def get_shell_command(name: str, r_command: str) -> str:
"""Handle conda env and call R code from command line."""
commands = []
if not is_current_conda_env(name=name):
commands.append(get_conda_activate_command(name=name))
r_command = _wrap_r_subprocess_command(r_command)
commands.append(r_command)
return " && ".join(commands)
def get_pip_version(name: str) -> Optional[str]:
"""Check for the version of pip (if installed)."""
if is_current_conda_env(name):
import pip
return pip.__version__
dependencies = get_dependencies(name=name)
return dependencies["conda"].get("pip", Package(name="pip")).version
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 pip_custom_install(name: str, package: Package):
"""Pip installing packages with custom urls"""
commands = []
if not is_current_conda_env(name):
commands.append(get_conda_activate_command(name=name))
pip_command = get_pip_custom_install_command(spec=package.spec)
logger.debug(f"Pip install command: {pip_command}")
commands.append(pip_command)
command = " && ".join(commands)
install = subprocess.run(command,
shell=True,
stderr=subprocess.PIPE,
encoding="UTF-8")
if install.returncode != 0:
raise PipInstallError(
f"Pip install {package.name} with custom url [{package.spec}] failed with message: {install.stderr}"
)
def pip_install(
name: str,
packages: Packages,
index_url: Union[str, ListLike] = PIP_DEFAULT_INDEX_URL,
) -> None:
"""Pip installing packages."""
commands = []
if not is_current_conda_env(name):
commands.append(get_conda_activate_command(name=name))
commands.append(get_pip_install_command(packages, index_url))
command = " && ".join(commands)
logger.debug(f"Pip install command: {command}")
install = subprocess.run(command,
shell=True,
stderr=subprocess.PIPE,
encoding="UTF-8")
if install.returncode != 0:
raise PipInstallError(
f"Pip install {[package.spec for package in packages]} failed with message: {install.stderr}"
)
def _ensure_correct_conda_env_activated(name: str, command: str):
"""If the current conda environment is not the named conda environment, then activate first."""
if not is_current_conda_env(name):
return get_conda_activate_command(name=name) + " && " + command
return command