[INFRA] PDF build on CI raises warnings: duplicate links

[sappelhoff]

I also find several issues in the "build pdf" step regarding images and characters not being available in a font. Worth investigating later.

These warnings look legitimate, especially in reference to the image files:

[WARNING] Duplicate link reference '[deprecated]' at line 2394 column 1
[WARNING] Duplicate link reference '[string]' at line 2396 column 1
[WARNING] Duplicate link reference '[strings]' at line 2398 column 1
[WARNING] Duplicate link reference '[uri]' at line 2414 column 1
[WARNING] Duplicate link reference '[strings]' at line 4302 column 1
[WARNING] Duplicate link reference '[string]' at line 4461 column 1
[WARNING] Duplicate link reference '[derived-dataset-description]' at line 4552 column 1
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pcasl_sequence.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pcasl_labeling_pulses.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pasl_boluscutoff_false.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png': replacing image with description
[WARNING] Could not fetch resource '../04-modality-specific-files/images/asl_flowchart.png': replacing image with description
[WARNING] Missing character: There is no └ (U+2514) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ─ (U+2500) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ─ (U+2500) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no └ (U+2514) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ─ (U+2500) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ─ (U+2500) in font [lmmono10-regular]:!
[WARNING] Missing character: There is no ├ (U+251C) in font [lmmono10-regular]:!

Originally posted by @sappelhoff in #759 (comment)

there is also another known warning :

[WARNING] Deprecated: markdown_github. Use gfm instead.

That's something we do deliberately, because gfm breaks our tables, if I remember correctly.

EDIT: The missing font characters for "pipe symbols" has been fixed in #837

[sappelhoff]

the issue on not-found images is due to the fact that pandoc searches for relative paths relative to the working directory.

And currently, the working directory (where pandoc is invoked) is in ./pdf_build_src/src_copy/src.

(src_copy/src is temporary, the build output will be in ./pdf_build_src)

I'll fix this in #767

[sappelhoff]

The warnings about missing characters can be fixed by setting a mono font that supports unicode in the header setup. Something like this \setmonofont{DejaVu Sans Mono} added below these lines:

bids-specification/pdf_build_src/header_setup.tex

Lines 4 to 5 in a280ae8

	\usepackage{fontspec}
	\setmainfont{Symbola}

However, that results in the following (screenshot):

I guess somebody needs to try a couple of fonts and find out what works and what doesn't.

The issue of missing characters isn't too bad, because even when they are missing, the rendering looks good:

[sappelhoff]

Finally, the "duplicate links" issue can probably be fixed reasonably well in

bids-specification/pdf_build_src/process_markdowns.py

Line 1 in a280ae8

"""Process the markdown files.

... but it's also not too bad, because it does not affect the rendering and/or usability.

[sappelhoff]

All issues have been picked off by other PRs. The only issue that remains is kind of a duplicate of #596 - so I am closing this one now.