mirror of
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synced 2026-02-19 22:40:57 -05:00
removed old templates
This commit is contained in:
parent
144eebbcfa
commit
e19f843e06
55 changed files with 0 additions and 3920 deletions
2
templates/r/.gitignore
vendored
2
templates/r/.gitignore
vendored
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data/*
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!data/.gitkeep
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@ -1,199 +0,0 @@
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# zk configuration file
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#
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# Uncomment the properties you want to customize.
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# NOTE SETTINGS
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#
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# Defines the default options used when generating new notes.
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[note]
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# Language used when writing notes.
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# This is used to generate slugs or with date formats.
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#language = "en"
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# The default title used for new note, if no `--title` flag is provided.
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#default-title = "Untitled"
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# Template used to generate a note's filename, without extension.
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extension = "md"
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filename = "docs/{{slug title}}-{{format-date now '%Y-%m-%d'}}-{{id}}"
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language = "en"
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# The file extension used for the notes.
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#extension = "md"
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# Template used to generate a note's content.
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# If not an absolute path or "~/unix/path", it's relative to .zk/templates/
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template = "default.md"
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# Path globs ignored while indexing existing notes.
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#exclude = [
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# "drafts/*",
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# "log.md"
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#]
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# Configure random ID generation.
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# The charset used for random IDs. You can use:
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# * letters: only letters from a to z.
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# * numbers: 0 to 9
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# * alphanum: letters + numbers
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# * hex: hexadecimal, from a to f and 0 to 9
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# * custom string: will use any character from the provided value
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#id-charset = "alphanum"
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# Length of the generated IDs.
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#id-length = 4
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# Letter case for the random IDs, among lower, upper or mixed.
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#id-case = "lower"
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# EXTRA VARIABLES
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#
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# A dictionary of variables you can use for any custom values when generating
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# new notes. They are accessible in templates with {{extra.<key>}}
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[extra]
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#key = "value"
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# GROUP OVERRIDES
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#
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# You can override global settings from [note] and [extra] for a particular
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# group of notes by declaring a [group."<name>"] section.
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#
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# Specify the list of directories which will automatically belong to the group
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# with the optional `paths` property.
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#
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# Omitting `paths` is equivalent to providing a single path equal to the name of
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# the group. This can be useful to quickly declare a group by the name of the
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# directory it applies to.
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#[group."<NAME>"]
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#paths = ["<DIR1>", "<DIR2>"]
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#[group."<NAME>".note]
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#filename = "{{format-date now}}"
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#[group."<NAME>".extra]
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#key = "value"
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# MARKDOWN SETTINGS
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[format.markdown]
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# Format used to generate links between notes.
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# Either "wiki", "markdown" or a custom template. Default is "markdown".
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link-format = "wiki"
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# Indicates whether a link's path will be percent-encoded.
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# Defaults to true for "markdown" format and false for "wiki" format.
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#link-encode-path = true
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# Indicates whether a link's path file extension will be removed.
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# Defaults to true.
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#link-drop-extension = true
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# Enable support for #hashtags.
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hashtags = false
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# Enable support for :colon:separated:tags:.
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colon-tags = true
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# Enable support for Bear's #multi-word tags#
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# Hashtags must be enabled for multi-word tags to work.
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multiword-tags = false
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# EXTERNAL TOOLS
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[tool]
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# Default editor used to open notes. When not set, the EDITOR or VISUAL
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# environment variables are used.
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#editor = "vim"
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# Pager used to scroll through long output. If you want to disable paging
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# altogether, set it to an empty string "".
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#pager = "less -FIRX"
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# Command used to preview a note during interactive fzf mode.
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# Set it to an empty string "" to disable preview.
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# bat is a great tool to render Markdown document with syntax highlighting.
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#https://github.com/sharkdp/bat
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#fzf-preview = "bat -p --color always {-1}"
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# LSP
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#
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# Configure basic editor integration for LSP-compatible editors.
