Replace niv with flakes
This commit is contained in:
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3d8e0fe114
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24d7820165
GPG Key ID:
9893DA236405AF57
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@ -0,0 +1,41 @@
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{
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"nodes": {
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"flake-utils": {
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"locked": {
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"lastModified": 1634851050,
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"narHash": "sha256-N83GlSGPJJdcqhUxSCS/WwW5pksYf3VP1M13cDRTSVA=",
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"owner": "numtide",
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"repo": "flake-utils",
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"rev": "c91f3de5adaf1de973b797ef7485e441a65b8935",
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"type": "github"
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},
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"original": {
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"owner": "numtide",
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"repo": "flake-utils",
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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": 1635865339,
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"narHash": "sha256-fmI8PxMmL7WXV/O8m6vT9/yW42buxvAYeRNpcABvnKs=",
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"owner": "NixOS",
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"repo": "nixpkgs",
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"rev": "26a56abd090ec5c8f4c6c9e1189fbfa4bcb8db3f",
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"type": "github"
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},
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"original": {
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"id": "nixpkgs",
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"type": "indirect"
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}
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},
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"root": {
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"inputs": {
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"flake-utils": "flake-utils",
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"nixpkgs": "nixpkgs"
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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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@ -0,0 +1,13 @@
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{
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description = ''
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locigenesis is a tool that generates a human T-cell receptor (TCR), runs
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it through a sequence reader simulation tool and extracts CDR3.
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'';
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inputs.flake-utils.url = "github:numtide/flake-utils";
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outputs = { self, nixpkgs, flake-utils }:
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flake-utils.lib.eachDefaultSystem (system:
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let pkgs = nixpkgs.legacyPackages.${system};
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in { devShell = import ./shell.nix { inherit pkgs; }; });
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}
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@ -1,26 +0,0 @@
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{
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"niv": {
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"branch": "master",
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"description": "Easy dependency management for Nix projects",
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"homepage": "https://github.com/nmattia/niv",
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"owner": "nmattia",
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"repo": "niv",
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"rev": "af958e8057f345ee1aca714c1247ef3ba1c15f5e",
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"sha256": "1qjavxabbrsh73yck5dcq8jggvh3r2jkbr6b5nlz5d9yrqm9255n",
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"type": "tarball",
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"url": "https://github.com/nmattia/niv/archive/af958e8057f345ee1aca714c1247ef3ba1c15f5e.tar.gz",
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"url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
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},
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"nixpkgs": {
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"branch": "release-20.09",
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"description": "Nix Packages collection",
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"homepage": "",
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"owner": "NixOS",
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"repo": "nixpkgs",
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"rev": "359e6542e1d41eb18df55c82bdb08bf738fae2cf",
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"sha256": "05v28njaas9l26ibc6vy6imvy7grbkli32bmv0n32x6x9cf68gf9",
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"type": "tarball",
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"url": "https://github.com/NixOS/nixpkgs/archive/359e6542e1d41eb18df55c82bdb08bf738fae2cf.tar.gz",
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"url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
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}
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}
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174
nix/sources.nix
174
nix/sources.nix
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@ -1,174 +0,0 @@
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# This file has been generated by Niv.
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let
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#
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# The fetchers. fetch_<type> fetches specs of type <type>.
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#
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fetch_file = pkgs: name: spec:
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let
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name' = sanitizeName name + "-src";
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in
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if spec.builtin or true then
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builtins_fetchurl { inherit (spec) url sha256; name = name'; }
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else
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pkgs.fetchurl { inherit (spec) url sha256; name = name'; };
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fetch_tarball = pkgs: name: spec:
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let
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name' = sanitizeName name + "-src";
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in
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if spec.builtin or true then
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builtins_fetchTarball { name = name'; inherit (spec) url sha256; }
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else
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pkgs.fetchzip { name = name'; inherit (spec) url sha256; };
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fetch_git = name: spec:
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let
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ref =
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if spec ? ref then spec.ref else
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if spec ? branch then "refs/heads/${spec.branch}" else
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if spec ? tag then "refs/tags/${spec.tag}" else
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abort "In git source '${name}': Please specify `ref`, `tag` or `branch`!";
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in
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builtins.fetchGit { url = spec.repo; inherit (spec) rev; inherit ref; };
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fetch_local = spec: spec.path;
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fetch_builtin-tarball = name: throw
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''[${name}] The niv type "builtin-tarball" is deprecated. You should instead use `builtin = true`.
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$ niv modify ${name} -a type=tarball -a builtin=true'';
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fetch_builtin-url = name: throw
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''[${name}] The niv type "builtin-url" will soon be deprecated. You should instead use `builtin = true`.
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$ niv modify ${name} -a type=file -a builtin=true'';
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#
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# Various helpers
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#
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# https://github.com/NixOS/nixpkgs/pull/83241/files#diff-c6f540a4f3bfa4b0e8b6bafd4cd54e8bR695
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sanitizeName = name:
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(
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concatMapStrings (s: if builtins.isList s then "-" else s)
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(
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builtins.split "[^[:alnum:]+._?=-]+"
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((x: builtins.elemAt (builtins.match "\\.*(.*)" x) 0) name)
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)
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);
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# The set of packages used when specs are fetched using non-builtins.
