A minimal working example to reproduce the margins when pdfing WikiPathways pathway maps using selenium.

mwe_selenium_wikipathways.py

import base64
from selenium import webdriver
from selenium.webdriver.chrome.options import Options
from selenium.webdriver.common.print_page_options import PrintOptions


url = "https://example.com/"
url = "https://pathway-viewer.toolforge.org/embed/WP1"

window_width, window_height = 800, 600

chrome_options = Options()
chrome_options.add_argument("--headless")
driver = webdriver.Chrome(options=chrome_options)
driver.set_window_size(window_width, window_height)
driver.get(url)
driver.save_screenshot("screenshot.png")

cm_per_px = 2.54 / 72
print_options = PrintOptions()
print_options.background = False
print_options.page_width = window_width * cm_per_px
print_options.page_height = window_height * cm_per_px
print_options.margin_top = 0
print_options.margin_left = 0
print_options.margin_bottom = 0
print_options.margin_right = 0
with open("screenshot.pdf", mode="wb") as f:
    f.write(base64.b64decode(driver.print_page(print_options)))

The following fix will remove the margins, but the pdf size will be 600*450.

- print_options.page_width = window_width * cm_per_px
- print_options.page_height = window_height * cm_per_px
+ print_options.page_width = window_height * cm_per_px
+ print_options.page_height = window_height**2 / window_width * cm_per_px