--- /dev/null
+{
+ "nodes": {
+ "flake-compat": {
+ "flake": false,
+ "locked": {
+ "lastModified": 1696426674,
+ "narHash": "sha256-kvjfFW7WAETZlt09AgDn1MrtKzP7t90Vf7vypd3OL1U=",
+ "owner": "edolstra",
+ "repo": "flake-compat",
+ "rev": "0f9255e01c2351cc7d116c072cb317785dd33b33",
+ "type": "github"
+ },
+ "original": {
+ "owner": "edolstra",
+ "repo": "flake-compat",
+ "type": "github"
+ }
+ },
+ "flake-compat_2": {
+ "flake": false,
+ "locked": {
+ "lastModified": 1696426674,
+ "narHash": "sha256-kvjfFW7WAETZlt09AgDn1MrtKzP7t90Vf7vypd3OL1U=",
+ "owner": "edolstra",
+ "repo": "flake-compat",
+ "rev": "0f9255e01c2351cc7d116c072cb317785dd33b33",
+ "type": "github"
+ },
+ "original": {
+ "owner": "edolstra",
+ "repo": "flake-compat",
+ "type": "github"
+ }
+ },
+ "flake-utils": {
+ "inputs": {
+ "systems": "systems"
+ },
+ "locked": {
+ "lastModified": 1710146030,
+ "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+ "owner": "numtide",
+ "repo": "flake-utils",
+ "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+ "type": "github"
+ },
+ "original": {
+ "owner": "numtide",
+ "repo": "flake-utils",
+ "type": "github"
+ }
+ },
+ "flake-utils_2": {
+ "inputs": {
+ "systems": "systems_2"
+ },
+ "locked": {
+ "lastModified": 1710146030,
+ "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
+ "owner": "numtide",
+ "repo": "flake-utils",
+ "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
+ "type": "github"
+ },
+ "original": {
+ "owner": "numtide",
+ "repo": "flake-utils",
+ "type": "github"
+ }
+ },
+ "git-hooks": {
+ "inputs": {
+ "flake-compat": "flake-compat",
+ "flake-utils": "flake-utils",
+ "gitignore": "gitignore",
+ "nixpkgs": [
+ "literate-phylomemy",
+ "nixpkgs"
+ ],
+ "nixpkgs-stable": "nixpkgs-stable"
+ },
+ "locked": {
+ "lastModified": 1715609711,
+ "narHash": "sha256-/5u29K0c+4jyQ8x7dUIEUWlz2BoTSZWUP2quPwFCE7M=",
+ "owner": "cachix",
+ "repo": "git-hooks.nix",
+ "rev": "c182c876690380f8d3b9557c4609472ebfa1b141",
+ "type": "github"
+ },
+ "original": {
+ "owner": "cachix",
+ "repo": "git-hooks.nix",
+ "type": "github"
+ }
+ },
+ "git-hooks_2": {
+ "inputs": {
+ "flake-compat": "flake-compat_2",
+ "flake-utils": "flake-utils_2",
+ "gitignore": "gitignore_2",
+ "nixpkgs": [
+ "literate-phylomemy",
+ "logic",
+ "nixpkgs"
+ ],
+ "nixpkgs-stable": "nixpkgs-stable_2"
+ },
+ "locked": {
+ "lastModified": 1715609711,
+ "narHash": "sha256-/5u29K0c+4jyQ8x7dUIEUWlz2BoTSZWUP2quPwFCE7M=",
+ "owner": "cachix",
+ "repo": "git-hooks.nix",
+ "rev": "c182c876690380f8d3b9557c4609472ebfa1b141",
+ "type": "github"
+ },
+ "original": {
+ "owner": "cachix",
+ "repo": "git-hooks.nix",
+ "type": "github"
+ }
+ },
+ "gitignore": {
+ "inputs": {
+ "nixpkgs": [
+ "literate-phylomemy",
+ "git-hooks",
+ "nixpkgs"
+ ]
+ },
+ "locked": {
+ "lastModified": 1709087332,
+ "narHash": "sha256-HG2cCnktfHsKV0s4XW83gU3F57gaTljL9KNSuG6bnQs=",
