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Recent Releases of reproducible

reproducible - v2.1.0

reproducible 2.1.0

New

  • new family of functions that are called inside postProcessTo that use sf::gdal_utils directly. These are still experimental and will only be activated with options("reproducible.gdalwarp" = TRUE)
  • default for gdalMask has changed default for "touches". Now has equivalent for terra::mask(..., touches = TRUE), using "-wo CUTLINE_ALL_TOUCHED=TRUE"
  • gdalProject now uses 2 threads, setting "-wo NUM_THREADS=2"; can be changed by user with options("reproducible.gdalwarpThreads" = X); see ?reproducibleOptions
  • gdal* functions now address datatype issues
  • gdal* defaults to FLT8S if datatype not passed
  • makeRelative, makeAbsolute and similar have been created to ease many issues encountered in preProcess

Changes

  • showSimilar (e.g., options(reproducible.showSimilar = 1)) now preferentially shows the most recent item in cache if there are several with equivalent matching.
  • overhaul of messaging in Cache and prepInputs families; functions are highlighted with a different colour; indent level reflects nesting of both Cache and prepInputs, so it is easier to identify which message goes with which function call.
  • preProcess is a lot faster now for large numbers of files; uses CHECKSUMS more effectively and fewer times
  • retry now captures its expr so it doesn't need a quote; is like try now.
  • showSimilar mechanisms now returns the most recent, if there are >1 similar that are equivalently similar
  • if a user is having troubles with googledrive for e.g., large files on spotting connections, instructions for using gdown are provided
  • showCache, clearCache now have extra arguments fun, cacheId, and ... now can take any arbitrary tag = value pair. The cacheId argument will be very fast if a user is not using useDBI() is FALSE.
  • .wrap and .unwrap can now deal with SpatVectorCollection (a terra class that does not have a wrap/unwrap method in terra)
  • ALTREP digesting when using spooky or fastdigest were not stable for integers and factors. There is now a work around in .robustDigest that stabilizes these by expanding them from their ALTREP representation first. Since they will be saved and recovered anyway, this will have little effect.
  • .wrap and .unwrap are becoming more mature and can handle many more classes effectively. Methods can still be written, if needed.

Testing

  • lots of testing with cacheSaveFormat = "qs", which previously was not reliable especially for environments. With all recent changes to .wrap and .unwrap, these appear stable now and should be able to be used for environments.

Bugfixes

  • switchDataType can now correctly switch between gdal formats and terra
  • many messaging fixes that were imprecise or missing

- R
Published by achubaty almost 2 years ago

reproducible - v2.0.12

reproducible 2.0.12

  • re-submission after removal from CRAN

- R
Published by achubaty almost 2 years ago

reproducible - v2.0.9

reproducible 2.0.9

Enhancements

  • new function isUpdated() to determine whether a cached object has been updated;
  • makeRelative() is now exported for use downstream (e.g., SpaDES.core);
  • new functions getRelative() and normPathRel() for improved symlink handling (#362);
  • messaging is improved for Cache with the function named instead of just cacheId
  • messaging for prepInputs: minor changes
  • more edge cases for Checksums dealt with, so fewer unneeded downloads
  • wrapSpatRaster (wrap for file-backed spatRaster objects) fixes for more edge cases
  • postProcessTo can now use sf::gdal_utils for the case of from is a gridded object and to is a polygon vector. This appears to be between 2x and 10x faster in tests.
  • postProcessTo does a pre-crop (with buffer) to make the projectTo faster. When both from and to are vector objects, this pre-crop appears to create slivers in some cases. This step is now skipped for these cases.
  • Cache can now deal with unnamed functions, e.g., Cache((function(x) x)(1)). It will be refered to as "headless".
  • terra would fail if internet was unavailable, even when internet is not necessary, due to needing to retrieve projection information. Many cases where this happens will now divert to use sf.
  • Cache can now skip calculating objSize, which can take a non-trivial amount of time for large, complicated objects; see reproducibleOptions()

Bug fixes

  • Filenames for some classes returned ""; now returns NULL so character vectors are only pointers to files
  • Cache on a terra object that writes file to disk, when quick argument is specified was failing, always creating the same object; fixed with #PR368
  • useDBI was incorrectly used if a user had set the option prior to package loading. Now works as expected.
  • several other minor
  • preProcess deals better with more cases of nested paths in archives.
  • more edge cases corrected for inputPaths

- R
Published by achubaty over 2 years ago

reproducible - v2.0.8

reproducible 2.0.8

Enhancements

  • minor formatting changes

Bug fixes

  • only use character strings when comparing getRVersion() <= "XXX"
  • fixes for assessDataType for categorical (factor) Raster and SpatRaster

- R
Published by achubaty over 2 years ago

reproducible - v2.0.7

reproducible 2.0.7

Enhancements

  • Address change in round with R > 4.3.1; now a primitive, that does method dispatch. Failure was identified with unit tests, by Luke Tierney who was making the change in base::round.

