From a09d5c9d9f7097dd4baf4e9611e488ee1d12ca2f Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Fri, 16 Dec 2022 10:57:55 +1100 Subject: init --- .gitignore | 1 + bin/cluster.hs | 88 ++++++ cabal.project | 7 + flake.lock | 900 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ flake.nix | 39 +++ package.yaml | 17 ++ phylogenies.cabal | 28 ++ 7 files changed, 1080 insertions(+) create mode 100644 .gitignore create mode 100644 bin/cluster.hs create mode 100644 cabal.project create mode 100644 flake.lock create mode 100644 flake.nix create mode 100644 package.yaml create mode 100644 phylogenies.cabal diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..fcfc4a1 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +result* diff --git a/bin/cluster.hs b/bin/cluster.hs new file mode 100644 index 0000000..70e22c7 --- /dev/null +++ b/bin/cluster.hs @@ -0,0 +1,88 @@ +{-# LANGUAGE ViewPatterns #-} + +module Main where + +import Data.Fixed (mod') +import Data.Foldable (toList) +import Data.List +import qualified Data.Map as M +import qualified Data.Vector.Unboxed as V +import Numeric.Log hiding (sum) +import PPL +import System.Random (mkStdGen, setStdGen) + +cumsum = scanl1 (+) + +first f xs = snd . head . filter (f . fst) $ zip xs [0 ..] + +stirling n = n * log n - n + +pois lambda (fromIntegral -> k) = lambda' ** k' * Exp (negate lambda) / Exp (stirling k) + where + lambda' = Exp $ log lambda + k' = Exp $ log k + +-- (infinite) binary trees +data Tree a = Empty | Tree a (Tree a) (Tree a) + deriving (Show) + +instance Foldable Tree where + foldMap f t = bftrav [t] + where + bftrav [] = mempty + bftrav (Empty : ts) = bftrav ts + bftrav ((Tree a l r) : ts) = f a <> bftrav (ts <> [l, r]) + +-- Infinite trees from infinite lists +-- NB: it's harder to partition a list so that it folds back to +-- equivalence. It doesn't really matter here since we're only +-- unfolding random uniforms anyway. +treeFromList (x : xs) = Tree x (treeFromList lpart) (treeFromList rpart) + where + (lpart, rpart) = unzip $ partition xs + partition (a : b : xs) = (a, b) : partition xs + +-- Constrain trees so leaves sum to node value +normTree :: Tree Double -> Tree Double +normTree (Tree x l r) = go $ Tree x l r + where + go (Tree x (Tree u l r) (Tree v l' r')) = + let s = x / (u + v) + in Tree x (go $ Tree (s * u) l r) (go $ Tree (s * v) l' r') + +drawTreeProbs = toList . normTree . treeFromList <$> iid uniform + +model xs = do + (clmuAcinar, clmuDuctal, params, clusters) <- sample $ do + -- Sample hyperparameters + a <- bounded 1 10 + + -- CRP style + dir <- cumsum <$> dirichletProcess a + rs <- iid uniform + clmuAcinar <- drawTreeProbs + clmuDuctal <- drawTreeProbs + let clusters = map (\r -> first (>= r) dir) rs + params = map (\i -> zip clmuAcinar clmuDuctal !! i) clusters + pure (clmuAcinar, clmuDuctal, params, clusters) + mapM_ scoreLog $ zipWith likelihood params (V.toList xs) + let cls = take (V.length xs) clusters + k = maximum cls + 1 + pure (take k clmuAcinar, take k clmuDuctal, cls) + where + likelihood (ap, dp) (ac, ad, dc, dd) = + max (pois (fromIntegral ad * ap) ac) (pois (fromIntegral ad * ap / 