def test_conda_env_parsing_pass(self):
""" Parse a conda environment file sucessfully """
builder_obj = builder.EnvBuilder(
pf(PATH_GOOD_R_PKS, "rpackages.txt"),
pf(PATH_GOOD_CONDA_ENV, "environment.yml")
)
builder_obj.build()
def test_rpackage_parsing_and_warn(self):
""" Parse a r package file and warn if empty """
builder_obj = builder.EnvBuilder(
pf(PATH_EMPTY_R_PKS, "rpackages.txt"),
pf(PATH_GOOD_CONDA_ENV, "environment.yml"))
builder_obj.check_rpkgs()
expectations = {"passed": 0, "warned": 2, "failed": 0}
self.assess_builder_status(builder_obj, **expectations)
def test_rpackage_resolving_and_pass(self):
""" Try to resolve a given R package dependency from either
Anaconda's 'r'- or 'bioconda'-channel """
builder_obj = builder.EnvBuilder(
pf(PATH_GOOD_R_PKS, "rpackages.txt"),
pf(PATH_GOOD_CONDA_ENV, "environment.yml"))
builder_obj.check_rpkgs()
expectations = {"passed": 2, "warned": 1, "failed": 0}
self.assess_builder_status(builder_obj, **expectations)
def test_conda_env_extension(self):
""" Check, that resolved R packages are listed as dependencies in the
environment.yml """
builder_obj = builder.EnvBuilder(
pf(PATH_GOOD_R_PKS, "rpackages.txt"),
pf(PATH_GOOD_CONDA_ENV, "environment.yml"))
builder_obj.check_rpkgs()
builder_obj.extend_conda_env()
expectations = {"passed": 3, "warned": 1, "failed": 0}
self.assess_builder_status(builder_obj, **expectations)
self.assertEquals(len(builder_obj.conda_env.get("dependencies")), 3)