Bug fixes

  • several identified and fixed (PRs by Ceres Barros, notably, PRs #341, #342, #343). These fix missing argument in a .unwrap call, and missing check in preProcess, when targetFilePath was NULL.
  • minor documentation updates

- R
Published by achubaty over 2 years ago

reproducible - v2.0.5

reproducible 2.0.5

Enhancements

  • Updates of Copy & new .wrap, .unwrap generics and methods to wrap classes that don't save well to disk as is. This uses the name similar to terra::wrap, but with slight differences internally to allow for SpatRaster objects who are file-backed and must have their files moved when they are unwrapped.
  • loadFiles updated for more cases
  • convert to using withr throughout testing for cleaning up
  • more methods for Filename added, including for Path class
  • Cache(..., useCloud = TRUE) had many cases that were not working; known cases are now working. Also, now file from file-backed cases are now placed inside the cacheOutputs folder rather than inside a separate folder (used to be "rasters")

Bugfixes

  • several small for edge cases

Dependency changes

  • none

- R
Published by achubaty over 2 years ago

reproducible - v2.0.4

reproducible 2.0.4

Enhancements

  • reproducible.useFuture now defaults to "multisession"
  • updated tests to deal with data.table development branch (#314)
  • removed all use of data.table::setattr to deal with "modified compiler constants" issue that was detected during CRAN checks at https://github.com/kalibera/cran-checks/blob/master/rcnst/results/reproducible/00check.log

Bugfixes

  • preProcess failed when googledrive url filename could be found, but destinationPath was not "."
  • normPath had different behaviour on *nix-alikes and Windows. Now it is the same.
  • Issue #316 -- SpatRaster objects if saved to a specific, non relative (to getwd()) path would not be recovered correctly.
  • Several other Issues that addressed edge cases for prepInputs and family.

Continuous integration

  • Improvements with testing on GitHub Actions

- R
Published by achubaty over 2 years ago

reproducible - v2.0.2

Known issues: https://github.com/PredictiveEcology/reproducible/issues

Version 2.0.2

Enhancements

  • new optional backend for Cache via options(reproducible.useDBI = FALSE) is single data files with the same basename as the cached object, i.e., with the same cacheId in the file name. This is a replacement for RSQLite and will likely become the default in the next release. This approach makes cloud caching easier as all metadata are available in small binary files for each cached object. This is simpler, faster and creates far fewer package dependencies (now 11 recursive; before 27 recursive). If a user has DBI and RSQLite installed, then the backend will default to use these currently, i.e., the previous behaviour. The user can change the backend without loss of Cache data.
  • moved raster and sp to Suggests; no more internal functions use these. User can still work with Raster and sp class objects as before.
  • preProcess can now handle google docs files, if type = ... is passed.
  • postProcess now uses terra and sf internally (with #253) throughout the family of postProcess functions. The previous *Input and *Output functions now redirect to the new *To* functions. These are faster, more stable, and cover vastly more cases than the previous *Inputs family. The old backends no longer work as before.
  • minor functions to assist with transition from raster to terra: maxFn, minFn, rasterRead
  • .dealWithClass and .dealWithClassOnRecovery are now exported generics, with several methods here, notably, list, environment, default
  • other miscellaneous changes to deal with raster to terra transition (e.g. studyAreaName can deal with SpatVector)
  • prepInputs now deals with archives that have sub-folder structure are now dealt with correctly in all examples and tests esp. #181.
  • prepInputs can now deal with .gdb files. Though, it is limited to sf out of the box, so e.g., Raster layers inside gdb files are not supported (yet?). User can pass fun = NA to not try to load it, but at least have the .gdb file locally on disk.
  • hardLinkOrCopy now uses linkOrCopy(symlink = FALSE); more cases dealt with especially nested directory structures that do not exist in the to.
  • many GitHub issues closed after transition to using terra and sf.
  • preProcess had multiple changes. The following now work: archives with subfolders, archives with subfolders with identical basenames (different dirnames), gdb files, other files where targetFile is a directory.
  • ~40 issues were closed with current release.
  • code coverage now approaching 85%
  • substantial changes to preProcess for minor efficiency gains, edge cases, code cleaning
  • new function CacheGeo that weaves together prepInputs and Cache to create a geo-spatial caching. See help and examples.
  • maskTo now allows touches arg for terra::mask
  • Spatial class is also "fixed" in fixErrorsIn
  • prepInputs and preProcess now capture dlFun, so user can pass unquoted dlFun
  • Copy method for SpatRaster, with and without file-backing
  • Cache(..., useCloud = TRUE) reworked so appears to be more robust than previously.
  • maskTo now works even if to is larger than from
  • netCDF works with prepInputs; thanks to user nbsmokee with PR #300.

Dependency changes

  • no spatial packages are automatically installed any more; to work with prepInputs and family, the user will have to install terra and sf at a minimum.
  • terra, sf are in Suggests
  • removed entirely: fasterize, fpCompare, magrittr
  • moved to Suggests: raster, sp, rlang
  • A normal (minimal) install of reproducible no longer installs DBI, nor does it use RSQLite. All cache repositories database files will be in binary individual files in the cacheOutputs file. If a user has DBI and a SQLite engine, then the previous behaviour will be used.

Defunct

  • reproducible.useNewDigestAlgorithm is not longer an option as the old algorithms do not work reliably.

