quarto: init at 1.1.189 #186697

MrTarantoga · 2022-08-14T19:17:30Z

Description of changes

Quarto® is an open-source scientific and technical publishing system built on Pandoc

The idea is, to add quarto support to RStudio.

Things done

tpwrules

Please also rearrange your commits to have the one adding yourself to the maintainer list first, then squash the rest into a single commit. You can use git rebase -i master to do this easily.

pkgs/development/libraries/quarto/default.nix

smancill · 2022-08-15T05:31:46Z

Use the proper format for the maintainers commit message: https://nixos.org/manual/nixpkgs/stable/#var-meta-maintainers

pkgs/development/libraries/quarto/default.nix

smancill · 2022-08-15T05:43:19Z

Do we really need to download precompiled binaries instead of building from source? What's the problem?

MrTarantoga · 2022-08-15T08:48:55Z

Use the proper format for the maintainers commit message: https://nixos.org/manual/nixpkgs/stable/#var-meta-maintainers

Solved in 7363e4d

MrTarantoga · 2022-08-15T08:50:22Z

Do we really need to download precompiled binaries instead of building from source? What's the problem?

Yes, the install phase of the source package does nothing else then downloading precompiled versions and install them. So, there I see no difference between the source and the distribution package.

pkgs/development/libraries/quarto/default.nix

ulysses4ever · 2022-09-06T18:40:09Z

@MrTarantoga you did an amazing job here already, thank you! Do you think you'll get a chance to finish it some time soon?

ulysses4ever · 2022-09-06T18:40:50Z

I'd also love to have quarto-cli as a separate package, but I can survive with RStudio stuff I guess.

MrTarantoga · 2022-09-06T18:49:31Z

@MrTarantoga you did an amazing job here already, thank you! Do you think you'll get a chance to finish it some time soon?

I am not sure if it will work with all features. It does not find the jupyter or R environment.

I have some struggle with patching the files to work as expected. The last 2 weeks I have no success with adaption.

leonvonrabenmond · 2022-09-06T19:17:44Z

I am not sure if it will work with all features. It does not find the jupyter or R environment.

I have some struggle with patching the files to work as expected. The last 2 weeks I have no success with adaption.

I have been playing around with your current patch and I encountered the same issue. Funnily enough, I found that if you add jupyter separately in a nix-shell it works perfectly fine, but when in the enviornment, it somehow can't seem to find it..

leonvonrabenmond · 2022-09-08T15:03:57Z

I managed to get Quarto to find jupyter (and other kernels, such as the IJulia one) after installing it as a python package, rather then the standard nix package. With Tex being installed it allows me to render to pdf perfectly, but it completely fails under HTML with

ERROR: NotFound: No such file or directory (os error 2), remove '/home/leon/.cache/quarto/sass/397ef2e52d54cf686e4908b90039e9db.css'

As far as I can tell this comes from Deno, but I have no clue what causes it.

pkgs/development/libraries/quarto/default.nix

SuperSandro2000 · 2022-09-08T15:14:06Z

pkgs/top-level/all-packages.nix

@@ -36449,4 +36449,6 @@ with pkgs;
  swift-corelibs-libdispatch = callPackage ../development/libraries/swift-corelibs-libdispatch { };

  swaysettings = callPackage ../applications/misc/swaysettings { };
+
+  quarto = callPackage ../development/libraries/quarto { };


This should be sorted alphabetically into the libraries section.

There are not all files sorted alphabetical. Also I do not identify a special library section. I hope that is what you mean: 32c7b9f

pkgs/development/libraries/quarto/default.nix

SuperSandro2000 · 2022-09-08T15:14:56Z

maintainers/maintainer-list.nix

@@ -14967,4 +14967,10 @@
    github = "yisuidenghua";
    githubId = 102890144;
  };
+  mrtarantoga = {


This list is sorted alphabetical.

MrTarantoga · 2022-09-08T20:08:48Z

I am not sure if it will work with all features. It does not find the jupyter or R environment.
I have some struggle with patching the files to work as expected. The last 2 weeks I have no success with adaption.

I have been playing around with your current patch and I encountered the same issue. Funnily enough, I found that if you add jupyter separately in a nix-shell it works perfectly fine, but when in the enviornment, it somehow can't seem to find it..

Yes, I think quarto expect the FHS and nix does not support this standard. I am reading currently the documentation to support this, but I am not sure if it is possible. Maybe there must be patched the javscript sources. I struggle with the FHS support in nix and in its packages, it is quite hard to understand how it works.

SuperSandro2000 · 2022-09-09T09:58:46Z

Did you already try to use buildFHSUserEnvBubblewrap ?

sepiabrown

Updated src and version. Edited according to comments by @smancill and @SuperSandro2000. Adjusted QUARTO_IMPORT_ARGMAP accordingly. Partially tested with quarto preview.

pkgs/development/libraries/quarto/default.nix

pkgs/development/libraries/quarto/fix-deno-path.patch

pkgs/development/libraries/quarto/default.nix

pkgs/development/libraries/quarto/fix-deno-path.patch

alienzj · 2022-09-25T00:12:11Z

Can we merge it?
Since Rstudio 2022.07.1+554 request new version quarto.

