[Doitsu]

AFAIK, a zipped epub archive needs be packed in certain sequence and the mimetype needs be added first and uncompressed.
The Sigil Plugin runner routines contain this Python 3 code that worked fine for me:

epub_mimetype = b'application/epub+zip'


def unzip_epub_to_dir(path_to_epub, destdir):
    f = open(pathof(path_to_epub), 'rb')
    sz = ZipFile(f)
    for name in sz.namelist():
        data = sz.read(name)
        name = name.replace("/", os.sep)
        filepath = os.path.join(destdir,name)
        basedir = os.path.dirname(filepath)
        if not os.path.isdir(basedir):
            os.makedirs(basedir)
        with open(filepath,'wb') as fp:
            fp.write(data)
    f.close()



def epub_zip_up_book_contents(ebook_path, epub_filepath):
    outzip = zipfile.ZipFile(pathof(epub_filepath), 'w')
    files = unipath.walk(ebook_path)
    if 'mimetype' in files:
        outzip.write(pathof(os.path.join(ebook_path, 'mimetype')), pathof('mimetype'), zipfile.ZIP_STORED)
    else:
        raise Exception('mimetype file is missing')
    files.remove('mimetype')
    for file in files:
        filepath = os.path.join(ebook_path, file)
        outzip.write(pathof(filepath),pathof(file),zipfile.ZIP_DEFLATED)
    outzip.close()

You can find the latest version (with all required imports, e.g. zipfile, os) on Github.

Since you're a Linux user, you could also use a shell script.

Alternatively, you could also run your Python code in Calibre Editor as a function or write a Sigil plugin.

This way all the packing and unpacking is handled by the hosting app.