Defunct and removed

  • removed assessDataTypeGDAL(), clearStubArtifacts(),
  • removed non-exported digestRasterLayer2(); evalArgsOnly(); .getSourceURL(); .getTargetCRS(); .checkSums(), .groupedMessage(); .checkForAuxililaryFiles()
  • option("reproducible.polygonShortcut") removed

Non exported function changes

  • .basename renamed to basename2

Bugfixes

  • Cache was incorrectly dealing with environment and environment-like objects. Since some objects, e.g., Spat* objects in terra, must be wrapped prior to saving, environments must be scanned for these classes of objects prior to saving. This previously only occurred for list objects;
  • When working with revdep SpaDES.core, there were some cases where the Cache was failing as it could not find the module name;
  • during transition from postProcess (using raster and sp) to postProcessTo, some cases are falling through the cracks; these have being addressed.

- R
Published by achubaty almost 3 years ago

reproducible - v1.2.16

Known issues: https://github.com/PredictiveEcology/reproducible/issues

Version 1.2.16

Dependency changes

  • none

Enhancements

  • Cache now captures the first argument passed to it without evaluating it, so Cache(rnorm(1)) now works as expected.
  • As a result of previous, Cache now works with base pipe |> (with R >= 4.1).
  • Due to some internal changes in the way arguments are evaluated and digested, there may be some cache entries that will be rerun. However, in simple cases of FUN passed to Cache, there should be no problems with previous cache databases being successfully recovered.
  • Added more unit tests
  • Reworked Cache internals so that digesting is more accurate, as the correct methods for functions are more accurately found, objects within functions are more precisely evaluated.
  • Improved documentation:
    • Examples were reworked, replaced, improved;
    • All user-facing exported functions and methods now have complete documentation;
    • Added () in DESCRIPTION for functions;
    • Added \value in .Rd files for exported methods (structure, the class, the output meaning);
    • Remove commented code in examples.

Bug fixes

  • postProcess now also checks resolution when assessing whether to project
  • prepInputs has an internal Cache call for loading the object into memory; this was incorrectly evaluating all files if there were more than one file downloaded and extracted. This resulted in cases, e.g. shapefiles, being considered identical if they had the identical geometries, even if their data were different. This is fixed now as it uses the digest of all files extracted.

Deprecated and defunct

  • remove defunct argument digestPathContent from Cache
  • options("reproducible.useGDAL") is now deprecated; the package is moving towards terra.

- R
Published by achubaty about 3 years ago

reproducible - v1.2.11

Known issues: https://github.com/PredictiveEcology/reproducible/issues

Version 1.2.11

Dependency changes

  • none

Enhancements

  • none

Bug fixes

  • fix tests for postProcessTerra to deal with changes in GDAL/PROJ/GEOS (#253; @rsbivand)
  • fixed issue with masking

- R
Published by achubaty over 3 years ago

reproducible - v1.2.10

Known issues: https://github.com/PredictiveEcology/reproducible/issues

Version 1.2.10

Dependency changes

  • Drop support for R 3.6 (#230)
  • remove gdalUtilities, gdalUtils, and rgeos from Suggests
  • Added minimum versions of raster and terra, because previous versions were causing collisions.

Enhancements

  • all direct calls to GDAL are removed: only terra and sf are used throughout
  • prepInputs can now take fun as a quoted expression on x, the object loaded by dlFun in preProcess
  • preProcess arg dlFun can now be a quoted expression
  • changes to the internals and outputs of objSize; now is primarily a wrapper around lobstr::obj_size, but has an option to get more detail for lists and environments.
  • .robustDigest now deals explicitly with numerics, which digest differently on different OSs. Namely, they get rounded prior to digesting. Through trial and error, it was found that setting options("reproducible.digestDigits" = 7) was sufficient for all known cases. Rounding to deeper than 7 decimal places was insufficient. There are also new methods for language, integer, data.frame (which does each column one at a time to address the numeric issue)
  • New version of postProcess called postProcessTerra. This will eventually replace postProcess as it is much faster in all cases and simpler code base thanks to the fantastic work of Robert Hijmans (terra) and all the upstream work that terra relies on
  • Minor message updates, especially for "adding to memoised copy...". The three dots made it seem like it was taking a long time. When in reality, it is instantaneous and is the last thing that happens in the Cache call. If there is a delay after this message, then it is the code following the Cache call that is (silently) slow.
  • retry can now return a named list for the exprBetween, which allows for more than one object to be modified between retries.

Bug fixes

  • .robustDigest was removing Cache attributes from objects under many conditions, when it should have left them there. It is unclear what the issues were, as this would likely not have impacted Cache. Now these attributes are left on.
  • data.table objects appear to not be recovered correctly from disk (e.g., from Cache repository. We have added data.table::copy when recovering from Cache repository
  • clearCache and cc did not correctly remove file-backed raster files (when not clearing whole CacheRepo); this may have resulted in a proliferation of files, each a filename with an underscore and a new higher number. This fix should eliminate this problem.
  • deal with development versions of GDAL in getGDALVersion() (#239)
  • fix issue with maskInputs() when not passing rasterToMatch.
  • fix issue with isna.SpatialFix when using postProcess.quosure