2) ac) + * max (pois (fromIntegral dd * dp) dc) (pois (fromIntegral dd * dp / 2) dc) + +main = do + setStdGen $ mkStdGen 42 + (hdr : lines) <- lines <$> readFile "/nix/store/9xkb2apajv9sy37akz24x3jj6kw5hn7h-bionix-dump-counts" + let parsed = V.fromList $ map ((\[_, ac, ad, dc, dd] -> (dbl ac, dbl ad, dbl dc, dbl dd)) . words) lines + dbl = round . read :: String -> Int + ((a, d, cl), _) <- foldl1' (\a c -> if mml a < mml c then a else c) . take 100000 <$> mh 0.3 (model parsed) + writeFile "/data/props" . unlines $ zipWith (\a b -> show a <> "," <> show b) a d + writeFile "/data/clusters" . unlines $ map show cl + where + mml ((a, d, cl), lik) = sum (map (log . (+ 1)) a) + sum (map (log . (+ 1)) d) + sum (map (log . (+ 1)) tab) - sum (map stirling tab) - ln lik + where + tab = M.elems $ M.fromListWith (+) [(c, 1) | c <- cl] diff --git a/cabal.project b/cabal.project new file mode 100644 index 0000000..265b3e2 --- /dev/null +++ b/cabal.project @@ -0,0 +1,7 @@ +packages: *.cabal + +source-repository-package + type: git + location: https://vk3.wtf/cgit/ppl.git + tag: b906da9afa6802bf8104dfabe26b67a6c673af91 + --sha256: 14gqgs4akf74q5wh3spn72fnggb28dgmmh52vi9a5kx7dc23pxj2 diff --git a/flake.lock b/flake.lock new file mode 100644 index 0000000..2f052dd --- /dev/null +++ b/flake.lock @@ -0,0 +1,900 @@ +{ + "nodes": { + "HTTP": { + "flake": false, + "locked": { + "lastModified": 1451647621, + "narHash": "sha256-oHIyw3x0iKBexEo49YeUDV1k74ZtyYKGR2gNJXXRxts=", + "owner": "phadej", + "repo": "HTTP", + "rev": "9bc0996d412fef1787449d841277ef663ad9a915", + "type": "github" + }, + "original": { + "owner": "phadej", + "repo": "HTTP", + "type": "github" + } + }, + "blank": { + "locked": { + "lastModified": 1625557891, + "narHash": "sha256-O8/MWsPBGhhyPoPLHZAuoZiiHo9q6FLlEeIDEXuj6T4=", + "owner": "divnix", + "repo": "blank", + "rev": "5a5d2684073d9f563072ed07c871d577a6c614a8", + "type": "github" + }, + "original": { + "owner": "divnix", + "repo": "blank", + "type": "github" + } + }, + "cabal-32": { + "flake": false, + "locked": { + "lastModified": 1603716527, + "narHash": "sha256-X0TFfdD4KZpwl0Zr6x+PLxUt/VyKQfX7ylXHdmZIL+w=", + "owner": "haskell", + "repo": "cabal", + "rev": "48bf10787e27364730dd37a42b603cee8d6af7ee", + "type": "github" + }, + "original": { + "owner": "haskell", + "ref": "3.2", + "repo": "cabal", + "type": "github" + } + }, + "cabal-34": { + "flake": false, + "locked": { + "lastModified": 1640353650, + "narHash": "sha256-N1t6M3/wqj90AEdRkeC8i923gQYUpzSr8b40qVOZ1Rk=", + "owner": "haskell", + "repo": "cabal", + "rev": "942639c18c0cd8ec53e0a6f8d120091af35312cd", + "type": "github" + }, + "original": { + "owner": "haskell", + "ref": "3.4", + "repo": "cabal", + "type": "github" + } + }, + "cabal-36": { + "flake": false, + "locked": { + "lastModified": 1641652457, + "narHash": "sha256-BlFPKP4C4HRUJeAbdembX1Rms1LD380q9s0qVDeoAak=", + "owner": "haskell", + "repo": "cabal", + "rev": "f27667f8ec360c475027dcaee0138c937477b070", + "type": "github" + }, + "original": { + "owner": "haskell", + "ref": "3.6", + "repo": "cabal", + "type": "github" + } + }, + "cardano-shell": { + "flake": false, + "locked": { + "lastModified": 