NEWS.md

Known issues: https://github.com/PredictiveEcology/SpaDES.core/issues

version 1.0.5

new features

• New experimental spades.futureEvents option. If set to TRUE, spades will run module events in a "future" (see future package), if they do not produce outputs for other modules.
• enable automated module code checking with GitHub Actions (use_gha() and corresponding vignette; #74)
• newProject creates Rstudio .Rproj file if invoked in Rstudio
• moved paddedFloatToChar to reproducible; but re-exported here, so still usable.

dependencies

• completely removed dplyr, lubridate, R.utils, tools, backports and rlang from dependencies
• move tcltk to Suggests
• remove devtools, microbenchmark from Suggests

bug fixes

• minor bug fixes
• use new all.equal(..., check.environment = FALSE) for internal testing

version 1.0.3

new features

• none

dependencies

• completely removed RCurl dependency (#120)
• Suggests sp because it's linked in documentation (#120)

bug fixes

• fix pkgDeps example for new version of Require
• minor bug fixes

version 1.0.2

new features

• desc argument in defineParameter, expectsInput, and createsOutput can now have extraneous spaces and End-of-Line characters. This means that they can now be written more easily with a single set of quotes, without needing paste. The accessor functions, moduleParams, moduleInputs, and moduleOutputs all will strip extraneous spaces and End-of-Line characters.
• new helper functions for debugging: writeEventInfo() and writeRNGInfo() to write info to file.

dependencies

• drop support for R < 3.6
• removed imports from stringi

bug fixes

• minor bug fixes in sample modules
• module template has full path instead of .. for moduleParams etc. This is more accurate.
• address changes to active bindings in R-devel
• fix CRAN check errors
• reduced the number of tests run on CRAN (extended tests still run on GitHub Actions)

version 1.0.1

new features

• Par is now an activeBinding (similar to mod) pointing to P(sim); this allows for tab autocomplete to function correctly.
• new helper functions to extract parameters, inputs, and outputs tables from module metadata: moduleParams(), moduleInputs(), moduleOutputs(). These are now used in default .Rmd template.
• better testing of memoryUse functionality
• A pointer to sim is now created at .pkgEnv$.sim at the start of spades call, rather than on.exit; failures due to "out of memory" were not completing the on.exit
• improved templating of new modules, including support for automated module code checking using GitHub Actions (newModule() sets useGitHub = TRUE by default).

dependencies

• add usethis to Suggests for use with GitHub Actions

deprecated

• none

bug fixes

• tests for Filenames function coming from reproducible package
• options('spades.recoverMode') was creating temp folders every event and not removing them; now it does.

version 1.0.0

new features

• several efforts made to reduce memory leaks over long simulations; if memory leaks are a problem, setting options('spades.recoveryMode' = 0) may further help
• Updates to deal with new backend with reproducible
• better assertions inside list elements of simInit, e.g., simInit(times = list(start = "test")) now fails because times must be a list of 2 numeric objects
• messaging is now all with message instead of a mixture of message, cat and print. This allows for easier suppressing of messaging, e.g., via suppressMessages. This was requested in a downstream package, SpaDES.experiment that was submitted to CRAN but rejected due to the now former inability to suppress messages.
• restartR saves simulation objects using qs::qsave() which is faster and creates smaller file sizes.

dependencies

• moved packages from Imports to Suggests: codetools, future, httr, logging, and tcltk
• removed archivist
• qs now used for improved object serialization to disk

deprecated

.objSizeInclEnviros and removed

bug fixes

• removed mention of 'demo' from intro vignette (#110)
• objectSynonyms caused a breakage under some conditions related to recovering a module from Cache.

version 0.2.8

new features

• Changed all internal print and cat statements to message to allow use of suppressMessages, as recommended by CRAN
• added file based logging via logging package, invoked by setting debug argument in spades function call to a list(...). ?spades describes details

bug fixes

• restartR minor bug fixes

version 0.2.7

dependencies

• Removed dependency packages DEoptim, future.apply, Matrix, parallel, pryr, purrr, and rgenoud, which are no longer required. See "deprecated" info below.
• added whisker to Imports to facilitate module file templating (#100)

new features

• memory and peak memory estimation is now available for *nix-type systems, when future is installed. See new vignette iv-advanced and ?memoryUse.
• new function and capacity: restartR. Restarts R mid-stream to deal with apparent memory leaks in R. In our experience with large projects that have long time horizons, there appears to be a memory leak at a low level in R (identified here: https://github.com/r-lib/fastmap). This has prevented projects from running to completion. Without diagnosing the root cause of the memory inflation, we have noticed that interrupting a simulation, saving the simList, restarting R, resets the memory consumption back to levels near the start of a simulation. The new functionality allows a user who is hitting this memory leak issue to restart R as a work around. See ?restartR for instructions.
• new function newProject to initialize a SpaDES project with subdirectories cache/, inputs/, modules/, and outputs/, and setPaths() accordingly.