- R
Published by achubaty over 3 years ago

reproducible - v1.2.8

Known issues: https://github.com/PredictiveEcology/reproducible/issues

Version 1.2.8

Dependency changes

  • lwgeom now a suggested package

Enhancements

  • terra class objects can now be correctly saved and recovered by Cache
  • fixErrors can now distinguish testValidity = NA meaning don't fix errors and testValidity = FALSE run buffering which fixes many errors, but don't test whether there are any invalid polygons first (maybe slow), or testValidity = TRUE meaning test for validity, then if some are invalid, then run buffer.
  • Change default option to reproducible.useNewDigestAlgorithm = 2 which will have user visible changes. To keep old behaviour, set options(reproducible.useNewDigestAlgorithm = 1)
  • minor changes to messaging when options(reproducible.showSimilar) is set. It is now more compact e.g., 3 lines instead of 5.
  • added sf methods to studyAreaName

Bug fixes

  • A small, but very impactful bug that created false positive Cache returns; i.e., a 2nd time through a Cache would return a cached copy, when some of the arguments were different. It occurred for when the differences were in unnamed arguments only.

- R
Published by achubaty over 4 years ago

reproducible - v1.2.7

Known issues: https://github.com/PredictiveEcology/reproducible/issues

Version 1.2.7

reproducible will be slowly changing the defaults for vector GIS datasets from the sp package to the sf package. There is a large user-visible change that will come (in the next release), which will cause prepInputs to read .shp files with sf::st_read instead of raster::shapefile, as it is much faster. To change now, set options("reproducible.shapefileRead" = "sf::st_read")

Enhancements

  • default fun in prepInputs for shapefiles (.shp) is now sf::st_read if the system has sf installed. This can be overridden with options("reproducible.shapefileRead" = "raster::shapefile"), and this is indicated with a message at the moment this is occurring, as it will cause different behaviour.
  • quick argument in Cache can now be a character vector, allowing individual character arguments to be digested as character vectors and others to be digested as files located at the specified path as represented by the character vector.
  • objSize previously included objects in namespaces, baseenv and emptyenv, so it was generally too large. Now uses the same criteria as pryr::object_size
  • improvements with messaging when unzip missing (thanks to C. Barros #202)
  • while unzipping, will also search for 7z.exe on Windows if the object is larger than 2GB, if can't find unzip.
  • fun argument in prepInputs and family can now be a quoted expression.
  • archive argument in prepInputs can now be NA which means to treat the file downloaded not as an archive, even if it has a .zip file extension
  • many minor improvements to functioning of esp. prepInputs
  • speed improvements during postProcess especially for very large objects (>5GB tested). Previously, it was running many fixErrors calls; now only calls fixErrors on fail of the proximate call (e.g., st_crop or whatever)
  • retry now has a new argument exprBetween to allow for doing something after the fail (for example, if an operation fails, e.g., st_crop, then run fixErrors, then return back to st_crop for the retry)
  • Cache now has MUCH better nested levels detection, with messaging... and control of how deep the Caching goes seems good, via useCache = 2 will only Cache 2 levels in...
  • archive argument in prepInputs family can now be NA ... meaning do not try to unzip even if it is a .zip file or other standard archive extension
  • gdb.zip files (e.g., a file with a .zip extension, but that should not be opened with an unzip-type program) can now be opened with prepInputs(url = "whateverUrl", archive = NA, fun = "sf::st_read")
  • fun argument in prepInputs can now be a quoted function call.
  • preProcess now does a better job with large archives that can't be correctly handled with the default zip and unzip with R, by trying system2 calls to possible 7z.exe or other options on Linux-alikes.

Bug fixes

  • Copy generic no longer has fileBackedDir argument. It is now passed through with the .... This was creating a bug with some cases where fileBackedDir was not being correctly executed.
  • fixErrors() now better handles sf polygons with mixed geometries that include points.
  • inadvertent deleting of file-backed rasters in multi-filed stacks during Cache
  • writeOutputs.Raster attempted to change datatype of Raster class objects using the setReplacement dataType<-, without subsequently writing to disk via writeRaster. This created bad values in the Raster* object. This now performs a writeRaster if there is a datatype passed to writeOutputs e.g., through prepInputs or postProcess.
  • updateSlotFilename has many more tests.
  • prepInputs(..., fun = NA) now is the correct specification for "do not load object into R". This essentially replicates preProcess with same arguments.
  • several minor bugfixes
  • Copy did not correctly copy RasterStacks when some of the RasterLayer objects were in memory, some on disk; raster::fromDisk returned FALSE in those cases, so Copy didn't occur on the file-backed layer files. Using Filenames instead to determine if there are any files that need copying.

- R
Published by achubaty almost 5 years ago

reproducible - v1.2.6

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 1.2.6

Enhancements

  • Optional (and may be default soon) -- An update to the internal digesting for file-backed Rasters that should be substantially faster, and smaller disk footprint. Set using options("reproducible.useNewDigestAlgorithm" = 2)
  • changed default of options("reproducible.polygonShortcut" = FALSE) as there were still too many edge cases that were not covered.

Bug fix

  • RasterStack objects with a single file (thus acting like a RasterBrick) are now handled correctly by Cache and prepInputs families, especially with new options("reproducible.useNewDigestAlgorithm" = 2), though in tests, it worked with default also
  • Fix issue #185, RSQLite now uses a RNG during dbAppend; this affected 2 tests.

