Fix newick output

[GavinHuttley]

Summary by Sourcery

Fix the Newick output formatting by removing quotes from the string representation of the tree dictionary. Enhance the 'ctree' function to handle cases where the tree is not generated by printing an error message and exiting. Update the test for 'ctree' to include the '-hp' flag in the arguments.

Bug Fixes:

• Fix the Newick tree output by ensuring the string representation of the tree dictionary is correctly formatted without quotes.

Enhancements:

• Add a check in the 'ctree' function to print an error message and exit if the tree is not generated.

Tests:

• Update the 'test_ctree' function to include the '-hp' flag in the arguments for testing.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR fixes issues with Newick tree output formatting by modifying the tree string representation and adding error handling. The changes also include some code cleanup by removing unnecessary blank lines.

Sequence diagram for ctree function error handling

sequenceDiagram
    participant User
    participant CLI as ctree CLI
    participant App as Application
    participant Util as dvs_util
    participant Sys as System

    User->>CLI: Run ctree command
    CLI->>App: Call app(seqs)
    alt Tree is None
        App-->>CLI: Return None
        CLI->>Util: Print error message
        CLI->>Sys: Exit with error
    else Tree is valid
        App-->>CLI: Return Tree
        CLI->>User: Write tree to outpath
    end

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File-Level Changes

Change	Details	Files
Modified tree string generation to properly handle Newick format	Added quote removal from tree string representation Added underscore_unmunge parameter to make_tree function call	src/diverse_seq/cluster.py
Added error handling for tree generation	Added check for invalid tree result Added error message display in red color Added system exit on tree generation failure	src/diverse_seq/cli.py
Updated CLI test configuration	Added -hp flag to hide progress in test command	tests/test_cli.py
Code cleanup	Removed unnecessary blank lines in multiple files	src/diverse_seq/cluster.py src/diverse_seq/cli.py src/diverse_seq/distance.py

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[sourcery-ai]

Hey @GavinHuttley - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟡 Testing: 1 issue found
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[coveralls]

Pull Request Test Coverage Report for Build 11715161343

Details

• 3 of 5 (60.0%) changed or added relevant lines in 2 files are covered.
• 2 unchanged lines in 2 files lost coverage.
• Overall coverage decreased (-0.1%) to 91.816%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/diverse_seq/cli.py	1	3	33.33%

Files with Coverage Reduction	New Missed Lines	%
src/diverse_seq/distance.py	1	91.27%
src/diverse_seq/cli.py	1	85.03%

Totals
Change from base Build 11623895953:	-0.1%
Covered Lines:	1178
Relevant Lines:	1283

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💛 - Coveralls