import re
from itertools import chain
from snakemake.linting import Linter, Lint, links, NAME_PATTERN
ABS_PATH_PATTERN = "(?P<quote>['\"])(?P<path>(?:/[^/\\n]+?)+?)(?P=quote)"
PATH_PATTERN = "(?P<quote>['\"])(?P<path>/?(?:[^/]+?/)+?(?:[^/]+?)?)(?P=quote)"
[docs]
class SnakefileLinter(Linter):
def item_desc_plain(self, snakefile):
return f"snakefile {snakefile}"
def item_desc_json(self, snakefile):
return {"snakefile": snakefile}
def read_item(self, snakefile):
return self.workflow.sourcecache.open(snakefile).read()
def lint_absolute_paths(self, snakefile, regex=re.compile(ABS_PATH_PATTERN)):
for match in regex.finditer(snakefile):
line = get_line(match, snakefile)
yield Lint(
title='Absolute path "{}" in line {}'.format(match.group("path"), line),
body="Do not define absolute paths inside of the workflow, since this "
"renders your workflow irreproducible on other machines. "
"Use path relative to the working directory instead, or make the path "
"configurable via a config file.",
links=[links.config],
)
def lint_mixed_func_and_rules(
self,
snakefile,
rule_regex=re.compile("rule .+?:"),
func_regex=re.compile("def .+?:"),
):
if rule_regex.search(snakefile) and func_regex.search(snakefile):
yield Lint(
title="Mixed rules and functions in same snakefile.",
body="Small one-liner functions used only once should be "
"defined as lambda expressions. Other functions should be collected "
"in a common module, e.g. 'rules/common.smk'. This makes the workflow "
"steps more readable.",
links=[links.includes],
)
def lint_path_add(
self,
snakefile,
regex1=re.compile(f"{NAME_PATTERN} *\\+ *{PATH_PATTERN}"),
regex2=re.compile(f"{PATH_PATTERN} *\\+ *{NAME_PATTERN}"),
):
for match in chain(regex1.finditer(snakefile), regex2.finditer(snakefile)):
line = get_line(match, snakefile)
yield Lint(
title=f"Path composition with '+' in line {line}",
body="This becomes quickly unreadable. Usually, it is better to endure some "
"redundancy against having a more readable workflow. Hence, just repeat common "
'prefixes. If path composition is unavoidable, use pathlib or (python >= 3.6) string formatting with f"...". ',
)
def lint_envvars(
self,
snakefile,
regex=re.compile(r"os.environ\[(?P<quote>['\"])(?P<name>.+)?(?P=quote)\]"),
):
for match in regex.finditer(snakefile):
line = get_line(match, snakefile)
name = match.group("name")
if name not in self.workflow.envvars:
yield Lint(
title="Environment variable {} used but not asserted with envvars directive in line {}.".format(
name, line
),
body="Asserting existence of environment variables with the envvars directive ensures proper error "
"messages if the user fails to invoke a workflow with all required environment variables defined. "
"Further, it allows snakemake to pass them on in case of distributed execution.",
links=[links.envvars],
)
def lint_singularity(self, snakefile, regex=re.compile("singularity:")):
for match in regex.finditer(snakefile):
line = get_line(match, snakefile)
yield Lint(
title="Deprecated singularity directive used for container definition in line {}.".format(
line
),
body="Use the container directive instead (it is agnostic of the underlying container runtime).",
links=[links.containers],
)
def lint_tab_usage(self, snakefile, regex=re.compile(r"^ *\t")):
for match in regex.finditer(snakefile):
line = get_line(match, snakefile)
yield Lint(
title=f"Tab usage in line {line}.",
body="Both Python and Snakemake can get confused when mixing tabs and spaces for indentation. "
"It is recommended to only use spaces for indentation.",
)
[docs]
def get_line(match, snakefile):
return snakefile[: match.start()].count("\n") + 1