- R
Published by achubaty about 5 years ago

reproducible - v1.2.1

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 1.2.1

New features

  • harmonized message colours that are use adjustable via options: reproducible.messageColourPrepInputs for all prepInputs functions; reproducible.messageColourCache for all Cache functions; and reproducible.messageColourQuestion for questions that require user input. Defaults are cyan, blue and green respectively. These are user-visible colour changes.
  • improved messaging for Cache cases where a file.link is used instead of saving.
  • with improved messaging, now options(reproducible.verbose = 0) will turn off almost all messaging.
  • postProcess and family now have filename2 = NULL as the default, so not saved to disk. This is a change.
  • verbose is now an argument throughout, whose default is getOption(reproducible.verbose), which is set by default to 1. Thus, individual function calls can be more or less verbose, or the whole session via option.

Bug fixes

  • RasterStack objects were not correctly saved to disk under some conditions in postProcess - fixed
  • several minor

- R
Published by achubaty over 5 years ago

reproducible - v1.1.1

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 1.1.1

New features

  • none

Dependency changes

  • none

bug fixes

  • fix CRAN test failure when file.link does not succeed.

- R
Published by achubaty almost 6 years ago

reproducible - v1.1.0

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 1.1.0

New features

  • begin to accommodate changes in GDAL/PROJ and associated updates to other spatial packages. More updates are expected as other spatial packages (namely raster) are updated.
  • can now change options('reproducible.cacheSaveFormat') on the fly; cache will look for the file by cacheId and write it using options('reproducible.cacheSaveFormat'). If it is in another format, Cache will load it and resave it with the new format. Experimental still.
  • new Copy methods for refClass objects, SQLite and moved environment method into ANY as it would be dispatched for unknown classes that inherit from environment, of which there are many and this should be intercepted
  • Require can now handle minimum version numbers, e.g., Require("bit (>=1.1-15.2)"); this can be worked into downstream tools. Still experimental.
  • Cache will do file.link or file.symlink if an existing Cache entry with identical output exists and it is large (currently 1e6 bytes); this will save disk space.
  • Cache database now has tags for elapsed time of "digest", "original call", and "subsequent recovery from file", elapsedTimeDigest, elapsedTimeFirstRun, and elapsedTimeLoad, respectively.
  • Better management of temporary files in package and tests, e.g., during downloading (preProcess). Includes 2 new functions, tempdir2 and tempfile2 for use with reproducible package
  • New option: reproducible.tempPath, which is used for the new control of temporary files. Defaults to file.path(tempdir(), "reproducible"). This feature was requested to help manage large amounts of temporary objects that were not being easily and automatically cleaned
  • Copying or moving of Cache directories now works automatically if using default drv and conn; user may need to manually call movedCache if cache is not responding correctly. File-backed Rasters are automatically updated with new paths.
  • Cache now treats file-backed Rasters as though they had a relative path instead of their absolute path. This means that Cache directories can be copied from one location to another and the file-backed Raster* will have their filenames updated on the fly during a Cache recovery. User doesn't need to do anything.
  • postProcess now will perform simple tests and skip cropInputs and projectInputs with a message if it can, rather than using Cache to "skip". This should speed up postProcess in many cases.
  • messaging with Cache has change. Now, cacheId is shown in all cases, making it easier to identify specific items in the cache.
  • Automatically cleanup temporary (intermediate) raster files (with #110).

Dependency changes

  • none

bug fixes

  • Copy only creates a temporary directory for filebacked rasters; previously any Copy command was creating a temporary directory, regardless of whether it was needed
  • cropInputs.spatialObjects had a bug when object was a large non-Raster class.
  • cropInputs may have failed due to "self intersection" error when x was a SpatialPolygons* object; now catches error, runs fixErrors and retries crop. Great reprex by @tati-micheletti. Fixed in commit 89e652ef111af7de91a17a613c66312c1b848847.
  • Filenames bugfix related to RasterBrick
  • prepInputs does a better job of keeping all temporary files in a temporary folder; and cleans up after itself better.
  • prepInputs now will not show message that it is loading object into R if fun = NULL (#135).

- R
Published by achubaty almost 6 years ago

reproducible - v1.0.0

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 1.0.0

New features

  • This version is not backwards-compatible out of the box. To maintain backwards compatibility, set: options("reproducible.useDBI" = FALSE)
  • A new backend was introduced that uses DBI package directly, without archivist. This has much improved speed.
  • New option: options("reproducible.cacheSaveFormat"). This can be either rds (default) or qs. All cached objects will be saved with this format. Previously it was rda.
  • Cache objects can now be saved with with qs::qsave. In many cases, this has much improved speed and file sizes compared to rds; however, testing across a wide range of conditions will occur before it becomes the default.
  • Changed default behaviour for memoising ... because Cache is now much faster, the default is to turn memoising off, via options("reproducible.useMemoise" = FALSE). In cases of large objects, memoising should still be faster, so user can still activate it, setting the option to TRUE.
  • Much better SQLite database handling for concurrent write attempts. Tested with dozens of write attempts per second by 3 cores with abundant locked database occurrences.
  • postProcess arg useGDAL can now take "force" as the default behaviour is to not use GDAL if the problem can fit into RAM and sf or raster tools will be faster than GDAL tools
  • useCloud argument in Cache and family has slightly modified functionality (see ?Cache new section useCloud) and now has more tests including edge cases, such as useCloud = TRUE, useCache = 'overwrite'. The cloud version now will also follow the "overwrite" command.