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# See https://github.com/zk-org/zk/blob/main/docs/editors-integration.md
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#
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[lsp]
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[lsp.diagnostics]
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# Each diagnostic can have for value: none, hint, info, warning, error
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# Report titles of wiki-links as hints.
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wiki-title = "hint"
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# Warn for dead links between notes.
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dead-link = "error"
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[lsp.completion]
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# Customize the completion pop-up of your LSP client.
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# Show the note title in the completion pop-up, or fallback on its path if empty.
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#note-label = "{{title-or-path}}"
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# Filter out the completion pop-up using the note title or its path.
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#note-filter-text = "{{title}} {{path}}"
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# Show the note filename without extension as detail.
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#note-detail = "{{filename-stem}}"
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# NAMED FILTERS
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#
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# A named filter is a set of note filtering options used frequently together.
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#
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[filter]
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# Matches the notes created the last two weeks. For example:
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# $ zk list recents --limit 15
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# $ zk edit recents --interactive
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#recents = "--sort created- --created-after 'last two weeks'"
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# COMMAND ALIASES
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#
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# Aliases are user commands called with `zk <alias> [<flags>] [<args>]`.
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#
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# The alias will be executed with `$SHELL -c`, please refer to your shell's
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# man page to see the available syntax. In most shells:
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# * $@ can be used to expand all the provided flags and arguments
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# * you can pipe commands together with the usual | character
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#
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[alias]
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# Here are a few aliases to get you started.
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# Shortcut to a command.
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#ls = "zk list $@"
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# Default flags for an existing command.
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#list = "zk list --quiet $@"
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# Edit the last modified note.
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#editlast = "zk edit --limit 1 --sort modified- $@"
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# Edit the notes selected interactively among the notes created the last two weeks.
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# This alias doesn't take any argument, so we don't use $@.
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#recent = "zk edit --sort created- --created-after 'last two weeks' --interactive"
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# Print paths separated with colons for the notes found with the given
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# arguments. This can be useful to expand a complex search query into a flag
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# taking only paths. For example:
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# zk list --link-to "`zk path -m potatoe`"
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#path = "zk list --quiet --format {{path}} --delimiter , $@"
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# Show a random note.
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#lucky = "zk list --quiet --format full --sort random --limit 1"
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# Returns the Git history for the notes found with the given arguments.
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# Note the use of a pipe and the location of $@.
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#hist = "zk list --format path --delimiter0 --quiet $@ | xargs -t -0 git log --patch --"
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# Edit this configuration file.
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#conf = '$EDITOR "$ZK_NOTEBOOK_DIR/.zk/config.toml"'
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Binary file not shown.
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@ -1,3 +0,0 @@
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# {{title}}
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{{content}}
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@ -1,4 +0,0 @@
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rverurl := 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv'
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update-r-version:
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RVER=$( wget -qO- {{rverurl}} | tail -n 2 | head -n 1 | cut -d',' -f4 | tr -d '"' ) &&\
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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
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103
templates/r/flake.lock
generated
103
templates/r/flake.lock
generated
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@ -1,103 +0,0 @@
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{
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"nodes": {
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"nCats": {
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"inputs": {
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"nixCats": "nixCats",
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"nixpkgs": [
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"nixpkgs"
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],
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"plugins-r": "plugins-r",
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"rixpkgs": "rixpkgs"
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},
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"locked": {
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"lastModified": 1748733634,
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"owner": "dwinkler1",
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"repo": "nixCatsConfig",
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"rev": "7e7ab54f9ab73daf585ef881aa30da1686aab524",
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"type": "github"
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},
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"original": {
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"owner": "dwinkler1",
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"repo": "nixCatsConfig",
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"type": "github"
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}
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},
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"nixCats": {
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"locked": {
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"lastModified": 1748230488,
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"owner": "BirdeeHub",
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"repo": "nixCats-nvim",
