factor
                    - Model types for network have been added to the bin to vtk tools (to identify correct output folders)
                - New tool to create heterogeneous network maps has been included
                - Output of three different fibre files added
                
    30/11/2022  - output files renamed from ".dat" to ".txt" for better portability with Windows
                - Main files now determine which OS is being used, and create folders/files differently for the different OS for compatability -> no need for different main files for Windows
                - Compile.bat file added to compile in Windows
                - Should now be fully compatible with Windows, Mac and Linux (other OS have not been considered)
                - *Intention to also optimise memory useage, but not been done yet* -> tried but it seemed to make no worthwhile difference


=====Version 1.1 Sub-cellular heterogeneity included, associated with Methods paper
    03/02/2021 - Extracellular concentrations added as run-time controllable parameters
	05/04/2020 - Functionality for sub-cellular heterogeneity and reading in maps added; documentation updated; "Sub_cellular_het_geometries" directory and single example map file added to "MSCSF_state_and_geometry_files"; example of using this added to Example_scripts/3D_cell; no 7 
    01/04/2020 - Arguments.c file updated to Windows format as default (works in all OS).


=====Version 1.0 Release.
    07/10/2019 - Fix:   In function "output_settings()", the order of variables Gleak and Gup was the incorrect way round relative to the text
    fprintf(so,"\t\t\t\tJup_scale  = %.02f || Jleak_scale = %.02f || || Jrel_scale = %0.2f\n\n", p.Gleak, p.Gup, p.Grel); 
    >>  fprintf(so,"\t\t\t\tJup_scale  = %.02f || Jleak_scale = %.02f || || Jrel_scale = %0.2f\n\n", p.Gup, p.Gleak, p.Grel);

    24/06/2019 - Documentation for installing the package on Windows computers has been included (thank you to Jakub Tomek for this implementation and associated documentation). This is provided ahead of a full version of the framework with included Visual Studio project files, which I intend to finish and upload soon.

    23/06/2019 - Fix:   Small issue with writing the settings file for all implementations other than single native, so it writes now to correct folder.
                        [E.g. output_settings_tissue(Sim, Tissue, directory) -> output_settings_tissue(Sim, Tissue, res_dir_full) in Tissue_native_main.cc and similar equivalents for all main files other than Single_cell_native.cc]

    20/06/2019 - Release version uploaded, with accompanying author revised version of the manuscript (currently under review at PLOS Comp. Biol).