Dependency changes

  • deprecating archivist; moved to Suggests.
  • removed imports for bitops, dplyr, fasterize, flock, git2r, lubridate, RcppArmadillo, RCurl and tidyselect. Some of these went to Suggests.

bug fixes

  • postProcess calls that use GDAL made more robust (including #93).
  • Several minor, edge cases were detected and fixed.

- R
Published by achubaty about 6 years ago

reproducible - v0.2.10

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.10

Dependency changes

  • made compatible with googledrive v 1.0.0 (#119)

New features

  • pkgDep2, a new convenience function to get the dependencies of the "first order" dependencies.
  • useCache, used in many functions (incl Cache, postProcess) can now be numeric, a qualitative indicator of "how deep" nested Cache calls should set useCache = TRUE -- implemented as 1 or 2 in postProcess currently. See ?Cache

bug fixes

  • pkgDep was becoming unreliable for unknown reasons. It has been reimplemented, much faster, without memoising. The speed gains should be immediately noticeable (6 second to 0.1 second for pkgDep("reproducible"))
  • improved retry to use exponential backoff when attempting to access online resources (#121)

- R
Published by achubaty over 6 years ago

reproducible - v0.2.9

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.9

New features

  • Cache has 2 new arguments, useCloud and cloudFolderID. This is a new approach to cloud caching. It has been tested with file backed RasterLayer, RasterStack and RasterBrick and all normal R objects. It will not work for any other class of disk-backed files, e.g., ff or bigmatrix, nor is it likely to work for R6 class objects.
  • Slowly deprecating cloudCache and family of functions in favour of a new approach using arguments to Cache, i.e., useCache and cloudFolderID
  • downloadData from GoogleDrive now protects against HTTP2 error by capturing error and retrying. This is a curl issue for interrupted connections.

Bug fixes

  • fixes for rcnst errors on R-devel, tested using devtools::check(env_vars = list("R_COMPILE_PKGS"=1, "R_JIT_STRATEGY"=4, "R_CHECK_CONSTANTS"=5))
  • other minor impovements, included fixes for #115

- R
Published by achubaty over 6 years ago

reproducible - v0.2.8

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.8

New features

  • new functions for accessing specific items from the cacheRepo: getArtifact, getCacheId, getUserTags
  • cloudSyncCache has more options that are implemented and many unitTests

bug fixes

  • prepInputs wasn't correctly passing useCache
  • cropInputs was reprojecting extent of y as a time saving approach, but this was incorrect if studyArea is a SpatialPolygon that is not close to filling the extent. It now reprojects studyArea directly which will be slower, but correct. -- fixes issue #93
  • other minor improvements

- R
Published by achubaty almost 7 years ago

reproducible - v0.2.7

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.7

New features

  • CHECKSUMS.txt should now be ordered consistently across operating systems (note: base::order will not succeed in doing this --> now using .orderDotsUnderscoreFirst)
  • cloudSyncCache has a new argument: cacheIds. Now user can control entries by cacheId, so can delete/upload individual objects by cacheId
  • Experimental support within the postProcess family for sf class objects

bug fixes

  • mostly minor
  • cloudCache bugfixes for more cases

- R
Published by achubaty about 7 years ago

reproducible - v0.2.6

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.6

Dependency changes

  • remove tibble from Imports as it's no longer being used

New features

  • remove %>% pipe that was long ago deprecated. User should use %C% if they want a pipe that is Cache-aware. See examples.
  • Full rewrite of all options descriptions now in reproducible, see ?reproducibleOptions
  • now cacheRepo and options("reproducible.cachePath") can take a vector of paths. Similar to how .libPaths() works for libraries, Cache will search first in the first entry in the cacheRepo, then the second etc. until it finds an entry. It will only write to the first entry.
  • new value for the option: options("reproducible.useCache" = "devMode"). The point of this mode is to facilitate using the Cache when functions and datasets are continually in flux, and old Cache entries are likely stale very often. In devMode, the cache mechanism will work as normal if the Cache call is the first time for a function OR if it successfully finds a copy in the cache based on the normal Cache mechanism. It differs from the normal Cache if the Cache call does not find a copy in the cacheRepo, but it does find an entry that matches based on userTags. In this case, it will delete the old entry in the cacheRepo (identified based on matching userTags), then continue with normal Cache. For this to work correctly, userTags must be unique for each function call. This should be used with caution as it is still experimental.
  • change to how hashes are calculated. This will cause existing caches to not work correctly. To allow a user to keep old behaviour (during a transition period), the "old" algorigthm can be used, with options("reproducible.useNewDigestAlgorithm" = FALSE). There is a message of this change on package load.
  • add experimental cloud* functions, especially cloudCache which allows sharing of Cache among collaborators. Currently only works with googledrive
  • updated assessDataType to consolidate assessDataTypeGDAL and assessDataType into single function (#71, @ianmseddy)
  • cc: new function -- a shortcut for some commonly used options for clearCache()
  • added experimental capacity for prepInputs to handle .rar archives, on systems with correct binaries to deal with them (#86, @tati-micheletti)
  • remove fastdigest::fastdigest as it is not return the identical hash across operating systems

