Recent Releases of casal2
casal2 - Casal2 v25.06
Casal2 Version 2025.06 (June) is a quality and bug fix release. This releases focuses on two major outcomes. 1. Implementing unit tests for all missing scientific code. All processes, observations etc now have at least one unit test. 2. Improving the way the user configuration is validated. A whole new validation system has been implemented that allows for declarative validation instead of functional. This ensures the code is more consistent and gaps in validation are easily identified and fixed. For example, You can just use myParameter->GreaterThanOrEqualTo(PARAM_OTHER) now instead of manually loading and doing the comparison. This extended to tables now as well which has resulted in a reduction of approximately 75% in the Observation validation code.
Breaking Changes: This version of Casal2 introduces one breaking change. When defining selectivities on an observation you must provide at least one selectivity label per category, including categories that have been combined. For example, defining categories male+female will require two selectivities instead of one. This has been introduced to standardise behaviour across the entire Casal2 platform.
Functional Fixes: 1. FIX: AddressableTransformation.Orthogonal had calculation error with restoring transform 2. FIX: Corrected the allowed likelihood types in Observation.Proportionsbycategory to Binomial 3. FIX: alpha parameter removed from Selecitivites.Compoundall as it's not used 4. FIX: alpha parameter removed from Selecitivites.Compoundleft as it's not used 5. FIX: alpha parameter removed from Selecitivites.Compoundmiddle as it's not used 6. FIX: alpha parameter removed from Selecitivites.Compoundright as it's not used 7. FIX: Selectivities.DoubleNormalPlateau correctly validates Beta in length models now 8. FIX: Process.Maturation was using 0 for non-specified years and projections instead of final year 9. CHG: Process.Maturation now has new parameters to ensure behaviour is known (MISSINGYEARSMETHOD, PROJECTIONYEARSMETHOD) 10. CHG: Process.Maturation missingyearsmethod defaults to error, will error if user doesn't provide all years 11. CHG: Process.Maturation now has zero or final years values for projectionyearsmethod and missingyearsmethod 12. FIX: AgeingError.Normal was not correctly applying k to the last row of the matrix resulting on only half-row being set to 0.0 13. FIX: AgeingError.OffByone was not correctly applying k to the last row of the matrix resulting on only half-row being set to 0.0 14. FIX: Length process Recruitment Beverton Holt has typos for initialmeanlength and initiallengthcv 15. FIX: GrowthIncrements was using the bitwise (&) instead of logical (&&) when checking for lengthplusgroup. 16. FIX: Timevarying.AnnualShift was over-writing the addressable parameter value, not shifting it. 17. CHG: TimeVarying.Linear has been disabled because it's very broken. 18. CHG: TimeVarying.RandomWalk has been disabld because it's very broken. 19. FIX: Process.Mortality.InitialisationEventBiomass wasn't doing any mortality as it wasn't finished. Fixed 20. CHG: Anywhere a selectivity could be defined with something other than selectivities (e.g. relativembyage) now also supports using selectivities keyword via a new parameter alias feature. 21. FIX: #426 - Observations Age.ProportionsAtLength and others now have correct selectivity iteration 22. FIX: Observations Age.TagRecaptureByAge, Age.ProportionsByCategory and Age.ProportionsByCategoryByLength now have correct category iterations with doing the comparisons. 23. FIX: Observations.Length.TagRecaptureByLengthForGrowth was ignoring user supplied process_error
General Improvements:
- FIX: Build system now works with Python 3.12+
- FIX: Github actions deprecated functions have been updated.
- FIX: Checking for correct values in Likelihood.Bernoulli to prevent calculation errors.
- FIX: Added better parameter validation in AddressableTransformations to prevent undefined behaviour.
- FIX: Optimised the MortalityDiseaseRate processes because they were calculating too much.
- ADD: The parameter system now has a new validation system to standardise parameter validation.
- ADD: The parameter system now has a new table validation system to standardise table validation.
- DEL: The documentation builder no longer scrapes the code for syntax building, this was obsolete.
- ADD: New TwoSexComplex test case model for better unit testing coverage
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Published by Zaita about 1 year ago
casal2 - Casal2 24.06
This release contains a bunch of improvements and bug fixes for Casal2.
- The user manual has been updated for both Age and Length variants.