1608537748, + "narHash": "sha256-PulY1GfiMgKVnBci3ex4ptk2UNYMXqGjJOxcPy2KYT4=", + "owner": "input-output-hk", + "repo": "cardano-shell", + "rev": "9392c75087cb9a3d453998f4230930dea3a95725", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "cardano-shell", + "type": "github" + } + }, + "devshell": { + "inputs": { + "flake-utils": [ + "haskellNix", + "tullia", + "std", + "flake-utils" + ], + "nixpkgs": [ + "haskellNix", + "tullia", + "std", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1663445644, + "narHash": "sha256-+xVlcK60x7VY1vRJbNUEAHi17ZuoQxAIH4S4iUFUGBA=", + "owner": "numtide", + "repo": "devshell", + "rev": "e3dc3e21594fe07bdb24bdf1c8657acaa4cb8f66", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "devshell", + "type": "github" + } + }, + "dmerge": { + "inputs": { + "nixlib": [ + "haskellNix", + "tullia", + "std", + "nixpkgs" + ], + "yants": [ + "haskellNix", + "tullia", + "std", + "yants" + ] + }, + "locked": { + "lastModified": 1659548052, + "narHash": "sha256-fzI2gp1skGA8mQo/FBFrUAtY0GQkAIAaV/V127TJPyY=", + "owner": "divnix", + "repo": "data-merge", + "rev": "d160d18ce7b1a45b88344aa3f13ed1163954b497", + "type": "github" + }, + "original": { + "owner": "divnix", + "repo": "data-merge", + "type": "github" + } + }, + "flake-compat": { + "flake": false, + "locked": { + "lastModified": 1635892615, + "narHash": "sha256-harGbMZr4hzat2BWBU+Y5OYXlu+fVz7E4WeQzHi5o8A=", + "owner": "input-output-hk", + "repo": "flake-compat", + "rev": "eca47d3377946315596da653862d341ee5341318", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "flake-compat", + "type": "github" + } + }, + "flake-compat_2": { + "flake": false, + "locked": { + "lastModified": 1650374568, + "narHash": "sha256-Z+s0J8/r907g149rllvwhb4pKi8Wam5ij0st8PwAh+E=", + "owner": "edolstra", + "repo": "flake-compat", + "rev": "b4a34015c698c7793d592d66adbab377907a2be8", + "type": "github" + }, + "original": { + "owner": "edolstra", + "repo": "flake-compat", + "type": "github" + } + }, + "flake-utils": { + "locked": { + "lastModified": 1667395993, + "narHash": "sha256-nuEHfE/LcWyuSWnS8t12N1wc105Qtau+/OdUAjtQ0rA=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "5aed5285a952e0b949eb3ba02c12fa4fcfef535f", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "flake-utils_2": { + "locked": { + "lastModified": 1644229661, + "narHash": "sha256-1YdnJAsNy69bpcjuoKdOYQX0YxZBiCYZo4Twxerqv7k=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "3cecb5b042f7f209c56ffd8371b2711a290ec797", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "flake-utils_3": { + "locked": { + "lastModified": 1653893745, + "narHash": "sha256-0jntwV3Z8//YwuOjzhV2sgJJPt+HY6KhU7VZUL0fKZQ=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "1ed9fb1935d260de5fe1c2f7ee0ebaae17ed2fa1", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "flake-utils_4": { + "locked": { + "lastModified": 1659877975, + "narHash": "sha256-zllb8aq3YO3h8B/U0/J1WBgAL8EX5yWf5pMj3G0NAmc=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "c0e246b9b83f637f4681389ecabcb2681b4f3af0", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "flake-utils_5": { + "locked": { + "lastModified": 