JEM Alligator Production Probability Model Change Log

• 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)

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

• Fix for grid artifacts in some locations across the output due to a problematic method of determining the input grid

index, which would lead to a duplication of the neighbor cell's calculated values

• Fix so that if an input grid cell has fill value, the output grid cell for that variable will also have fill value

• Fix for command line year range: make sure lower & upper years are valid and adjust as necessary, like UI does

• Further improved modeling time by reading input data in even more efficient chunks
• Fix for command line year range option being +1 year in the future

• Tree island heights file now optional; added selectors for CSV columns
• Gator holes file now optional; added selectors for CSV columns
• Percent Edge Habitat can now be disabled
• Automatically determine output file name
• Indicate which files are required on the UI & update layout slightly
• More descriptive errors when files are missing & better exception trapping

• Ensure parent folders of specified output file exist or can be created
• Change zip and extracted folder name for easier integration with headless scripting tools

• Bug fix: do not require salinity file to run the model

• Allow running on partial season data and to produce a subset of metrics when data are available
• Allow selection of NcML files for depth data
• Automatically convert units of input depth data (e.g. cm -> mm)
• Detect coordinate axes order for depth and salinity data (e.g. t,y,x vs. t,x,y)
• UI: Expand text controls for output parameters, remove tab folder
• Fix for date ranges: use closed interval instead of open interval

• Update to allow headless execution (see --headless --help)
• Improved modeling time by reading input data in more efficient chunks
• More granular reporting of modeling progress
• Fix for potential resource problems (files left open in the event of errors)
• Fix for "duplicate salinity" error when loading parameters file
• Fix for salinity file not resetting when loading from parameters file
• Fix for year range choice from user occasionally not being retained
• Fix for occasional errors when saving parameters file

• Added bug reporting capability (Help > Report Bug); integrated "Report Bug..." button to Eclipse error dialog
• Bug fix: inter year dates (breeding start to nest flooding end) are now hh:mm:ss adjusted to the

depth input dates. If an exact match between dates cannot be found during processing, a close

match is found and used

• More verbose logging in model processor:
• layer names & variable names;
• output variable names, types, and units;
• output spatial parameters, time parameter;
• dates read from depth file and salinity file (if provided);
• inter year dates used; inexact date matches logged;
• Log CDL of input depth file (http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/CDL-Syntax.html)

• Updated mean clutch top height equation in nest building component as requested by the modeler
• Bug fix: changed constant value in same clutch height equation from 25 cm to 42 cm to represent typical

height of clutch

• Fixed bug where gator holes spatial extent might extend beyond output grid extent, causing a nondescript error
• Fixed bug where model year range may not be set properly when loading from parameters file
• Allow salinity input file to be optional

• Updated to Eclipse 4 platform
• Update to NetCDF-Java 4.3
• Defer reading of output parameters from depth file until "Run" is clicked or requested by the user
• Fixed bug where output parameters were not being properly updated to the model before running
• Fixed bug where multiple dialogs were being displayed when model run completed

• Bug fix: do not require output file to exist before running

• Allow selection of data variable from NetCDF if default is not found

• Converted to cross-platform GUI application

• CLI application created