+ "owner": "hercules-ci",
+ "repo": "gitignore.nix",
+ "rev": "637db329424fd7e46cf4185293b9cc8c88c95394",
+ "type": "github"
+ },
+ "original": {
+ "owner": "hercules-ci",
+ "repo": "gitignore.nix",
+ "type": "github"
+ }
+ },
+ "gitignore_2": {
+ "inputs": {
+ "nixpkgs": [
+ "literate-phylomemy",
+ "logic",
+ "git-hooks",
+ "nixpkgs"
+ ]
+ },
+ "locked": {
+ "lastModified": 1709087332,
+ "narHash": "sha256-HG2cCnktfHsKV0s4XW83gU3F57gaTljL9KNSuG6bnQs=",
+ "owner": "hercules-ci",
+ "repo": "gitignore.nix",
+ "rev": "637db329424fd7e46cf4185293b9cc8c88c95394",
+ "type": "github"
+ },
+ "original": {
+ "owner": "hercules-ci",
+ "repo": "gitignore.nix",
+ "type": "github"
+ }
+ },
+ "literate-phylomemy": {
+ "inputs": {
+ "git-hooks": "git-hooks",
+ "logic": "logic",
+ "nixpkgs": "nixpkgs_2"
+ },
+ "locked": {
+ "lastModified": 1728381939,
+ "narHash": "sha256-flmlzK5Megm15OwY8WSeI5NBA54gpRzCgDNgPSRJxc4=",
+ "ref": "refs/heads/main",
+ "rev": "8c2a19dbf52c13f8bfc9356740ad4687efa0318e",
+ "revCount": 1,
+ "type": "git",
+ "url": "https://seed.radicle.garden/z2364hmzZUAGy1nKdSFa1gLSoUE2M.git"
+ },
+ "original": {
+ "type": "git",
+ "url": "https://seed.radicle.garden/z2364hmzZUAGy1nKdSFa1gLSoUE2M.git"
+ }
+ },
+ "logic": {
+ "inputs": {
+ "git-hooks": "git-hooks_2",
+ "nixpkgs": "nixpkgs"
+ },
+ "locked": {
+ "lastModified": 1719224209,
+ "narHash": "sha256-9wLe/nHEJ55MP7j/xFeLbkYUIJDrQ5MHfw2lZn7ynfQ=",
+ "ref": "refs/heads/main",
+ "rev": "68250d2551950b4ac2a76a31e3e8f0274fec5040",
+ "revCount": 1,
+ "type": "git",
+ "url": "https://radicle-mermet.sourcephile.fr/z3795BqJN8hSMGkyAUr8hHviEEi2H.git"
+ },
+ "original": {
+ "type": "git",
+ "url": "https://radicle-mermet.sourcephile.fr/z3795BqJN8hSMGkyAUr8hHviEEi2H.git"
+ }
+ },
+ "nixpkgs": {
+ "locked": {
+ "lastModified": 1716793392,
+ "narHash": "sha256-ex3nO87EEQhshXd19QSVW5UIXL0pbPuew4q8TdEJQBY=",
+ "owner": "NixOS",
+ "repo": "nixpkgs",
+ "rev": "67a8b308bae9c26be660ccceff3e53a65e01afe1",
+ "type": "github"
+ },
+ "original": {
+ "id": "nixpkgs",
+ "type": "indirect"
+ }
+ },
+ "nixpkgs-stable": {
+ "locked": {
+ "lastModified": 1710695816,
+ "narHash": "sha256-3Eh7fhEID17pv9ZxrPwCLfqXnYP006RKzSs0JptsN84=",
+ "owner": "NixOS",
+ "repo": "nixpkgs",
+ "rev": "614b4613980a522ba49f0d194531beddbb7220d3",
+ "type": "github"
+ },
+ "original": {
+ "owner": "NixOS",
+ "ref": "nixos-23.11",
+ "repo": "nixpkgs",
+ "type": "github"
+ }
+ },
+ "nixpkgs-stable_2": {
+ "locked": {
+ "lastModified": 1710695816,
+ "narHash": "sha256-3Eh7fhEID17pv9ZxrPwCLfqXnYP006RKzSs0JptsN84=",
+ "owner": "NixOS",
+ "repo": "nixpkgs",
+ "rev": "614b4613980a522ba49f0d194531beddbb7220d3",
+ "type": "github"
+ },
+ "original": {
+ "owner": "NixOS",
+ "ref": "nixos-23.11",
+ "repo": "nixpkgs",
+ "type": "github"
+ }
+ },
+ "nixpkgs_2": {
+ "locked": {
+ "lastModified": 1727264057,
