Issues building site: character coding issues with filenames

[lintool]

I'm having this issue cloning this repo;

% git clone git@github.com:gwf-uwaterloo/gwf-publications.git
Cloning into 'gwf-publications'...
remote: Enumerating objects: 78775, done.
remote: Total 78775 (delta 0), reused 0 (delta 0), pack-reused 78775
Receiving objects: 100% (78775/78775), 77.32 MiB | 5.54 MiB/s, done.
Resolving deltas: 100% (38243/38243), done.
Updating files: 100% (12192/12192), done.
warning: the following paths have collided (e.g. case-sensitive paths
on a case-insensitive filesystem) and only one from the same
colliding group is in the working tree:

  'docs/people/M/Mats-P-Björkman/index.html'
  'docs/people/M/Mats-P-Björkman/index.html'

Can we fix the path collisions?

[lintool]

Recipe for building site on my Mac:

conda deactivate
conda create -n gwf python=3.8
conda activate gwf
git clone git@github.com:gwf-uwaterloo/gwf-publications.git
pip install -r bin/requirements.txt
brew install hugo
brew install bibutils

ANTHOLOGY_PREFIX="https://gwf-uwaterloo.github.io/gwf-publications" make

I get to this error:

INFO     Converting BibTeX files to MODS XML...
xargs: bin/bib2xml_wrapper: Permission denied
make: *** [build/.mods] Error 126

Which can be fixed by:

chmod +x bin/bib2xml_wrapper

Also, similar error:

chmod +x bin/xml2end_wrapper

[lintool]

Got to this point, below.

Probably related to the directory collision errors above.

INFO     Converting MODS XML files to EndNote...
INFO     Running Hugo... this may take a while.
Start building sites … 
hugo v0.106.0+extended darwin/amd64 BuildDate=unknown
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
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ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
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ERROR 2022/11/23 17:59:07 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
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ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/H/Hanna-Lee.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/H/Hjalte MR-Mann.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/I/Ingibjörg Svala-Jónsdóttir.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/I/Isabel C-Barrio.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/I/Isla H-Myers-Smith.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/J/J Hans C-Cornelissen.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
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ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/J/Jeffrey M-Welker.md": page not found
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ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/J/Jill T-Anderson.md": page not found
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ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/J/Jonas J-Lembrechts.md": page not found
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ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/R/Rachel-Slatyer.md": page not found
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ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/R/Robert-Way.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/S/Sarah C-Elmendorf.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/S/Shengwei-Zong.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/S/Signe-Lett.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/S/Sonja-Wipf.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/S/Sonya R-Geange.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/S/Stef-Bokhorst.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/S/Stephen J-Coulson.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/S/Susanna-Venn.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/T/Toke Thomas-Høye.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:08 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/T/T’ai GW-Forte.md": page not found
ERROR 2022/11/23 17:59:09 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
ERROR 2022/11/23 17:59:09 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "people/V/Vigdis-Vandvik.md": page not found
ERROR 2022/11/23 17:59:09 [en] REF_NOT_FOUND: Ref "/people/M/Mats P-Björkman.md" from page "papers/G22/G22-41001.md": page not found
Error: Error building site: logged 144 error(s)
Total in 5625 ms
make: *** [build/.hugo] Error 255

[lintool]

Now at commit c5737cd950ffd04a2c783dba18090aa7643e5e7f - after doing a fresh checkout, getting this error:

(gwf) jimmylin@iMac-Pro gwf-publications % git status
On branch main
Your branch is up to date with 'origin/main'.

Untracked files:
  (use "git add <file>..." to include in what will be committed)
    "docs/people/M/Mats-P-Bj\303\266rkman/"

nothing added to commit but untracked files present (use "git add" to track)

This appears to be a Mac error, as I don't get the same error on Linux.

[lintool]

Somehow we're generating two different versions of the directory?

>>> print(hashlib.md5('docs/people/M/Mats-P-Björkman/index.html'.encode('utf-8')).hexdigest())
de9ab2b63fff3ce4863b08f0bca97ac2
>>> print(hashlib.md5('docs/people/M/Mats-P-Björkman/index.html'.encode('utf-8')).hexdigest())
3f4aedabae399d5361387405bda10860

I think the ö is different somehow?