1653893745, + "narHash": "sha256-0jntwV3Z8//YwuOjzhV2sgJJPt+HY6KhU7VZUL0fKZQ=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "1ed9fb1935d260de5fe1c2f7ee0ebaae17ed2fa1", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "ghc-8.6.5-iohk": { + "flake": false, + "locked": { + "lastModified": 1600920045, + "narHash": "sha256-DO6kxJz248djebZLpSzTGD6s8WRpNI9BTwUeOf5RwY8=", + "owner": "input-output-hk", + "repo": "ghc", + "rev": "95713a6ecce4551240da7c96b6176f980af75cae", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "ref": "release/8.6.5-iohk", + "repo": "ghc", + "type": "github" + } + }, + "gomod2nix": { + "inputs": { + "nixpkgs": "nixpkgs_2", + "utils": "utils" + }, + "locked": { + "lastModified": 1655245309, + "narHash": "sha256-d/YPoQ/vFn1+GTmSdvbSBSTOai61FONxB4+Lt6w/IVI=", + "owner": "tweag", + "repo": "gomod2nix", + "rev": "40d32f82fc60d66402eb0972e6e368aeab3faf58", + "type": "github" + }, + "original": { + "owner": "tweag", + "repo": "gomod2nix", + "type": "github" + } + }, + "hackage": { + "flake": false, + "locked": { + "lastModified": 1671063994, + "narHash": "sha256-4YZ6+JUSFPBlK0zNErqBY8GLvBVbS8q1ldNcBwqSuME=", + "owner": "input-output-hk", + "repo": "hackage.nix", + "rev": "f42f80c9eda52453b6042aee6f614302d076b852", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "hackage.nix", + "type": "github" + } + }, + "haskellNix": { + "inputs": { + "HTTP": "HTTP", + "cabal-32": "cabal-32", + "cabal-34": "cabal-34", + "cabal-36": "cabal-36", + "cardano-shell": "cardano-shell", + "flake-compat": "flake-compat", + "flake-utils": "flake-utils_2", + "ghc-8.6.5-iohk": "ghc-8.6.5-iohk", + "hackage": "hackage", + "hpc-coveralls": "hpc-coveralls", + "hydra": "hydra", + "iserv-proxy": "iserv-proxy", + "nixpkgs": [ + "haskellNix", + "nixpkgs-unstable" + ], + "nixpkgs-2003": "nixpkgs-2003", + "nixpkgs-2105": "nixpkgs-2105", + "nixpkgs-2111": "nixpkgs-2111", + "nixpkgs-2205": "nixpkgs-2205", + "nixpkgs-2211": "nixpkgs-2211", + "nixpkgs-unstable": "nixpkgs-unstable", + "old-ghc-nix": "old-ghc-nix", + "stackage": "stackage", + "tullia": "tullia" + }, + "locked": { + "lastModified": 1671065520, + "narHash": "sha256-Mbcbyx0DKTdzNWmDj17nzfaazL7qg/cNAzJFKZ1i92E=", + "owner": "input-output-hk", + "repo": "haskell.nix", + "rev": "af2c47f5909c5c74c28124f8793539736680d606", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "haskell.nix", + "type": "github" + } + }, + "hpc-coveralls": { + "flake": false, + "locked": { + "lastModified": 1607498076, + "narHash": "sha256-8uqsEtivphgZWYeUo5RDUhp6bO9j2vaaProQxHBltQk=", + "owner": "sevanspowell", + "repo": "hpc-coveralls", + "rev": "14df0f7d229f4cd2e79f8eabb1a740097fdfa430", + "type": "github" + }, + "original": { + "owner": "sevanspowell", + "repo": "hpc-coveralls", + "type": "github" + } + }, + "hydra": { + "inputs": { + "nix": "nix", + "nixpkgs": [ + "haskellNix", + "hydra", + "nix", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1646878427, + "narHash": "sha256-KtbrofMtN8GlM7D+n90kixr7QpSlVmdN+vK5CA/aRzc=", + "owner": "NixOS", + "repo": "hydra", + "rev": "28b682b85b7efc5cf7974065792a1f22203a5927", + "type": "github" + }, + "original": { + "id": "hydra", + "type": "indirect" + } + }, + "iserv-proxy": { + "flake": false, + "locked": { + "lastModified": 