- A large number of basic code improvements, error handling and user messages have been updated.
- Building Casal2 and associated documentation has been fixed.
- GitHub Actions have been fixed.
- A new writing your first model tutorial is now available at: https://casal2.readthedocs.io/en/latest/
- Contributor guides, github.io pages etc have all been updated.
- README has been updated.
- Broken unit tests and builds on various Linux platforms and compilers have been fixed.
- Casal2 now supports multiple input configuration files with the -c command like argument
- Added sqrt transformations to manual
- Added mortality constant exploitation process
- Implemented double tag loss
- Added disease mortaloty as an age model process
- Added constant difference parameter transformation
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Published by Zaita about 2 years ago
casal2 - Production release 2022-10
This version of Casal2 was built from the main development branch on 2022-10-10.
Model output will include "Version: v22.10".
Windows files (built on Windows Server 2019): Casal2-Windows-build.zip Debian/Ubuntu Linux files (built on Ubuntu 20.04): Casal2-Linux-build.zip Older Linux files (built on CentOS 7.9): Casal2.tar.gz
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Published by NIWAFisheriesModelling almost 4 years ago
casal2 - Production release 2022-08
Release notes are available on the Casal2 GitHub webpages.
This version of Casal2 was built from the main development branch on 2022-08-31.
Model output will include "Version: v22.08 (2022-08-31)".
Windows files (built on Windows Server 2019): Casal2-Windows-build.zip Debian/Ubuntu Linux files (built on Ubuntu 20.04): Casal2-Linux-build.zip Older Linux files (built on CentOS 7.9): Casal2.tar.gz
What's Changed
- Length based model 202204 by @Craig44 in https://github.com/NIWAFisheriesModelling/CASAL2/pull/386
- Sim casal2 202206 by @Craig44 in https://github.com/NIWAFisheriesModelling/CASAL2/pull/394
- Age size observation 202206 by @Craig44 in https://github.com/NIWAFisheriesModelling/CASAL2/pull/397
- ADD fishing mortality process, plus improvements 202207 by @Craig44 in https://github.com/NIWAFisheriesModelling/CASAL2/pull/400
- Recruitment ycs syntax change 202208 by @Craig44 in https://github.com/NIWAFisheriesModelling/CASAL2/pull/404
Full Changelog: https://github.com/NIWAFisheriesModelling/CASAL2/compare/v21.11...v22.08
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Published by NIWAFisheriesModelling almost 4 years ago
casal2 - Development release 2022-07
This version of Casal2 was built from the main development branch on 2022-07-28.
Model output will include "Version: v22.07".
Windows files (built on Windows Server 2019): Casal2-Windows-build.zip Debian/Ubuntu Linux files (built on Ubuntu 20.04): Casal2-Linux-build.zip Older Linux files (built on CentOS 7.9): Casal2.tar.gz
What's Changed
- Age size observation 202206 by @Craig44 in https://github.com/NIWAFisheriesModelling/CASAL2/pull/397
Full Changelog: https://github.com/NIWAFisheriesModelling/CASAL2/compare/dev.202206...dev.2207
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Published by NIWAFisheriesModelling almost 4 years ago
casal2 - Development release 2022-06
This version of Casal2 was built from the main development branch on 2022-06-29.
Model output will include "Version: v22.06".
Windows files (built on Windows Server 2019): Casal2-Windows-build.zip Debian/Ubuntu Linux files (built on Ubuntu 20.04): Casal2-Linux-build.zip Older Linux files (built on CentOS 7.9): Casal2.tar.gz
What's Changed
- Sim casal2 202206 by @Craig44 in https://github.com/NIWAFisheriesModelling/CASAL2/pull/394
Full Changelog: https://github.com/NIWAFisheriesModelling/CASAL2/compare/dev.202205...dev.202206
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Published by NIWAFisheriesModelling about 4 years ago
casal2 - Development release 2022-05
This version of Casal2 was built from the main development branch on 2022-05-24.
Model output will include "Version: v22.05".
