Quarto: Difference between revisions

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Quarto is an open-source technical publishing system that allows you to render markdown and code chunks into technical documents. It supports several kinds of formats including HTML, PDF, and word documents.

The quarto package from nixpkgs by itself will render "qmd" markdown without any extra ~~dependencies~~. However in order to render R, Python, or other code chunks, you will need to include those tools in your ~~path~~. ~~For example~~, ~~consider~~ the following "default.nix" file:

The quarto package from nixpkgs by itself will render <code>qmd</code> markdown without any extra requirements. However in order to render R, Python, or other code chunks, you will need to include those tools.

You can use the following in your system's <code>configuration.nix</code> file:<syntaxhighlight lang="nix">environment.systemPackages = let

myPythonPackages = ps: with ps; [

pandas

statsmodels

scikit-learn

sympy

];

myRPackages = with pkgs.rPackages; [

reticulate # wanted by quarto to execute Python when using R.

# any other RPackages - you can reuse this list for R and RStudio

]

patchedQuarto = (pkgs.quarto.override {

extraPythonPackages = myPythonPackages;

extraRPackages = myRPackages;

}).overrideAttrs (oldAttrs: { # Remove this overrideAttrs patch when fixed. See https://github.com/NixOS/nixpkgs/issues/519484#issuecomment-4667477454

postPatch = (oldAttrs.postPatch or "") + ''

substituteInPlace bin/quarto.js \

--replace-fail "syntax-highlighting" "highlight-style"

'';

});

in with pkgs; [

#### next generation of Rmarkdown for Python, Julia, R, and JS:

patchedQuarto

#### Your command-line Python:

(python3.withPackages (myPythonPackages))

#### R and RStudio:

(rWrapper.override {packages = myRPackages; })

(rstudioWrapper.override { packages = myRPackages; })

];</syntaxhighlight>similarly a `flake.nix` file with `nix develop`:<syntaxhighlight lang="nix">

{

description = "Minimal Quarto and SymPy environment";

inputs = {

nixpkgs.url = "github:Nixos/nixpkgs/nixos-unstable";

};

outputs = { self, nixpkgs }:

let

system = "x86_64-linux";

pkgs = nixpkgs.legacyPackages.${system};

myPythonPackages = ps: with ps; [ sympy ];

myRPackages = with pkgs.rPackages; [ reticulate ];

pythonEnv = pkgs.python3.withPackages (myPythonPackages);

in

{

devShells.${system}.default = pkgs.mkShell {

packages = [

((pkgs.quarto.override {

extraPythonPackages = myPythonPackages;

extraRPackages = myRPackages;

}).overrideAttrs (oldAttrs: {

# Remove this overrideAttrs patch when fixed.

# See https://github.com/NixOS/nixpkgs/issues/519484#issuecomment-4667477454

postPatch = (oldAttrs.postPatch or "") + ''

substituteInPlace bin/quarto.js \

--replace-fail "syntax-highlighting" "highlight-style"

'';

}))

pythonEnv

(pkgs.rWrapper.override {packages = myRPackages; })

];

shellHook = ''

echo "Quarto Environment Active (Pure Flake)"

echo "Quickstart: run 'quarto render document.qmd'"

'';

};

}

</syntaxhighlight>Or you can use the following <code>default.nix</code> or <code>shell.nix</code> file with <code>nix-shell</code> (and you don't have to pass in your Python packages via <code>override</code>):

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packages = with pkgs; [

# The core tool can render markdown without any additional ~~dependencies~~.

#### The core tool can render markdown without any additional requirements:

quarto

# quarto # commenting until this is fixed in nixpkgs - until then use below patch,

#### see https://github.com/NixOS/nixpkgs/issues/519484#issuecomment-4667477454

(quarto.overrideAttrs (oldAttrs: {

postPatch = (oldAttrs.postPatch or "") + ''

substituteInPlace bin/quarto.js \

--replace-fail "syntax-highlighting" "highlight-style"

'';

}))

# Render python code chunks.

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This nix shell gives you the tools render markdown documents with different kinds of code chunks. The following snippet can be placed in a "main.qmd" file.

