fix: Issue #1253 (problems editing Jupyter Notebooks) #1255
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bhjolly
changed the title
johanneskoester
requested changes
Nov 17, 2021
snakemake/notebook.py
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| @@ -42,12 +42,12 @@ def draft(self, listen): | |||
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| nb["cells"].append(nbformat.v4.new_code_cell("# start coding here")) | |||
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| 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.
snakemake/script.py
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| @@ -393,7 +393,7 @@ def evaluate(self, edit=False): | |||
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| @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.
johanneskoester
approved these changes
Nov 23, 2021
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Kudos, SonarCloud Quality Gate passed!
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Description
Snakemake 6.10 was unable to open Jupyter Notebooks for editing as the use of LocalSourceFile objects for file paths was not supported in notebook.py or script.py (affecting Notebooks). This PR addresses that issue (logged as GH Issue #1253 )
QC
docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).