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fix: Issue #1253 (problems editing Jupyter Notebooks) #1255

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merged 2 commits into from Nov 23, 2021
Merged

fix: Issue #1253 (problems editing Jupyter Notebooks) #1255

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e5e96da
fix bug introduced by LocalSourceFile paths
bhjolly Nov 10, 2021
dafcec9
Use get_path_or_uri from SourceFile.
johanneskoester Nov 23, 2021
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8 changes: 4 additions & 4 deletions snakemake/notebook.py
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Expand Up @@ -42,12 +42,12 @@ def draft(self, listen):

nb["cells"].append(nbformat.v4.new_code_cell("# start coding here"))

os.makedirs(os.path.dirname(self.local_path), exist_ok=True)
os.makedirs(os.path.dirname(str(self.local_path)), exist_ok=True)
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Can you use self.local_path.get_path_or_uri() here? That is more idiomatic with the new API.

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And in all str() occurrences below as well.


with open(self.local_path, "wb") as out:
with open(str(self.local_path), "wb") as out:
out.write(nbformat.writes(nb).encode())

self.source = open(self.local_path).read()
self.source = open(str(self.local_path)).read()

self.evaluate(edit=listen)

Expand Down Expand Up @@ -101,7 +101,7 @@ def execute_script(self, fname, edit=None):
for cell in nb["cells"]:
cell["outputs"] = []

nbformat.write(nb, self.local_path)
nbformat.write(nb, str(self.local_path))

def insert_preamble_cell(self, preamble, notebook):
import nbformat
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2 changes: 1 addition & 1 deletion snakemake/script.py
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Expand Up @@ -393,7 +393,7 @@ def evaluate(self, edit=False):

@property
def local_path(self):
path = self.path[7:]
path = str(self.path)#[7:]
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Here, I'd rather rely on the SourceFile methods for checking whether the path is absolute or not and so on.

if not os.path.isabs(path):
return smart_join(self.basedir, path)
return path
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