Fix list parameter handling

[t0mdavid-m]

Caused issues with isobaric quantification

Summary by CodeRabbit

• Bug Fixes

  • Improved command execution for external tools: certain text-based options that were previously ignored are now correctly recognized and applied, ensuring tool runs reflect the specified parameters.

• Chores

  • Updated application version to 0.9.5 across configuration.
  • Refreshed Windows build artifacts and installer naming to use the new version.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

Incremented version identifiers from 0.9.4 to 0.9.5 in the Windows build workflow and settings. Adjusted CommandExecutor.run_topp to forward non-boolean, non-multiline string parameters as "- " when constructing TOPP tool commands.

Changes

Cohort / File(s)	Summary
Version bump (workflow & config) .github/workflows/build-windows-executable-app.yaml, settings.json	Updated APP_NAME to FLASHApp-0.9.5 and settings.json version to 0.9.5; no logic changes.
TOPP command construction logic src/workflow/CommandExecutor.py	Added branch to include plain string params (excluding 'true'/'false' and multiline) as "- " in command assembly.

Sequence Diagram(s)

sequenceDiagram
  autonumber
  actor User
  participant App
  participant ParameterManager as ParamManager
  participant CommandExecutor
  participant TOPPTool

  User->>App: Trigger TOPP run
  App->>ParamManager: Get parameters
  ParamManager-->>App: {key: value}*
  App->>CommandExecutor: run_topp(params)
  CommandExecutor->>CommandExecutor: Build command
  alt boolean true
    Note right of CommandExecutor: Append "-key"
  else boolean false
    Note right of CommandExecutor: Append nothing
  else multiline string
    Note right of CommandExecutor: Existing handling (unchanged)
  else plain string (new)
    Note right of CommandExecutor: Append "-key value"
  else non-string
    Note right of CommandExecutor: Append "-key str(value)"
  end
  CommandExecutor->>TOPPTool: Execute built command
  TOPPTool-->>CommandExecutor: Return status
  CommandExecutor-->>App: Result
  App-->>User: Report completion

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Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Fix sequence view #18 — Similar version/APP_NAME bumps in the same workflow and settings files.
• Make zip cross-os compatible #27 — Updates APP_NAME and settings.json version in parallel areas.
• Update Front Page #35 — Cohesive version alignment across workflow and settings as in this PR.

Poem

A hop, a skip—now nine point five,
I thump the ground: our builds alive!
Strings once shy now join the call,
“-key value” marching all.
Carrots queued, commands aligned,
Installer’s new—release time! 🍀🐇

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📥 Commits

Reviewing files that changed from the base of the PR and between d2e6f27 and b69ed07.

📒 Files selected for processing (3)

• .github/workflows/build-windows-executable-app.yaml (1 hunks)
• settings.json (1 hunks)
• src/workflow/CommandExecutor.py (1 hunks)

✨ Finishing Touches

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🧪 Generate unit tests

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix_list_parameter_handling

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