Script to (recursively) literally include all \input or \include, and put all files in the root folder (for submission in journals with an awful UI system)

flatten.py

"""
This script flattens the structure of this project in the output folder.
"""
import os
import re
import sys
import shutil
from datetime import date
from pathlib import Path


today = str(date.today())
OUTPUT_FOLDER = f"submission_{today}"

output_f = Path(OUTPUT_FOLDER)
if output_f.exists():
    shutil.rmtree(output_f)
output_f.mkdir(exist_ok=True)


def replace_contents(fname:str, reps):
    with open(fname, "rt") as f:
        data = f.read()
        for k in reps:
            data = data.replace(k, reps[k])
    with open(fname, "wt") as f:
        f.write(data)
        f.close()
        
        
def flatten(main_name:str):
    """ Taken and adapted from https://github.com/rekka/latex-flatten/blob/master/latex-flatten.py """
    with open(main_name,'r') as main:
        out = []
        for line in main.readlines():
            s = re.split('%', line, 2)
            tex = s[0]
            if len(s) > 1:
                comment = '%' + s[1]
            else:
                comment = ''

            chunks = re.split(r'\\(?:input|include)\{[^}]+\}', tex)

            if len(chunks) > 1:
                for (c, t) in zip(chunks, re.finditer(r'\\(input|include)\{([^}]+)\}', tex)):
                    cmd_name = t.group(1)
                    include_name = t.group(2)
                    if '.' not in include_name: include_name = include_name + '.tex'
                    if c.strip(): output.write(c + '\n')
                    out.append('% BEGIN \\' + cmd_name + '{' + include_name + '}\n')
                    include = flatten(include_name)
                    out.append(include)
                    out.append('% END \\' + cmd_name + '{' + include_name + '}\n')
                tail = chunks[-1] + comment
                if tail.strip(): output.write(tail)
            else:
                out.append(line)
    return "".join(out)


replacements = {}

for p in output_f.parent.rglob("*"):
    if p.is_dir():
        continue
    if str(p)[0] == "." or "/." in str(p):
        continue
    if str(p).startswith(OUTPUT_FOLDER):
        continue
    
    if str(p) == "main.tex":
        newmain = flatten(p)
        with open(output_f / "main.tex", "w") as f:
            f.write(newmain)
    
    if p.name.endswith(".tex"):
        continue
    
    needs_move = os.path.sep in str(p)
    
    print(str(p))
    if needs_move:
        newname = str(p).replace(os.path.sep, "_")
        shutil.copy(p, output_f / newname)
        replacements[str(p)] = newname
    else:
        shutil.copy(p, output_f)


for p in output_f.rglob("main.tex"):
    data = replace_contents(p, replacements)
    
os.system(f"cd {OUTPUT_FOLDER}; pdflatex main.tex; bibtex main; pdflatex main.tex; bibtex main; pdflatex main.tex; rm main.acn; main.aux; rm main.bbl; rm main.glo; rm main.ist;rm main.log ;rm main.out")