1639165170, + "narHash": "sha256-QsWL/sBDL5GM8IXd/dE/ORiL4RvteEN+aok23tXgAoc=", + "rev": "6e95df7be6dd29680f983db07a057fc2f34f81f6", + "revCount": 7, + "type": "git", + "url": "https://gitlab.haskell.org/ghc/iserv-proxy.git" + }, + "original": { + "rev": "6e95df7be6dd29680f983db07a057fc2f34f81f6", + "type": "git", + "url": "https://gitlab.haskell.org/ghc/iserv-proxy.git" + } + }, + "lowdown-src": { + "flake": false, + "locked": { + "lastModified": 1633514407, + "narHash": "sha256-Dw32tiMjdK9t3ETl5fzGrutQTzh2rufgZV4A/BbxuD4=", + "owner": "kristapsdz", + "repo": "lowdown", + "rev": "d2c2b44ff6c27b936ec27358a2653caaef8f73b8", + "type": "github" + }, + "original": { + "owner": "kristapsdz", + "repo": "lowdown", + "type": "github" + } + }, + "mdbook-kroki-preprocessor": { + "flake": false, + "locked": { + "lastModified": 1661755005, + "narHash": "sha256-1TJuUzfyMycWlOQH67LR63/ll2GDZz25I3JfScy/Jnw=", + "owner": "JoelCourtney", + "repo": "mdbook-kroki-preprocessor", + "rev": "93adb5716d035829efed27f65f2f0833a7d3e76f", + "type": "github" + }, + "original": { + "owner": "JoelCourtney", + "repo": "mdbook-kroki-preprocessor", + "type": "github" + } + }, + "n2c": { + "inputs": { + "flake-utils": "flake-utils_5", + "nixpkgs": [ + "haskellNix", + "tullia", + "std", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1665039323, + "narHash": "sha256-SAh3ZjFGsaCI8FRzXQyp56qcGdAqgKEfJWPCQ0Sr7tQ=", + "owner": "nlewo", + "repo": "nix2container", + "rev": "b008fe329ffb59b67bf9e7b08ede6ee792f2741a", + "type": "github" + }, + "original": { + "owner": "nlewo", + "repo": "nix2container", + "type": "github" + } + }, + "nix": { + "inputs": { + "lowdown-src": "lowdown-src", + "nixpkgs": "nixpkgs", + "nixpkgs-regression": "nixpkgs-regression" + }, + "locked": { + "lastModified": 1643066034, + "narHash": "sha256-xEPeMcNJVOeZtoN+d+aRwolpW8mFSEQx76HTRdlhPhg=", + "owner": "NixOS", + "repo": "nix", + "rev": "a1cd7e58606a41fcf62bf8637804cf8306f17f62", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "2.6.0", + "repo": "nix", + "type": "github" + } + }, + "nix-nomad": { + "inputs": { + "flake-compat": "flake-compat_2", + "flake-utils": [ + "haskellNix", + "tullia", + "nix2container", + "flake-utils" + ], + "gomod2nix": "gomod2nix", + "nixpkgs": [ + "haskellNix", + "tullia", + "nixpkgs" + ], + "nixpkgs-lib": [ + "haskellNix", + "tullia", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1658277770, + "narHash": "sha256-T/PgG3wUn8Z2rnzfxf2VqlR1CBjInPE0l1yVzXxPnt0=", + "owner": "tristanpemble", + "repo": "nix-nomad", + "rev": "054adcbdd0a836ae1c20951b67ed549131fd2d70", + "type": "github" + }, + "original": { + "owner": "tristanpemble", + "repo": "nix-nomad", + "type": "github" + } + }, + "nix2container": { + "inputs": { + "flake-utils": "flake-utils_3", + "nixpkgs": "nixpkgs_3" + }, + "locked": { + "lastModified": 