Changelog

Source: NEWS.md

CHANGES IN BioCro VERSION 3.1.3

CRAN release: 2024-04-30

• This is the first version of BioCro to be accepted by CRAN! Most of the changes since version 3.1.0 were needed to comply with CRAN policies and requirements.

• Several changes have been made to reduce the package size from over 20 MB to less than 5 MB:

  • Crop model regression tests only store 1 of every 24 rows (one time point from each day)
  • The stored weather data has been rounded to 3 significant digits
    • The solar values have been rounded to the nearest integer
    • The rh values have been rounded to 2 significant digits
  • The stored crop model regression test data has been rounded to 5 significant digits
  • All previously-existing vignettes were converted to “web only,” meaning they will be available through the pkgdown website but not included with the package itself
  • A new vignette has been added (BioCro.Rmd) that simply redirects readers to the documentation website

• Moved the included boost libraries from inc to src/inc since CRAN will not allow a nonstandard top-level directory. Some paths were shortened during this move.

• Added the Boost organization to the authors as a copyright holder to comply with CRAN policies

• Addressed a missing-field-initializers warning from the compiler by explicitly setting iterations to 0 in the output from rue_leaf_photosynthesis

• Addressed a mistake in thermal_time_and_frost_senescence.h where the leaf death rate due to frost had been unintentionally set to 0 in all conditions. This mistake was caught by a compiler that reported a “ignoring return value of function declared with ‘nodiscard’ attribute” warning.

• Changed the minimum version of macOS checked by the R-CMD-check from 3.6.0 to 4.2.0

  • CRAN now only provides R versions 4.1.0 and above for Mac
  • The deSolve package cannot be built on Mac for R versions below 4.2.0

CHANGES IN BioCro VERSION 3.1.2

• Variable-length arrays were eliminated from the module library code and replaced with std::vector.

CHANGES IN BioCro VERSION 3.1.1

• The package date in its DESCRIPTION file was updated to meet CRAN submission requirements (must be less than one month old)

CHANGES IN BioCro VERSION 3.1.0

MINOR USER-FACING CHANGES

• Another bug was corrected in src/module_library/c3photoC.cpp: The photorespiration value Rp is now calculated using the value of Ci from the current loop iteration (rather than the previous loop iteration).

• Modified some testing-related functions so that warnings due to mismatched framework versions do not trigger test failures: the tryCatch call in test_module now only catches errors (not warnings) when evaluating the module, and test_plant_model (in crop_model_testing_helper_functions.R) now uses expect_no_error instead of expect_silent.

• Changed the energy_par_content constant to 0.219. This is a conversion rate from photon flux density (in micromoles per square meter per second) to energy flux density (in joules per square meter per second or watts per square meter) for photosynthetically active radiation (PAR). It equals 1/4.57, 4.57 being a commonly used constant to convert PAR in W m^-2 to micromole m^-2 s^-1. Users should take care to ensure that if processing of radiation data is required to prepare it for use with BioCro, the same conversion factor is used. See more details in Plant Growth Chamber Handbook. CHAPTER 1 – RADIATION– John C. Sager and J. Craig McFarlane. Table 2, Pg 3 (https://www.controlledenvironments.org/wp-content/uploads/sites/6/2017/06/Ch01.pdf)

• The C++ framework has been updated to v1.1.3. Since the framework is included as a git submodule, it will be necessary to use the --recurse-submodule flag when using git pull, git checkout, or git switch to update a local copy of the BioCro repository, or to move to or from this branch.

• Replaced the inc/boost directory with a submodule pointing to the new biocro/boost repository.

• The (unexported) lightME function has been removed from the R package, since its functionality can be reproduced using the BioCro:solar_position_michalsky and BioCro:shortwave_atmospheric_scattering modules.

OTHER CHANGES

• All instances of fabs or unqualified abs have been replaced by std::abs. The use of unqualified abs in src/module_library/c3photoC.cpp had been causing test failures when running BioCro on Windows using R version 3.6.0.

• This version adds a description of the BioCro git branching model to contribution_guidelines.Rmd and clarifies the process of updating NEWS.md.

• The R-CMD-check workflow has been changed in the following ways:

  • When the check workflow is run manually, there are two new input options:

    • The user can now choose whether or not to run R CMD check with the –as-cran option. Formerly, this was always used.

    • The user can choose whether and when to throw an error on R CMD check failures. Formerly, an error was thrown whenever the R CMD check failure was either “warning” or “error”.

  • Output that was formerly shown only on manual runs when the “debug” checkbox was selected is now always shown. The “debug” option has been changed to “dry-run”, which results in the debug output being shown but the actual check, and those set-up steps needed only to carry out the check, are skipped.

  • The debug output steps are grouped together when possible, and the output is shown earlier on in the workflow.

  • The R-CMD-check workflow has been modified to work around a problem with testing R version 3.6.0 on Windows. And for all platforms, we now specify the tested minimum R version as 3.6.0 rather than simply 3.6 in order to ensure that we are actually testing the minimum required R version specified in the DESCRIPTION file, rather than some later 3.6.x version such as version 3.6.3.

• Modified the R-CMD-check workflow so that the manual is not checked when the workflow runs automatically. This has also been made the default when the workflow is run manually.

