Ichthyop

New features

- Automatic compilation tests using GitHub actions
- Badges on README.md.
- New License to allow connections with Zenodo (GPL-3)
- Adding debugging stuff that saves W computed by Ichthyop and leaves program

Bug fixes

- Deactivate the `compile on save` Netbeans feature (compilation errors not always detected)
- Correction of a bug in the `TxtFileRelease` class. In 3.3.4, changes were made to insure that the output drifter dimension has the same size as the effectively released particles, but in fact the file has a 0 drifter dimension. Moved back to previous state, with the display of a warning message.

Bug fixes

- Correction in the reading of gdepT/gdepW in NemoDataset (use of `round` instead of `floor`)
- Possibility to use DEB length criterion for the RecruitmentAction (no more conflict with traditional growth actions like linear)
- Debugging the configuration update manager (work from resource stream rather than URL, which failed when running the jar file directly)

New features

- Adding NEMO in 2D
- Possibility to read Roms W field instead of computing it (not fully satisfying though)
- Nyctemeral migration not active if the target depth is below the local sea floor
- Moving to Maven Java system (easier compilation using `mvn -B package`).
- Adding possibility to run Ichthyop in map coordinates rather than in lon/lat (developped for polar application, Dennis Jongsomjit).
- Adding functional response to linear growth action (implies reading food variable if activated)

Bug fixes

- Correction in the calculation of W in NEMO dataset using divergence equation.

New features

- Taking into account partial steps in NEMO dataset.

Bug fixes:
Multi release events - Some particles were overwritten at new release event.
Mapping - The JVM would often crash (architecture and version dependant) when trying to retrieve map background though the computer is offline or behind a proxy. Created and offline tile factory.
Bactracking - Multi release event did not work in backward mode.

New features:
Dataset - Ichthyop can read Symphonie (http://sirocco.omp.obs-mip.fr/outils/Symphonie/Accueil/SymphoAccueil.htm) NetCDF output files.
Lethal temperature - Added a hot lethal temperature. Lethal temperatures (both cold and hot) can be provided as a function of particle age, in a CSV file.
Buoyancy - Egg density can be provided as a function of age, in a CSV file.

Bug fixes:
Configuration panel - Crashed at displaying a block with no visible parameter.
Backtracking - Used to crash for particles reaching the edge of the domain.
Backtracking - Did not work in batch neither SERIAL mode.
Backtracking - Time spans were incorrectly defined for KMZ export.
Backtracking - Multiple release events was not supported.
Zone editor - Ensured all floating numbers are dot-separated. Bathymetric mask was always enabled even though the checkbox was not selected.
Release particles - Application did not warn the user when attempting to release particles under the bottom or above the surface.
Dataset - Application used to throw an 'IOException, two many files opened' when working with many NetCDF input files.
OPA NEMO - computation of the vertical velocity was not correct. Now requires fields e3u_ps & e3v_ps.
Configuration menu - Save as button did not work.
Gregorian calendar - The time converter generated a 24h offset on leap years only.
ROMS Dataset - Wrong calculation of the NEW type of vertical coordinate.
Coastal advection -


New features:
Coastline behavior - Now there is a parameter to control coastal behavior. Particle might beach, bounce on the coastline as a billiard ball or just standstill.
Mars - Handles generalized sigma level (Mars V8).
Mars - Handles rotated domains (lon & lat as two dimensional fields).
WMS - Broaden the zoom range.
Recruitment stain - Look for recruited particles within an area defined by a central point and a radius.
NetCDF library updated to last version (4.2 April 2011)
Dataset - Added an option to deactivate a thorough and expensive sorting of the NetCDF input files when the files are already chronologically sorted.


Release notes for Ichthyop python

Run Ichthyop

Double click on the JAR file or run it from commmand line 'java -jar ichthyop-3.3.jar'

License information

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

For details about the GNU General Public License, please see http://www.gnu.org/licenses/

Description of files and folders

% Files
ichthyop-3.3.jar, java exectuable
readme.txt --> this document

% Directories
cfg --> Ichthyop configuration folder
lib --> Necessary libraries to run the program
input --> Basic NetCDF input files used for the examples