+ "narHash": "sha256-KQPI8CTTnB9CrJ7LrmLC4VWbKZfljEPBXOFGZFRpxao=",
+ "owner": "NixOS",
+ "repo": "nixpkgs",
+ "rev": "759537f06e6999e141588ff1c9be7f3a5c060106",
+ "type": "github"
+ },
+ "original": {
+ "id": "nixpkgs",
+ "type": "indirect"
+ }
+ },
+ "nixpkgs_3": {
+ "locked": {
+ "lastModified": 1727264057,
+ "narHash": "sha256-KQPI8CTTnB9CrJ7LrmLC4VWbKZfljEPBXOFGZFRpxao=",
+ "owner": "NixOS",
+ "repo": "nixpkgs",
+ "rev": "759537f06e6999e141588ff1c9be7f3a5c060106",
+ "type": "github"
+ },
+ "original": {
+ "id": "nixpkgs",
+ "type": "indirect"
+ }
+ },
+ "root": {
+ "inputs": {
+ "literate-phylomemy": "literate-phylomemy",
+ "nixpkgs": "nixpkgs_3"
+ }
+ },
+ "systems": {
+ "locked": {
+ "lastModified": 1681028828,
+ "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+ "owner": "nix-systems",
+ "repo": "default",
+ "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+ "type": "github"
+ },
+ "original": {
+ "owner": "nix-systems",
+ "repo": "default",
+ "type": "github"
+ }
+ },
+ "systems_2": {
+ "locked": {
+ "lastModified": 1681028828,
+ "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
+ "owner": "nix-systems",
+ "repo": "default",
+ "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
+ "type": "github"
+ },
+ "original": {
+ "owner": "nix-systems",
+ "repo": "default",
+ "type": "github"
+ }
+ }
+ },
+ "root": "root",
+ "version": 7
+}
--- /dev/null
+# SPDX-FileCopyrightText: 2024 Jane Doe <jane@example.org>
+# SPDX-License-Identifier: CC0-1.0
+{
+ description = "A phylomemy script example";
+ inputs = {
+ # Update with:
+ # nix flake lock --override-input nixpkgs github:NixOS/nixpkgs
+ nixpkgs.url = "flake:nixpkgs";
+ literate-phylomemy.url = "git+https://seed.radicle.garden/z2364hmzZUAGy1nKdSFa1gLSoUE2M.git";
+ };
+ outputs =
+ inputs:
+ let
+ lib = inputs.nixpkgs.lib;
+ # Helper to build for each system in `lib.systems.flakeExposed`.
+ perSystem =
+ f:
+ lib.genAttrs lib.systems.flakeExposed (
+ system:
+ f rec {
+ inherit system;
+ pkgs = import inputs.nixpkgs { inherit system; };
+ haskellPackages = pkgs.haskellPackages;
+ }
+ );
+ in
+ {
+ # `nix -L build`
+ packages = perSystem (
+ { pkgs, system, haskellPackages, ... }:
+ {
+ # The Glasgow Haskell Compiler (GHC)
+ # Here made available as `.#ghc` for script.hs's shebang
+ ghc = haskellPackages.ghcWithPackages (
+ haskellPackages: [
+ # Extra Haskell packages available
+ inputs.literate-phylomemy.packages.${system}.default
+ haskellPackages.bytestring
+ haskellPackages.turtle
+ haskellPackages.pretty-show
+ ]
+ );
+ ghcid = pkgs.ghcid;
+ xdot = pkgs.xdot;
+ # A compiled version of `script.hs`
+ # (instead of an interpreted one when run as `./script.hs`)
+ # To avoid writing a `.cabal` file, `ghc --make` is called directly here,
+ # but should the script become a full fledge executable,
+ # a `.cabal` file should be written instead.
