add manuscript

Author: aeiwz

figures/graphical_abstract.png

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+"""
+Convert metbit_manuscript.md → metbit_manuscript.docx
+Handles: headings, paragraphs, bold/italic/code inline, tables, images,
+         horizontal rules, bullet lists, and blank-line paragraph breaks.
+"""
+
+import re
+import os
+from pathlib import Path
+
+from docx import Document
+from docx.shared import Pt, Cm, RGBColor, Inches
+from docx.enum.text import WD_ALIGN_PARAGRAPH
+from docx.enum.style import WD_STYLE_TYPE
+from docx.oxml.ns import qn
+from docx.oxml import OxmlElement
+
+HERE = Path(__file__).parent
+
+
+# ── helpers ───────────────────────────────────────────────────────────────────
+
+def set_run_font(run, name="Times New Roman", size=11, bold=False,
+                 italic=False, color=None):
+    run.font.name = name
+    run.font.size = Pt(size)
+    run.bold = bold
+    run.italic = italic
+    if color:
+        run.font.color.rgb = RGBColor(*color)
+
+
+def add_horizontal_rule(doc):
+    """Add a thin bottom-border paragraph as a visual divider."""
+    p = doc.add_paragraph()
+    p.paragraph_format.space_before = Pt(4)
+    p.paragraph_format.space_after  = Pt(4)
+    pPr = p._p.get_or_add_pPr()
+    pBdr = OxmlElement('w:pBdr')
+    bottom = OxmlElement('w:bottom')
+    bottom.set(qn('w:val'), 'single')
+    bottom.set(qn('w:sz'), '6')
+    bottom.set(qn('w:space'), '1')
+    bottom.set(qn('w:color'), '999999')
+    pBdr.append(bottom)
+    pPr.append(pBdr)
+
+
+def add_inline_runs(para, text, base_size=11, base_font="Times New Roman"):
+    """
+    Parse inline markdown (* ** ` [text](url)) and add styled runs.
+    Handles: **bold**, *italic*, `code`, **bold *nested italic* bold**
+    """
+    # tokenise into segments: (text, bold, italic, code)
+    # Strategy: walk character by character through a simple state machine
+    segments = []
+    i = 0
+    bold = False
+    italic = False
+    code = False
+    buf = []
+
+    def flush():
+        if buf:
+            segments.append((''.join(buf), bold, italic, code))
+            buf.clear()
+
+    while i < len(text):
+        # code span
+        if text[i] == '`' and not code:
+            flush()
+            code = True
+            i += 1
+            continue
+        if text[i] == '`' and code:
+            flush()
+            code = False
+            i += 1
+            continue
+
+        # bold (**) — must check before single *
+        if text[i:i+2] == '**' and not code:
+            flush()
+            bold = not bold
+            i += 2
+            continue
+
+        # italic (*)
+        if text[i] == '*' and not code:
+            flush()
+            italic = not italic
+            i += 1
+            continue
+
+        # skip markdown image syntax entirely — handled at block level
+        if text[i:i+2] == '![':
+            j = text.find(')', i)
+            i = j + 1 if j != -1 else i + 1
+            continue
+
+        # markdown link [label](url) → keep label only
+        if text[i] == '[' and not code:
+            end_bracket = text.find(']', i)
+            if end_bracket != -1 and end_bracket + 1 < len(text) and text[end_bracket+1] == '(':
+                end_paren = text.find(')', end_bracket)
+                if end_paren != -1:
+                    flush()
+                    label = text[i+1:end_bracket]
+                    buf.append(label)
+                    flush()
+                    i = end_paren + 1
+                    continue
+        buf.append(text[i])
+        i += 1
+
+    flush()
+
+    for seg_text, is_bold, is_italic, is_code in segments:
+        if not seg_text:
+            continue
+        run = para.add_run(seg_text)
+        if is_code:
+            run.font.name = "Courier New"
+            run.font.size = Pt(base_size - 0.5)
+            run.font.color.rgb = RGBColor(0x8B, 0x00, 0x00)
+        else:
+            run.font.name = base_font
+            run.font.size = Pt(base_size)
+            run.bold   = is_bold
+            run.italic = is_italic
+
+
+def parse_table(lines, doc):
+    """Convert markdown table lines into a docx table."""
