Changes in version 0.99.6                        

Date: 2025-09-26 This version includes minor changes in Vignette to
align with Bioconductor submission standards.

                       Changes in version 0.99.5                        

Date: 2025-09-05

Fixes a merge issue between branches without adding changes to the
package.

                       Changes in version 0.99.4                        

Date: 2025-07-17

This version includes a major refactoring to align with Bioconductor
submission standards, addressing all points from the initial review.

SIGNIFICANT CHANGES

  - The runPsScan() function has been completely refactored. It no
    longer downloads files to the working directory. Instead, it now
    uses BiocFileCache to download and cache the ps_scan.pl script,
    prosite.dat, and pfscan executables. This makes the function robust,
    reproducible, and compliant with Bioconductor guidelines for
    handling external data.

  - All system calls have been updated to use system2() instead of
    system() or shell(), providing a safer and more portable way to run
    the external Perl script.

  - The interactive OS confirmation prompt (readline()) has been removed
    from runPsScan() to make the function fully non-interactive and
    suitable for automated scripts.

IMPROVEMENTS

  - Code Style:
    
      - All function names have been standardized to use camelCase for
        consistency (e.g., read.prosite is now readProsite,
        extract_protein_motifs is now extractProteinMotifs, etc.).
    
      - Removed all print() and cat() statements from package functions.
        Status updates now correctly use message().
    
      - Replaced paste() in stop() and warning() calls with sprintf().
    
      - Removed all uses of suppressWarnings(), ensuring that important
        data coercion warnings are visible to the user.

  - Documentation:
    
      - Added a package-level manual page, accessible via ?PMScanR.
    
      - Added examples to all exported functions, including an
        interactive() example for runPMScanRShiny().

  - Vignette:
    
      - The vignette has been updated to include the standard
        Bioconductor installation instructions.
    
      - Removed setwd() and unnecessary if (file.exists(...)) checks to
        make the code cleaner and more focused on workflow.

  - DESCRIPTION file:
    
      - Added URL and BugReports fields pointing to the GitHub
        repository.
    
      - Added Perl to the SystemRequirements field.
    
      - Added BiocFileCache to Imports.

  - NAMESPACE:
    
      - Removed all broad import() statements. The package now
        exclusively uses specific importFrom() tags for all dependencies
        (bslib, bsicons, reshape2, etc.), preventing namespace
        conflicts.

  - Unit Tests:
    
      - Added a suite of unit tests using testthat for core data
        processing functions (gff2matrix, extractProteinMotifs,
        freqPie), increasing package robustness.

BUG FIXES

  - Fixed a bug in gff2matrix() where it would error on empty data frame
    input. It now correctly returns an empty matrix.

  - Fixed a bug in extractProteinMotifs() where the regular expression
    failed to correctly parse motif headers, causing it to return an
    empty list. The parsing logic is now more robust.