Bug fixes

  • prepInputs on GIS objects that don't use raster::raster to load object were skipping postProcess. Fixed.
  • under some circumstances, the prepInputs would cause virtually all entries in CHECKSUMS.txt to be deleted. 2 cases where this happened were identified and corrected.
  • data.table class objects would give an error sometimes due to use of attr(DT). Internally, attributes are now added with data.table::setattr to deal with this.
  • calling gdalwarp from prostProcess now correctly matches extent (#73, @tati-micheletti)
  • files from url that have unknown extension are now guessed with by preProcess (#92, @tati-micheletti)

- R
Published by achubaty about 7 years ago

reproducible - v0.2.5

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.5

Dependency changes

  • Added remotes to Imports and removed devtools

New features

  • New value possible for options(reproducible.useCache = 'overwrite'), which allows use of Cache in cases where the function call has an entry in the cacheRepo, will purge it and add the output of the current call instead.
  • New option reproducible.inputPaths (default NULL) and reproducible.inputPathsRecursive (default FALSE), which will be used in prepInputs as possible directory sources (searched recursively or not) for files being downloaded/extracted/prepared. This allows the using of local copies of files in (an)other location(s) instead of downloading them. If local location does not have the required files, it will proceed to download so there is little cost in setting this option. If files do exist on local system, the function will attempt to use a hardlink before making a copy.
  • dlGoogle() now sets options(httr_oob_default = TRUE) if using Rstudio Server.
  • Files in CHECKSUMS now sorted alphabetically.
  • Checksums can now have a CHECKSUMS.txt file located in a different place than the destinationPath
  • Attempt to select raster resampling method based on raster type if no method supplied (#63, @ianmseddy)
  • projectInputs

  • new function assessDataTypeGDAL, used in postProcess, to identify smallest datatype for large Raster* objects passed to GDAL system call

    • when masking and reprojecting large Raster objects, enact gdalwarp system call if raster::canProcessInMemory(x,4) = FALSE for faster and memory-safe processing
    • better handling of various data types in Raster objects, including factor rasters

Bug fixes

  • Work around internally inside extractFromArchive for large (>2GB) zip files. In the R help manual, unzip fails for zip files >2GB. This uses a system call if the zip file is too large and fails using base::unzip.
  • Work around for raster::getData issues.
  • Speed up of Cache() when deeply nested, due to grep(sys.calls(), ...) that would take long and hang.
  • Bugfix for preProcess(url = NULL) (#65, @tati-micheletti)
  • Improved memory performance of clearCache (#67), especially for large Raster objects that are stored as binary R files (i.e., .rda)
  • Other minor bugfixes

Other changes

  • Deal with new raster package changes in development version of raster package
  • Added checks for float point number issues in raster resolutions produced by raster::projectRaster
  • .robustDigest now does not include Cache-added attributes
  • Additonal tests for preProcess() (#68, @tati-micheletti)
  • Many new unit tests written, which caught several minor bugs

- R
Published by achubaty over 7 years ago

reproducible - v0.2.3

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.3

  • fix and skip downloading test on CRAN

- R
Published by achubaty over 7 years ago

reproducible - v0.2.2

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.2

Dependency changes

  • Add future to Suggests.

New features

  • new option on non-Windows OSs to use future for Cache saving to SQLite database, via options("reproducible.futurePlan"), if the future package is installed. This is FALSE by default.
  • If a do.call function is Cached, previously, it would be labelled in the database as do.call. Now it attempts to extract the actual function being called by the do.call. Messaging is similarly changed.
  • new option reproducible.ask, logical, indicating whether clearCache should ask for deletions when in an interactive session
  • prepInputs, preProcess and downloadFile now have dlFun, to pass a custom function for downloading (e.g., "raster::getData")
  • prepInputs will automatically use readRDS if the file is a .rds.
  • prepInputs will return a list if fun = "base::load", with a message; can still pass an envir to obtain standard behaviour of base::load.
  • clearCache - new argument ask.
  • new function assessDataType, used in postProcess, to identify smallest datatype for Raster* objects, if user does not pass an explicity datatype in prepInputs or postProcess (#39, @CeresBarros).

Bug fixes

  • fix problems with tests introduced by recent git2r update (@stewid, #36).
  • .prepareRasterBackedFile -- now will postpend an incremented numeric to a cached copy of a file-backed Raster object, if it already exists. This mirrors the behaviour of the .rda file. Previously, if two Cache events returned the same file name backing a Raster object, even if the content was different, it would allow the same file name. If either cached object was deleted, therefore, it would cause the other one to break as its file-backing would be missing.
  • options were wrongly pointing to spades.XXX and should have been reproducible.XXX.
  • copyFile did not perform correctly under all cases; now better handling of these cases, often sending to file.copy (slower, but more reliable)
  • extractFromArchive needed a new Checksum function call under some circumstances
  • several other minor bug fixes.
  • extractFromArchive -- when dealing with nested zips, not all args were passed in recursively (#37, @CeresBarros)
  • prepInputs -- arguments that were same as Cache were not being correctly passed internally to Cache, and if wrapped in Cache, it was not passed into prepInputs. Fixed.
  • .prepareFileBackedRaster was failing in some cases (specifically if it was inside a do.call) (#40, @CeresBarros).
  • Cache was failing under some cases of Cache(do.call, ...). Fixed.
  • Cache -- when arguments to Cache were the same as the arguments in FUN, Cache would "take" them. Now, they are correctly passed to the FUN.
  • preProcess -- writing to checksums may have produced a warning if CHECKSUMS.txt was not present. Now it does not.
  • numerous other minor bugfixes

Minor changes

  • most tests now use a standardized approach to attaching libraries, creating objects, paths, enabling easier, error resistent test building

- R
Published by achubaty over 7 years ago

reproducible - v0.2.1

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.1

New features

  • new functions:

    • convertPaths and convertRasterPaths to assist with renaming moved files.

