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Use Sequence instead of list[] in parameters to build_primer_pairs() #86

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merged 3 commits into from
Nov 14, 2024

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@tfenne tfenne commented Nov 13, 2024

Fixes #84

@tfenne tfenne requested a review from msto November 13, 2024 22:27
@tfenne tfenne requested a review from nh13 as a code owner November 13, 2024 22:27
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codecov bot commented Nov 13, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 96.64%. Comparing base (8cbc1a2) to head (82cd798).
Report is 2 commits behind head on main.

Additional details and impacted files
@@           Coverage Diff           @@
##             main      #86   +/-   ##
=======================================
  Coverage   96.63%   96.64%           
=======================================
  Files          26       26           
  Lines        1696     1697    +1     
  Branches      330      330           
=======================================
+ Hits         1639     1640    +1     
  Misses         31       31           
  Partials       26       26           

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coderabbitai bot commented Nov 13, 2024

Walkthrough

The pull request introduces changes to two primary components: the .gitignore file and the picking.py module. In the .gitignore file, the directory .idea/ has been added to the list of ignored files, preventing version control from tracking this directory typically used by JetBrains IDEs. In the picking.py module, the build_primer_pairs function has been updated to change the parameter types for left_primers and right_primers from list[Oligo] to Sequence[Oligo], enhancing flexibility for the types of collections that can be accepted. An import statement for Sequence from collections.abc has been included to support this change. The score function remains unchanged, and the overall functionality and error handling of the build_primer_pairs function are preserved.

Assessment against linked issues

Objective Addressed Explanation
Update build_primer_pairs() to accept Iterable[Oligo] or Sequence[Oligo] (#84)

Possibly related PRs

Suggested reviewers

  • nh13: Suggested for review due to familiarity with the picking.py module and related changes.

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 33dfeb9 and 82cd798.

📒 Files selected for processing (1)
  • .gitignore (1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
  • .gitignore

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Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 8cbc1a2 and 33dfeb9.

📒 Files selected for processing (2)
  • .gitignore (1 hunks)
  • prymer/api/picking.py (2 hunks)
🔇 Additional comments (2)
prymer/api/picking.py (2)

19-19: LGTM! Good choice of using Sequence type.

Using Sequence from collections.abc is more appropriate than Iterable as it provides index access which is needed for accessing the primers in the function.


94-95: LGTM! Parameter type change improves flexibility while maintaining compatibility.

The change from list[Oligo] to Sequence[Oligo] successfully:

  • Allows subclasses of Oligo to be used (e.g., for storing QC attributes)
  • Maintains backward compatibility as list implements Sequence
  • Preserves all existing functionality as the function only needs sequence operations

Let's verify that the function only uses sequence operations:

✅ Verification successful

Parameter type change to Sequence[Oligo] is safe and appropriate

After analyzing the implementation, the function only uses sequence operations that are compatible with the Sequence protocol:

  • Basic iteration using for loops
  • Boolean check with any()
  • No list-specific methods or operations are used

The change improves API flexibility while maintaining full compatibility with existing code.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify that the function only uses operations compatible with Sequence
# Expected: Only sequence operations (iteration, len, indexing) should be found

# Search for method calls on left_primers and right_primers
rg -U --multiline '(left|right)_primers\.[a-zA-Z_]+\(' prymer/api/picking.py

# Search for any special list operations
rg -U --multiline '(left|right)_primers\[(.*?)\]' prymer/api/picking.py

Length of output: 152


Script:

#!/bin/bash
# Let's try a different approach to verify sequence operations
# Get the entire function implementation to analyze usage

# First, find the function name that contains these parameters
rg -l "left_primers.*right_primers.*Sequence\[Oligo\]" prymer/api/picking.py

# Then get the full function implementation with context
rg -U --multiline "def.*left_primers.*right_primers.*Sequence\[Oligo\]" -A 50 prymer/api/picking.py

Length of output: 180


Script:

#!/bin/bash
# Let's try a simpler approach to get the function content
# First, get the file content to see the actual implementation
cat prymer/api/picking.py

Length of output: 7063

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I don't see any reason not to implement coderabbit's suggestion here, I never would have caught that

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tfenne commented Nov 14, 2024

I don't see any reason not to implement coderabbit's suggestion here, I never would have caught that

I went the other way - the JetBrains section at the bottom was commented out and not that useful, and I think it's nice to have the ignores for all the IDEs in the same place.

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msto commented Nov 14, 2024

Makes sense to me.

I was more commenting that I never would have noticed the duplication - I'm pretty lenient about additions to the gitignore 😅

@tfenne tfenne merged commit 8c39970 into main Nov 14, 2024
7 checks passed
@tfenne tfenne deleted the tf_build_primers_list_to_sequence branch November 14, 2024 23:09
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Update build_primer_pairs() to accept Iterable[Oligo] or Sequence[Oligo]
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