• GitHub workflows and actions in the repository have been updated to use the latest versions of all GitHub and 3rd-party actions.

• Updates related to changing the GitHub hosting organization from “ebimodeling” to “biocro”:

  Most references to the ebimodeling GitHub organization have been removed; references to ebimodeling/biocro have been updated to point to biocro/biocro instead. Most of these occurred in various places in the documentation. Most links to the online documentation have been replaced with links to https://biocro.github.io, with (in some cases) instructions on how to navigate to the particular section of the documentation of interest. This decreases dependence on the precise layout of the online documentation. Some other changes and clarifications to the documentation have been made as well.

• Addressed some format-security compiler warnings related to calling Rf_error and Rprintf without a format specifier; a format specifier of "%s" should always be used when printing the value of a string variable.

CHANGES IN BioCro VERSION 3.0.2

MINOR CHANGES

• This version adds several missing references to the main README.

CHANGES IN BioCro VERSION 3.0.1

MINOR CHANGES

• This version pertains only to the GitHub documentation workflow. It changes the publication location to the biocro/BioCro-documentation repository, and it changes the triggers of the workflow so that automatic publication happens when a new release is published. Additionally, a symlink is created to link the URL https://biocro.github.io/BioCro-documentation/latest/pkgdown/ to https://biocro.github.io/BioCro-documentation//pkgdown/, where is the tag name for the new release.

CHANGES IN BioCro VERSION 3.0.0

MAJOR CHANGES

• This version introduces the concept of distinct module libraries, allowing users to develop modules in private and to create collections of related modules. There is an associated syntax change, where modules must now be specified using fully-qualified names that include a module library name and the local name of a module within that library; for example, the module that was previously known as thermal_time_linear must now be referred to as BioCro:thermal_time_linear.

• Any R package representing a BioCro module library must now have four non-exported functions related to accessing its modules: get_all_modules, get_all_quantities, module_creators, and framework_version. When a fully-qualified module name such as library_name:local_module_name is passed to a function such as module_info, an internal call to library_name:::module_creators(module_name) will be made to retrieve a pointer to a module. Hence, library_name must be the same as the module library package name. This is a required part of a method for passing C objects from a module library to the core BioCro framework via R; the full details are not discussed here.

• The code in the src directory has been reorganized to reflect the division between framework code, module code, and “R-to-C” code discussed in the manuscript; now, src/framework contains the core C++ code, src/module_library contains the module code, and the “R-to-C” code can be found directly in src.

• The C++ framework code in src/framework has been moved to a separate repository and licensed under the GNU LGPL; it is included in the BioCro R package repository as a Git submodule. This allows us to use a permissive license for the BioCro R package while still protecting the code that assembles and solves models. Associated with this change, the BioCro R package is now licensed under the MIT license. See LICENSE.note for details.

MINOR CHANGES

• The soil_type_selector module has been removed and replaced with a data object called soil_parameters. For crop models that previously set the soil_type_indicator to 6 to choose the soil parameter values, this parameter has been replaced with the values from soil_parameters$clay_loam.

• Crop model definitions are now stored as single lists rather than as multiple objects; for example, soybean_parameters and soybean_initial_values are now stored as two elements of the soybean list: soybean$parameters and soybean$initial_values.

• The function returned by partial_run_biocro can now properly respond to vectors and lists of named elements.

• Module testing functions have been added to the package namespace.

• Many small improvements have been made to the documentation and the module code in src/module_library; these changes are too numerous to list here.

BUG FIXES

• The elements of the arg_names input to partial_run_biocro can now be in any order; previously, they were required to be supplied in the same order as the appear in the other inputs to partial_run_biocro, for example, the names of any initial values were required to come before the names of any parameters. If the arguments were supplied in the wrong order, then the inputs to the function returned by partial_run_biocro would be interpreted in the wrong order.

• A bug that sometimes caused the last time point of a simulation to contain NaN for all quantities has been fixed; this was related to an out-of-bounds error when accessing vector elements in the C++ function dynamical_system::update_drivers.

CHANGES IN BioCro VERSION 2.0.0

MAJOR CHANGES

• This version is a major update to the design of BioCro. In this version, subsets of a model are called modules. The design attempts to meet the following goals:
  • Make it easier to reuse modules between species, such as the C3 photosynthesis modules.
  • Make it easier to swap related modules for comparison, for example, comparing the Farquhar-von-Caemmerer-Berry model to a radiation use efficiency model.
  • Simplify parameter optimization and sensitivity analysis by providing an interface readily useable by common optimizers and similar functions.
• More details can be found in the peer-reviewed publication in in silico Plants Lochocki et al., 2022 and in the vignettes included with the package:
  • A Practical Guide to BioCro
  • Quantitative Comparison Between Two Photosynthesis Models
  • An Introduction to BioCro for Those Who Want to Add Models
  PDF versions of these vignettes corresponding to the latest version of BioCro can be obtained online from the Articles menu at the BioCro documentation website.

BioCro VERSION 0.951

• This is the last release of the original version of BioCro, which was first described in Miguez et al., 2009 and updated over the years to add more crop models and R functions. A full change log for this version and previous versions is not available in this document.