+ default = pkgs.stdenv.mkDerivation {
+ name = "script";
+ src = ./.;
+ buildInputs = [
+ inputs.self.packages.${system}.ghc
+ ];
+ buildPhase = ''
+ mkdir -p $out/bin
+ ghc -o "$out/bin/script" -O2 --make ./script.hs
+ '';
+ };
+ }
+ );
+ # `nix develop` or `direnv allow`
+ devShells = perSystem (
+ { pkgs, system, ... }:
+ {
+ default = pkgs.mkShell {
+ nativeBuildInputs = [
+ inputs.self.packages.${system}.ghc
+ pkgs.haskellPackages.haskell-language-server
+ pkgs.haskellPackages.hlint
+ pkgs.reuse
+ pkgs.xdot
+ ];
+ };
+ }
+ );
+ };
+}
--- /dev/null
+#!/usr/bin/env -S nix -L shell .#ghc .#ghcid .#xdot --command ghcid --test :main
+-- Alternatively: #!/usr/bin/env -S nix -L shell .#ghc .#xdot --command runghc
+-- SPDX-FileCopyrightText: 2024 Jane Doe <jane@example.org>
+-- SPDX-License-Identifier: CC0-1.0
+{-# LANGUAGE OverloadedLists #-}
+{-# LANGUAGE OverloadedStrings #-}
+{-# LANGUAGE ParallelListComp #-}
+
+import Control.Concurrent.Async qualified as Async
+import Data.ByteString.Builder qualified as BS
+import Data.Either (fromRight)
+import Data.Map.Strict qualified as Map
+import Data.Sequence qualified as Seq
+import Logic
+import Logic.Theory.Arithmetic
+import Logic.Theory.Ord
+import Numeric.Probability
+import Phylomemy qualified as Phylo
+import System.IO qualified as Sys
+import System.Process qualified as Sys
+import Text.Pretty.Simple
+
+main = do
+ let minSupp = assertStrictlyPositive 1
+ let minSize = assertStrictlyPositive 2
+
+ letName rangeToDocs0 $ \rangeToDocs ->
+ letName ["a", "b", "c", "d", "e", "f", "g"] $ \roots -> do
+ let clusters =
+ Phylo.clusterize roots minSupp minSize rangeToDocs
+
+ let msf :: Phylo.MaximalSpanningForest Pos Phylo.Cluster =
+ Phylo.maximalSpanningForest Phylo.similarityJaccard (unName <$> clusters)
+ let phylomemy :: Phylo.MaximalSpanningForest Pos Phylo.Cluster =
+ let Just lambda = probability 0.3
+ in letName (Phylo.predictionMeasureF lambda) $ \predMeasure ->
+ Phylo.msfSplit predMeasure roots msf
+ let dot = Phylo.dotMaximalSpanningForest phylomemy
+
+ pPrint ("Number of maximal spanning trees", length phylomemy)
+ Sys.withFile "phylomemy.dot" Sys.WriteMode (`BS.hPutBuilder` dot)
+ Sys.callProcess "xdot" ["phylomemy.dot"]
+
+rangeToDocs0 :: Pos Phylo.:-> Seq.Seq (Phylo.Document Pos)
+rangeToDocs0 =
+ Map.fromList
+ [ ( Pos rangeIndex
+ , Seq.fromList
+ [ Phylo.Document
+ { Phylo.documentPosition = Pos (2 * rangeIndex + 3 * docIndex)
+ , Phylo.documentRoots = Map.fromList [(r, ()) | r <- roots]
+ }
+ | roots <- docs
+ | docIndex <- [1 ..]
+ ]
+ )
+ | docs <-
+ [ [["a", "b", "c"], ["a", "d", "e"], ["e", "f", "g"]]
+ , [["a", "b"], ["d", "f"]]
+ , [["f"], ["d", "f"], ["f", "g", "a"]]
+ , [["b", "c", "e"], ["a", "d", "e"], ["a", "b", "c"]]
+ , [["d", "f", "g"], ["b", "f"], ["a", "c", "d"], ["a", "f"]]
+ , [["c", "d", "g"], ["b", "c", "g"], ["a", "b", "c"], ["e", "g"]]
+ ]
+ | rangeIndex <- [1 ..]
+ ]
+
+assertStrictlyPositive :: (Ord a) => (Zeroable a) => a -> () ::: a / () > Zero
+assertStrictlyPositive i = unitName i Logic./ fromRight undefined (prove (unitName i Logic.Theory.Ord.> zero))
+
+newtype Pos = Pos Int deriving (Eq, Ord, Show, Num)
+instance Phylo.ShowHuman Pos where
+ showHuman (Pos x) = show x
sourcephile / git / literate-phylomemy-example1.git / commitdiff