added full julia, python, r setup

templates/py/flake.nix

@@ -0,0 +1,143 @@
+{
+  description = "Project Template";
+  inputs = {
+    rixpkgs.url = "https://github.com/rstats-on-nix/nixpkgs/archive/2025-05-19.tar.gz";
+    nixpkgs.url = "github:nixos/nixpkgs/nixpkgs-unstable";
+    nCats.url = "github:dwinkler1/nixCatsConfig";
+    nCats.inputs.nixpkgs.follows = "nixpkgs";
+    pyproject-nix = {
+      url = "github:pyproject-nix/pyproject.nix";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+
+    uv2nix = {
+      url = "github:pyproject-nix/uv2nix";
+      inputs.pyproject-nix.follows = "pyproject-nix";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+
+    pyproject-build-systems = {
+      url = "github:pyproject-nix/build-system-pkgs";
+      inputs.pyproject-nix.follows = "pyproject-nix";
+      inputs.uv2nix.follows = "uv2nix";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
+  outputs = {
+    self,
+    nixpkgs,
+    nCats,
+    ...
+  } @ inputs: let
+    forSystems = nixpkgs.lib.genAttrs nixpkgs.lib.platforms.all;
+  in {
+    packages = forSystems (
+      system: let
+        inherit (nCats) utils;
+        finalPackage = nCats.packages.${system}.default.override (prev: {
+          dependencyOverlays =
+            prev.dependencyOverlays
+            ++ [
+              (utils.standardPluginOverlay inputs)
+              (final: prev: {
+                rpkgs = inputs.rixpkgs.legacyPackages.${system};
+              })
+              (final: prev: let
+                # Load a uv workspace from a workspace root.
+                # Uv2nix treats all uv projects as workspace projects.
+                workspace = uv2nix.lib.workspace.loadWorkspace {workspaceRoot = ./.;};
+
+                # Create package overlay from workspace.
+                overlay = workspace.mkPyprojectOverlay {
+                  # Prefer prebuilt binary wheels as a package source.
+                  # Sdists are less likely to "just work" because of the metadata missing from uv.lock.
+                  # Binary wheels are more likely to, but may still require overrides for library dependencies.
+                  sourcePreference = "wheel"; # or sourcePreference = "sdist";
+                  # Optionally customise PEP 508 environment
+                  # environ = {
+                  #     platform_release = "5.10.65";
+                  # };
+                };
+
+                # Extend generated overlay with build fixups
+                #
+                # Uv2nix can only work with what it has, and uv.lock is missing essential metadata to perform some builds.
+                # This is an additional overlay implementing build fixups.
+                # See:
+                # - https://pyproject-nix.github.io/uv2nix/FAQ.html
+                pyprojectOverrides = _final: _prev: {
+                  # Implement build fixups here.
+                  # Note that uv2nix is _not_ using Nixpkgs buildPythonPackage.
+                  # It's using https://pyproject-nix.github.io/pyproject.nix/build.html
+                };
+
+                # Construct package set
+                pythonSet =
+                  # Use base package set from pyproject.nix builders
+                  (pkgs.callPackage pyproject-nix.build.packages {inherit python;}).overrideScope
+                  (
+                    lib.composeManyExtensions [
+                      pyproject-build-systems.overlays.default
+                      overlay
+                      pyprojectOverrides
+                    ]
+                  );
+              in {
+                venv = pythonSet.mkVirtualEnv builtins.toString ./. workspace.deps.default;
+              })
+              (import (builtins.path {
+                path = ./rpkgs.nix;
+                name = "my-rpackages";
+              }))
+            ];
+          categoryDefinitions = utils.mergeCatDefs prev.categoryDefinitions (
+            {
+              pkgs,
+              settings,
+              categories,
+              name,
+              extra,
+              mkPlugin,
+              ...
+            } @ packageDef: let
+              myPy = pkgs.python313;
+            in {
+              lspsAndRuntimeDeps.rdev = with pkgs; [
+                myPy
+                uv
+                nodejs
+                ruff
+                just
+                wget
+                python313Packages.python-lsp-server
+              ];
+              environmentVariables.rdev = {
+                # Prevent uv from managing Python downloads
+                UV_PYTHON_DOWNLOADS = "never";
+                # Force uv to use nixpkgs Python interpreter
+                UV_PYTHON = myPy.interpreter;
+              };
+            }
+          );
+
+          packageDefinitions =
+            prev.packageDefinitions
+            // {
+              nixCats = utils.mergeCatDefs prev.packageDefinitions.nixCats (
+                {...}: {
+                  settings = {
+                    suffix-path = false;
+                    suffix-LD = false;
+                  };
+                  categories = {
+                    rdev = true;
+                  };
+                }
+              );
+            };
+        });
+      in
+        utils.mkAllWithDefault finalPackage
+    );
+  };
+}