+    # filter out separator rows (|---|---|)
+    data_rows = [l for l in lines
+                 if not re.match(r'^\s*\|[\s\-|:]+\|\s*$', l)]
+    if not data_rows:
+        return
+
+    rows = []
+    for row in data_rows:
+        cells = [c.strip() for c in row.strip().strip('|').split('|')]
+        rows.append(cells)
+
+    ncols = max(len(r) for r in rows)
+    table = doc.add_table(rows=len(rows), cols=ncols)
+    table.style = 'Table Grid'
+
+    for r_idx, row in enumerate(rows):
+        for c_idx, cell_text in enumerate(row):
+            if c_idx >= ncols:
+                break
+            cell = table.cell(r_idx, c_idx)
+            cell.text = ''
+            p = cell.paragraphs[0]
+            p.paragraph_format.space_before = Pt(2)
+            p.paragraph_format.space_after  = Pt(2)
+
+            is_header = (r_idx == 0)
+            add_inline_runs(p, cell_text, base_size=9.5)
+            if is_header:
+                for run in p.runs:
+                    run.bold = True
+                # shade header row
+                tc = cell._tc
+                tcPr = tc.get_or_add_tcPr()
+                shd = OxmlElement('w:shd')
+                shd.set(qn('w:val'), 'clear')
+                shd.set(qn('w:color'), 'auto')
+                shd.set(qn('w:fill'), '1B4F72')
+                tcPr.append(shd)
+                for run in p.runs:
+                    run.font.color.rgb = RGBColor(0xFF, 0xFF, 0xFF)
+
+    doc.add_paragraph()   # spacing after table
+
+
+def insert_image(doc, img_path_rel):
+    """Try to insert an image; skip gracefully if not found."""
+    img_path = HERE / img_path_rel
+    if img_path.exists():
+        try:
+            doc.add_picture(str(img_path), width=Inches(5.8))
+            last_para = doc.paragraphs[-1]
+            last_para.alignment = WD_ALIGN_PARAGRAPH.CENTER
+        except Exception as e:
+            doc.add_paragraph(f"[Image: {img_path_rel}]")
+    else:
+        doc.add_paragraph(f"[Image not found: {img_path_rel}]")
+
+
+# ── document setup ────────────────────────────────────────────────────────────
+
+def build_document(md_path: Path, out_path: Path):
+    doc = Document()
+
+    # Page margins
+    for section in doc.sections:
+        section.top_margin    = Cm(2.54)
+        section.bottom_margin = Cm(2.54)
+        section.left_margin   = Cm(3.17)
+        section.right_margin  = Cm(3.17)
+
+    # ── custom styles ─────────────────────────────────────────────────────────
+    styles = doc.styles
+
+    def _get_or_create(name, style_type=WD_STYLE_TYPE.PARAGRAPH):
+        return styles[name] if name in [s.name for s in styles] \
+               else styles.add_style(name, style_type)
+
+    # Title style
+    title_style = styles['Title']
+    title_style.font.name = "Times New Roman"
+    title_style.font.size = Pt(16)
+    title_style.font.bold = True
+    title_style.font.color.rgb = RGBColor(0x15, 0x43, 0x60)
+    title_style.paragraph_format.alignment = WD_ALIGN_PARAGRAPH.CENTER
+    title_style.paragraph_format.space_after = Pt(10)
+
+    # Heading 1
+    h1 = styles['Heading 1']
+    h1.font.name = "Times New Roman"
+    h1.font.size = Pt(13)
+    h1.font.bold = True
+    h1.font.color.rgb = RGBColor(0x15, 0x43, 0x60)
+    h1.paragraph_format.space_before = Pt(14)
+    h1.paragraph_format.space_after  = Pt(4)
+
+    # Heading 2
+    h2 = styles['Heading 2']
+    h2.font.name = "Times New Roman"
+    h2.font.size = Pt(11.5)
+    h2.font.bold = True
+    h2.font.italic = True
+    h2.font.color.rgb = RGBColor(0x1A, 0x52, 0x76)
+    h2.paragraph_format.space_before = Pt(10)
+    h2.paragraph_format.space_after  = Pt(3)
+
+    # Heading 3
+    h3 = styles['Heading 3']
+    h3.font.name = "Times New Roman"
+    h3.font.size = Pt(11)
+    h3.font.bold = True
+    h3.font.color.rgb = RGBColor(0x0E, 0x66, 0x55)
+    h3.paragraph_format.space_before = Pt(8)
+    h3.paragraph_format.space_after  = Pt(2)
+
+    # Normal body
+    normal = styles['Normal']
+    normal.font.name = "Times New Roman"
+    normal.font.size = Pt(11)
+    normal.paragraph_format.space_after  = Pt(6)
+    normal.paragraph_format.first_line_indent = Cm(0)
+
+    # ── parse markdown ────────────────────────────────────────────────────────
+    raw = md_path.read_text(encoding='utf-8')