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"rev": "2a2f15a6c085524ac121f5da9a73ee2155c53d70",
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"type": "github"
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},
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"original": {
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"owner": "BirdeeHub",
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"repo": "nixCats-nvim",
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"type": "github"
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}
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},
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"nixpkgs": {
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"locked": {
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"lastModified": 1748662220,
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"owner": "nixos",
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"repo": "nixpkgs",
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"rev": "59138c7667b7970d205d6a05a8bfa2d78caa3643",
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"type": "github"
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},
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"original": {
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"owner": "nixos",
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"ref": "nixpkgs-unstable",
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"repo": "nixpkgs",
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"type": "github"
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}
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},
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"plugins-r": {
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"flake": false,
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"locked": {
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"lastModified": 1748371931,
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"owner": "R-nvim",
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"repo": "R.nvim",
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"rev": "382858fcf23aabbf47ff06279baf69d52260b939",
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"type": "github"
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},
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"original": {
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"owner": "R-nvim",
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"repo": "R.nvim",
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"type": "github"
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}
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},
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"rixpkgs": {
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"locked": {
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"lastModified": 1746476429,
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"narHash": "sha256-KHNAOy8ILpIlz5rtwxURpcVOqbWRMoT/rXRgpy1pyG8=",
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"type": "tarball",
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"url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-04-29.tar.gz"
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},
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"original": {
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"type": "tarball",
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"url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-04-29.tar.gz"
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}
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},
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"rixpkgs_2": {
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"locked": {
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"lastModified": 1747664360,
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"narHash": "sha256-DskCWKtHNGApsP3PI/HB+fETs3qXpwul3PtSgTb++N4=",
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"type": "tarball",
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"url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-05-19.tar.gz"
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},
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"original": {
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"type": "tarball",
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"url": "https://github.com/rstats-on-nix/nixpkgs/archive/2025-05-19.tar.gz"
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}
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},
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"root": {
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"inputs": {
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"nCats": "nCats",
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"nixpkgs": "nixpkgs",
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"rixpkgs": "rixpkgs_2"
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}
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}
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},
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"root": "root",
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"version": 7
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}
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@ -1,71 +0,0 @@
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{
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description = "Project Template";
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inputs = {
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rixpkgs.url = "https://github.com/rstats-on-nix/nixpkgs/archive/2025-05-19.tar.gz";
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nixpkgs.url = "github:nixos/nixpkgs/nixpkgs-unstable";
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nCats.url = "github:dwinkler1/nixCatsConfig";
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nCats.inputs.nixpkgs.follows = "nixpkgs";
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};
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outputs = {
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self,
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nixpkgs,
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nCats,
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...
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} @ inputs: let
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forSystems = nixpkgs.lib.genAttrs nixpkgs.lib.platforms.all;
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in {
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packages = forSystems (
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system: let
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inherit (nCats) utils;
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finalPackage = nCats.packages.${system}.default.override (prev: {
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dependencyOverlays =
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prev.dependencyOverlays
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++ [
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|
||||||
(utils.standardPluginOverlay inputs)
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(final: prev: {
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rpkgs = inputs.rixpkgs.legacyPackages.${system};
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})
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(import (builtins.path {
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||||||
path = ./rpkgs.nix;
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name = "my-rpackages";
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}))
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];
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categoryDefinitions = utils.mergeCatDefs prev.categoryDefinitions (
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{
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pkgs,
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settings,
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||||||
categories,
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||||||
name,
|
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||||||
extra,
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||||||
mkPlugin,
|
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||||||
...