1658567952, + "narHash": "sha256-XZ4ETYAMU7XcpEeAFP3NOl9yDXNuZAen/aIJ84G+VgA=", + "owner": "nlewo", + "repo": "nix2container", + "rev": "60bb43d405991c1378baf15a40b5811a53e32ffa", + "type": "github" + }, + "original": { + "owner": "nlewo", + "repo": "nix2container", + "type": "github" + } + }, + "nixago": { + "inputs": { + "flake-utils": [ + "haskellNix", + "tullia", + "std", + "flake-utils" + ], + "nixago-exts": [ + "haskellNix", + "tullia", + "std", + "blank" + ], + "nixpkgs": [ + "haskellNix", + "tullia", + "std", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1661824785, + "narHash": "sha256-/PnwdWoO/JugJZHtDUioQp3uRiWeXHUdgvoyNbXesz8=", + "owner": "nix-community", + "repo": "nixago", + "rev": "8c1f9e5f1578d4b2ea989f618588d62a335083c3", + "type": "github" + }, + "original": { + "owner": "nix-community", + "repo": "nixago", + "type": "github" + } + }, + "nixpkgs": { + "locked": { + "lastModified": 1632864508, + "narHash": "sha256-d127FIvGR41XbVRDPVvozUPQ/uRHbHwvfyKHwEt5xFM=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "82891b5e2c2359d7e58d08849e4c89511ab94234", + "type": "github" + }, + "original": { + "id": "nixpkgs", + "ref": "nixos-21.05-small", + "type": "indirect" + } + }, + "nixpkgs-2003": { + "locked": { + "lastModified": 1620055814, + "narHash": "sha256-8LEHoYSJiL901bTMVatq+rf8y7QtWuZhwwpKE2fyaRY=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "1db42b7fe3878f3f5f7a4f2dc210772fd080e205", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-20.03-darwin", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs-2105": { + "locked": { + "lastModified": 1659914493, + "narHash": "sha256-lkA5X3VNMKirvA+SUzvEhfA7XquWLci+CGi505YFAIs=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "022caabb5f2265ad4006c1fa5b1ebe69fb0c3faf", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-21.05-darwin", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs-2111": { + "locked": { + "lastModified": 1659446231, + "narHash": "sha256-hekabNdTdgR/iLsgce5TGWmfIDZ86qjPhxDg/8TlzhE=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "eabc38219184cc3e04a974fe31857d8e0eac098d", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-21.11-darwin", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs-2205": { + "locked": { + "lastModified": 1663981975, + "narHash": "sha256-TKaxWAVJR+a5JJauKZqibmaM5e/Pi5tBDx9s8fl/kSE=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "309faedb8338d3ae8ad8f1043b3ccf48c9cc2970", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-22.05-darwin", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs-2211": { + "locked": { + "lastModified": 1669997163, + "narHash": "sha256-vhjC0kZMFoN6jzK0GR+tBzKi5KgBXgehadfidW8+Va4=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "6f87491a54d8d64d30af6663cb3bf5d2ee7db958", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-22.11-darwin", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs-regression": { + "locked": { + "lastModified": 1643052045, + "narHash": "sha256-uGJ0VXIhWKGXxkeNnq4TvV3CIOkUJ3PAoLZ3HMzNVMw=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "215d4d0fd80ca5163643b03a33fde804a29cc1e2", + "type": "github" + }, + "original": { + "id": "nixpkgs", + "rev": "215d4d0fd80ca5163643b03a33fde804a29cc1e2", + "type": "indirect" + } + }, + "nixpkgs-unstable": { + "locked": { + "lastModified": 