Fix: Sort mrtarantoga alphabetical

Quarto is a library/support package for several pandoc projects. Fix: Remove trailing whitespace Add final newline to default.nix Fix indention and newline errors Fix: Missed unpackPhase resolved Add: sourceProvenance Suggestion of: NixOS#186697 (comment) Fix: reduce imports Fix: use version attribute in download string Fix: reduce path expression Fix: add runHook {pre/post}Install as common practice Fix: replace gpl2 with gpl2Plus Fix: change maintainers description Fix: do not use symlinks, use the PATH instead Fix wrong platforms ++ means concatenation and is not correct in this context. Co-authored-by: Sandro <sandro.jaeckel@gmail.com> Change structure to support fixed output derivations Co-authored-by: Sandro <sandro.jaeckel@gmail.com> Fix Fix Apply suggestion Co-authored-by: Suwon Park <35622998+sepiabrown@users.noreply.github.com> Fix suggestion Bundle makeProgram function call Co-authored-by: Suwon Park <35622998+sepiabrown@users.noreply.github.com> Update library version from 1.0.38 to 1.1.189 Co-authored-by: Suwon Park <35622998+sepiabrown@users.noreply.github.com> Add missing dependencies Co-authored-by: Suwon Park <35622998+sepiabrown@users.noreply.github.com> pandoc, deno, esbuild can be hooked into QUARTO_* environment variables, so they are not needed in buildInputs. Co-authored-by: Suwon Park <35622998+sepiabrown@users.noreply.github.com> Fix deno-path patch Co-authored-by: Suwon Park <35622998+sepiabrown@users.noreply.github.com> Remove wrong spaces Add python3 jupyter host support Fix spacing Co-authored-by: Suwon Park <35622998+sepiabrown@users.noreply.github.com> Sort quarto in all-packages.nix alphabetical Remove lib prefix from maintainers Co-authored-by: Sebastián Mancilla <238528+smancill@users.noreply.github.com> Simplify mkdir command Co-authored-by: Sandro <sandro.jaeckel@gmail.com> Fix missusage of makeBinPath Co-authored-by: Sandro <sandro.jaeckel@gmail.com> Remove python3Packages -> not used Co-authored-by: Sandro <sandro.jaeckel@gmail.com> Remove punctuation from description Co-authored-by: Sandro <sandro.jaeckel@gmail.com> Fix review Error in NixOS#186697 (comment) Fix wrong path for import_map.json Do not strip downloaded binary

MrTarantoga · 2022-09-25T09:04:15Z

I squashed now all commits. You can merge if you want, there no constraints from my side.

pkgs/development/libraries/quarto/default.nix

alienzj · 2022-09-26T22:02:55Z

Thanks all!

DPDmancul · 2022-09-28T22:04:07Z

Is there a way to make the engines dependency optional?
For example if I want to use this with Julia or without an engine it downloads and uselessly installs also R, python and jupyter.

I'm not skilled in Nix yet but maybe changing ${python3... with ${pkgs.python3... (and the same for R) should print the path without ensuring the dependency to be installed. Then maybe some overidable options can be added to install engines (which can be defaulted to true in order to not making a breaking change).

SuperSandro2000 · 2022-09-28T22:08:44Z

I'm not skilled in Nix yet but maybe changing ${python3... with ${pkgs.python3... (and the same for R) should print the path without ensuring the dependency to be installed. Then maybe some overidable options can be added to install engines (which can be defaulted to true in order to not making a breaking change).

That change wouldn't work. Also making options for everything increases the package complexity and all combinations are never tested. The best option would be if quarto would just pickup the packages from PATH and they are not set in the wrapper.

leonvonrabenmond · 2022-09-29T10:17:06Z

The best option would be if quarto would just pickup the packages from PATH and they are not set in the wrapper.

If I recall correctly, we did manage to partially get this to work in parts atleast, but the issue was, among others, that some packages did not set their PATHs correctly.

For example if I want to use this with Julia

Julia uses the IJulia kernel for jupyter, but the sadly, quarto does not find jupyter unless it is installed directly as a python package. We could maybe makes this work if we fix all the PATHs. I believe python3 gets found normally, but I have no clue about R.

We could either try and fix the jupyter pathing issue or just remove all but it (assuming R is found normally) I guess...

06kellyjac · 2022-10-07T09:31:03Z

FYI share is full of stuff, should probably be in a subdir

ls ./result/share/
 build   capabilities   conf   COPYING.md ... etc ...

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das-g mentioned this pull request Aug 22, 2022

Package quarto-cli #160911

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MrTarantoga force-pushed the add-quarto-1.0.38 branch from 1e26752 to 5d6eeb6 Compare September 20, 2022 10:04

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MrTarantoga added 2 commits September 25, 2022 11:02

Add me as a maintainer of the package

2bc8cde

Fix: Sort mrtarantoga alphabetical

MrTarantoga force-pushed the add-quarto-1.0.38 branch from 556de34 to 3be6403 Compare September 25, 2022 09:03

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quarto: fix formatting

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MrTarantoga mentioned this pull request Oct 2, 2022

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quarto: init at 1.1.189 #186697

quarto: init at 1.1.189 #186697

MrTarantoga commented Aug 14, 2022

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06kellyjac commented Oct 7, 2022

quarto: init at 1.1.189 #186697

quarto: init at 1.1.189 #186697

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MrTarantoga commented Aug 14, 2022

Description of changes

Things done

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smancill commented Aug 15, 2022

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