A new vignette has been added (BioCro.Rmd
) that simply redirects readers
to the documentation website
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.
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.
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.
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.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.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.
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.
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
.
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:
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.
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