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} @ packageDef: {
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||||||
lspsAndRuntimeDeps.rdev = with pkgs; [
|
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rWrapper
|
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||||||
just
|
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||||||
wget
|
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||||||
];
|
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||||||
}
|
|
||||||
);
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packageDefinitions =
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prev.packageDefinitions
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// {
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nixCats = utils.mergeCatDefs prev.packageDefinitions.nixCats (
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{...}: {
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||||||
settings = {
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||||||
suffix-path = false;
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|
||||||
suffix-LD = false;
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|
||||||
};
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||||||
categories = {
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rdev = true;
|
|
||||||
};
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|
||||||
}
|
|
||||||
);
|
|
||||||
};
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||||||
});
|
|
||||||
in
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||||||
utils.mkAllWithDefault finalPackage
|
|
||||||
);
|
|
||||||
};
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|
||||||
}
|
|
||||||
|
|
@ -1,34 +0,0 @@
|
||||||
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;};
|
|
||||||
}
|
|
||||||
5
templates/sci/.gitignore
vendored
5
templates/sci/.gitignore
vendored
|
|
@ -1,5 +0,0 @@
|
||||||
data
|
|
||||||
!data/raw/.gitkeep
|
|
||||||
!data/processed/.gitkeep
|
|
||||||
.venv
|
|
||||||
__marimo__
|
|
||||||
|
|
@ -1,67 +0,0 @@
|
||||||
[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
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
3.12
|
|
||||||
|
|
@ -1,199 +0,0 @@
|
||||||
# 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 "$ZK_NOTEBOOK_DIR/.zk/config.toml"'
|
|
||||||
Binary file not shown.
|
|
@ -1,3 +0,0 @@
|
||||||
# {{title}}
|
|
||||||
|
|
||||||
{{content}}
|
|
||||||
|
|
@ -1,4 +0,0 @@
|
||||||
rverurl := 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv'
|
|
||||||
update-r-version:
|
|
||||||
RVER=$( 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
|
|
||||||
121
templates/sci/flake.lock
generated
121
templates/sci/flake.lock
generated
|
|
@ -1,121 +0,0 @@
|
||||||
{
|
|
||||||
"nodes": {
|
|
||||||
"nCats": {
|
|
||||||
"inputs": {
|
|
||||||
"nixCats": "nixCats",
|
|
||||||
"nixpkgs": [
|
|
||||||
"nixpkgs"
|
|
||||||
],
|
|
||||||
"plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
|
|
||||||
"plugins-r": "plugins-r",
|
|
||||||
"rixpkgs": "rixpkgs"
|
|
||||||
},
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1750580429,
|
|
||||||
"narHash": "sha256-JK+bWsMRFyCHseiIS9olgpRM1McJ4vM1HwSCG49+M3E=",
|
|
||||||
"owner": "dwinkler1",
|
|
||||||
"repo": "nixCatsConfig",
|
|
||||||
"rev": "5037594b13921e6c83acec8de704e47669ceca41",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "dwinkler1",
|
|
||||||
"repo": "nixCatsConfig",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"nixCats": {
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1750385661,
|
|
||||||
"owner": "BirdeeHub",
|
|
||||||
"repo": "nixCats-nvim",
|
|
||||||
"rev": "04379fef2fbd4c9d8f4c9a6203cef135ab0b1acd",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "BirdeeHub",
|
|
||||||
"repo": "nixCats-nvim",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"nixpkgs": {
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1750731501,
|
|
||||||
"narHash": "sha256-Ah4qq+SbwMaGkuXCibyg+Fwn00el4KmI3XFX6htfDuk=",
|
|
||||||
"owner": "nixos",
|
|
||||||
"repo": "nixpkgs",
|
|
||||||
"rev": "69dfebb3d175bde602f612915c5576a41b18486b",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "nixos",
|
|
||||||
"ref": "nixpkgs-unstable",
|
|
||||||
"repo": "nixpkgs",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"plugins-cmp-pandoc-references": {
|
|
||||||
"flake": false,
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1743491695,
|
|
||||||
"owner": "jmbuhr",
|
|
||||||
"repo": "cmp-pandoc-references",
|
|
||||||
"rev": "130eae4f75029d6495808e0ea4b769fa1ce4c9ac",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "jmbuhr",
|
|
||||||
"repo": "cmp-pandoc-references",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"plugins-r": {
|
|
||||||
"flake": false,
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1749130465,
|
|
||||||
"owner": "R-nvim",
|
|
||||||
"repo": "R.nvim",
|
|
||||||
"rev": "65f772c012240bc1a1706da11049d2c9801275dc",
|
|
||||||
"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
|
|
||||||
}
|
|
||||||
|
|
@ -1,140 +0,0 @@
|
||||||
{
|
|
||||||
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.${system};
|
|
||||||
})
|
|
||||||
(import (builtins.path {
|
|
||||||
path = ./rpkgs.nix;
|
|
||||||
name = "my-rpackages";
|
|
||||||
}))
|
|
||||||
(import (builtins.path {
|
|
||||||
path = ./pypkgs.nix;
|
|
||||||
name = "my-pypackages";
|
|
||||||
}))
|
|
||||||
];
|
|
||||||
categoryDefinitions = utils.mergeCatDefs prev.categoryDefinitions (
|
|
||||||
{
|
|
||||||
pkgs,
|
|
||||||
settings,
|
|
||||||
categories,
|
|
||||||
name,
|
|
||||||
extra,
|
|
||||||
mkPlugin,
|
|
||||||
...
