def test_r_install_double_quotes(setup_env, quote_mark, mocker):
double_quote_command = "install.packages('h2o')"
expected_command = double_quote_command.replace("'", r"\"")
command = double_quote_command.replace("'", quote_mark)
env = setup_env["env"]
env_io = setup_env["env_io"]
expected = copy.deepcopy(setup_env["expected"])
run_mock = mocker.patch("conda_env_tracker.gateways.r.run_command")
run_mock.configure_mock(**{
"return_value.failed": False,
"return_value.stderr": ""
})
mocker.patch(
"conda_env_tracker.env.get_r_dependencies",
mocker.Mock(return_value={"h2o": Package("h2o", "h2o", "3.24.0.3")}),
)
h2o = Package("h2o", command)
packages = Packages([h2o])
RHandler(env=env).install(packages=packages)
expected["logs"].append(f'R --quiet --vanilla -e "{expected_command}"')
expected["packages"]["r"] = {"h2o": h2o}
actual = env_io.get_history()
assert actual.logs == expected["logs"]
assert actual.packages == expected["packages"]
assert actual.actions[-1] == expected["logs"][-1]
actual_install_r = (env_io.env_dir / "install.R").read_text()
assert actual_install_r == command
def test_custom_r_install(setup_env, mocker):
command = 'install.packages("h2o")'
env = setup_env["env"]
env_io = setup_env["env_io"]
expected = copy.deepcopy(setup_env["expected"])
run_mock = mocker.patch("conda_env_tracker.gateways.r.run_command")
run_mock.configure_mock(**{
"return_value.failed": False,
"return_value.stderr": ""
})
mocker.patch(
"conda_env_tracker.env.get_r_dependencies",
mocker.Mock(return_value={"h2o": "3.24.0.3"}),
)
h2o = Package("h2o", command)
packages = Packages([h2o])
RHandler(env=env).install(packages=packages)
expected["logs"].append(f"R --quiet --vanilla -e '{command}'")
expected["packages"]["r"] = {"h2o": h2o}
actual = env_io.get_history()
assert actual.logs == expected["logs"]
assert actual.packages == expected["packages"]
assert actual.actions[-1] == expected["logs"][-1]
actual_install_r = (env_io.env_dir / "install.R").read_text()
assert actual_install_r == command
def test_two_same_package_r_install(setup_env, mocker):
"""Test that the second command replaces the first command (and updates the version of the package)"""
command_h2o_1 = 'install.packages("h2o")'
escaped_command_1 = command_h2o_1.replace('"', r"\"")
command_h2o_2 = 'install.packages("h2o", type="source", repos=(c("http://h2o-release.s3.amazonaws.com/h2o/latest_stable_R")))'
escaped_command_2 = command_h2o_2.replace('"', r"\"")
env = setup_env["env"]
env_io = setup_env["env_io"]
expected = copy.deepcopy(setup_env["expected"])
run_mock = mocker.patch("conda_env_tracker.gateways.r.run_command")
run_mock.configure_mock(**{
"return_value.failed": False,
"return_value.stderr": ""
})
mocker.patch(
"conda_env_tracker.env.get_r_dependencies",
side_effect=[
{
"h2o": Package("h2o", "h2o", "3.4.0.1")
},
{
"h2o": Package("h2o", "h2o", "3.24.0.5")
},
],
)
h2o_1 = Package("h2o", command_h2o_1)
h2o_2 = Package("h2o", command_h2o_2)
packages_1 = Packages([h2o_1])
packages_2 = Packages([h2o_2])
RHandler(env=env).install(packages=packages_1)
RHandler(env=env).install(packages=packages_2)
expected["logs"].append(f'R --quiet --vanilla -e "{escaped_command_1}"')
expected["logs"].append(f'R --quiet --vanilla -e "{escaped_command_2}"')
expected["packages"]["r"] = {"h2o": h2o_2}
actual = env_io.get_history()
assert actual.logs == expected["logs"]
assert actual.packages == expected["packages"]
assert actual.actions[-1] == expected["logs"][-1]
actual_install_r = (env_io.env_dir / "install.R").read_text()
assert actual_install_r == command_h2o_2
def r_remove(name: str, specs=ListLike, yes: bool = False) -> Environment:
"""R remove spec"""
env = Environment.read(name=name)
check_r_base_package(env=env)
packages = Packages.from_specs(specs)
RHandler(env=env).remove(packages=packages)
_ask_user_to_sync(name=name, yes=yes)
return env
def _handle_r_extra_log(env: Environment, history: History,
index: int) -> Environment:
log = history.logs[index]
if "remove.packages(" in log:
packages = history.logs.extra_removed_packages(index=index)
RHandler(env=env).remove(packages=packages)
else:
package_names = [
package_name
for package_name in history.revisions.diffs[index]["r"]["upsert"]
]
packages = Packages()
for package_name in package_names:
packages.append(
history.revisions.packages[index]["r"][package_name])
RHandler(env=env).install(packages=packages)
return env
def test_two_custom_r_install(setup_env, mocker):
