From 8539fe8b65c3b6f6de0afd61811dbc6bd9519b30 Mon Sep 17 00:00:00 2001 From: Julien Moutinho Date: Tue, 2 Sep 2025 01:18:56 +0200 Subject: [PATCH] maintenance(deps): update `nixpkgs`, `literate-phylomemy` and `logic` --- flake.lock | 154 +++++++++++++++++++++++++++++++++++++++++++++++------ flake.nix | 6 +++ script.hs | 6 ++- 3 files changed, 148 insertions(+), 18 deletions(-) diff --git a/flake.lock b/flake.lock index afa629c..282b41e 100644 --- a/flake.lock +++ b/flake.lock @@ -32,6 +32,22 @@ "type": "github" } }, + "flake-compat_3": { + "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" @@ -68,6 +84,24 @@ "type": "github" } }, + "flake-utils_3": { + "inputs": { + "systems": "systems_3" + }, + "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", @@ -119,6 +153,31 @@ "type": "github" } }, + "git-hooks_3": { + "inputs": { + "flake-compat": "flake-compat_3", + "flake-utils": "flake-utils_3", + "gitignore": "gitignore_3", + "nixpkgs": [ + "logic", + "nixpkgs" + ], + "nixpkgs-stable": "nixpkgs-stable_3" + }, + "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": [ @@ -164,18 +223,42 @@ "type": "github" } }, + "gitignore_3": { + "inputs": { + "nixpkgs": [ + "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" + "nixpkgs": [ + "nixpkgs" + ] }, "locked": { - "lastModified": 1728381939, - "narHash": "sha256-flmlzK5Megm15OwY8WSeI5NBA54gpRzCgDNgPSRJxc4=", + "lastModified": 1756768038, + "narHash": "sha256-9fusT9axRRc/uQoYTAp+tJeyF/6lSyK8PdtthnsLkS0=", "ref": "refs/heads/main", - "rev": "8c2a19dbf52c13f8bfc9356740ad4687efa0318e", - "revCount": 1, + "rev": "e4084b41cd821b32180e3a94490a1333477a08f2", + "revCount": 3, "type": "git", "url": "https://seed.radicle.garden/z2364hmzZUAGy1nKdSFa1gLSoUE2M.git" }, @@ -203,6 +286,27 @@ "url": "https://radicle-mermet.sourcephile.fr/z3795BqJN8hSMGkyAUr8hHviEEi2H.git" } }, + "logic_2": { + "inputs": { + "git-hooks": "git-hooks_3", + "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, @@ -249,27 +353,29 @@ "type": "github" } }, - "nixpkgs_2": { + "nixpkgs-stable_3": { "locked": { - "lastModified": 1727264057, - "narHash": "sha256-KQPI8CTTnB9CrJ7LrmLC4VWbKZfljEPBXOFGZFRpxao=", + "lastModified": 1710695816, + "narHash": "sha256-3Eh7fhEID17pv9ZxrPwCLfqXnYP006RKzSs0JptsN84=", "owner": "NixOS", "repo": "nixpkgs", - "rev": "759537f06e6999e141588ff1c9be7f3a5c060106", + "rev": "614b4613980a522ba49f0d194531beddbb7220d3", "type": "github" }, "original": { - "id": "nixpkgs", - "type": "indirect" + "owner": "NixOS", + "ref": "nixos-23.11", + "repo": "nixpkgs", + "type": "github" } }, - "nixpkgs_3": { + "nixpkgs_2": { "locked": { - "lastModified": 1727264057, - "narHash": "sha256-KQPI8CTTnB9CrJ7LrmLC4VWbKZfljEPBXOFGZFRpxao=", + "lastModified": 1755704039, + "narHash": "sha256-gKlP0LbyJ3qX0KObfIWcp5nbuHSb5EHwIvU6UcNBg2A=", "owner": "NixOS", "repo": "nixpkgs", - "rev": "759537f06e6999e141588ff1c9be7f3a5c060106", + "rev": "9cb344e96d5b6918e94e1bca2d9f3ea1e9615545", "type": "github" }, "original": { @@ -280,7 +386,8 @@ "root": { "inputs": { "literate-phylomemy": "literate-phylomemy", - "nixpkgs": "nixpkgs_3" + "logic": "logic_2", + "nixpkgs": "nixpkgs_2" } }, "systems": { @@ -312,6 +419,21 @@ "repo": "default", "type": "github" } + }, + "systems_3": { + "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", diff --git a/flake.nix b/flake.nix index a87037a..e8f67f2 100644 --- a/flake.nix +++ b/flake.nix @@ -7,6 +7,11 @@ # nix flake lock --override-input nixpkgs github:NixOS/nixpkgs nixpkgs.url = "flake:nixpkgs"; literate-phylomemy.url = "git+https://seed.radicle.garden/z2364hmzZUAGy1nKdSFa1gLSoUE2M.git"; + literate-phylomemy.inputs.nixpkgs.follows = "nixpkgs"; + # When working on a local clone: + #literate-phylomemy.url = "git+file:///home/julm/work/sourcephile/haskell/literate-phylomemy"; + logic.url = "git+https://radicle-mermet.sourcephile.fr/z3795BqJN8hSMGkyAUr8hHviEEi2H.git"; + logic.inputs.nixpkgs.follows = "nixpkgs"; }; outputs = inputs: @@ -35,6 +40,7 @@ haskellPackages: [ # Extra Haskell packages available inputs.literate-phylomemy.packages.${system}.default + inputs.logic.packages.${system}.default haskellPackages.bytestring haskellPackages.turtle haskellPackages.pretty-show diff --git a/script.hs b/script.hs index 079b8df..82da066 100755 --- a/script.hs +++ b/script.hs @@ -34,8 +34,10 @@ main = do 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 + Phylo.msfPrune predMeasure roots msf + let scaleTodot = Phylo.dotMaximalSpanningForest phylomemy + let scale = 3 + let dot = scaleTodot Map.! scale pPrint ("Number of maximal spanning trees", length phylomemy) Sys.withFile "phylomemy.dot" Sys.WriteMode (`BS.hPutBuilder` dot) -- 2.49.0