|
|
||||||
} @ packageDef: {
|
|
||||||
lspsAndRuntimeDeps = {
|
|
||||||
meta = with pkgs; [
|
|
||||||
just
|
|
||||||
wget
|
|
||||||
gh
|
|
||||||
];
|
|
||||||
rdev = with pkgs; [
|
|
||||||
rWrapper
|
|
||||||
];
|
|
||||||
pydev = with pkgs; [
|
|
||||||
py
|
|
||||||
uv
|
|
||||||
pyright
|
|
||||||
nodejs
|
|
||||||
];
|
|
||||||
jldev = with pkgs; [
|
|
||||||
julia-bin
|
|
||||||
];
|
|
||||||
quarto = with pkgs; [
|
|
||||||
quarto
|
|
||||||
];
|
|
||||||
};
|
|
||||||
|
|
||||||
environmentVariables = {
|
|
||||||
rdev = {
|
|
||||||
R_LIBS_USER = "./.Rlibs";
|
|
||||||
};
|
|
||||||
pydev = {
|
|
||||||
# Prevent uv from managing Python downloads
|
|
||||||
UV_PYTHON_DOWNLOADS = "never";
|
|
||||||
# Force uv to use nixpkgs Python interpreter
|
|
||||||
UV_PYTHON = pkgs.py.interpreter;
|
|
||||||
};
|
|
||||||
};
|
|
||||||
extraWrapperArgs = {
|
|
||||||
pydev = [
|
|
||||||
"--unset PYTHONPATH"
|
|
||||||
];
|
|
||||||
};
|
|
||||||
bashBeforeWrapper = {
|
|
||||||
pydev = [
|
|
||||||
"export UV_PYTHON=${pkgs.py.interpreter}"
|
|
||||||
"export UV_PYTHON_DOWNLOADS=\"never\""
|
|
||||||
"${pkgs.uv}/bin/uv sync"
|
|
||||||
];
|
|
||||||
};
|
|
||||||
}
|
|
||||||
);
|
|
||||||
|
|
||||||
packageDefinitions =
|
|
||||||
prev.packageDefinitions
|
|
||||||
// {
|
|
||||||
nixCats = utils.mergeCatDefs prev.packageDefinitions.nixCats (
|
|
||||||
{pkgs, name, ...}: {
|
|
||||||
settings = {
|
|
||||||
suffix-path = false;
|
|
||||||
suffix-LD = false;
|
|
||||||
hosts = {
|
|
||||||
python3.enable = true;
|
|
||||||
marimo = {
|
|
||||||
enable = true;
|
|
||||||
path = {
|
|
||||||
value = "${pkgs.uv}/bin/uv";
|
|
||||||
args = ["--add-flags" "run marimo edit"];
|
|
||||||
};
|
|
||||||
};
|
|
||||||
neovide = {
|
|
||||||
enable = true;
|
|
||||||
path = {
|
|
||||||
value = "${pkgs.neovide}/bin/neovide";
|
|
||||||
args = [
|
|
||||||
"--add-flags"
|
|
||||||
"--neovim-bin ${name}"
|
|
||||||
];
|
|
||||||
};
|
|
||||||
};
|
|
||||||
};
|
|
||||||
};
|
|
||||||
categories = {
|
|
||||||
meta = true;
|
|
||||||
rdev = true;
|
|
||||||
pydev = true;
|
|
||||||
jldev = true;
|
|
||||||
quarto = true;
|
|
||||||
};
|
|
||||||
}
|
|
||||||
);
|
|
||||||
};
|
|
||||||
});
|
|
||||||
in
|
|
||||||
utils.mkAllWithDefault finalPackage
|
|
||||||
);
|
|
||||||
};
|
|
||||||
}
|
|
||||||
|
|
@ -1,8 +0,0 @@
|
||||||
final: prev: let
|
|
||||||
