tests/testthat/test-install.R

In LTLA/jormungandR: Freezing Python Dependencies Inside Bioconductor Packages

# This checks that the version-controlling behavior of setupBasiliskEnv is correct.
# library(testthat); library(basilisk); source("setup.R"); source("test-install.R"); 

basilisk.utils::installConda()
target <- file.path(client.dir, "thingo")

test_that("setupBasiliskEnv refuses to work without all specified versions", {
    basilisk.utils::unlink2(target)
    expect_error(setupBasiliskEnv(target, "numpy"), "versions must be explicitly specified")
    expect_error(setupBasiliskEnv(target, "numpy>=10"), "versions must be explicitly specified")
    expect_error(setupBasiliskEnv(target, "numpy<=10"), "versions must be explicitly specified")
})

test_that("setupBasiliskEnv obtains the correct version of the packages", {
    basilisk.utils::unlink2(target)
    setupBasiliskEnv(target, c(test.pandas, test.pandas.deps))
    incoming <- basilisk:::.basilisk_freeze(target)
    expect_true(test.pandas %in% incoming)
    expect_true(all(test.pandas.deps %in% incoming))

    basilisk.utils::unlink2(target)
    setupBasiliskEnv(target, c(old.pandas, old.pandas.deps))
    incoming <- basilisk:::.basilisk_freeze(target)
    expect_true(old.pandas %in% incoming)
    expect_true(all(old.pandas.deps %in% incoming))

    # Listers also work as expected.
    expect_match(listPythonVersion(target), "^3")
    info <- listPackages(target)
    expect_true("pandas" %in% info$package)
})

test_that("setupBasiliskEnv will install Python 2.7 if requested", {
    # Python 2.7 binaries aren't provided for Arm64, so we'll just skip it.
    skip_on_os(c("mac", "linux"), arch="aarch64")

    basilisk.utils::unlink2(target)
    setupBasiliskEnv(target, "python=2.7")
    env.py <- basilisk.utils::getPythonBinary(target)
    py.ver <- system2(env.py, "--version", stderr=TRUE, stdout=TRUE)
    expect_match(py.ver, "2\\.7")

    # Same if we use the lister.
    expect_match(listPythonVersion(target), "^2\\.7")
})

test_that("setupBasiliskEnv works with PyPi-hosted packages", {
    basilisk.utils::unlink2(target)
    setupBasiliskEnv(target, old.pandas.deps, pip=old.pandas)

    incoming <- basilisk:::.basilisk_freeze(target)
    expect_true(old.pandas %in% incoming)
    expect_true(all(old.pandas.deps %in% incoming))
})

test_that("setupBasiliskEnv works with local packages", {
    basilisk.utils::unlink2(target)
    setupBasiliskEnv(target, packages=character(0), paths=system.file("example", "inst", "test_dummy", package="basilisk"))
    incoming <- basilisk:::.basilisk_freeze(target)
    expect_true("test_dummy==0.1" %in% incoming)
})

test_that("setupBasiliskEnv destroys directory on error", {
    basilisk.utils::unlink2(target)
    expect_error(setupBasiliskEnv(target, package="WHHEEEEEEEEEEEEEEEEEE==0.0.1"), 'failed to install')
    expect_false(file.exists(target))
})