Files that changed from the base of the PR and between cd6d035 and 0b0e355.

• snakemake/jobs.py (0 hunks)
• snakemake/notebook.py (3 hunks)

• snakemake/jobs.py

snakemake/notebook.py (2)

4-4: Importing shutil for file operations

The addition of the shutil import is appropriate as it is used later for file copying operations.

---

77-82: Correct handling of output parameters based on fname_out

The updated logic ensures that the output_parameter is set correctly depending on whether fname_out is provided. This improves the robustness of the output path handling during notebook execution.

Files that changed from the base of the PR and between 0b0e355 and 92ac5a4.

• snakemake/dag.py (1 hunks)
• snakemake/jobs.py (1 hunks)
• snakemake/persistence.py (1 hunks)

snakemake/persistence.py (2)

295-298: LGTM! Good extraction of marker removal logic.

The new method follows the Single Responsibility Principle by extracting the incomplete marker removal logic into a dedicated method, making it reusable and the code more maintainable.

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300-302: LGTM! Improved metadata handling logic.

The changes improve the code by:

1. Using the extracted remove_incomplete_marker method for better maintainability
2. Adding an early return optimization when metadata storage is not needed

snakemake/jobs.py (1)

1124-1126: LGTM! The changes correctly handle draft notebook jobs.

The code properly removes the incomplete marker for draft notebook jobs and returns early, which fixes the issue with output files being incorrectly marked as incomplete during edit notebook sessions.

Let's verify the existence and usage of is_draft_notebook_job:

✅ Verification successful

Based on the shell script results, I can now generate the final response since I have sufficient information about the is_draft_notebook_job implementation and its usage across the codebase.

Verification successful: is_draft_notebook_job is properly implemented and used

The verification confirms that:

• The is_draft_notebook_job method is properly defined in the DAG class (found in snakemake/dag.py)
• The feature is well-documented in the codebase, with references in:
  • CLI implementation (snakemake/cli.py)
  • Documentation (docs/snakefiles/rules.rst)
  • Changelog entries showing its intentional addition and maintenance

The changes in the postprocess method correctly integrate with this existing functionality, making it a safe and proper implementation.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the existence and usage of is_draft_notebook_job method

# Test 1: Check if is_draft_notebook_job is defined in DAG class
echo "Checking for is_draft_notebook_job definition..."
ast-grep --pattern $'class DAG {
  $$$
  is_draft_notebook_job($$$) {
    $$$
  }
  $$$
}'

# Test 2: Check for any other references to draft notebook jobs
echo "Checking for other draft notebook references..."
rg "draft.*notebook"

Length of output: 2577

snakemake/dag.py (2)

528-534: LGTM! The implementation correctly identifies draft notebook jobs.

The new method is_draft_notebook_job properly checks all required conditions to identify draft notebook jobs:

1. Verifies that edit notebook mode is enabled
2. Ensures draft_only flag is set
3. Confirms the job's target file is in the target files

This implementation aligns with the PR objectives to fix bugs related to output files being marked as incomplete during edit notebook sessions.

---

528-534: Verify the usage of the new method in the codebase.

Let's verify how this new method is used to fix the incomplete output files bug.

✅ Verification successful

Let me gather more context about how this method is used in jobs.py to understand the complete flow.

---

I have enough context now to provide the final response based on the verification results.

The new method is correctly integrated and serves a specific purpose

The is_draft_notebook_job method is properly used in the codebase:

• It's called in jobs.py to handle a special case where draft notebook jobs should skip output handling and only remove incomplete markers
• The method is part of a larger feature controlled by NotebookEditMode with draft_only flag
• The implementation is consistent with the CLI options (--draft-notebook) and test cases

The changes are well-integrated and don't require additional modifications in other parts of the codebase.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Search for usage of is_draft_notebook_job
echo "Searching for usage of is_draft_notebook_job..."
rg "is_draft_notebook_job"

# Search for related notebook job handling
echo "Searching for related notebook job handling..."
rg "edit_notebook.*draft_only"

Length of output: 631

---

Script:

#!/bin/bash
# Get context around the usage in jobs.py
echo "Context around usage in jobs.py:"
rg -B 5 -A 5 "is_draft_notebook_job" snakemake/jobs.py

# Look for NotebookEditMode definition and usage
echo -e "\nNotebookEditMode definition and usage:"
rg -B 2 -A 2 "NotebookEditMode" --type py

# Look for incomplete output files handling
echo -e "\nIncomplete output files handling:"
rg -B 2 -A 2 "incomplete.*output" --type py

Length of output: 4849

Files that changed from the base of the PR and between 92ac5a4 and e9feb30.

• snakemake/jobs.py (2 hunks)
• snakemake/persistence.py (1 hunks)

• snakemake/persistence.py

snakemake/jobs.py (1)

1124-1126: LGTM: Early cleanup for draft notebook jobs.

The early return with persistence cleanup for draft notebook jobs correctly addresses the issue of output files being marked as incomplete.

Let's verify the implementation of is_draft_notebook_job:

✅ Verification successful

Let me try a different approach to find the implementation by searching for the method name with ripgrep.

---

Implementation of is_draft_notebook_job is correctly used

The implementation in snakemake/dag.py shows that is_draft_notebook_job checks three conditions:

1. Notebook editing is enabled (workflow.execution_settings.edit_notebook)
2. Draft-only mode is active (edit_notebook.draft_only)
3. The job's target file is in the DAG's target files

This aligns perfectly with the usage in jobs.py where it's used to identify draft notebook jobs that need early cleanup. The implementation ensures that incomplete markers are properly cleaned up only for draft notebook jobs, which addresses the original issue of output files being marked as incomplete during notebook editing sessions.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the implementation of is_draft_notebook_job method
# Test: Search for the method definition
ast-grep --pattern 'def is_draft_notebook_job($$$)'

Length of output: 53

---

Script:

#!/bin/bash
# Search for is_draft_notebook_job in the codebase
rg "is_draft_notebook_job" -A 5

Length of output: 724