context("Dictionary") # we check that all pipeops that are exported are also in the dictionary, and can be constructed from there. test_that("Dictionary contains all PipeOps", { skip_on_cran() oldwarn = options(warn = 2) # make sure all caching private member vars are extended inflate = function(x) { x$label x$param_set$values$content$label x } # abstract pipeops that don't need to be in mlr_pipeops abstracts = c("PipeOp", "PipeOpEnsemble", "PipeOpTaskPreproc", "PipeOpTaskPreprocSimple", "PipeOpImpute", "PipeOpTargetTrafo") # param set values not hashable, because functions pval_unhashable = "missind" # constructor-args that have no defaults initargs = list( PipeOpBranch = list(options = 2), PipeOpChunk = list(outnum = 2), PipeOpCopy = list(outnum = 2), PipeOpFeatureUnion = list(innum = 2), PipeOpImputeLearner = list(learner = mlr_learners$get("classif.rpart")), PipeOpLearner = list(learner = mlr_learners$get("classif.rpart")), PipeOpLearnerCV = list(learner = mlr_learners$get("classif.rpart")), PipeOpClassifAvg = list(innum = 2), PipeOpRegrAvg = list(innum = 2), PipeOpUnbranch = list(options = 2), PipeOpFilter = list(filter = mlr3filters::FilterVariance$new(), param_vals = list(filter.nfeat = 1)), PipeOpMultiplicityExply = list(outnum = 2)) # The PipeOps that may have a default ID different from the mlr_pipeops key unequal_id = c("PipeOpLearner", "PipeOpLearnerCV", "PipeOpFilter") # function that recursively checks if an R6 Class Generator generates a subclass of PipeOp (*without* constructing it) inherits_from_pipeop = function(r6cg) { if (r6cg$classname == "PipeOp") { return(TRUE) } upper = r6cg$get_inherit() if (is.null(upper)) { return(FALSE) } inherits_from_pipeop(upper) } # get a list of objects that are exported by the mlr3pipelines package nspath = dirname(system.file("NAMESPACE", package = "mlr3pipelines")) exports = parseNamespaceFile(basename(nspath), dirname(nspath))$exports pkgenv = asNamespace("mlr3pipelines") pipeops = Filter(function(x) { objgen = get(x, pkgenv) "R6ClassGenerator" %in% class(objgen) && inherits_from_pipeop(objgen) }, ls(pkgenv, all.names = TRUE)) pipeops = intersect(pipeops, exports) pipeops = setdiff(pipeops, abstracts) # now 'pipeops' contains the names of all PipeOps that need to be present in the dictionary. # for each pipeop that *should* be in the dictionary, get the corresponding mlr_pipeops "key" # (or __NOT_FOUND__ if the pipeop is not in the dictionary) dictnames = map_chr(pipeops, function(pipe) { c(names(mlr_pipeops$items)[map_lgl(mlr_pipeops$items, function(gen) { identical(gen$value, get(pipe, pkgenv)) })], "__NOT_FOUND__")[1] }) expect("__NOT_FOUND__" %nin% dictnames, "Not all exported non-abstract PipeOps are in mlr_pipeops") tmp = setdiff(mlr_pipeops$keys(), dictnames) expect(length(tmp) == 0, sprintf("PipeOps in mlr_pipeops that are not exported: %s", paste(tmp, collapse = ","))) # as.atomic: converts non-atomic things to NULL as.atomic = function(x) if (is.atomic(x)) x # the loop now checks whether we can construct each pipeop from the dictionary *and* by itself for (idx in seq_along(dictnames)) { if (dictnames[[idx]] == "filter") next # TODO: remove this when https://github.com/mlr-org/mlr3filters/issues/162 is solved pogen = get(pipeops[idx], pkgenv) # the constructor, as found in the package namespace dictname = dictnames[idx] # the "key" in the mlr_pipeops dictionary args = initargs[[pipeops[idx]]] %??% list() # the required arguments, if any. e.g. 'outnum' for PipeOpCopy. test_obj = do.call(pogen$new, args) # test_obj: PipeOp object, constructed from constructor # check that mlr_pipeops key is the default ID if (pipeops[idx] %nin% unequal_id) { expect_equal(test_obj$id, dictname) } # check that mlr_pipeops$get() gives the same object as PipeOpXXX$new() does other_obj = do.call(mlr_pipeops$get, c(list(dictname), args)) expect_equal(other_obj, test_obj, info = paste(dictname, "$new test")) if (!dictname %in% pval_unhashable) { expect_equal(other_obj$hash, test_obj$hash, info = paste(dictname, "$new test")) } expect_equal(other_obj$phash, test_obj$phash, info = paste(dictname, "$new test")) # check that ID can be changed args$id = "TESTID" other_obj = do.call(mlr_pipeops$get, c(list(dictname), args)) expect_false(isTRUE(all.equal(other_obj, test_obj)), info = paste(dictname, "$new id test")) expect_false(isTRUE(all.equal(other_obj$hash, test_obj$hash)), info = paste(dictname, "$new id test")) expect_false(isTRUE(all.equal(other_obj$phash, test_obj$phash)), info = paste(dictname, "$new id test")) test_obj$id = "TESTID" other_obj = inflate(do.call(mlr_pipeops$get, c(list(dictname), args))) expect_equal(other_obj, test_obj, info = paste(dictname, "$new id test 2")) if (!dictname %in% pval_unhashable) { expect_equal(other_obj$hash, test_obj$hash, info = paste(dictname, "$new id test 2")) } expect_equal(other_obj$phash, test_obj$phash, info = paste(dictname, "$new id test 2")) expect_equal(inflate(do.call(pogen$new, args)), test_obj, info = dictname) tops = test_obj$param_set # we now check if hyperparameters can be changed through construction # we do this by automatically generating a hyperparameter value that deviates from the automatically constructed one. # However, for ParamUty we can't do that, so if there are only 'ParamUty' parameter we skip this part. eligibleparams = which( tops$class != "ParamUty" & # filter out discrete params with only one level, or the numeric parameters with $lower == $upper # Note that numeric parameters have 0 levels, and discrete parameters have $lower == $upper (== NA) ( (!is.na(tops$lower) & tops$lower != tops$upper) | (is.finite(tops$nlevels) & tops$nlevels > 1) ) ) if (length(eligibleparams)) { testingparam = tops$ids()[[eligibleparams[[1]]]] # we want to construct an object where the parameter value is *different* from the value it gets on construction by default. # For this we take a few candidate values and `setdiff` the original value origval = as.atomic(test_obj$param_set$values[[testingparam]]) if (tops$class[[testingparam]] %in% c("ParamLgl", "ParamFct")) { candidates = tops$levels[[testingparam]] } else { candidates = Filter(function(x) is.finite(x) && !is.na(x), c(tops$lower[[testingparam]], tops$upper[[testingparam]], tops$lower[[testingparam]] + 1, 0, origval + 1)) } val = setdiff(candidates, origval)[1] # construct the `param_vals = list(PARNAME = PARVAL)` construction argument args$param_vals = list(val) names(args$param_vals) = testingparam # check that the constructed object is different from the test_obj, but setting the test_obj's parameter # makes them equal again. dict_constructed = do.call(mlr_pipeops$get, c(list(dictname), args)) gen_constructed = do.call(pogen$new, args) expect_false(isTRUE(all.equal(dict_constructed, test_obj)), dictname) expect_false(isTRUE(all.equal(dict_constructed$hash, test_obj$hash)), dictname) # phash should be independent of this! expect_true(isTRUE(all.equal(dict_constructed$phash, test_obj$phash)), dictname) test_obj$param_set$values[[testingparam]] = val expect_equal(touch(dict_constructed), test_obj) expect_equal(inflate(touch(gen_constructed)), test_obj) } # $help() works and gives expected result expect_equal(test_obj$man, paste0("mlr3pipelines::", pipeops[idx]), info = paste(dictname, test_obj$man, "vs", paste0("mlr3pipelines::", pipeops[idx]))) # $label can be retrieved expect_string(test_obj$label) help_metainfo = paste(capture.output(print(str(test_obj$help()))), sep = "\n") expect_false(grepl("^LABEL COULD NOT BE RETRIEVED$", test_obj$label), info = paste(dictname, help_metainfo, sep = "\n")) if (identical(help, utils::help)) { # different behaviour if pkgload / devtools are doing help vs. vanilla R help() expect_equal( c(help(pipeops[idx], package = "mlr3pipelines")), c(test_obj$help()), info = paste("help for", dictname) ) expect_equal( # use c() to strip all attributes; they indicate the actual help()-call which is obviously different here. c(help(paste0("mlr_pipeops_", dictname), package = "mlr3pipelines")), c(test_obj$help()), info = paste("help for", dictname, "II") ) } else { expect_equal( help(pipeops[idx], package = "mlr3pipelines"), test_obj$help(), info = paste("help for", dictname) ) } } options(warn = oldwarn$warn) }) test_that("data.table of pipeops looks as it should", { potable = as.data.table(mlr_pipeops) expect_set_equal(colnames(potable), c("key", "label", "packages", "tags", "feature_types", "input.num", "output.num", "input.type.train", "input.type.predict", "output.type.train", "output.type.predict")) expect_equal(nrow(potable), length(mlr_pipeops$keys())) expect_set_equal(potable$key, mlr_pipeops$keys()) expect_equal(potable["branch"]$output.num, NA_integer_) expect_equal(potable["unbranch"]$input.num, NA_integer_) expect_equal(potable["branch"]$output.type.train, list("*")) expect_equal(potable["featureunion"]$input.type.train, list("Task")) expect_equal(potable["learner"]$output.type.train, list("NULL")) expect_equal(potable["learner_cv"]$input.type.train, list("TaskClassif")) }) test_that("GraphLearner is in mlr_learners", { expect_data_table(as.data.table(mlr_learners)) # can construct mlr_learners table # unfortunately we don't add GraphLearner to mlr_learners #expect_equal( # mlr_learners$get("graph", graph = PipeOpLearner$new(lrn("classif.rpart"))), # GraphLearner$new(Graph$new()$add_pipeop(PipeOpLearner$new(lrn("classif.rpart")))) #) # FIXME: depends on mlr-org/mlr3#328 # expect_error(mlr_learners$get("graph"), "'graph'.*'graph'") # Needs the argument 'graph' to construct 'graph' }) test_that("mlr_graphs dictionary", { expect_r6(mlr_graphs) dt = as.data.table(mlr_graphs) expect_data_table(dt, col.names = "unique") expect_true("key" %in% colnames(dt)) }) test_that("Cannot add pipeops with keys that invalidates the convenience for id incrementation", { copy = mlr_pipeops$clone(deep = TRUE) expect_error(copy$add("name_1", PipeOp), regexp = "grepl") })