Windows files (built on Windows Server 2019): Casal2-Windows-build.zip Debian/Ubuntu Linux files (built on Ubuntu 20.04): Casal2-Linux-build.zip Older Linux files (built on CentOS 7.9): Casal2.tar.gz
What's Changed
- Length based model 202204 by @Craig44 in https://github.com/NIWAFisheriesModelling/CASAL2/pull/386
Full Changelog: https://github.com/NIWAFisheriesModelling/CASAL2/compare/dev.202204...dev.202205
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Published by NIWAFisheriesModelling about 4 years ago
casal2 - Development release 2022-04
THIS SOFTWARE HAS NOT BEEN VALIDATED
This version of Casal2 was built from the main development branch on 2022-04-13.
Model output will include "Version: v22.04 (2022-04-13)".
Windows files (built on Windows Server 2019): Casal2-Windows-build.zip Debian/Ubuntu Linux files (built on Ubuntu 20.04): Casal2-Linux-build.zip Older Linux files (built on CentOS 7.9): Casal2.tar.gz
Full Changelog: https://github.com/NIWAFisheriesModelling/CASAL2/compare/dev.202203...dev.202204
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Published by NIWAFisheriesModelling about 4 years ago
casal2 - dev.202203
THIS SOFTWARE HAS NOT BEEN VALIDATED.
This version of Casal2 was built from the main development branch on 2022-03-17.
Model output will include "Version: v22.03 (2022-03-17)".
Windows files (built on Windows Server 2019): Casal2-Windows-build.zip Debian/Ubuntu Linux files (built on Ubuntu 20.04): Casal2-Linux-build.zip
Full Changelog: https://github.com/NIWAFisheriesModelling/CASAL2/compare/dev.202202...dev.202203
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Published by NIWAFisheriesModelling over 4 years ago
casal2 - Development version as of 2022-02-28
THIS SOFTWARE HAS NOT BEEN VALIDATED.
This version of Casal2 was built from the main development branch on 2022-02-25.
Model output will include "Version: v22.02 (2022-02-25)".
Windows files: Casal2-Windows-build.zip Debian/Ubuntu Linux files: Casal2-Linux-build.zip CentOS Linux files: Casal2.tar.gz
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Published by NIWAFisheriesModelling over 4 years ago
casal2 - Production version 2021-11
Release notes are available at the Casal2 GitHub webpages.
This version of Casal2 was built from the main development branch on 2021-12-03.
Model output will include "Version: v21.11 (2021-11-24)".
Windows files (built on Windows 2016): Casal2-Windows-build.zip Linux files (built on Ubuntu 20.04): Casal2-Windows-build.zip Linux files (built on CentOS 7.9): Casal2.tar.gz
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Published by NIWAFisheriesModelling over 4 years ago
casal2 - Development version as of 2021-10-07
THIS SOFTWARE HAS NOT BEEN VALIDATED.
This version of Casal2 was built from the main development branch on 2021-10-07.
Model output will include "Version: v21.10 (2021-10-06)".
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Published by NIWAFisheriesModelling almost 5 years ago
casal2 - Demonstration version 202110
THIS SOFTWARE HAS NOT BEEN VALIDATED.
This version of Casal2 is for demonstration purposes. It was built from the agelengthredesign202109_ branch on 2021-10-04.
Model output will include "Version: v21.10 (2021-10-04)".
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Published by NIWAFisheriesModelling almost 5 years ago
casal2 - Production version 1.1.0 (interim release)
Release notes are available at the Casal2 GitHub webpages
Windows installation package: casal2_setup.exe Windows files: Casal2.windows.zip Debian/Ubuntu Linux installation package: Casal2.deb Linux files: Casal2.tar.gz and Casal2.linux.zip
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Published by NIWAFisheriesModelling almost 5 years ago
casal2 - Production version 1.0.0
Release notes are available at https://casal2.github.io
Windows installation package: casal2_setup.exe Windows installation files: Casal2.windows.zip Debian/Ubuntu Linux installation package: Casal2.deb Linux installation files: Casal2.tar.gz and Casal2.linux.zip
Docker image available at https://hub.docker.com/r/casal2/casal2
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Published by NIWAFisheriesModelling almost 6 years ago
casal2 - Development version as of 2019-07-29
Windows installation package: casal2_setup.exe Windows installation files: Casal2.zip Debian or Ubuntu Linux installation package: Casal2.deb Linux installation files: Casal2.tar.gz
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Published by NIWAFisheriesModelling over 6 years ago