Some links do not rendered in the PDF

[Remi-Gau]

Note that some links are not rendered in the pdf.

For example the link at the top of the genetic section:

[`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

I think this is because of the back tick in the square brackets.

Originally posted by @Remi-Gau in #1711 (comment)

[Remi-Gau]

OK the solution to this one (so far)

The following won't be turned into a link during the pdd build
-   [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
-   [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb) 

This will
[`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

[sappelhoff]

interesting, thanks for investigating!

So we'd have to:

1. in the PDF build, check if list items are links
2. turn these selective lists that contain such items into non-lists

??

what about:

will this link render?
    -   A link follows: [`a link`](https://google.com)

[Remi-Gau]

OK I tried a bunch of things:

!!! example "Example datasets"

    The following example dataset with genetics data have been formatted using this specification
    and can be used for practical guidance when curating a new dataset.

    -   [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
    -   foo bar [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
    -   [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

-   [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
-   foo bar [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
-   [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

- [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
- foo bar [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

[`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

and I got this:

[sappelhoff]

so the admonitions are the problem 🤔

don't get it though, as your script removes the admonition completely:

bids-specification/pdf_build_src/remove_admonitions.py

Lines 16 to 54 in 4c642bd

	def remove_admonitions(
	input_folder: str | Path, output_folder: str | Path, indent: str = None
	):
	if indent is None:
	indent = INDENT
	md_files = Path(input_folder).glob("**/*.md")
	for file in md_files:
	with open(file, "r", encoding="utf8") as f:
	content = f.readlines()
	output_file = Path(output_folder) / file.relative_to(input_folder)
	output_file.parent.mkdir(parents=True, exist_ok=True)
	print(f"processing: {file}\n to: {output_file}")
	with open(output_file, "w", encoding="utf8") as f:
	is_admonition = False
	counter = 0
	for line in content:
	if any(line.startswith(x) for x in ADMONITION_DELIMITERS):
	is_admonition = True
	counter = 0
	continue
	# skip first line after admonition
	if is_admonition and counter == 0:
	counter += 1
	continue
	if not line.startswith(indent):
	is_admonition = False
	if is_admonition:
	line = line.lstrip(indent)

[Remi-Gau]

let me test the script the blurb above

[Remi-Gau]

OK if I run the remove_admonition code on the blurb above it gives this

The following example dataset with genetics data have been formatted using this specification
and can be used for practical guidance when curating a new dataset.

    -   [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
    -   foo bar [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
    -   [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

-   [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
-   foo bar [`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
-   [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

- [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)
- foo bar [UK biobank](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

[`UK biobank`](https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb)

So my code is too silly... Will try to fix.