def diff(name: str) -> ListLike:
"""Get the difference between history yaml and local conda environment"""
env = Environment.read(name=name)
env_reader = EnvIO(env_directory=USER_ENVS_DIR / name)
version_diff_pkges, new_pkges, missing_pkges = History.history_diff(
env_name=name, env=env, env_reader=env_reader)
return missing_pkges + version_diff_pkges + new_pkges
def conda_update(
name: str,
specs: ListLike = (),
channels: ListLike = None,
all=False,
yes: bool = False,
strict_channel_priority: bool = True,
) -> Environment:
"""Install conda packages into the environment."""
env = Environment.read(name=name)
cleaned = process_specs(specs)
if all:
CondaHandler(env=env).update_all(
packages=cleaned,
channels=channels,
yes=yes,
strict_channel_priority=strict_channel_priority,
)
else:
CondaHandler(env=env).install(
packages=cleaned,
channels=channels,
yes=yes,
strict_channel_priority=strict_channel_priority,
)
_ask_user_to_sync(name=name, yes=yes)
return env
def pip_remove(name: str, specs: ListLike, yes: bool = False) -> Environment:
"""Remove pip packages including custom packages"""
env = Environment.read(name=name)
check_pip(env=env)
cleaned = process_specs(specs)
PipHandler(env=env).remove(packages=cleaned, yes=yes)
_ask_user_to_sync(name=name, yes=yes)
return env
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 test_missing_r_base():
with pytest.raises(RError) as err:
env = Environment.read(name="test_env_name_that_does_not_exist")
check_r_base_package(env=env)
assert (
str(err.value)
== f'"r-base" not installed.\nFound conda packages:\n[]\nMust have "r-base" conda installed to install R packages.'
)
def conda_remove(
name: str, specs: ListLike, channels: ListLike = None, yes: bool = False
) -> Environment:
"""Remove conda packages into the environment."""
env = Environment.read(name=name)
cleaned = clean_specs(specs)
CondaHandler(env=env).remove(packages=cleaned, channels=channels, yes=yes)
_ask_user_to_sync(name=name, yes=yes)
return env
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 pip_custom_install(
name: str, package: str, url_path: str, yes: bool = False
) -> Environment:
"""Install custom pip package"""
env = Environment.read(name=name)
check_pip(env=env)
cleaned = Package(name=package.lower(), spec=url_path)
PipHandler(env=env).custom_install(package=cleaned)
_ask_user_to_sync(name=name, yes=yes)
return env
def update_packages(name: str, specs: ListLike, remove: ListLike) -> Environment:
"""Update the history with local packages installed without cet cli."""
# pylint: disable=redefined-outer-name
env = Environment.read(name=name)
handler = CondaHandler(env=env)
if remove:
cleaned_remove = clean_specs(remove)
handler.update_history_remove(packages=cleaned_remove)
if specs:
cleaned = clean_specs(specs)
handler.update_history_install(packages=cleaned)
env.export()
return env
def pip_install(
name: str,
specs: ListLike,
index_url: Union[str, ListLike] = PIP_DEFAULT_INDEX_URL,
yes: bool = False,
) -> Environment:
"""Install pip packages into the environment."""
env = Environment.read(name=name)
check_pip(env=env)
cleaned = process_specs(specs, check_custom=True)
PipHandler(env=env).install(packages=cleaned, index_url=index_url)
_ask_user_to_sync(name=name, yes=yes)
return env
def conda_install(
name: str,
specs: ListLike,
channels: ListLike = None,
yes: bool = False,
strict_channel_priority: bool = True,
) -> Environment:
"""Install conda packages into the environment."""
env = Environment.read(name=name)
cleaned = process_specs(specs)
CondaHandler(env=env).install(
packages=cleaned,
channels=channels,
yes=yes,
strict_channel_priority=strict_channel_priority,
)
if not yes:
jupyter_kernel_install_query(name=name, packages=cleaned)
_ask_user_to_sync(name=name, yes=yes)
return env
def pull(name: str, yes: bool = False) -> Environment:
"""Pull the remote changes to local"""
env = Environment.read(name=name)
return _pull(env=env, yes=yes)
def push(name: str) -> Environment:
"""Push the local changes to remote"""
env = Environment.read(name=name)
return _push(env=env)
def remove(name: str, yes=False) -> None:
"""Remove the cet environment. Conda environment and any associated files."""
env = Environment.read(name=name)
env.remove(yes=yes)
def rebuild(name: str) -> Environment:
"""Rebuild the conda environment."""
env = Environment.read(name=name)
env.rebuild()
return env
def update_channels(name: str, channels: ListLike) -> Environment:
"""Add channels to the cet for future installs."""
env = Environment.read(name=name)
env.append_channels(channels)
return env
def test_missing_pip_pip_install():
env = Environment.read(name="test_env_name_that_does_not_exist")
env.dependencies = {"conda": {"python": "3.7"}}
with pytest.raises(PipInstallError) as err:
check_pip(env=env)
assert str(err.value) == ("Must have pip installed to install pip packages")
def pkg_list(name: str) -> dict:
"""A function to print the list of packages in the environment"""
env = Environment.read(name=name)
packages = get_packages(env)
print_package_list(packages)
return packages
def sync(name: str, yes: bool = False) -> Environment:
"""Automatically pull and push any changes needed"""
env = Environment.read(name=name)
env = _pull(env=env, yes=yes)
return _push(env=env)