def infer(cls, name: str, packages: Packages, channels: ListLike = None):
"""create conda_env_tracker environment by inferring to existing conda environment"""
if name == "base":
raise CondaEnvTrackerCondaError(
"Environment can not be created using default name base"
)
if name not in get_all_existing_environment():
raise CondaEnvTrackerCondaError(
f"Environment {name} can not be inferred, does not exist"
)
existing_packages = get_dependencies(name=name)
if "r-base" in existing_packages["conda"]:
existing_r_packages = get_r_dependencies(name=name)
else:
existing_r_packages = {}
user_packages = {"conda": Packages(), "pip": Packages(), "r": Packages()}
for package in packages:
if package.name in existing_packages.get("conda", Packages()):
user_packages["conda"].append(package)
elif package.name in existing_packages.get("pip", Packages()):
user_packages["pip"].append(package)
elif package.name in existing_r_packages:
raise RError(
"Cannot infer R packages, must run follow-up R install command.\n"
f"Found '{package.name}' in installed R packages {existing_r_packages}."
)
else:
raise CondaEnvTrackerCondaError(
f"Environment {name} does not have {package.spec} installed"
)
conda_create_cmd = get_conda_create_command(
name, user_packages["conda"], channels
)
specs = Actions.get_package_specs(
packages=user_packages["conda"], dependencies=existing_packages["conda"]
)
history = History(
name=name,
channels=Channels(channels),
packages=HistoryPackages.create(user_packages["conda"]),
logs=Logs.create(conda_create_cmd),
actions=Actions.create(name=name, specs=specs, channels=Channels(channels)),
debug=Debug.create(name=name),
)
env = cls(name=name, history=history)
if user_packages["pip"]:
handler = PipHandler(env=env)
handler.update_history_install(packages=user_packages["pip"])
env = handler.env
env.export()
return env
def __init__(self, name: str, history: Optional[History] = None):
self.name = name
self.history = history
self.local_io = EnvIO(env_directory=USER_ENVS_DIR / name)
self.dependencies = {}
if self.history:
self.dependencies = get_dependencies(name=self.name)
if self.history.packages.get("r"):
self.dependencies["r"] = get_r_dependencies(name=self.name)
def __init__(
self,
name: str,
history: Optional[History] = None,
dependencies: Optional[dict] = None,
):
self.name = name
self.history = history
self.local_io = EnvIO(env_directory=USER_ENVS_DIR / name)
if dependencies:
self.dependencies = dependencies
else:
self.dependencies = {}
if self.history:
self.dependencies = get_dependencies(name=self.name)
if self.history.packages.get("r"):
self.dependencies["r"] = get_r_dependencies(name=self.name)
if history:
self.history.packages.update_versions(dependencies=self.dependencies)
def test_parse_r_packages(mocker):
stdout = f"""> {r.LIST_R_PACKAGES}
Package Version
checkpoint 0.4.5
jsonlite 1.6
praise 1.0.0
utf8 1.1.4
>
>
"""
run_mock = mocker.patch("conda_env_tracker.gateways.r.subprocess.run")
run_mock.configure_mock(**{
"return_value.stdout": stdout,
"return_value.returncode": 0
})
actual = r.get_r_dependencies(name="env_name")
escaped_list_r_packages = r.LIST_R_PACKAGES.replace('"', r"\"")
expected_command = (f"source {CONDA_SH_PATH} && "
"conda activate env_name && "
f'R --quiet --vanilla -e "{escaped_list_r_packages}"')
run_mock.assert_called_once_with(
expected_command,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True,
encoding="UTF-8",
)
expected = {
"checkpoint": Package("checkpoint", "checkpoint", "0.4.5"),
"jsonlite": Package("jsonlite", "jsonlite", "1.6"),
"praise": Package("praise", "praise", "1.0.0"),
"utf8": Package("utf8", "utf8", "1.1.4"),
}
assert actual == expected
def update_dependencies(self, update_r_dependencies=False):
"""Update the list of all conda, pip, and R dependencies installed."""
self.dependencies = get_dependencies(name=self.name)
if update_r_dependencies:
self.dependencies["r"] = get_r_dependencies(name=self.name)