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fix: Draft notebook filename with wildcards and params. #1352

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merged 2 commits into from Jan 28, 2022
Merged

fix: Draft notebook filename with wildcards and params. #1352

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d71efa4
fix: Draft notebook filename with wildcards and params.
bilke Jan 26, 2022
b60fee4
fix: report generation with notebook wildcards / params.
bilke Jan 26, 2022
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2 changes: 2 additions & 0 deletions snakemake/notebook.py
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Expand Up @@ -13,6 +13,7 @@
from snakemake.common import is_local_file
from snakemake.common import ON_WINDOWS
from snakemake.sourcecache import SourceCache, infer_source_file
from snakemake.utils import format

KERNEL_STARTED_RE = re.compile(r"Kernel started: (?P<kernel_id>\S+)")
KERNEL_SHUTDOWN_RE = re.compile(r"Kernel shutdown: (?P<kernel_id>\S+)")
Expand Down Expand Up @@ -262,6 +263,7 @@ def notebook(
Load a script from the given basedir + path and execute it.
"""
draft = False
path = format(path, wildcards=wildcards, params=params)
if edit is not None:
if is_local_file(path):
if not os.path.isabs(path):
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6 changes: 5 additions & 1 deletion snakemake/report/__init__.py
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Expand Up @@ -281,7 +281,11 @@ def code(self):
self._rule.notebook
):
_, source, language, _ = script.get_source(
self._rule.notebook, self._rule.workflow.sourcecache, self._rule.basedir
self._rule.notebook,
self._rule.workflow.sourcecache,
self._rule.basedir,
wildcards=self.wildcards,
params=self.params,
)
language = language.split("_")[1]
sources = notebook.get_cell_sources(source)
Expand Down