+    lines = raw.splitlines()
+
+    # group consecutive table lines into blocks
+    processed = []
+    i = 0
+    while i < len(lines):
+        line = lines[i]
+        # detect start of a table block
+        if re.match(r'^\s*\|', line):
+            block = []
+            while i < len(lines) and re.match(r'^\s*\|', lines[i]):
+                block.append(lines[i])
+                i += 1
+            processed.append(('TABLE', block))
+        else:
+            processed.append(('LINE', line))
+            i += 1
+
+    # ── render ────────────────────────────────────────────────────────────────
+    for kind, payload in processed:
+        if kind == 'TABLE':
+            parse_table(payload, doc)
+            continue
+
+        line = payload
+
+        # ── headings ──────────────────────────────────────────────────────────
+        if line.startswith('#### '):
+            p = doc.add_paragraph(line[5:].strip(), style='Heading 3')
+            continue
+        if line.startswith('### '):
+            p = doc.add_paragraph(line[4:].strip(), style='Heading 3')
+            continue
+        if line.startswith('## '):
+            p = doc.add_paragraph(line[3:].strip(), style='Heading 1')
+            continue
+        if line.startswith('# '):
+            p = doc.add_paragraph(line[2:].strip(), style='Title')
+            continue
+
+        # ── horizontal rule ───────────────────────────────────────────────────
+        if re.match(r'^-{3,}\s*$', line):
+            add_horizontal_rule(doc)
+            continue
+
+        # ── blank line → paragraph break (already implicit, skip) ─────────────
+        if line.strip() == '':
+            continue
+
+        # ── image ─────────────────────────────────────────────────────────────
+        img_match = re.match(r'^!\[([^\]]*)\]\(([^)]+)\)\s*$', line)
+        if img_match:
+            insert_image(doc, img_match.group(2))
+            continue
+
+        # ── bullet list ───────────────────────────────────────────────────────
+        bullet_match = re.match(r'^(\s*)[-*]\s+(.+)$', line)
+        if bullet_match:
+            indent = len(bullet_match.group(1)) // 2
+            p = doc.add_paragraph(style='List Bullet')
+            p.paragraph_format.left_indent = Cm(0.75 + indent * 0.5)
+            p.paragraph_format.space_after = Pt(2)
+            add_inline_runs(p, bullet_match.group(2), base_size=10.5)
+            continue
+
+        # ── italic-only figure caption line (*Figure …*) ──────────────────────
+        if re.match(r'^\*Figure', line) or re.match(r'^\*\*Figure', line):
+            p = doc.add_paragraph()
+            p.alignment = WD_ALIGN_PARAGRAPH.CENTER
+            p.paragraph_format.space_before = Pt(4)
+            p.paragraph_format.space_after  = Pt(10)
+            add_inline_runs(p, line, base_size=9.5)
+            continue
+
+        # ── meta lines: Authors / affiliations / corresponding ────────────────
+        if line.startswith('**Authors**'):
+            p = doc.add_paragraph()
+            p.paragraph_format.space_before = Pt(4)
+            p.paragraph_format.space_after  = Pt(2)
+            p.alignment = WD_ALIGN_PARAGRAPH.CENTER
+            add_inline_runs(p, line, base_size=11)
+            continue
+
+        # ── general paragraph ─────────────────────────────────────────────────
+        p = doc.add_paragraph()
+        p.paragraph_format.space_after  = Pt(6)
+        p.paragraph_format.alignment = WD_ALIGN_PARAGRAPH.JUSTIFY
+
+        # affiliation / small-print lines (¹ ² * lines)
+        if line.startswith(('¹', '²', '³', '\\*', '*Contributor')):
+            p.paragraph_format.alignment = WD_ALIGN_PARAGRAPH.CENTER
+            add_inline_runs(p, line.lstrip('\\'), base_size=9.5)
+            continue
+
+        # keywords line
+        if line.startswith('**Keywords'):
+            p.paragraph_format.space_before = Pt(4)
+            add_inline_runs(p, line, base_size=10)
+            continue
+
+        add_inline_runs(p, line, base_size=11)
+
+    doc.save(str(out_path))
+    print(f"Saved → {out_path}")
+
+
+# ── entry point ───────────────────────────────────────────────────────────────
+if __name__ == '__main__':
+    md   = HERE / 'metbit_manuscript.md'
+    docx = HERE / 'metbit_manuscript.docx'
+    build_document(md, docx)