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mkPkgs = sources: system:
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let
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sourcesNixpkgs =
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import (builtins_fetchTarball { inherit (sources.nixpkgs) url sha256; }) { inherit system; };
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hasNixpkgsPath = builtins.any (x: x.prefix == "nixpkgs") builtins.nixPath;
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hasThisAsNixpkgsPath = <nixpkgs> == ./.;
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in
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if builtins.hasAttr "nixpkgs" sources
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then sourcesNixpkgs
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else if hasNixpkgsPath && ! hasThisAsNixpkgsPath then
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import <nixpkgs> {}
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else
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abort
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''
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Please specify either <nixpkgs> (through -I or NIX_PATH=nixpkgs=...) or
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add a package called "nixpkgs" to your sources.json.
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'';
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# The actual fetching function.
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fetch = pkgs: name: spec:
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if ! builtins.hasAttr "type" spec then
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abort "ERROR: niv spec ${name} does not have a 'type' attribute"
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else if spec.type == "file" then fetch_file pkgs name spec
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else if spec.type == "tarball" then fetch_tarball pkgs name spec
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else if spec.type == "git" then fetch_git name spec
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else if spec.type == "local" then fetch_local spec
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else if spec.type == "builtin-tarball" then fetch_builtin-tarball name
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else if spec.type == "builtin-url" then fetch_builtin-url name
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else
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abort "ERROR: niv spec ${name} has unknown type ${builtins.toJSON spec.type}";
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# If the environment variable NIV_OVERRIDE_${name} is set, then use
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# the path directly as opposed to the fetched source.
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replace = name: drv:
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let
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saneName = stringAsChars (c: if isNull (builtins.match "[a-zA-Z0-9]" c) then "_" else c) name;
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ersatz = builtins.getEnv "NIV_OVERRIDE_${saneName}";
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in
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if ersatz == "" then drv else
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# this turns the string into an actual Nix path (for both absolute and
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# relative paths)
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if builtins.substring 0 1 ersatz == "/" then /. + ersatz else /. + builtins.getEnv "PWD" + "/${ersatz}";
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# Ports of functions for older nix versions
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# a Nix version of mapAttrs if the built-in doesn't exist
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mapAttrs = builtins.mapAttrs or (
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f: set: with builtins;
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listToAttrs (map (attr: { name = attr; value = f attr set.${attr}; }) (attrNames set))
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);
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# https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/lists.nix#L295
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range = first: last: if first > last then [] else builtins.genList (n: first + n) (last - first + 1);
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# https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L257
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stringToCharacters = s: map (p: builtins.substring p 1 s) (range 0 (builtins.stringLength s - 1));
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# https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L269
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stringAsChars = f: s: concatStrings (map f (stringToCharacters s));
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concatMapStrings = f: list: concatStrings (map f list);
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concatStrings = builtins.concatStringsSep "";
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# https://github.com/NixOS/nixpkgs/blob/8a9f58a375c401b96da862d969f66429def1d118/lib/attrsets.nix#L331
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optionalAttrs = cond: as: if cond then as else {};
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# fetchTarball version that is compatible between all the versions of Nix
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builtins_fetchTarball = { url, name ? null, sha256 }@attrs:
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let
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inherit (builtins) lessThan nixVersion fetchTarball;
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in
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if lessThan nixVersion "1.12" then
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fetchTarball ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; }))
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else
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fetchTarball attrs;
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# fetchurl version that is compatible between all the versions of Nix
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builtins_fetchurl = { url, name ? null, sha256 }@attrs:
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let
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inherit (builtins) lessThan nixVersion fetchurl;
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in
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if lessThan nixVersion "1.12" then
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fetchurl ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; }))
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else
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fetchurl attrs;
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# Create the final "sources" from the config
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mkSources = config:
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mapAttrs (
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name: spec:
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if builtins.hasAttr "outPath" spec
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then abort
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"The values in sources.json should not have an 'outPath' attribute"
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else
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spec // { outPath = replace name (fetch config.pkgs name spec); }
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) config.sources;
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# The "config" used by the fetchers
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mkConfig =
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{ sourcesFile ? if builtins.pathExists ./sources.json then ./sources.json else null
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, sources ? if isNull sourcesFile then {} else builtins.fromJSON (builtins.readFile sourcesFile)
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, system ? builtins.currentSystem
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, pkgs ? mkPkgs sources system
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}: rec {
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# The sources, i.e. the attribute set of spec name to spec
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inherit sources;
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# The "pkgs" (evaluated nixpkgs) to use for e.g. non-builtin fetchers
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inherit pkgs;
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};
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in
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mkSources (mkConfig {}) // { __functor = _: settings: mkSources (mkConfig settings); }
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@ -1,4 +1,4 @@
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{ sources ? import ./nix/sources.nix, pkgs ? import sources.nixpkgs { } }:
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{ pkgs ? import <nixpkgs> { } }:
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with pkgs;
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@ -6,8 +6,7 @@ let
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CuReSim = stdenv.mkDerivation rec {
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name = "CuReSim";
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version = "1.3";
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src = fetchzip {
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url =
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src = fetchzip { url =
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"http://www.pegase-biosciences.com/wp-content/uploads/2015/08/${name}${version}.zip";
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sha256 = "1hvlpgy4haqgqq52mkxhcl9i1fx67kgwi6f1mijvqzk0xff77hkp";
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stripRoot = true;
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