bug fixes

• newModule() now uses open = interactive() as default to prevent files being left open during tests.
• various bug fixes and improvements.

deprecated

• experiment(), experiment2(), and POM() have been moved to the SpaDES.experiment package

version 0.2.6

dependencies

• R 3.5.0 is the minimum version required for SpaDES.core. Too many dependency packages are not maintaining their backwards compatibility.
• added backports to Imports for R-oldrel support
• removed googledrive dependency (this functionality moved to reproducible)

documentation

• improved documentation for P, params, and parameters, thanks to Louis-Etienne Robert.

new features

• update objSize.simList method with 2 new arguments from reproducible package
• .robustDigest method for simList class objects now does only includes parameters that are listed within the module metadata, if Cache or .robustDigest is called within a module. This means that changes to parameter values in "other" modules will not affect the Caching of "the current" module.
• New function outputObjectNames will extract just the object names of all outputObjects across modules
• New function restartSpades and its associated options(spades.recoveryMode = 1), the new default, which is still experimental. Its purpose is to be able to restart a simulation in the case of an error or interruption.
• Now gives better errors if modules are missing main .R file or if they are missing entirely
• More silent tests
• mod is now an active binding to sim[[currentModule(sim)]]$.objects (move from sim[[currentModule(sim)]]) and its parent environment is emptyenv(). This should cause no changes to users who use mod$..., but it will cause a change if user was calling objects directly via sim[[currentModule(sim)]]$.... This change is to separate the function enclosing environments and object enclosing environments, which should be different.
• sim@completed is now an environment instead of a list. Of the three event queues, this one can become the largest. The list would get increasingly slow as the number of completed events increased. There should be no user visible changes when using completed(sim)

User visible changes to default options

spades.debug is now set to 1 spades.recoveryMode is new and set to 1 (i.e., the current event will be kept at its initial state)

bug fixes

• Internal bugs during simInit especially in some weird cases of childModules.
• packages listed in reqdPkgs not being loaded when only listed in child modules. Fixed in 5cd79ac95bc8d190e954313f125928458b0108d2.
• fixed issue with saving simulation outputs at simulation end time.

version 0.2.5

• improved messaging and fixed test failures when GLPK installed but not used by igraph
• compatibility with RandomFields >= 3.3.4

version 0.2.4

package dependencies

• archivist and devtools added to Suggests because they are used in vignettes
• minimium reproducible version 0.2.6

new features

• new vignette on caching SpaDES simulations moved from SpaDES package.

• simList environment now has emptyenv() as its parent.env. The biggest user-facing changes are:

  • functions placed in the envir(sim) (unusual, but may occur) won't find objects in the .GlobalEnv;
  • lighter memory footprint, as functions take RAM due to the objects in the parent.env in which they are defined (little know fact identified here: http://adv-r.had.co.nz/memory.html#gc identified as a possible source of memory leaks).

• module's function environment in the simList now has its parent asNamespace("SpaDES.core") instead of the envir(sim) (as mentioned above), i.e,. parent.env(sim[[currentModule(sim)]]) is asNamespace("SpaDES.core"). The main user-noticeable changes of this are that module functions will not accidentally find objects in the simList unless they are actually passed in explicitly as arguments.

• New active binding, mod that works as a module-specific variable, similar to a private object, i.e., mod$a is a local object inside the module that persists across events. It is a pointer to sim[[currentModule(sim)]]$a

• New function scheduleConditionalEvent, which allows an event to be scheduled based on a condition. Still experimental.

• An experimental new function and feature, objectSynonyms, which will create active bindings of two names to a single object

• User can now specify modulePath as a character vector, e.g., simInit(..., paths = list(modulePath = c(".", "test"))). This means that a user can organize the modules in different locations.

