def process_r_specs(package_names: ListLike, commands: ListLike) -> Packages:
"""Generate the install commands for R packages and return as the package spec."""
if len(package_names) != len(commands):
raise RError(
f"Must have same number of package names ({len(package_names)}) and install commands ({len(commands)})."
)
packages = Packages()
for package_name, command in zip(package_names, commands):
packages.append(Package(package_name, spec=command))
return packages
def parse(cls, history_section: dict):
"""Parse the history file and create the packages."""
packages_instance = cls()
for source, packages in history_section.items():
source_packages = Packages()
for name, spec in packages.items():
if spec == "*":
source_packages.append_spec(name)
else:
source_packages.append(Package(name, spec))
packages_instance.update_packages(packages=source_packages,
source=source)
return packages_instance
def clean_r_specs(package_names: ListLike, commands: ListLike) -> Packages:
"""Cleaning all R package specs and converting to a package class."""
packages = Packages()
for package_name, command in zip_longest(package_names, commands):
if not package_name or not command:
raise RError(
(
"Must have same number of R package names and install commands.\n"
f"Package names: {package_names}\n"
f"and install commands: {commands}"
)
)
packages.append(Package(package_name, command))
return packages
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 parse(cls, history_section: dict):
"""Parse the history file and create the packages."""
packages_instance = cls()
for source, packages in history_section.items():
source_packages = Packages()
for name, spec in packages.items():
if spec == "*":
source_packages.append_spec(name)
elif spec[0].isdigit() and all(
letter.isalnum() or letter in [".", "=", "_"]
for letter in spec):
source_packages.append_spec(name + cls.separators[source] +
spec)
else:
source_packages.append(Package(name, spec))
packages_instance.update_packages(packages=source_packages,
source=source)
return packages_instance
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 extract_r_packages(self, index: int) -> Optional[Packages]:
"""Extract R packages with versions (if the version was specified in the log)."""
if self[index].startswith(R_COMMAND):
r_packages = Packages()
quote = '"'
package_names = self._get_r_package_names(self[index])
start = self[index].index(quote) + len(quote)
r_commands = self[index]
for package_name in package_names:
i_name = r_commands.index(package_name)
try:
end = r_commands.index(";", i_name)
except ValueError:
end = r_commands.rindex(quote, i_name)
spec = r_commands[start:end].strip()
start = end + 1
r_packages.append(
Package(package_name, spec.replace(r"\"", '"')))
return r_packages
return None