Casal2 v26.01

Casal2 Version 2026.01

This is a bug fix and merge release. Bug fixes from Alistair Dunn fork have been merged into the Casal2 origin main branch and a new release is being published.

The following changes have been included in this release:
ADD HarvestStrategyRampU option for using a reference year range
ADD Derived quantity observation (draft)
FIX Manual and minor fixes
ADD HarvestStrategyRampU option for using a reference year range
FIX: Orthogonal transformation, ProportionsbyCategory observations
FIX: Calculation error in the orthogonal transformation
FIX: Rewrite of ProportionsByCategory observations to work as it should
UPD: User Manual updates and changes to reflect above changes
RENAME: \length\ProportionsByCategoryByLength to \length\ProportionsByCategory
CHG: Removed some defined PARAM_XX variables that are not used from English_UK.h
CHG: Renamed some PARAM_XX parameters to better reflect consistency for the ProportionsByCategory observations
ADD: Additional prior of type Sum
ADD: lognormal bias adjustment (optional false)
ADD: Harvest strategy projections
UPD: Add biomass_index_scalar to U harvest strategies
ADD: Biomass index derived quantity catchability argument for survey indices

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.Proportions_by_category to Binomial
3. FIX: alpha parameter removed from Selecitivites.Compound_all as it's not used
4. FIX: alpha parameter removed from Selecitivites.Compound_left as it's not used
5. FIX: alpha parameter removed from Selecitivites.Compound_middle as it's not used
6. FIX: alpha parameter removed from Selecitivites.Compound_right 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 (MISSING_YEARS_METHOD, PROJECTION_YEARS_METHOD)
10. CHG: Process.Maturation missing_years_method defaults to error, will error if user doesn't provide all years
11. CHG: Process.Maturation now has zero or final years values for projection_years_method and missing_years_method
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 initial_mean_length and initial_length_cv
15. FIX: GrowthIncrements was using the bitwise (&) instead of logical (&&) when checking for length_plus_group.
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.Random_Walk 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. relative_m_by_age) 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:

1. FIX: Build system now works with Python 3.12+
2. FIX: Github actions deprecated functions have been updated.
3. FIX: Checking for correct values in Likelihood.Bernoulli to prevent calculation errors.
4. FIX: Added better parameter validation in AddressableTransformations to prevent undefined behaviour.
5. FIX: Optimised the MortalityDiseaseRate processes because they were calculating too much.
6. ADD: The parameter system now has a new validation system to standardise parameter validation.
7. ADD: The parameter system now has a new table validation system to standardise table validation.
8. DEL: The documentation builder no longer scrapes the code for syntax building, this was obsolete.
9. ADD: New TwoSexComplex test case model for better unit testing coverage

Casal2 24.06

This release contains a bunch of improvements and bug fixes for Casal2.

1. The user manual has been updated for both Age and Length variants.
2. A large number of basic code improvements, error handling and user messages have been updated.
3. Building Casal2 and associated documentation has been fixed.
4. GitHub Actions have been fixed.
5. A new writing your first model tutorial is now available at: https://casal2.readthedocs.io/en/latest/
6. Contributor guides, github.io pages etc have all been updated.
7. README has been updated.
8. Broken unit tests and builds on various Linux platforms and compilers have been fixed.
9. Casal2 now supports multiple input configuration files with the -c command like argument
10. Added sqrt transformations to manual
11. Added mortality constant exploitation process
12. Implemented double tag loss
13. Added disease mortaloty as an age model process
14. Added constant difference parameter transformation

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

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 #386
• Sim casal2 202206 by @Craig44 in #394
• Age size observation 202206 by @Craig44 in #397
• ADD fishing mortality process, plus improvements 202207 by @Craig44 in #400
• Recruitment ycs syntax change 202208 by @Craig44 in #404

Full Changelog: v21.11...v22.08

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 #397

Full Changelog: dev.202206...dev.2207

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 #394

Full Changelog: dev.202205...dev.202206

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 #386

Full Changelog: dev.202204...dev.202205

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: dev.202203...dev.202204

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: dev.202202...dev.202203