reqPkgs = (pyPackages: with pyPackages;[
|
|
||||||
requests
|
|
||||||
]);
|
|
||||||
in {
|
|
||||||
py = prev.python3.withPackages reqPkgs;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
@ -1,16 +0,0 @@
|
||||||
[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",
|
|
||||||
]
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
{ "venvPath": ".", "venv": ".venv" }
|
|
||||||
|
|
@ -1,35 +0,0 @@
|
||||||
final: prev: let
|
|
||||||
reqPkgs = with prev.rpkgs.rPackages; [
|
|
||||||
Hmisc
|
|
||||||
broom
|
|
||||||
data_table
|
|
||||||
dplyr
|
|
||||||
ggplot2
|
|
||||||
gt
|
|
||||||
janitor
|
|
||||||
psych
|
|
||||||
tidyr
|
|
||||||
quarto
|
|
||||||
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;};
|
|
||||||
}
|
|
||||||
1152
templates/sci/uv.lock
generated
1152
templates/sci/uv.lock
generated
File diff suppressed because it is too large
Load diff
5
templates/sci_minimal/.gitignore
vendored
5
templates/sci_minimal/.gitignore
vendored
|
|
@ -1,5 +0,0 @@
|
||||||
data
|
|
||||||
!data/raw/.gitkeep
|
|
||||||
!data/processed/.gitkeep
|
|
||||||
.venv
|
|
||||||
__marimo__
|
|
||||||
|
|
@ -1,67 +0,0 @@
|
||||||
[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
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
3.12
|
|
||||||
|
|
@ -1,199 +0,0 @@
|
||||||
# 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 "$ZK_NOTEBOOK_DIR/.zk/config.toml"'
|
|
||||||
Binary file not shown.
|
|
@ -1,3 +0,0 @@
|
||||||
# {{title}}
|
|
||||||
|
|
||||||
{{content}}
|
|
||||||
|
|
@ -1,4 +0,0 @@
|
||||||
rverurl := 'https://raw.githubusercontent.com/ropensci/rix/refs/heads/main/inst/extdata/available_df.csv'
|
|
||||||
update-r-version:
|
|
||||||
RVER=$( 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
|
|
||||||
121
templates/sci_minimal/flake.lock
generated
121
templates/sci_minimal/flake.lock
generated
|
|
@ -1,121 +0,0 @@
|
||||||
{
|
|
||||||
"nodes": {
|
|
||||||
"nCats": {
|
|
||||||
"inputs": {
|
|
||||||
"nixCats": "nixCats",
|
|
||||||
"nixpkgs": [
|
|
||||||
"nixpkgs"
|
|
||||||
],
|
|
||||||
"plugins-cmp-pandoc-references": "plugins-cmp-pandoc-references",
|
|
||||||
"plugins-r": "plugins-r",
|
|
||||||
"rixpkgs": "rixpkgs"
|
|
||||||
},
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1750580429,
|
|
||||||
"narHash": "sha256-JK+bWsMRFyCHseiIS9olgpRM1McJ4vM1HwSCG49+M3E=",
|
|
||||||
"owner": "dwinkler1",
|
|
||||||
"repo": "nixCatsConfig",
|
|
