JEM Apple Snail Change log

• Relax grid overlap check between water and temperature to not require same starting x & y
• Allow water coordinates to drive output dataset footprint

• 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

• Set time variable as "unlimited" to fix errors like "Variable starting pos=3434677996 may not exceed 2147483647"

• 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)

• Javadocs, address compiler warnings, use primitives, general refactoring
• Remove IDataWriter & DataWriter, refactor to use CERP NetCDF library in AppleSnailProcessor
• Move AlleeFunctionType & AleeParameter to constants package
• Add NcVariable, NcVariableImpl, and NcVariables
• Add OutputNcVariable
• Summarize variable mins and maxes after processing
• Add "min", "max" attributes to output variables
• Add "title", "summary", "keywords" attributes to global attributes
• Log model parameterization (input files, variables, selected dates, output file, variables)
• Log output file header and run time after processing
• Add CLI option "--output-variables" to allow limiting output variables produced
• Fix potential bug when comparing cell sizes of hydro and temp datasets
• Add org.geotools.plugin;bundle-version="23.0.0"

• Fix bug (since 2.4.0) that caused eggPopulation and snailPopulationJuveniles to be 0

• 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",
• gov.usgs.jem.spatial.model;bundle-version="1.4.0",
• com.google.auto.value;bundle-version="1.7.2"

• Refactored the Parameters tab to use ExpandBar and Expand Items with a vertical scroll bar.
• Added a new Allee option to select which type of allee function to use, Hill (previous) or Log.

• Improved modeling time significantly by restructuring the way data are read, processed, and written
• Update UI to use list control for date selection instead of combo control
• Updated command line options with --date-range (remove --date-index-range) to specify YYYYMMDD lower and upper

bounds for model run

• Added fish mortality simulation and unit tests; New parameters: Dsd min water level, minimum days above water level,

and the fish mortality factor

• Minor folder structure change: moved the tests to its own test source folder.
• Added Reproduction delay to the UI
• Added Allee Factors to the UI and the reproduction simulation

• Headless: better model validation and setting of automatic defaults (variable names, output folder, date range)

• Update to allow headless execution (see --headless --help)
• Fixes for changes in NetCDF library and fill value
• Minor bug fix related to dates in NetCDFReaderModel
• Adjustment of kgrowth parameter default value from 0. 05 to 0.1
• Bug fix to survival equation in SurvivalSimulation
• Added the ability to have a negative date index to indicate the min / max of that index
• Include default parameters XML file

• Update to Eclipse 4 framework
• Update to NetCDF-Java 4.3

pre-1.0

• Initial release