templates/sci/.gitignore

@@ -0,0 +1,2 @@
+data/*
+!data/.gitkeep

templates/sci/.marimo.toml

@@ -0,0 +1,67 @@
+[formatting]
+line_length = 79
+
+[keymap]
+preset = "vim"
+[keymap.overrides]
+
+[runtime]
+auto_instantiate = true
+std_stream_max_bytes = 1000000
+on_cell_change = "autorun"
+reactive_tests = true
+default_sql_output = "auto"
+auto_reload = "off"
+watcher_on_save = "lazy"
+output_max_bytes = 8000000
+
+[language_servers.pylsp]
+enable_pydocstyle = false
+enable_flake8 = false
+enable_ruff = true
+enable_mypy = true
+enable_pylint = false
+enabled = true
+enable_pyflakes = false
+
+[experimental]
+
+[completion]
+activate_on_typing = true
+copilot = "github"
+
+[server]
+browser = "default"
+follow_symlink = false
+
+[ai]
+rules = ""
+[ai.google]
+
+[ai.bedrock]
+
+[ai.open_ai]
+
+[ai.anthropic]
+
+[diagnostics]
+
+[package_management]
+manager = "uv"
+
+[snippets]
+include_default_snippets = true
+custom_paths = []
+
+[display]
+default_table_page_size = 10
+code_editor_font_size = 14
+cell_output = "below"
+dataframes = "rich"
+theme = "dark"
+default_width = "medium"
+
+[save]
+format_on_save = false
+autosave = "after_delay"
+autosave_delay = 1000

templates/sci/.python-version

@@ -0,0 +1 @@
+3.12

templates/sci/.zk/config.toml

@@ -0,0 +1,199 @@
+# zk configuration file
+#
+# Uncomment the properties you want to customize.
+
+# NOTE SETTINGS
+#
+# Defines the default options used when generating new notes.
+[note]
+
+# Language used when writing notes.
+# This is used to generate slugs or with date formats.
+#language = "en"
+
+# The default title used for new note, if no `--title` flag is provided.
+#default-title = "Untitled"
+
+# Template used to generate a note's filename, without extension.
+extension = "md"
+filename = "docs/{{slug title}}-{{format-date now '%Y-%m-%d'}}-{{id}}"
+language = "en"
+
+# The file extension used for the notes.
+#extension = "md"
+
+# Template used to generate a note's content.
+# If not an absolute path or "~/unix/path", it's relative to .zk/templates/
+template = "default.md"
+
+# Path globs ignored while indexing existing notes.
+#exclude = [
+#    "drafts/*",
+#    "log.md"
+#]
+
+# Configure random ID generation.
+
+# The charset used for random IDs. You can use:
+#   * letters: only letters from a to z.
+#   * numbers: 0 to 9
+#   * alphanum: letters + numbers
+#   * hex: hexadecimal, from a to f and 0 to 9
+#   * custom string: will use any character from the provided value
+#id-charset = "alphanum"
+
+# Length of the generated IDs.
+#id-length = 4
+
+# Letter case for the random IDs, among lower, upper or mixed.
+#id-case = "lower"
+
+
+# EXTRA VARIABLES
+#
+# A dictionary of variables you can use for any custom values when generating
+# new notes. They are accessible in templates with {{extra.<key>}}
+[extra]
+
+#key = "value"
+
+
+# GROUP OVERRIDES
+#
+# You can override global settings from [note] and [extra] for a particular
+# group of notes by declaring a [group."<name>"] section.
+#
+# Specify the list of directories which will automatically belong to the group
+# with the optional `paths` property.
+#
+# Omitting `paths` is equivalent to providing a single path equal to the name of
+# the group. This can be useful to quickly declare a group by the name of the
+# directory it applies to.
+
+#[group."<NAME>"]
+#paths = ["<DIR1>", "<DIR2>"]
+#[group."<NAME>".note]
+#filename = "{{format-date now}}"
+#[group."<NAME>".extra]
+#key = "value"
+
+
+# MARKDOWN SETTINGS
+[format.markdown]
+
+# Format used to generate links between notes.
+# Either "wiki", "markdown" or a custom template. Default is "markdown".
+link-format = "wiki"
+# Indicates whether a link's path will be percent-encoded.
+# Defaults to true for "markdown" format and false for "wiki" format.
+#link-encode-path = true
+# Indicates whether a link's path file extension will be removed.
+# Defaults to true.
+#link-drop-extension = true
+
+# Enable support for #hashtags.
+hashtags = false
+# Enable support for :colon:separated:tags:.
+colon-tags = true
+# Enable support for Bear's #multi-word tags#
+# Hashtags must be enabled for multi-word tags to work.
+multiword-tags = false
+
+
+# EXTERNAL TOOLS
+[tool]
+
+# Default editor used to open notes. When not set, the EDITOR or VISUAL
+# environment variables are used.
+#editor = "vim"
+
+# Pager used to scroll through long output. If you want to disable paging
+# altogether, set it to an empty string "".
+#pager = "less -FIRX"
+
+# Command used to preview a note during interactive fzf mode.
+# Set it to an empty string "" to disable preview.
+
+# bat is a great tool to render Markdown document with syntax highlighting.
+#https://github.com/sharkdp/bat
+#fzf-preview = "bat -p --color always {-1}"
+
+
+# LSP
+#
+#   Configure basic editor integration for LSP-compatible editors.
+#   See https://github.com/zk-org/zk/blob/main/docs/editors-integration.md
+#
+[lsp]
+
+[lsp.diagnostics]
+# Each diagnostic can have for value: none, hint, info, warning, error
+
+# Report titles of wiki-links as hints.
+wiki-title = "hint"
+# Warn for dead links between notes.
+dead-link = "error"
+
+[lsp.completion]
+# Customize the completion pop-up of your LSP client.
+
+# Show the note title in the completion pop-up, or fallback on its path if empty.
+#note-label = "{{title-or-path}}"
+# Filter out the completion pop-up using the note title or its path.
+#note-filter-text = "{{title}} {{path}}"
+# Show the note filename without extension as detail.
+#note-detail = "{{filename-stem}}"
+
+
+# NAMED FILTERS
+#
+#    A named filter is a set of note filtering options used frequently together.
+#
+[filter]
+
+# Matches the notes created the last two weeks. For example:
+#    $ zk list recents --limit 15
+#    $ zk edit recents --interactive
+#recents = "--sort created- --created-after 'last two weeks'"
+
+
+# COMMAND ALIASES
+#
+#   Aliases are user commands called with `zk <alias> [<flags>] [<args>]`.
+#
+#   The alias will be executed with `$SHELL -c`, please refer to your shell's
+#   man page to see the available syntax. In most shells:
+#     * $@ can be used to expand all the provided flags and arguments
+#     * you can pipe commands together with the usual | character
+#
+[alias]
+# Here are a few aliases to get you started.
+
+# Shortcut to a command.
+#ls = "zk list $@"
+
+# Default flags for an existing command.
+#list = "zk list --quiet $@"
+
+# Edit the last modified note.
+#editlast = "zk edit --limit 1 --sort modified- $@"
+
+# Edit the notes selected interactively among the notes created the last two weeks.
+# This alias doesn't take any argument, so we don't use $@.
+#recent = "zk edit --sort created- --created-after 'last two weeks' --interactive"
+
+# Print paths separated with colons for the notes found with the given
+# arguments. This can be useful to expand a complex search query into a flag
+# taking only paths. For example:
+#   zk list --link-to "`zk path -m potatoe`"
+#path = "zk list --quiet --format {{path}} --delimiter , $@"
+
+# Show a random note.
+#lucky = "zk list --quiet --format full --sort random --limit 1"
+
+# Returns the Git history for the notes found with the given arguments.
+# Note the use of a pipe and the location of $@.
+#hist = "zk list --format path --delimiter0 --quiet $@ | xargs -t -0 git log --patch --"
+
+# Edit this configuration file.
+#conf = '$EDITOR "$ZK_NOTEBOOK_DIR/.zk/config.toml"'

templates/sci/.zk/templates/default.md

@@ -0,0 +1,3 @@
+# {{title}}
+
+{{content}}

templates/sci/Justfile

@@ -0,0 +1,4 @@
+rverurl := 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv'
+update-r-version:
+    RVER=$( wget -qO- {{rverurl}} | tail -n 2 | head -n 1 | cut -d',' -f4 | tr -d '"' ) &&\
+     sed -i  "s|rixpkgs.url = \"https://github.com/rstats-on-nix/nixpkgs/archive/[0-9]\{4\}-[0-9]\{2\}-[0-9]\{2\}\.tar\.gz\";|rixpkgs.url = \"https://github.com/rstats-on-nix/nixpkgs/archive/$RVER.tar.gz\";|" flake.nix

templates/sci/flake.lock

@@ -0,0 +1,103 @@
+{
+  "nodes": {
+    "nCats": {
+      "inputs": {
+        "nixCats": "nixCats",
+        "nixpkgs": [
+          "nixpkgs"
+        ],
+        "plugins-r": "plugins-r",
+        "rixpkgs": "rixpkgs"
+      },
+      "locked": {
+        "lastModified": 1748808131,
+        "owner": "dwinkler1",
+        "repo": "nixCatsConfig",
+        "rev": "b5cbf7502b5d7d58cd5dc8c73ac40a5744f2e767",
+        "type": "github"
+      },
+      "original": {
+        "owner": "dwinkler1",
+        "repo": "nixCatsConfig",
+        "type": "github"
+      }
+    },
+    "nixCats": {
+      "locked": {
+        "lastModified": 1748230488,
+        "owner": "BirdeeHub",
+        "repo": "nixCats-nvim",
+        "rev": "2a2f15a6c085524ac121f5da9a73ee2155c53d70",
+        "type": "github"
+      },
+      "original": {
+        "owner": "BirdeeHub",
+        "repo": "nixCats-nvim",
+        "type": "github"
+      }
+    },
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1748662220,
+        "owner": "nixos",
+        "repo": "nixpkgs",
+        "rev": "59138c7667b7970d205d6a05a8bfa2d78caa3643",
+        "type": "github"
+      },
+      "original": {
+        "owner": "nixos",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "plugins-r": {
+      "flake": false,
+      "locked": {
+        "lastModified": 1748371931,
+        "owner": "R-nvim",
+        "repo": "R.nvim",
+        "rev": "382858fcf23aabbf47ff06279baf69d52260b939",
+        "type": "github"
+      },
+      "original": {
+        "owner": "R-nvim",
+        "repo": "R.nvim",
+        "type": "github"
+      }
+    },
+    "rixpkgs": {
+      "locked": {
+        "lastModified": 1746476429,
+        "narHash": "sha256-KHNAOy8ILpIlz5rtwxURpcVOqbWRMoT/rXRgpy1pyG8=",
+        "type": "tarball",
+        "url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-04-29.tar.gz"
+      },
+      "original": {
+        "type": "tarball",
+        "url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-04-29.tar.gz"
+      }
+    },
+    "rixpkgs_2": {
+      "locked": {
+        "lastModified": 1747664360,
+        "narHash": "sha256-DskCWKtHNGApsP3PI/HB+fETs3qXpwul3PtSgTb++N4=",
+        "type": "tarball",
+        "url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-05-19.tar.gz"
+      },
+      "original": {
+        "type": "tarball",
+        "url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-05-19.tar.gz"
+      }
+    },
+    "root": {
+      "inputs": {
+        "nCats": "nCats",
+        "nixpkgs": "nixpkgs",
+        "rixpkgs": "rixpkgs_2"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

templates/sci/flake.nix

@@ -0,0 +1,119 @@
+{
+  description = "Project Template";
+  inputs = {
+    rixpkgs.url = "https://github.com/rstats-on-nix/nixpkgs/archive/2025-05-19.tar.gz";
+    nixpkgs.url = "github:nixos/nixpkgs/nixpkgs-unstable";
+    nCats.url = "github:dwinkler1/nixCatsConfig";
+    nCats.inputs.nixpkgs.follows = "nixpkgs";
+  };
+  outputs = {
+    self,
+    nixpkgs,
+    nCats,
+    ...
+  } @ inputs: let
+    forSystems = nixpkgs.lib.genAttrs nixpkgs.lib.platforms.all;
+  in {
+    packages = forSystems (
+      system: let
+        inherit (nCats) utils;
+        finalPackage = nCats.packages.${system}.default.override (prev: {
+          dependencyOverlays =
+            prev.dependencyOverlays
+            ++ [
+              (utils.standardPluginOverlay inputs)
+              (final: prev: {
+                rpkgs = inputs.rixpkgs.legacyPackages.${system};
+              })
+              (import (builtins.path {
+                path = ./rpkgs.nix;
+                name = "my-rpackages";
+              }))
+              (import (builtins.path {
+                path = ./pypkgs.nix;
+                name = "my-pypackages";
+              }))
+            ];
+          categoryDefinitions = utils.mergeCatDefs prev.categoryDefinitions (
+            {
+              pkgs,
+              settings,
+              categories,
+              name,
+              extra,
+              mkPlugin,
+              ...
+            } @ packageDef: {
+              lspsAndRuntimeDeps = {
+                meta = with pkgs; [
+                  just
+                  wget
+                  gh
+                ];
+                rdev = with pkgs; [
+                  rWrapper
+                ];
+                pydev = with pkgs; [
+                  py
+                  uv
+                  pyright
+                  nodejs
+                ];
+                jldev = with pkgs; [
+                  julia-bin
+                ];
+              };
+
+              environmentVariables = {
+                rdev = {
+                  R_LIBS_USER = "./.Rlibs";
+                };
+                pydev = {
+                  # Prevent uv from managing Python downloads
+                  UV_PYTHON_DOWNLOADS = "never";
+                  # Force uv to use nixpkgs Python interpreter
+                  UV_PYTHON = pkgs.py.interpreter;
+                };
+              };
+              extraWrapperArgs = {
+                pydev = [
+                  "--unset PYTHONPATH"
+                ];
+              };
+            }
+          );
+
+          packageDefinitions =
+            prev.packageDefinitions
+            // {
+              nixCats = utils.mergeCatDefs prev.packageDefinitions.nixCats (
+                {pkgs, ...}: {
+                  settings = {
+                    suffix-path = false;
+                    suffix-LD = false;
+                    hosts = {
+                      python3.enable = true;
+                      m = {
+                        enable = true;
+                        path = {
+                          value = "${pkgs.uv}/bin/uv";
+                          args = [ "--add-flags" "run marimo edit"];
+                        };
+                      };
+                    };
+                  };
+                  categories = {
+                    meta = true;
+                    rdev = true;
+                    pydev = true;
+                    jldev = true;
+                  };
+                }
+              );
+            };
+        });
+      in
+        utils.mkAllWithDefault finalPackage
+    );
+  };
+}

templates/sci/pypkgs.nix

@@ -0,0 +1,9 @@
+final: prev: let
+  reqPkgs = (pyPackages: with pyPackages;[
+    pandas
+    requests
+  ]);
+in {
+  py = prev.python3.withPackages reqPkgs;
+}
+

templates/sci/pyproject.toml

@@ -0,0 +1,16 @@
+[project]
+name = "sci"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "marimo[recommended]>=0.13.15",
+    "polars>=1.30.0",
+    "pytest>=8.3.5",
+    "python-lsp-ruff>=2.2.2",
+    "python-lsp-server>=1.12.2",
+    "vegafusion>=2.0.2",
+    "vl-convert-python>=1.8.0",
+    "websockets>=15.0.1",
+]

templates/sci/pyrightconfig.json

@@ -0,0 +1 @@
+{ "venvPath": ".", "venv": ".venv" }

templates/sci/rpkgs.nix

@@ -0,0 +1,34 @@
+final: prev: let
+  reqPkgs = with prev.rpkgs.rPackages; [
+    Hmisc
+    broom
+    data_table
+    dplyr
+    ggplot2
+    gt
+    janitor
+    psych
+    tidyr
+    languageserver
+    (buildRPackage {
+      name = "nvimcom";
+      src = prev.rpkgs.fetchFromGitHub {
+        owner = "R-nvim";
+        repo = "R.nvim";
+        rev = "382858fcf23aabbf47ff06279baf69d52260b939";
+        sha256 = "sha256-j2rXXO7246Nh8U6XyX43nNTbrire9ta9Ono9Yr+Eh9M=";
+      };
+      sourceRoot = "source/nvimcom";
+      buildInputs = with prev.rpkgs; [
+        R
+        stdenv.cc.cc
+        gnumake
+      ];
+      propagatedBuildInputs = [];
+    })
+  ];
+in {
+  quarto = prev.rpkgs.quarto.override {extraRPackages = reqPkgs;};
+  rWrapper = prev.rpkgs.rWrapper.override {packages = reqPkgs;};
+  radianWrapper = prev.rpkgs.radianWrapper.override {packages = reqPkgs;};
+}