<syntaxhighlight>---

---

title: Quarto Document

---

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import os

os.listdir()

```

```</syntaxhighlight>

</syntaxhighlight>

You can render this document into various formats:

@@ Line 1: / Line 1: @@
 Quarto is an open-source technical publishing system that allows you to render markdown and code chunks into technical documents. It supports several kinds of formats including HTML, PDF, and word documents.
-The quarto package from nixpkgs by itself will render "qmd" markdown without any extra dependencies. However in order to render R, Python, or other code chunks, you will need to include those tools in your path. For example, consider the following "default.nix" file:
+The quarto package from nixpkgs by itself will render <code>qmd</code> markdown without any extra requirements. However in order to render R, Python, or other code chunks, you will need to include those tools.
+You can use the following in your system's <code>configuration.nix</code> file:<syntaxhighlight lang="nix">environment.systemPackages = let
+    myPythonPackages = ps: with ps; [
+      pandas
+      statsmodels
+      scikit-learn
+      sympy
+    ];
+    myRPackages = with pkgs.rPackages; [
+      reticulate # wanted by quarto to execute Python when using R.
+      # any other RPackages - you can reuse this list for R and RStudio
+    ]
+    patchedQuarto = (pkgs.quarto.override {
+        extraPythonPackages = myPythonPackages;
+        extraRPackages = myRPackages;
+      }).overrideAttrs (oldAttrs: { # Remove this overrideAttrs patch when fixed. See https://github.com/NixOS/nixpkgs/issues/519484#issuecomment-4667477454
+      postPatch = (oldAttrs.postPatch or "") + ''
+        substituteInPlace bin/quarto.js \
+          --replace-fail "syntax-highlighting" "highlight-style"
+      '';
+    });
+  in with pkgs; [
+    #### next generation of Rmarkdown for Python, Julia, R, and JS:
+    patchedQuarto
+    #### Your command-line Python:
+    (python3.withPackages (myPythonPackages))
+    #### R and RStudio:
+    (rWrapper.override {packages = myRPackages; })
+    (rstudioWrapper.override { packages = myRPackages; })
+  ];</syntaxhighlight>similarly a `flake.nix` file with `nix develop`:<syntaxhighlight lang="nix">
+{
+  description = "Minimal Quarto and SymPy environment";
+  inputs = {
+    nixpkgs.url = "github:Nixos/nixpkgs/nixos-unstable";
+  };
+  outputs = { self, nixpkgs }:
+    let
+      system = "x86_64-linux";
+      pkgs = nixpkgs.legacyPackages.${system};
+      myPythonPackages = ps: with ps; [ sympy ];
+      myRPackages = with pkgs.rPackages; [ reticulate ];
+      pythonEnv = pkgs.python3.withPackages (myPythonPackages);
+    in
+    {
+      devShells.${system}.default = pkgs.mkShell {
+        packages = [
+          ((pkgs.quarto.override {
+            extraPythonPackages = myPythonPackages;
+            extraRPackages = myRPackages;
+          }).overrideAttrs (oldAttrs: {
+            # Remove this overrideAttrs patch when fixed.
+            # See https://github.com/NixOS/nixpkgs/issues/519484#issuecomment-4667477454
+            postPatch = (oldAttrs.postPatch or "") + ''
+              substituteInPlace bin/quarto.js \
+                --replace-fail "syntax-highlighting" "highlight-style"
+            '';
+          }))
+          pythonEnv
+          (pkgs.rWrapper.override {packages = myRPackages; })
+        ];
+        shellHook = ''
+          echo "Quarto Environment Active (Pure Flake)"
+          echo "Quickstart: run 'quarto render document.qmd'"
+        '';
+      };
+    };
+}
+</syntaxhighlight>Or you can use the following <code>default.nix</code> or <code>shell.nix</code> file with <code>nix-shell</code> (and you don't have to pass in your Python packages via <code>override</code>):
 <syntaxhighlight lang="nix">
@@ Line 10: / Line 78: @@
    packages = with pkgs; [
-     # The core tool can render markdown without any additional dependencies.
+     #### The core tool can render markdown without any additional requirements:
-     quarto
+    # quarto # commenting until this is fixed in nixpkgs - until then use below patch,
+    #### see https://github.com/NixOS/nixpkgs/issues/519484#issuecomment-4667477454
+     (quarto.overrideAttrs (oldAttrs: {
+      postPatch = (oldAttrs.postPatch or "") + ''
+        substituteInPlace bin/quarto.js \
+          --replace-fail "syntax-highlighting" "highlight-style"
+      '';
+    }))
      # Render python code chunks.
@@ Line 34: / Line 109: @@
 This nix shell gives you the tools render markdown documents with different kinds of code chunks. The following snippet can be placed in a "main.qmd" file.
-<syntaxhighlight>
+<syntaxhighlight>---
----
 title: Quarto Document
 ---
@@ Line 55: / Line 129: @@
 import os
 os.listdir()
-```
+```</syntaxhighlight>
-</syntaxhighlight>
 You can render this document into various formats: