From 24d78201657d935191a81451b5c2efc4862578f7 Mon Sep 17 00:00:00 2001 From: coolneng Date: Tue, 2 Nov 2021 16:11:17 +0100 Subject: [PATCH] Replace niv with flakes --- flake.lock | 41 +++++++++++ flake.nix | 13 ++++ nix/sources.json | 26 ------- nix/sources.nix | 174 ----------------------------------------------- shell.nix | 5 +- 5 files changed, 56 insertions(+), 203 deletions(-) create mode 100644 flake.lock create mode 100644 flake.nix delete mode 100644 nix/sources.json delete mode 100644 nix/sources.nix diff --git a/flake.lock b/flake.lock new file mode 100644 index 0000000..70e897b --- /dev/null +++ b/flake.lock @@ -0,0 +1,41 @@ +{ + "nodes": { + "flake-utils": { + "locked": { + "lastModified": 1634851050, + "narHash": "sha256-N83GlSGPJJdcqhUxSCS/WwW5pksYf3VP1M13cDRTSVA=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "c91f3de5adaf1de973b797ef7485e441a65b8935", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "nixpkgs": { + "locked": { + "lastModified": 1635865339, + "narHash": "sha256-fmI8PxMmL7WXV/O8m6vT9/yW42buxvAYeRNpcABvnKs=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "26a56abd090ec5c8f4c6c9e1189fbfa4bcb8db3f", + "type": "github" + }, + "original": { + "id": "nixpkgs", + "type": "indirect" + } + }, + "root": { + "inputs": { + "flake-utils": "flake-utils", + "nixpkgs": "nixpkgs" + } + } + }, + "root": "root", + "version": 7 +} diff --git a/flake.nix b/flake.nix new file mode 100644 index 0000000..a6aa45c --- /dev/null +++ b/flake.nix @@ -0,0 +1,13 @@ +{ + description = '' + locigenesis is a tool that generates a human T-cell receptor (TCR), runs + it through a sequence reader simulation tool and extracts CDR3. + ''; + + inputs.flake-utils.url = "github:numtide/flake-utils"; + + outputs = { self, nixpkgs, flake-utils }: + flake-utils.lib.eachDefaultSystem (system: + let pkgs = nixpkgs.legacyPackages.${system}; + in { devShell = import ./shell.nix { inherit pkgs; }; }); +} diff --git a/nix/sources.json b/nix/sources.json deleted file mode 100644 index 51d340c..0000000 --- a/nix/sources.json +++ /dev/null @@ -1,26 +0,0 @@ -{ - "niv": { - "branch": "master", - "description": "Easy dependency management for Nix projects", - "homepage": "https://github.com/nmattia/niv", - "owner": "nmattia", - "repo": "niv", - "rev": "af958e8057f345ee1aca714c1247ef3ba1c15f5e", - "sha256": "1qjavxabbrsh73yck5dcq8jggvh3r2jkbr6b5nlz5d9yrqm9255n", - "type": "tarball", - "url": "https://github.com/nmattia/niv/archive/af958e8057f345ee1aca714c1247ef3ba1c15f5e.tar.gz", - "url_template": "https://github.com///archive/.tar.gz" - }, - "nixpkgs": { - "branch": "release-20.09", - "description": "Nix Packages collection", - "homepage": "", - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "359e6542e1d41eb18df55c82bdb08bf738fae2cf", - "sha256": "05v28njaas9l26ibc6vy6imvy7grbkli32bmv0n32x6x9cf68gf9", - "type": "tarball", - "url": "https://github.com/NixOS/nixpkgs/archive/359e6542e1d41eb18df55c82bdb08bf738fae2cf.tar.gz", - "url_template": "https://github.com///archive/.tar.gz" - } -} diff --git a/nix/sources.nix b/nix/sources.nix deleted file mode 100644 index 1938409..0000000 --- a/nix/sources.nix +++ /dev/null @@ -1,174 +0,0 @@ -# This file has been generated by Niv. - -let - - # - # The fetchers. fetch_ fetches specs of type . - # - - fetch_file = pkgs: name: spec: - let - name' = sanitizeName name + "-src"; - in - if spec.builtin or true then - builtins_fetchurl { inherit (spec) url sha256; name = name'; } - else - pkgs.fetchurl { inherit (spec) url sha256; name = name'; }; - - fetch_tarball = pkgs: name: spec: - let - name' = sanitizeName name + "-src"; - in - if spec.builtin or true then - builtins_fetchTarball { name = name'; inherit (spec) url sha256; } - else - pkgs.fetchzip { name = name'; inherit (spec) url sha256; }; - - fetch_git = name: spec: - let - ref = - if spec ? ref then spec.ref else - if spec ? branch then "refs/heads/${spec.branch}" else - if spec ? tag then "refs/tags/${spec.tag}" else - abort "In git source '${name}': Please specify `ref`, `tag` or `branch`!"; - in - builtins.fetchGit { url = spec.repo; inherit (spec) rev; inherit ref; }; - - fetch_local = spec: spec.path; - - fetch_builtin-tarball = name: throw - ''[${name}] The niv type "builtin-tarball" is deprecated. You should instead use `builtin = true`. - $ niv modify ${name} -a type=tarball -a builtin=true''; - - fetch_builtin-url = name: throw - ''[${name}] The niv type "builtin-url" will soon be deprecated. You should instead use `builtin = true`. - $ niv modify ${name} -a type=file -a builtin=true''; - - # - # Various helpers - # - - # https://github.com/NixOS/nixpkgs/pull/83241/files#diff-c6f540a4f3bfa4b0e8b6bafd4cd54e8bR695 - sanitizeName = name: - ( - concatMapStrings (s: if builtins.isList s then "-" else s) - ( - builtins.split "[^[:alnum:]+._?=-]+" - ((x: builtins.elemAt (builtins.match "\\.*(.*)" x) 0) name) - ) - ); - - # The set of packages used when specs are fetched using non-builtins. - mkPkgs = sources: system: - let - sourcesNixpkgs = - import (builtins_fetchTarball { inherit (sources.nixpkgs) url sha256; }) { inherit system; }; - hasNixpkgsPath = builtins.any (x: x.prefix == "nixpkgs") builtins.nixPath; - hasThisAsNixpkgsPath = == ./.; - in - if builtins.hasAttr "nixpkgs" sources - then sourcesNixpkgs - else if hasNixpkgsPath && ! hasThisAsNixpkgsPath then - import {} - else - abort - '' - Please specify either (through -I or NIX_PATH=nixpkgs=...) or - add a package called "nixpkgs" to your sources.json. - ''; - - # The actual fetching function. - fetch = pkgs: name: spec: - - if ! builtins.hasAttr "type" spec then - abort "ERROR: niv spec ${name} does not have a 'type' attribute" - else if spec.type == "file" then fetch_file pkgs name spec - else if spec.type == "tarball" then fetch_tarball pkgs name spec - else if spec.type == "git" then fetch_git name spec - else if spec.type == "local" then fetch_local spec - else if spec.type == "builtin-tarball" then fetch_builtin-tarball name - else if spec.type == "builtin-url" then fetch_builtin-url name - else - abort "ERROR: niv spec ${name} has unknown type ${builtins.toJSON spec.type}"; - - # If the environment variable NIV_OVERRIDE_${name} is set, then use - # the path directly as opposed to the fetched source. - replace = name: drv: - let - saneName = stringAsChars (c: if isNull (builtins.match "[a-zA-Z0-9]" c) then "_" else c) name; - ersatz = builtins.getEnv "NIV_OVERRIDE_${saneName}"; - in - if ersatz == "" then drv else - # this turns the string into an actual Nix path (for both absolute and - # relative paths) - if builtins.substring 0 1 ersatz == "/" then /. + ersatz else /. + builtins.getEnv "PWD" + "/${ersatz}"; - - # Ports of functions for older nix versions - - # a Nix version of mapAttrs if the built-in doesn't exist - mapAttrs = builtins.mapAttrs or ( - f: set: with builtins; - listToAttrs (map (attr: { name = attr; value = f attr set.${attr}; }) (attrNames set)) - ); - - # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/lists.nix#L295 - range = first: last: if first > last then [] else builtins.genList (n: first + n) (last - first + 1); - - # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L257 - stringToCharacters = s: map (p: builtins.substring p 1 s) (range 0 (builtins.stringLength s - 1)); - - # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L269 - stringAsChars = f: s: concatStrings (map f (stringToCharacters s)); - concatMapStrings = f: list: concatStrings (map f list); - concatStrings = builtins.concatStringsSep ""; - - # https://github.com/NixOS/nixpkgs/blob/8a9f58a375c401b96da862d969f66429def1d118/lib/attrsets.nix#L331 - optionalAttrs = cond: as: if cond then as else {}; - - # fetchTarball version that is compatible between all the versions of Nix - builtins_fetchTarball = { url, name ? null, sha256 }@attrs: - let - inherit (builtins) lessThan nixVersion fetchTarball; - in - if lessThan nixVersion "1.12" then - fetchTarball ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; })) - else - fetchTarball attrs; - - # fetchurl version that is compatible between all the versions of Nix - builtins_fetchurl = { url, name ? null, sha256 }@attrs: - let - inherit (builtins) lessThan nixVersion fetchurl; - in - if lessThan nixVersion "1.12" then - fetchurl ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; })) - else - fetchurl attrs; - - # Create the final "sources" from the config - mkSources = config: - mapAttrs ( - name: spec: - if builtins.hasAttr "outPath" spec - then abort - "The values in sources.json should not have an 'outPath' attribute" - else - spec // { outPath = replace name (fetch config.pkgs name spec); } - ) config.sources; - - # The "config" used by the fetchers - mkConfig = - { sourcesFile ? if builtins.pathExists ./sources.json then ./sources.json else null - , sources ? if isNull sourcesFile then {} else builtins.fromJSON (builtins.readFile sourcesFile) - , system ? builtins.currentSystem - , pkgs ? mkPkgs sources system - }: rec { - # The sources, i.e. the attribute set of spec name to spec - inherit sources; - - # The "pkgs" (evaluated nixpkgs) to use for e.g. non-builtin fetchers - inherit pkgs; - }; - -in -mkSources (mkConfig {}) // { __functor = _: settings: mkSources (mkConfig settings); } diff --git a/shell.nix b/shell.nix index ef1b156..fe20f8f 100644 --- a/shell.nix +++ b/shell.nix @@ -1,4 +1,4 @@ -{ sources ? import ./nix/sources.nix, pkgs ? import sources.nixpkgs { } }: +{ pkgs ? import { } }: with pkgs; @@ -6,8 +6,7 @@ let CuReSim = stdenv.mkDerivation rec { name = "CuReSim"; version = "1.3"; - src = fetchzip { - url = + src = fetchzip { url = "http://www.pegase-biosciences.com/wp-content/uploads/2015/08/${name}${version}.zip"; sha256 = "1hvlpgy4haqgqq52mkxhcl9i1fx67kgwi6f1mijvqzk0xff77hkp"; stripRoot = true;