INFO: === SciTeX Writer v2.0.0a0 ===
INFO: Running ./scripts/shell/compile_supplementary.sh...
SUCC:     Configuration Loaded for supplementary (v2.0.0a0)

INFO: Running ./scripts/shell/compile_supplementary.sh...
INFO: [02:23:51] Starting: Dependency Check

INFO: Running ./scripts/shell/modules/check_dependancy_commands.sh...
INFO:     Warmup: 3ms
INFO:     Parallel checks: 281ms
SUCC:     Required tools:
      pdflatex             ✓
      bibtex               ✓
      latexdiff            ✓
      texcount             ✓
      xlsx2csv             ✓
      csv2latex            ✓
      parallel             ✓
SUCC: [02:23:52] Completed: Dependency Check (1s elapsed, 4s total)
INFO: [02:23:52] Starting: Bibliography Merge
SUCC: [02:23:52] Completed: Bibliography Merge (0s elapsed, 4s total)
INFO: [02:23:52] Starting: Citation Style
SUCC: Citation style already set to: unsrtnat
SUCC: [02:23:52] Completed: Citation Style (0s elapsed, 4s total)
INFO: [02:23:52] Starting: Parallel Processing (Figures, Tables, Word Count)
INFO:   Figure Processing:
    
    INFO: Running ./scripts/shell/modules/process_figures.sh ...
    INFO:     No figure source files found, creating placeholders only...
    INFO:     Cleaning jpg_for_compilation directory...
    INFO:     Skipping conversion pipeline (no source files)
    INFO:     Checking for missing figures...
    INFO:     Optimizing figures with Python script...
INFO:   Table Processing:
    
    INFO: Running ./scripts/shell/modules/process_tables.sh ...
    INFO:   [02:23:52] Initializing tables
    SUCC:   [02:23:52] Initializing tables (0s)
    INFO:   [02:23:52] Converting XLSX to CSV
    SUCC:   [02:23:52] Converting XLSX to CSV (0s)
    INFO:   [02:23:52] Ensuring captions exist
    SUCC:   [02:23:52] Ensuring captions exist (0s)
    INFO:   [02:23:52] Converting CSV to LaTeX
    INFO:     Using csv2latex for table processing
    SUCC:   [02:23:52] Converting CSV to LaTeX (0s)
    INFO:   [02:23:52] Gathering table files
    INFO:     Created table header template with instructions
    SUCC:     1 tables compiled
    SUCC:   [02:23:52] Gathering table files (0s)
INFO:   Word Count:
    
    INFO: Running ./scripts/shell/modules/count_words.sh ...
    SUCC:     Word counts updated:
    SUCC:       Figures: 0
    SUCC:       Tables: 0
    SUCC:       Supplementary text: 1077 words
SUCC: [02:23:52] Completed: Parallel Processing (0s elapsed, 4s total)
INFO: [02:23:52] Starting: TeX Compilation (Structure)

INFO: Running ./scripts/shell/modules/compilation_structure_tex_to_compiled_tex.sh ...
SUCC:     ./02_supplementary/supplementary.tex compiled
SUCC: [02:23:52] Completed: TeX Compilation (Structure) (0s elapsed, 4s total)
INFO: [02:23:52] Starting: PDF Generation

INFO: Running ./scripts/shell/modules/compilation_compiled_tex_to_compiled_pdf.sh ...
INFO:     Converting ./02_supplementary/supplementary.tex to PDF...
INFO:     Using latexmk (intelligent compilation)
WARN:     Compilation completed with warnings (check citations/references)
SUCC:     Total compilation: 2s
SUCC:     ./02_supplementary/supplementary.pdf ready (264K)
SUCC:     Symlink updated: ./02_supplementary/manuscript-latest.pdf -> supplementary.pdf (no archive yet)
SUCC: [02:23:55] Completed: PDF Generation (3s elapsed, 7s total)
INFO: [02:23:55] Starting: Diff Generation

INFO: Running ./scripts/shell/modules/process_diff.sh ...
INFO:     Creating diff between archive...
SUCC:     ./02_supplementary/supplementary_diff.tex created
INFO:     Compiling diff document...
INFO:     Using latexmk (intelligent compilation)
Rc files read:
  /etc/LatexMk
Latexmk: Run number 1 of rule 'pdflatex'
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
 \write18 enabled.
entering extended mode
Latexmk: Missing bbl file '02_supplementary/supplementary_diff.bbl' in following:
 No file supplementary_diff.bbl.
Latexmk: Summary of warnings from last run of *latex:
  Latex failed to resolve 2 reference(s)
Collected error summary (may duplicate other messages):
  pdflatex: Command for 'pdflatex' gave return code 1
      Refer to '02_supplementary/supplementary_diff.log' for details
Latexmk: Use the -f option to force complete processing,
 unless error was exceeding maximum runs, or warnings treated as errors.
SUCC:     ./02_supplementary/supplementary_diff.pdf ready (264K)
INFO:     Total time: 3s
SUCC: [02:23:58] Completed: Diff Generation (3s elapsed, 10s total)
INFO: [02:23:58] Starting: Archive/Versioning

INFO: Running ./scripts/shell/modules/process_archive.sh...
SUCC:     Version allocated as: v003
SUCC: [02:23:58] Completed: Archive/Versioning (0s elapsed, 10s total)
INFO: [02:23:58] Starting: Cleanup

INFO: Running ./scripts/shell/modules/cleanup.sh...
INFO:     Removing versioned files from current directory...
SUCC: [02:23:58] Completed: Cleanup (0s elapsed, 10s total)
INFO: [02:23:58] Starting: Directory Tree

INFO: ./scripts/shell/modules/custom_tree.sh...
SUCC:     ./02_supplementary/docs/tree.txt created
SUCC: [02:23:58] Completed: Directory Tree (0s elapsed, 10s total)

SUCC: ====================================================
SUCC: TOTAL COMPILATION TIME: 10s
SUCC: ====================================================
SUCC: See ./02_supplementary/logs/global.log