con / opfvta-reexecution

Container-based Replication of https://doi.org/10.1038/s41398-022-01812-5
Apache License 2.0
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latexmk needs to exit (0) #26

Closed asmacdo closed 1 year ago

asmacdo commented 1 year ago

make container-article

(see the transcript file for additional information)
Output written on article.pdf (7 pages).
Transcript written on article.log.
Latexmk: Missing bbl file 'article.bbl' in following:
 No file article.bbl.
Latexmk: Getting log file 'article.log'
Latexmk: Examining 'article.fls'
Latexmk: Examining 'article.log'
Latexmk: Log file says output to 'article.pdf'
Latexmk: Bibliography file(s) form .bcf file:
  ./bibliography.bib
Latexmk: 'pdflatex': source file 'article.bbl' doesn't exist. I'll try making it...
------------
Running 'make "article.bbl"'
------------
make: *** No rule to make target 'article.bbl'.  Stop.
Latexmk: All targets () are up-to-date
Collected error summary (may duplicate other messages):
  biber article: gave an error in previous invocation of latexmk.

make: *** [Makefile:65: container-article] Error 12

This works in that the pdf is generated, but because the exit code isn't 0, the next line in the Makefile doesnt complete:

https://github.com/con/opfvta-replication-2023/blob/master/paper/source/Makefile#L66

That is the line that should move the pdf from the paper dir and into the generated dir. Once thats fixed, we should be able to remove the rm -f article.pdf.

Additionally, it would be good if that move also includes datetime information, or maybe even incorporates a datalade save.

Finally, (this maybe should be a different issue, but the cleanup should do something with these extra files:

asmacdo@typhon:~/devel/opfvta-replication-2023/paper/source$ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
    modified:   figs/paperdiff_pages.pdf
    modified:   figs/topology.pdf

Untracked files:
  (use "git add <file>..." to include in what will be committed)
    .cache/
    article.run.xml

no changes added to commit (use "git add" and/or "git commit -a")

asmacdo@typhon:~/devel/opfvta-replication-2023/paper/source$ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
    modified:   figs/paperdiff_pages.pdf
    modified:   figs/topology.pdf

Untracked files:
  (use "git add <file>..." to include in what will be committed)
    .cache/
    article.run.xml
asmacdo commented 1 year ago

It worked!