  • prepInputs -- new features

    • alsoExtract now has more options (NULL, NA, "similar") and defaults to extracting all files in an archive (NULL).
    • skips postProcess altogether if no studyArea or rasterToMatch. Previously, this would invoke Cache even if there was nothing to postProcess.

Bug fixes

  • copyFile correctly handles directory names containing spaces.
  • makeMemoisable fixed to handle additonal edge cases.
  • other minor bug fixes.

- R
Published by achubaty over 7 years ago

reproducible - v0.2.0

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.2.0

New features

  • new functions:

    • prepInputs to aid in data downloading and preparation problems, solved in a reproducible, Cache-aware way.
    • postProcess which is a wrapper for sequences of several other new functions (cropInputs, fixErrors, projectInputs, maskInputs, writeOutputs, and determineFilename)
    • downloadFile can handle Google Drive and ftp/http(s) files
    • zipCache and mergeCache
    • compareNA does comparisons with NA as a possible value e.g., compareNA(c(1,NA), c(2, NA)) returns FALSE, TRUE

  • Cache -- new features:

    • new arguments showSimilar, verbose which can help with debugging
    • new argument useCache which allows turning caching on and off at a high level (e.g., options("useCache"))
    • new argument cacheId which allows user to hard code a result from a Cache
    • deprecated arguments: digestPathContent --> quick, compareRasterFileLength --> length
    • Cache arguments now propagate inward to nested Cache function calls, unless explicitly set on the inner functions
    • more precise messages provided upon each use
    • many more userTags added automatically to cache entries so much more powerful searching via showCache(userTags="something")

  • clearCache and showCache now give messages and require user intervention if request to clearCache would be large quantities of data deleted

  • memoise::memoise now used on 3rd run through an identical Cache call, dramatically speeding up in most cases

  • new options: reproducible.cachePath, reproducible.quick, reproducible.useMemoise, reproducible.useCache, reproducible.useragent, reproducible.verbose

  • asPath has a new argument indicating how deep should the path be considered when included in caching (only relevant when quick = TRUE)

  • New vignette on using Cache

  • Cache is parallel-safe, meaning there are tryCatch around every attempt at writing to SQLite database so it can be used safely on multi-threaded machines

  • bug fixes, unit tests, more imports for packages e.g., stats

  • updates for R 3.6.0 compact storage of sequence vectors

  • experimental pipes (%>%, %C%) and assign %<%

  • several performance enhancements

- R
Published by achubaty over 7 years ago

reproducible - v0.1.4

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.1.4

  • Cached pipe operator %C% -- use to begin a pipe sequence, e.g., Cache() %C% ...
  • Cache arg sideEffect can now be a path
  • Cache arg digestPathContent default changed from FALSE (was for speed) to TRUE (for content accuracy)
  • New function, searchFull, which shows the full search path, known alternatively as "scope", or "binding environments". It is where R will search for a function when requested by a user.
  • Uses memoise::memoise for several functions (loadFromLocalRepo, pkgDep, package_dependencies, available.packages) for speed -- will impact memory at the expense of speed

  • New Require function

    • attempts to create a lighter weight package reproducibility chain. This function is usable in a reproducible workflow: it includes both installing and loading of packages, it can maintain version numbers, and uses smart caching for speed. In tests, it can evaluate whether 20 packages and their dependencies (~130 packages) are installed and loaded quickly (i.e., if all TRUE, ~0.1 seconds). This is much slower than running require on those 20 packages, but require does not check for dependencies and deal with them if missing: it just errors. This speed should be fast enough for many purposes.
    • can accept uncommented name, if length 1.

  • remove dplyr from Imports

  • Add RCurl to Imports

  • change name of digestRaster to .digestRaster

- R
Published by achubaty about 8 years ago

reproducible - v0.1.3

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.1.3

  • fix R CMD check errors on Solaris that were not previously resolved

- R
Published by achubaty over 8 years ago

reproducible - v0.1.2

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.1.2

  • fix solaris check errors
  • fix bug in digestRaster affecting in-memory rasters
  • move rgdal to Suggests

- R
Published by achubaty over 8 years ago

reproducible - v0.1.1

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.1.1

  • cleanup examples and do run them (per CRAN)
  • add tests to ensure all exported (non-dot) functions have examples

- R
Published by achubaty over 8 years ago

reproducible - v0.1.0

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 0.1.0

  • A new package, which takes all caching utilities out of the SpaDES package.

- R
Published by achubaty over 8 years ago