||||||
"rev": "5037594b13921e6c83acec8de704e47669ceca41",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "dwinkler1",
|
|
||||||
"repo": "nixCatsConfig",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"nixCats": {
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1750385661,
|
|
||||||
"owner": "BirdeeHub",
|
|
||||||
"repo": "nixCats-nvim",
|
|
||||||
"rev": "04379fef2fbd4c9d8f4c9a6203cef135ab0b1acd",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "BirdeeHub",
|
|
||||||
"repo": "nixCats-nvim",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"nixpkgs": {
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1750731501,
|
|
||||||
"narHash": "sha256-Ah4qq+SbwMaGkuXCibyg+Fwn00el4KmI3XFX6htfDuk=",
|
|
||||||
"owner": "nixos",
|
|
||||||
"repo": "nixpkgs",
|
|
||||||
"rev": "69dfebb3d175bde602f612915c5576a41b18486b",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "nixos",
|
|
||||||
"ref": "nixpkgs-unstable",
|
|
||||||
"repo": "nixpkgs",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"plugins-cmp-pandoc-references": {
|
|
||||||
"flake": false,
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1743491695,
|
|
||||||
"owner": "jmbuhr",
|
|
||||||
"repo": "cmp-pandoc-references",
|
|
||||||
"rev": "130eae4f75029d6495808e0ea4b769fa1ce4c9ac",
|
|
||||||
"type": "github"
|
|
||||||
},
|
|
||||||
"original": {
|
|
||||||
"owner": "jmbuhr",
|
|
||||||
"repo": "cmp-pandoc-references",
|
|
||||||
"type": "github"
|
|
||||||
}
|
|
||||||
},
|
|
||||||
"plugins-r": {
|
|
||||||
"flake": false,
|
|
||||||
"locked": {
|
|
||||||
"lastModified": 1749130465,
|
|
||||||
"owner": "R-nvim",
|
|
||||||
"repo": "R.nvim",
|
|
||||||
"rev": "65f772c012240bc1a1706da11049d2c9801275dc",
|
|
||||||
"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
|
|
||||||
}
|
|
||||||
|
|
@ -1,140 +0,0 @@
|
||||||
{
|
|
||||||
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.${system};
|
|
||||||
})
|
|
||||||
(import (builtins.path {
|
|
||||||
path = ./rpkgs.nix;
|
|
||||||
name = "my-rpackages";
|
|
||||||
}))
|
|
||||||
(import (builtins.path {
|
|
||||||
path = ./pypkgs.nix;
|
|
||||||
name = "my-pypackages";
|
|
||||||
}))
|
|
||||||
];
|
|
||||||
categoryDefinitions = utils.mergeCatDefs prev.categoryDefinitions (
|
|
||||||
{
|
|
||||||
pkgs,
|
|
||||||
settings,
|
|
||||||
categories,
|
|
||||||
name,
|
|
||||||
extra,
|
|
||||||
mkPlugin,
|
|
||||||
...