"""Test that the second custom command replaces the first command (and updates the version of the package)"""
custom_command_h2o = 'install.packages("h2o")'
custom_command_trelliscopejs = (
'library("devtools"); install_github("hafen/trelliscopejs")')
env = setup_env["env"]
env_io = setup_env["env_io"]
expected = copy.deepcopy(setup_env["expected"])
run_mock = mocker.patch("conda_env_tracker.gateways.r.run_command")
run_mock.configure_mock(**{
"return_value.failed": False,
"return_value.stderr": ""
})
mocker.patch(
"conda_env_tracker.env.get_r_dependencies",
return_value={
"h2o": Package("h2o", "h2o", "3.4.0.1"),
"trelliscopejs": Package("trelliscopejs", "trelliscopejs",
"0.1.7"),
},
)
h2o = Package("h2o", custom_command_h2o)
trelliscopejs = Package("trelliscopejs", custom_command_trelliscopejs)
RHandler(env=env).install(packages=Packages([h2o]))
RHandler(env=env).install(packages=Packages([trelliscopejs]))
expected["logs"].append(f"R --quiet --vanilla -e '{custom_command_h2o}'")
expected["logs"].append(
f"R --quiet --vanilla -e '{custom_command_trelliscopejs}'")
expected["packages"]["r"] = {"h2o": h2o, "trelliscopejs": trelliscopejs}
actual = env_io.get_history()
assert actual.logs == expected["logs"]
assert actual.packages == expected["packages"]
assert actual.actions[-1] == expected["logs"][-1]
actual_install_r = (env_io.env_dir / "install.R").read_text()
expected_install_r = "\n".join(
[custom_command_h2o, custom_command_trelliscopejs])
assert actual_install_r == expected_install_r
def r_install(
name: str, package_names: ListLike, commands: ListLike, yes: bool = False
) -> Environment:
"""Install R packages with corresponding R command."""
env = Environment.read(name=name)
check_r_base_package(env=env)
packages = clean_r_specs(package_names=package_names, commands=commands)
RHandler(env=env).install(packages=packages)
_ask_user_to_sync(name=name, yes=yes)
return env
def test_remove_r_package(setup_env, mocker):
env = setup_env["env"]
env_io = setup_env["env_io"]
expected = copy.deepcopy(setup_env["expected"])
r_command = 'install.packages("h2o")'
escaped_command = r_command.replace('"', r"\"")
run_mock = mocker.patch("conda_env_tracker.gateways.r.run_command")
run_mock.configure_mock(**{
"return_value.failed": False,
"return_value.stderr": ""
})
mocker.patch(
"conda_env_tracker.env.get_r_dependencies",
mocker.Mock(return_value={"h2o": Package("h2o", "h2o", "3.24.0.3")}),
)
handler = RHandler(env=env)
h2o = Package("h2o", r_command)
packages = Packages([h2o])
handler.install(packages=packages)
install_log = f'R --quiet --vanilla -e "{escaped_command}"'
expected["logs"].append(install_log)
expected["packages"]["r"] = {"h2o": h2o}
actual = env_io.get_history()
assert actual.logs == expected["logs"]
assert actual.packages == expected["packages"]
assert actual.actions[-1] == install_log
expected_install_r = r_command
actual_install_r = (env_io.env_dir / "install.R").read_text()
assert actual_install_r == expected_install_r
mocker.patch("conda_env_tracker.r.r_remove")
handler.remove(packages=packages)
actual = env_io.get_history()
command = r"remove.packages(c(\"h2o\"))"
expected["packages"].pop("r")
expected["logs"].append(f'R --quiet --vanilla -e "{command}"')
assert actual.logs == expected["logs"]
assert actual.packages == expected["packages"]
assert actual.actions[-1] == expected["logs"][-1]
assert not (env_io.env_dir / "install.R").exists()
def _install_missing_r_packages(
env: Environment, local_history: History, remote_history: History
) -> Environment:
local_r_packages = local_history.packages.get("r", {})
remote_r_packages = remote_history.packages.get("r", {})
handler = RHandler(env=env)
packages_to_install = Packages()
packages_to_add_to_history = Packages()
for package_name, package in local_r_packages.items():
if package_name not in remote_r_packages:
if package_name in env.dependencies.get("r", {}):
packages_to_add_to_history.append(package)
else:
packages_to_install.append(package)
if packages_to_install:
handler.install(packages_to_install)
if packages_to_add_to_history:
handler.update_history_install(packages_to_add_to_history)
return env
def _handle_r_extra_log(env: Environment, history: History, index: int) -> Environment:
log = history.logs[index]
if "remove.packages(" in log:
packages = history.logs.extra_removed_packages(index=index)
RHandler(env=env).remove(packages=packages)
return env