JEM Small Fish Density Model Change Log

• Add --psus-required option to CLI, which is enabled by default and requires all PSUs to map to input grid(s).

• Update for Java 11
• Move Software Requirements to README.txt file
• Update to supporting libraries that have been migrated to Java 11
• Add javax.annotation to dependencies
• Update org.eclipse.jdt.core.prefs and org.eclipse.jdt.ui.prefs for Java 11 and warn on missing javadocs for private visibility

• Library updates (some may not apply):
• edu.ucar.unidata.netcdf;bundle-version="5.3.3",
• gov.usgs.jem.cerp.netcdf;bundle-version="3.0.0",
• gov.usgs.jem.cerp.netcdf.ug;bundle-version="3.0.0",
• gov.usgs.jem.spatial.model;bundle-version="2.0.0",
• gov.usgs.jem.spatial.expressions;bundle-version="2.0.0",
• gov.usgs.jem.hydro.processing;bundle-version="2.0.0",
• gov.usgs.jem.netcdf.depthcreator.ui;bundle-version="2.0.0",
• gov.usgs.jem.netcdf.ncmlcreator.ui;bundle-version="2.0.0",
• gov.usgs.jem.thredds.ui;bundle-version="2.0.0"
• Attempt to resolve the majority of compiler warnings through a combination of mechanisms:
• refactor deprecated to current usage where possible, suppress deprecation otherwise;
• add javadocs in some cases, but suppress where documentation was largely ignored or code is not otherwise actively maintained;
• suppress or address other compiler warnings (e.g. resource; unused)

• com.google.auto.value;bundle-version="1.7.2"
• guava;bundle-version="29.0.0",
• org.geotools.plugin;bundle-version="23.0.0",
• edu.ucar.unidata.netcdf;bundle-version="5.1.0",
• gov.usgs.jem.cerp.netcdf;bundle-version="2.0.0",
• org.apache.commons.csv;bundle-version="1.8.0",
• gov.usgs.jem.spatial.model;bundle-version="1.4.0",
• gov.usgs.jem.hydro.processing;bundle-version="1.4.0"

• Removed invalid parameters (i.e regions: HOLEY,LO,PENN,PM) from modeling_parameters.xml file.

• Upgraded SQLite to latest version (v3.21.0) to fix issue on MacOS when running large / multiple input files

• Load button click shows user three choices:

1. NetCDFs Folder Scan: Allows the user to browse to a folder containing multiple NetCDF scenarios files.

2. NcMLs Folder Scan: Allows the user to browse to a folder containing multiple NcML files.

3. NetCDF Timeseries: Allows the user to select multiple NetCDF timeseries files. The application will create NcML file

from the selected timeseries NetCDF files (files ordered on time ranges).

• Allow users to add additional NetCDf or NcML files to table viewer without removing previously added files
• Preferences page includes text boxes to edit default file names of Modeling parameters file, Region shape file, and

PSU CSV file (requires restart for these changes to take effect).

• Help documentation is updated with three choices of load button and Preferences page text boxes
• Update to help documentation with invalid OutputFiles link in index html page
• Headless: Renamed "--input-folder" option to "--input-nc-folder"
• Headless: --input-file option now also accepts ncml file
• Headless: Added two new options
• --input-ncml-folder: Specify input folder containing multiple ncml files which the application will scan for.
• --input-timeseries-nc-files : Specify multiple NetCDF files from the same timeseries to create a new aggregated scenario

• Initial release of application
• Output includes:
• DSD & TOTFISH CSV files for PSUs
• TOTFISH change and % change (scenario - baseline) CSV files for PSUs
• DSD (change and % change, scenario - baseline) CSV files for regions
• TOTFISH (change and % change, scenario - baseline) CSV files for regions
• TOTFISH landscape average CSV files
• TOTFISH time series average CSV files
• DSD differences by region (scenario - baseline) time series charts
• TOTFISH, cumulative TOTFISH, and cumulative TOTFISH difference (scenario - baseline) time series charts
• TOTFISH temporal average, change, and % change (scenario - baseline) maps for PSUs