|
|
||||||
} @ packageDef: {
|
|
||||||
lspsAndRuntimeDeps = {
|
|
||||||
meta = with pkgs; [
|
|
||||||
just
|
|
||||||
wget
|
|
||||||
gh
|
|
||||||
];
|
|
||||||
rdev = with pkgs; [
|
|
||||||
rWrapper
|
|
||||||
];
|
|
||||||
pydev = with pkgs; [
|
|
||||||
py
|
|
||||||
uv
|
|
||||||
pyright
|
|
||||||
nodejs
|
|
||||||
];
|
|
||||||
jldev = with pkgs; [
|
|
||||||
julia-bin
|
|
||||||
];
|
|
||||||
quarto = with pkgs; [
|
|
||||||
quarto
|
|
||||||
];
|
|
||||||
};
|
|
||||||
|
|
||||||
environmentVariables = {
|
|
||||||
rdev = {
|
|
||||||
R_LIBS_USER = "./.Rlibs";
|
|
||||||
};
|
|
||||||
pydev = {
|
|
||||||
# Prevent uv from managing Python downloads
|
|
||||||
UV_PYTHON_DOWNLOADS = "never";
|
|
||||||
# Force uv to use nixpkgs Python interpreter
|
|
||||||
UV_PYTHON = pkgs.py.interpreter;
|
|
||||||
};
|
|
||||||
};
|
|
||||||
extraWrapperArgs = {
|
|
||||||
pydev = [
|
|
||||||
"--unset PYTHONPATH"
|
|
||||||
];
|
|
||||||
};
|
|
||||||
bashBeforeWrapper = {
|
|
||||||
pydev = [
|
|
||||||
"export UV_PYTHON=${pkgs.py.interpreter}"
|
|
||||||
"export UV_PYTHON_DOWNLOADS=\"never\""
|
|
||||||
"${pkgs.uv}/bin/uv sync"
|
|
||||||
];
|
|
||||||
};
|
|
||||||
}
|
|
||||||
);
|
|
||||||
|
|
||||||
packageDefinitions =
|
|
||||||
prev.packageDefinitions
|
|
||||||
// {
|
|
||||||
nixCats = utils.mergeCatDefs prev.packageDefinitions.nixCats (
|
|
||||||
{pkgs, name, ...}: {
|
|
||||||
settings = {
|
|
||||||
suffix-path = false;
|
|
||||||
suffix-LD = false;
|
|
||||||
hosts = {
|
|
||||||
python3.enable = true;
|
|
||||||
marimo = {
|
|
||||||
enable = true;
|
|
||||||
path = {
|
|
||||||
value = "${pkgs.uv}/bin/uv";
|
|
||||||
args = ["--add-flags" "run marimo edit"];
|
|
||||||
};
|
|
||||||
};
|
|
||||||
neovide = {
|
|
||||||
enable = true;
|
|
||||||
path = {
|
|
||||||
value = "${pkgs.neovide}/bin/neovide";
|
|
||||||
args = [
|
|
||||||
"--add-flags"
|
|
||||||
"--neovim-bin ${name}"
|
|
||||||
];
|
|
||||||
};
|
|
||||||
};
|
|
||||||
};
|
|
||||||
};
|
|
||||||
categories = {
|
|
||||||
meta = true;
|
|
||||||
rdev = true;
|
|
||||||
pydev = true;
|
|
||||||
jldev = true;
|
|
||||||
quarto = true;
|
|
||||||
};
|
|
||||||
}
|
|
||||||
);
|
|
||||||
};
|
|
||||||
});
|
|
||||||
in
|
|
||||||
utils.mkAllWithDefault finalPackage
|
|
||||||
);
|
|
||||||
};
|
|
||||||
}
|
|
||||||
|
|
@ -1,8 +0,0 @@
|
||||||
final: prev: let
|
|
||||||
reqPkgs = (pyPackages: with pyPackages;[
|
|
||||||
requests
|
|
||||||
]);
|
|
||||||
in {
|
|
||||||
py = prev.python3.withPackages reqPkgs;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
@ -1,16 +0,0 @@
|
||||||
[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",
|
|
||||||
]
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
{ "venvPath": ".", "venv": ".venv" }
|
|
||||||
|
|
@ -1,35 +0,0 @@
|
||||||
final: prev: let
|
|
||||||
reqPkgs = with prev.rpkgs.rPackages; [
|
|
||||||
Hmisc
|
|
||||||
broom
|
|
||||||
data_table
|
|
||||||
dplyr
|
|
||||||
ggplot2
|
|
||||||
gt
|
|
||||||
janitor
|
|
||||||
psych
|
|
||||||
tidyr
|
|
||||||
quarto
|
|
||||||
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;};
|
|
||||||
}
|
|
||||||
1152
templates/sci_minimal/uv.lock
generated
1152
templates/sci_minimal/uv.lock
generated
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