1663905476, + "narHash": "sha256-0CSwRKaYravh9v6qSlBpM0gNg0UhKT2lL7Yn6Zbx7UM=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "e14f9fb57315f0d4abde222364f19f88c77d2b79", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_2": { + "locked": { + "lastModified": 1653581809, + "narHash": "sha256-Uvka0V5MTGbeOfWte25+tfRL3moECDh1VwokWSZUdoY=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "83658b28fe638a170a19b8933aa008b30640fbd1", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixos-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_3": { + "locked": { + "lastModified": 1654807842, + "narHash": "sha256-ADymZpr6LuTEBXcy6RtFHcUZdjKTBRTMYwu19WOx17E=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "fc909087cc3386955f21b4665731dbdaceefb1d8", + "type": "github" + }, + "original": { + "owner": "NixOS", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_4": { + "locked": { + "lastModified": 1665087388, + "narHash": "sha256-FZFPuW9NWHJteATOf79rZfwfRn5fE0wi9kRzvGfDHPA=", + "owner": "nixos", + "repo": "nixpkgs", + "rev": "95fda953f6db2e9496d2682c4fc7b82f959878f7", + "type": "github" + }, + "original": { + "owner": "nixos", + "ref": "nixpkgs-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "old-ghc-nix": { + "flake": false, + "locked": { + "lastModified": 1631092763, + "narHash": "sha256-sIKgO+z7tj4lw3u6oBZxqIhDrzSkvpHtv0Kki+lh9Fg=", + "owner": "angerman", + "repo": "old-ghc-nix", + "rev": "af48a7a7353e418119b6dfe3cd1463a657f342b8", + "type": "github" + }, + "original": { + "owner": "angerman", + "ref": "master", + "repo": "old-ghc-nix", + "type": "github" + } + }, + "root": { + "inputs": { + "flake-utils": "flake-utils", + "haskellNix": "haskellNix", + "nixpkgs": [ + "haskellNix", + "nixpkgs-unstable" + ] + } + }, + "stackage": { + "flake": false, + "locked": { + "lastModified": 1670890221, + "narHash": "sha256-kV7irjUr4Ot3b2MwTcgVKYuEe+legxhGh4ApBeESy1s=", + "owner": "input-output-hk", + "repo": "stackage.nix", + "rev": "56f59c2d4ecdb237348a0774274f38874f81a3ca", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "stackage.nix", + "type": "github" + } + }, + "std": { + "inputs": { + "blank": "blank", + "devshell": "devshell", + "dmerge": "dmerge", + "flake-utils": "flake-utils_4", + "makes": [ + "haskellNix", + "tullia", + "std", + "blank" + ], + "mdbook-kroki-preprocessor": "mdbook-kroki-preprocessor", + "microvm": [ + "haskellNix", + "tullia", + "std", + "blank" + ], + "n2c": "n2c", + "nixago": "nixago", + "nixpkgs": "nixpkgs_4", + "yants": "yants" + }, + "locked": { + "lastModified": 1665513321, + "narHash": "sha256-D6Pacw9yf/HMs84KYuCxHXnNDL7v43gtcka5URagFqE=", + "owner": "divnix", + "repo": "std", + "rev": "94a90eedb9cfc115b12ae8f6622d9904788559e4", + "type": "github" + }, + "original": { + "owner": "divnix", + "repo": "std", + "type": "github" + } + }, + "tullia": { + "inputs": { + "nix-nomad": "nix-nomad", + "nix2container": "nix2container", + "nixpkgs": [ + "haskellNix", + "nixpkgs" + ], + "std": "std" + }, + "locked": { + "lastModified": 