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Implementing the snipe qc command. #11

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merged 7 commits into from
Oct 15, 2024
Merged

Implementing the snipe qc command. #11

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89cb1d6
remove dead usecase
mr-eyes Oct 13, 2024
c0a5618
FracMinHash not MinHash as description
mr-eyes Oct 13, 2024
dbbab13
checkpoint in QC
mr-eyes Oct 14, 2024
4f216f1
separating SnipeSig
mr-eyes Oct 14, 2024
4ac09c3
more testing
mr-eyes Oct 14, 2024
5e4d6dd
adding var options
mr-eyes Oct 15, 2024
2f8b29d
handling empty signatures
mr-eyes Oct 15, 2024
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1 change: 1 addition & 0 deletions .pylintrc
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
disable=line-too-long
4 changes: 4 additions & 0 deletions .vscode/settings.json
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Expand Up @@ -2,4 +2,8 @@
"python.analysis.extraPaths": [
"./src"
]
// # show line numbers in jupyter notebooks
// "jupyter.lineNumbers": "on",
// # show line numbers in jup

}
3 changes: 3 additions & 0 deletions docs/docs/Sketch.md
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@@ -0,0 +1,3 @@
# Python API Documentation

::: snipe.api.sketch
2 changes: 1 addition & 1 deletion docs/docs/SnipeSig.md
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@@ -1,3 +1,3 @@
# Python API Documentation

::: snipe.api
::: snipe.api.snipe_sig
1 change: 1 addition & 0 deletions docs/mkdocs.yml
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Expand Up @@ -82,6 +82,7 @@ nav:
- API:
- SnipeSig: SnipeSig.md
- ReferenceQC: ReferenceQC.md
- Sketch: Sketch.md
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💡 Codebase verification

Action Required: Update Documentation Path

The file Sketch.md was found at docs/docs/Sketch.md, but the navigation entry references it as Sketch.md under the docs directory. Please update the navigation path in mkdocs.yml to docs/docs/Sketch.md or move Sketch.md to docs/Sketch.md to ensure consistency.

  • Option 1: Update mkdocs.yml: 
    - Sketch: docs/docs/Sketch.md
  • Option 2: Move Sketch.md to docs/Sketch.md
🔗 Analysis chain

LGTM! New API documentation added.

The addition of "Sketch: Sketch.md" to the API section of the navigation is consistent with the existing structure and naming conventions.

To ensure the new documentation file exists, run the following command:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Verify the existence of the Sketch.md file
fd -t f "Sketch.md" docs

Length of output: 49

Script:

#!/bin/bash
# Perform a case-insensitive search for Sketch.md in the docs directory
fd -ti f "sketch\.md" docs

Length of output: 197

Script:

#!/bin/bash
# Perform a case-insensitive search for Sketch.md in the docs directory
fd -t f -i "sketch\.md" docs

Length of output: 50

- CLI: cli.md


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4 changes: 4 additions & 0 deletions pyproject.toml
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Expand Up @@ -29,6 +29,10 @@ dependencies = [
"numpy",
"pyfastx",
"pathos",
"pandas",
"tqdm",
"lzstring",
"rapidfuzz",
]

[project.optional-dependencies]
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