• modulePath now has a new argument, module, where user can specify (a) specific module(s)'s path. Modifications were implemented to dataPath to utilize this new feature

• simInit and spades now call setPaths(paths) or setPaths(sim$paths), unsetting them on.exit internally to make the paths used for functions e.g., reproducible::Cache to use the correct path

• under-the-hood speed improvements for the DES (about 20% faster) -- 38 microseconds per event under ideal conditions

• improved default path settings in .inputObjects (#83)

• following reproducible package updates, now uses data.table::setattr internally to avoid copying of objects (this may have very little/no effect on simList objects)

• suppliedElsewhere has a new argument, returnWhere, a logical which will cause a logical of length 3 to be returned, indicating in which of the 3 other places the object may have been supplied, instead of length 1, still the default.

bug fixes

• fix to work with latest data.table v1.12.0 (#85, @mattdowle)
• several minor, including to Copy (error existed because function inheritance persisted even though the location of the function was moved)

version 0.2.3

package dependencies

• add RandomFields to Suggests, as it is in the Suggests of SpaDES.tools and used in examples/tests.

new features

• new option and default setting: options("spades.saveSimOnExit" = TRUE). This will save the state of the simList to an object as SpaDES.core:::.pkgEnv$.sim, with a message, if there is a hard exist. There is virtually no computational cost to this, as the object is already in RAM.
• simList internals changed. It now inherits from environment. Amongst other things, this means that tab autocomplete in RStudio now works for objects in the simList. Also, we removed several associated methods, $, [[, ls, ls.str, objects, as the defaults for environments work correctly with the simList now
• debug arg in spades call can now take numeric, currently 1 or 2, giving a few pre-packaged informative messaging each event
• new function elapsedTime which gives a summary of the clock time used by each module or event
• most metadata entries now have accessor of same name, e.g., inputObjects(sim) returns the inputObjects data.frame.
• new function citation replaces utils::citation with an S4 generic. If package arg is a character, it dispatches utils::citation; if a simList, it gives the citation for the module(s)
• improved messaging when GLPK not installed (e.g., on macOS)
• downloadModule() now prints the module version downloaded (#77)

bug fixes

• resolved .inputObjects() name conflict (internal .inputObjects renamed to ._inputObjectsDF; .outputObjects renamed to ._outputObjectsDF)
• module .inputObjects evaluated based on module load order (#72)
• .robustDigest fix for simLists -- needed to omit ._startClockTime and .timestamp

version 0.2.2

package dependencies

• remove sp from imports

new features

• none

bug fixes

• fix issues with failing tests on macOS

version 0.2.1

package dependencies

• requires new version of reproducible (>=0.2.2)

new features

• new option spades.useRequire: a logical which causes simInit to load packages with Require or require. Lower case is generally faster, but will not handle the case of uninstalled packages, so should only be used once all packages are installed.

• • • new option spades.keepCompleted: a logical which causes spades() to keep (TRUE) or not keep a record of completed events. Keeping track of completed events when they are many (>1e5) gets slow enough that it may be worth turning it off.

• more robust and faster tests are used now, care of helper functions in tests

• all.equal.simList now removes all time dependent attributes, e.g., ._startClockTime and .timestamp

• speed enhancements for Discrete Event Simulator; now overhead is 1.3 seconds for 5000 events or, per event, 260 microseconds (185 microseconds if options("spades.keepCompleted" = FALSE)

bug fixes

• Improvements to caching of functions with simList objects:

  • Cached functions with a simList in the arguments would erroneously return cached copies of functions. These now are copied through from argument simList, rather than cached simList. This means that changes to the function definitions in a module will persist (e.g., debugging via browser() will work correctly)
  • functions with simList in arguments that return a simList will now do a post digest of the output. This will be compared with the predigest, and only those object which changed in the simList will be modified.
  • caching of .inputObjects function was incorrect. Fixed.

version 0.2.0

new features

• module metadata now in named lists inside depends(sim)

• new debugging -- if debug is not FALSE, then any error will trigger a browser() call inside the event function. User can continue (c) or quit (Q) as per normal. c will trigger a reparse and events will continue as scheduled.

• introduction of code checking for modules, currently turned on or off by an option spades.moduleCodeChecks, which is TRUE by default. Code checking includes various types:

  • use codetools to check for various code problems
  • detects conflicts with known common functions (raster::level, raster::scale, quickPlot::Plot)
  • use checkCodeEnv on every function inside a module
  • checking for sim$xxx occurrences in modules, comparing to outputObjects in metadata if used in assignment (i.e., left hand side of assign operator), or comparing to inputObjects if used on the right hand side
  • check that all objects declared in inputObjects have default values assigned in the .inputObjects function
  • messages colour coded, and separated by file with absolute path explicit

• option spades.debug set to TRUE by default, instead of FALSE. This is better for new users.