1668711738, + "narHash": "sha256-CBjky16o9pqsGE1bWu6nRlRajgSXMEk+yaFQLibqXcE=", + "owner": "input-output-hk", + "repo": "tullia", + "rev": "ead1f515c251f0e060060ef0e2356a51d3dfe4b0", + "type": "github" + }, + "original": { + "owner": "input-output-hk", + "repo": "tullia", + "type": "github" + } + }, + "utils": { + "locked": { + "lastModified": 1653893745, + "narHash": "sha256-0jntwV3Z8//YwuOjzhV2sgJJPt+HY6KhU7VZUL0fKZQ=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "1ed9fb1935d260de5fe1c2f7ee0ebaae17ed2fa1", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "yants": { + "inputs": { + "nixpkgs": [ + "haskellNix", + "tullia", + "std", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1660507851, + "narHash": "sha256-BKjq7JnVuUR/xDtcv6Vm9GYGKAblisXrAgybor9hT/s=", + "owner": "divnix", + "repo": "yants", + "rev": "0b895ca02a8fa72bad50b454cb3e7d8a66407c96", + "type": "github" + }, + "original": { + "owner": "divnix", + "repo": "yants", + "type": "github" + } + } + }, + "root": "root", + "version": 7 +} diff --git a/flake.nix b/flake.nix new file mode 100644 index 0000000..90d4b35 --- /dev/null +++ b/flake.nix @@ -0,0 +1,39 @@ +{ + nixConfig = { + extra-trusted-public-keys = ["hydra.iohk.io:f/Ea+s+dFdN+3Y/G+FDgSq+a5NEWhJGzdjvKNGv0/EQ="]; + extra-substituters = ["https://cache.iog.io"]; + }; + description = "Bayesian phylogentic playground"; + inputs.haskellNix.url = "github:input-output-hk/haskell.nix"; + inputs.nixpkgs.follows = "haskellNix/nixpkgs-unstable"; + inputs.flake-utils.url = "github:numtide/flake-utils"; + outputs = { + self, + nixpkgs, + flake-utils, + haskellNix, + }: + flake-utils.lib.eachSystem ["x86_64-linux"] (system: let + overlays = [ + haskellNix.overlay + (final: prev: { + phylogenies = final.haskell-nix.project' { + src = ./.; + compiler-nix-name = "ghc925"; + shell.tools = { + hlint = {}; + ormolu = {}; + }; + shell.buildInputs = with pkgs; [ + ]; + }; + }) + ]; + pkgs = import nixpkgs { + inherit system overlays; + inherit (haskellNix) config; + }; + flake = pkgs.phylogenies.flake {}; + in + flake // { packages.default = flake.packages."phylogenies:exe:phylogenies";}); +} diff --git a/package.yaml b/package.yaml new file mode 100644 index 0000000..4d96c25 --- /dev/null +++ b/package.yaml @@ -0,0 +1,17 @@ +name: phylogenies +version: 0.0.1 +synopsis: phylogeny playground +maintainer: Justin Bedo +license: MIT + +executable: + main: cluster.hs + source-dirs: bin + ghc-options: [-rtsopts] + dependencies: + - base >= 4.9 && < 5 + - ppl + - containers + - log-domain + - vector + - random diff --git a/phylogenies.cabal b/phylogenies.cabal new file mode 100644 index 0000000..15db8d9 --- /dev/null +++ b/phylogenies.cabal @@ -0,0 +1,28 @@ +cabal-version: 1.12 + +-- This file has been generated from package.yaml by hpack version 0.34.7. +-- +-- see: https://github.com/sol/hpack + +name: phylogenies +version: 0.0.1 +synopsis: phylogeny playground +maintainer: Justin Bedo +license: MIT +build-type: Simple + +executable phylogenies + main-is: cluster.hs + other-modules: + Paths_phylogenies + hs-source-dirs: + bin + ghc-options: -rtsopts + build-depends: + base >=4.9 && <5 + , containers + , log-domain + , ppl + , random + , vector + default-language: Haskell2010 -- cgit v1.2.3