def conda_update_all(name: str,
channels: str,
packages: Packages = (),
yes: bool = False) -> str:
"""Conda update all packages."""
update_cmd = get_conda_update_all_command(name, packages, yes=yes)
run_command(f"{update_cmd} {channels}", error=CondaEnvTrackerCondaError)
return update_cmd
def update_conda_environment(env_dir: PathLike) -> None:
"""Update the given environment with using environment yaml file.
This file only contains packages the user has specifically asked for
and does not contain dependencies.
"""
env_dir = Path(env_dir)
env_file = _get_env_file(env_dir)
run_command(f'conda env update --prune --file "{env_file}"',
error=CondaEnvTrackerCondaError)
def conda_install(name: str,
packages: Packages,
channel_command: str,
yes: bool = False) -> str:
"""Conda install the packages"""
install_cmd = get_conda_install_command(name, packages, yes)
run_command(f"{install_cmd} {channel_command}",
error=CondaEnvTrackerCondaError)
return install_cmd
def conda_remove(name: str,
packages: Packages,
channel_command: str,
yes: bool = False) -> str:
"""Conda remove the packages"""
remove_cmd = get_conda_remove_command(name, packages, yes=yes)
run_command(f"{remove_cmd} {channel_command}",
error=CondaEnvTrackerCondaError)
return remove_cmd
def pip_remove(name: str, packages: Packages, yes):
"""Pip uninstall package, can handle custom package removal"""
commands = []
if not is_current_conda_env(name):
commands.append(get_conda_activate_command(name=name))
commands.append(get_pip_remove_command(packages, yes))
command = " && ".join(commands)
logger.debug(f"Pip remove command: {command}")
run_command(command, error=PipRemoveError)
def test_exit_with_user_no(mocker):
run_mock = mocker.patch("conda_env_tracker.gateways.utils.run")
attrs = {
"return_value.return_code": 0,
"return_value.stderr": "",
"return_value.stdout": "Proceed ([y]/n)? n\n",
}
run_mock.configure_mock(**attrs)
with pytest.raises(SystemExit):
run_command(command="command", error=CondaEnvTrackerCondaError)
def test_run_command_error_message(mocker, caplog):
mocker.patch(
"conda_env_tracker.gateways.utils.run",
return_value=mocker.Mock(failed=True,
stdout="",
stderr="Error message"),
)
class CustomException(Exception):
"""Custom Exception"""
with pytest.raises(CustomException) as err:
run_command("command", CustomException)
assert caplog.records[0].message == "command"
assert str(err.value) == "Error message"
def conda_create(
name: str,
packages: Packages,
channels: ListLike = None,
yes: bool = False,
strict_channel_priority: bool = True,
) -> str:
"""Create a conda environment."""
create_cmd = get_conda_create_command(
name,
packages,
channels,
yes=yes,
strict_channel_priority=strict_channel_priority,
)
logger.debug(f"Conda creation command:\n{create_cmd}")
run_command(create_cmd, error=CondaEnvTrackerCondaError)
return create_cmd
def _run_r_remove(name: str, r_command: str) -> str:
"""Run r remove command"""
command = get_shell_command(name=name, r_command=r_command)
process = run_command(command, error=RError)
if process.failed:
raise RError(
f"Error removing R packages:\n{process.stderr}\nenvironment='{name}' and command='{r_command}'."
)
return command
def _run_r_install(name: str, packages: Packages, r_command: str) -> str:
"""Run r install command"""
command = get_shell_command(name=name, r_command=r_command)
process = run_command(command, error=RError)
if process.failed or _cannot_install_r_package(process.stderr, packages):
raise RError(
f"Error installing R packages:\n{process.stderr}\nenvironment='{name}' and command='{r_command}'."
)
return command
def update_r_environment(name: str, env_dir: PathLike) -> None:
"""Update the R packages in the environment."""
install_r = Path(env_dir) / "install.R"
if install_r.exists():
r_update_command = f'source("{install_r.absolute()}")'
command = get_shell_command(name=name, r_command=r_update_command)
process = run_command(command, error=RError)
if process.failed:
raise RError(
f"Error updating R packages in environment:\n{process.stderr}")