Fix citations and travis build #100
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Pandoc is not installed including citeproc.
JamesOwers
changed the title
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This is 99% there. Travis build passes for all commands bar If this can be fixed, this will be a decent PR to merge Current stack trace for the errorMy next step would be to check the issue is not due to travis brew being out of date...Currently in the build log, we have: Travis config currently has: So google around this issue. |
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For EditReviewing advice here and the linked linux texlive install advice it links to here, it may be best to comment out the linux part of the travis build and raise a separate PR for that. Next steps for linuxFollow advice here to install a vanilla distribution: https://www.tug.org/texlive/debian.html |
Hopefully this solves some issues and maybe even cuts the build time
This issue suggests we could be using an old install of texlive. Conda should be putting pandoc on the path anyway. I wonder how it choses what tex version to use. https://tex.stackexchange.com/questions/567050/how-can-i-install-l3backend-pdfmode-def
Trying this to compare with previous build
Else we get the following stack:
```
brew
Installing Homebrew Packages
6.51s$ rvm $brew_ruby do brew bundle --verbose --global
/usr/local/bin/brew tap homebrew/bundle
==> Tapping homebrew/bundle
Cloning into '/usr/local/Homebrew/Library/Taps/homebrew/homebrew-bundle'...
remote: Enumerating objects: 101, done.
remote: Counting objects: 100% (101/101), done.
remote: Compressing objects: 100% (95/95), done.
remote: Total 101 (delta 4), reused 28 (delta 1), pack-reused 0
Receiving objects: 100% (101/101), 51.37 KiB | 2.23 MiB/s, done.
Resolving deltas: 100% (4/4), done.
Tapped (109 files, 268.1KB).
Error: Unknown command: bundle
before_install.1
0.01s$ echo $PATH
0.05s$ if [ "$TRAVIS_OS_NAME" = "osx" ]; then
eval "$(/usr/libexec/path_helper)"
sudo tlmgr update --self
elif [ "$TRAVIS_OS_NAME" = "linux" ]; then
tlmgr init-usertree
echo MSG FROM JO:
echo on linux we cannot update apt installed texlive
echo next steps to fix see commit msg: tompollard@85fd9e7
echo c.f. https://tex.stackexchange.com/questions/551383/cant-run-tex-lives-tlmgr-in-a-github-action
echo and https://tex.stackexchange.com/questions/1092/how-to-install-vanilla-texlive-on-debian-or-ubuntu
fi
sudo: tlmgr: command not found
```
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Ok, that's the build fixed for mac. Paved the way for fixing for linux next PR. |
Added: * Troubleshooting * More info to "how does it work"?
Also added comments re updating all
* Section references - chapter 1
* Uses plain LaTeX \ref{...} to indicate how to refer to each section.
* Use of URL links - chapter 1
Still todo:
* footnotes
* label arbitrary sections like it was an equation (e.g. the code snippet)
I think this makes sense, given that we are tracking both thesis.pdf (a large binary file), and thesis.html (a file which refers to these images).
Debatable whether this is really required. I do it for completeness. I don't know if we will be able to track changes the the file i.e. will it stay the same if we generate from the same markdown?
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This is phenomenal work! Thank you for putting the time in to make all of these improvements. There are a few other PRs (#97 and #96) that I'm also wanting to merge, but I'm going to review yours first, as I think having a more through CI process will mean less headaches down the road. This will probably take a second, so bear with me. |
dendrondal
reviewed
Jan 28, 2021
| @@ -37,6 +37,8 @@ For bold, add ** on either side of the text | |||
| For bold and italic, add _** on either side of the text | |||
| --> | |||
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| This is a brief outline of what went into each chapter. **Chapter 1** gives a background on duis tempus justo quis arcu consectetur sollicitudin. **Chapter 2** discusses morbi sollicitudin gravida tellus in maximus. **Chapter 3** discusses vestibulum eleifend turpis id turpis sollicitudin aliquet. **Chapter 4** shows how phasellus gravida non ex id aliquet. Proin faucibus nibh sit amet augue blandit varius. | |||
| This is a brief outline of what went into each chapter, and a section which shows how to reference headers (which are labelled automatically for you). This chapter, +@sec:introduction-with-a-citation, shows how to use citations and how to reference section headers. \*@sec:literature-review-with-maths shows how use and reference equations. \*@sec:first-research-study-with-code shows how to use and reference code. \*@sec:research-containing-a-figure shows how to use, reference, and resize pdf and jpg figures. \*@sec:research-containing-a-table shows how to use and reference tables. \*@sec:final-research-study is truly revolutionary (but shows nothing functional). **[Appendix 1](#appendix-1-some-extra-stuff)** shows how to add chapters which are not numbered, and has to be referenced manually, as does **[Appendix 2](#appendix-2-some-more-extra-stuff)**. See the base [`README.md`](https://github.com/tompollard/phd_thesis_markdown/blob/master/README.md) for how References are handled - leave `*_references.md` alone, and provide it to `pandoc` last. | |||
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Kudos for adding this, I didn't realize we had no secnos examples in here.
dendrondal
reviewed
Jan 28, 2021
| @@ -152,13 +158,36 @@ | |||
| \fi | |||
| $endif$ | |||
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| % $if(csl-refs)$ | |||
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What is the purpose of this block?
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good question - I just looked at what the current pandoc standard template was and fiddled until I fixed things! It was necessary to make the references section to actually work.
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Check out pandoc -D latex to see what the standard template currently is.
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Huh, interesting. Whatever works, and it certainly doesn't seem to be breaking anything!
Open
As an aside - I'm v happy to help in future since I'll be using this template to write my phd actively. The linux travis build is nearly there, I could have a crack at that next. |
Absolutely! If you want to add docker integration to the |
Yeah will do. Never used docker before so should be fun. This PR is complicated enough so I’ll wait for this to merge (fixing any changes you’d like), then raise a separate PR for Linux + docker travis improvements. |
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I definitely think it's a good idea to have that as a separate request. I think this is ready to merge. |
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@JamesOwers @dendrondal thanks for all of your work on this! |
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Issue
Unfortunately,
pandoc-citeprocis depreciated; citeproc-hs is now installed by default and used by pandoc. This means the installation (either via travis, install.sh, or hacking through the README.md) is broken (because installing pandoc-citeproc kicks a depreciation error).If the user proceeds without
pandoc-citeproc, citations don't work!Fix
tests both mac and linux nowlinux needs work to install texlive (see comments below, it's 90% done though)make installaccounts for the diff files and uses the correct one automaticallysource/*.mdby:--citeprocargumentstyle/template.texwith new contents ofpandoc -D latexrelating to citationsOther minor contributions
source/*.mdfiles including:pandoc-secnosthesis.{pdf,tex,html,docx}, such that it is obvious if changes are made (not true for docx, so there's an argument we shouldn't version control that file since it is large)make allto generatethesis.{pdf,tex,html,docx}with one command