• moduleMetadata argument order changed, so sim is first, more consistent with all other simList accessors.

• downloadData has changed dramatically, now it is a wrapper around reproducible::prepInputs which does more checking.

• extractURL will extract the sourceURL from metadata, given an object name.

• makeMemoiseable and unmakeMemoisable, new methods, each the inverse of the other, to deal with imperfect memoised returns under some cases of simList.

• new option, spades.keepCompleted, TRUE by default, which can be useful for dramatically speeding up the DES when there are many (>10,000) events.

deprecated, defunct, and removed features

• remove fileExt -- use tools::file_ext instead

bug fixes

• fix tests based on data.table changes (@mattdowle, #64).
• re-export start and end.
• newModule template modified slightly based on workshop feedback.
• setPaths now only sets the directories that are passed into it.
• all.equal.simList method strips a small number of attributes that are used internally that create false failures.
• speed enhancements.
• other minor bug fixes.

package dependency changes

• add package imports tools, pryr.
• removed package imports rgeos, RCurl and googledrive.

version 0.1.1

• uses reproducible::Require instead of SpaDES.core::loadPackages to load required packages. Currently, does not use version control for packages, but does use installing (from CRAN or GitHub), and loading (via require). This means a module can indicate a github package, e.g,. achubaty/amc@development

• environments in modules are now as follows:

  • Functions defined in a module are sourced into an environment located here: sim@.envir$<moduleName>, and it is a is a child of sim@.envir. Functions can be found in this environment, but prefixing functions is not necessary, because modules functions are within this environment already.
  • sim@.envir is a child of SpaDES.core

• scoping from within a function that is defined in a module is thus:

  • sim@.envir$<moduleName> --> sim@.envir --> SpaDES.core --> all imported packages including base --> .GlobalEnv --> search()

• speed improvements:

  • the core DES is now built around lists, rather than data.table objects. For small objects (e.g., the eventQueue) that have fewer than 200 objects, lists are faster. Accessors (e.g., events(sim), completed(sim)) of the event queues still show data.table objects, but these are made on the fly.
  • .parseModule and .parseModuePartial now put their parsed content into a temporary environment (sim@.envir$.parsedFiles$<Full Filename>) during the simInit, which gets re-used. Previously, files were parsed multiple times in a given simInit call. Several functions now have envir argument to pass this through (including moduleVersion, packages, checkParams)

• parsing of modules is now more intelligent, allowing for modules to contain functions (the current norm) and but they can also create objects at the module level. These can use the sim object in their definition. These objects can, for example, be used to help define parameters, for example, e.g., startSimPlus1 <- start(sim) + 1 can be defined in the module and used in defineModule

• remove grDevices from Imports as it was not used (#1)

• remove chron and CircStats dependencies

• remove functions dwrpnorm2 and move to package SpaDES.tools

• remove unused function F() due to conflicts with F/FALSE.

• improved download of module data: added new quickCheck argument

• improved download of modules: use fuzzy matching

• new option: spades.switchPkgNamespaces which allows the user to turn off the SpaDES feature that loads and unloads libraries specific to each module. While useful, it slows down computations, in some cases, by a lot.

• bug fixes:

  • in zipModule that omitted the checksum file from being included when data = FALSE (#3)
  • caching of .inputObjects functions was evaluating outputObjects instead of inputObjects. Now corrected.

• If .inputObjects contains arguments other than just sim, these will be evaluated as function inputs by the Cache mechanism (via .useCache), therefore correctly assessing when those inputs changed, e.g., if they are files and the arg is wrapped in asPath, then any change to the underlying file will cause a re-cache. e.g., .inputObjects <- function(sim, importantFile = asPath(file.path(inputPath(sim), "theFile.rdata"))) { ... }

• default debug option in spades() now uses the package option spades.debug and default is set to FALSE (#5)

• various other speed improvements and bug fixes

• convert P to a function, rather than S4 generic and method, for speed.

• importFrom only used functions from utils due to name conflicts with raster::stack and utils::stack

• new function remoteFileSize to check the size of remote files

• new namespaced function dataPath will return file.path(modulePath(sim), currentModule(sim), "data"), which will return a different path, depending on which module it is placed inside.

• add crayon to imports -- now messages are more colour coded

• bug fix in 'inputs' for the case of loading objects from the global environment, either from the same object to the same object, or from different global objects overwriting on the same simList object

version 0.1.0

• A new package, which takes all core DES functionality out of the SpaDES package:

  • see ?SpaDES.core for an overview

• various speed improvements and bug fixes