maintenance(deps): update `nixpkgs`, `literate-phylomemy` and `logic`

diff --git a/flake.lock b/flake.lock
index afa629cecf39bdc348bf59189beabf41cbbcf459..282b41e313dab34a1e704cb4a35462ab970873f4 100644 (file)
--- a/flake.lock
+++ b/flake.lock
@@ -32,6 +32,22 @@
         "type": "github"
       }
     },
         "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"
     "flake-utils": {
       "inputs": {
         "systems": "systems"


@@ -68,6 +84,24 @@
         "type": "github"
       }
     },
         "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",
     "git-hooks": {
       "inputs": {
         "flake-compat": "flake-compat",


@@ -119,6 +153,31 @@
         "type": "github"
       }
     },
         "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": [
     "gitignore": {
       "inputs": {
         "nixpkgs": [


@@ -164,18 +223,42 @@
         "type": "github"
       }
     },
         "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",
     "literate-phylomemy": {
       "inputs": {
         "git-hooks": "git-hooks",
         "logic": "logic",

-        "nixpkgs": "nixpkgs_2"
+        "nixpkgs": [
+          "nixpkgs"
+        ]

       },
       "locked": {
       },
       "locked": {

-        "lastModified": 1728381939,
-        "narHash": "sha256-flmlzK5Megm15OwY8WSeI5NBA54gpRzCgDNgPSRJxc4=",
+        "lastModified": 1756768038,
+        "narHash": "sha256-9fusT9axRRc/uQoYTAp+tJeyF/6lSyK8PdtthnsLkS0=",

         "ref": "refs/heads/main",
         "ref": "refs/heads/main",

-        "rev": "8c2a19dbf52c13f8bfc9356740ad4687efa0318e",
-        "revCount": 1,
+        "rev": "e4084b41cd821b32180e3a94490a1333477a08f2",
+        "revCount": 3,

         "type": "git",
         "url": "https://seed.radicle.garden/z2364hmzZUAGy1nKdSFa1gLSoUE2M.git"
       },
         "type": "git",
         "url": "https://seed.radicle.garden/z2364hmzZUAGy1nKdSFa1gLSoUE2M.git"
       },


@@ -203,6 +286,27 @@
         "url": "https://radicle-mermet.sourcephile.fr/z3795BqJN8hSMGkyAUr8hHviEEi2H.git"
       }
     },
         "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,
     "nixpkgs": {
       "locked": {
         "lastModified": 1716793392,


@@ -249,27 +353,29 @@
         "type": "github"
       }
     },
         "type": "github"
       }
     },

-    "nixpkgs_2": {
+    "nixpkgs-stable_3": {

       "locked": {
       "locked": {

-        "lastModified": 1727264057,
-        "narHash": "sha256-KQPI8CTTnB9CrJ7LrmLC4VWbKZfljEPBXOFGZFRpxao=",
+        "lastModified": 1710695816,
+        "narHash": "sha256-3Eh7fhEID17pv9ZxrPwCLfqXnYP006RKzSs0JptsN84=",

         "owner": "NixOS",
         "repo": "nixpkgs",
         "owner": "NixOS",
         "repo": "nixpkgs",

-        "rev": "759537f06e6999e141588ff1c9be7f3a5c060106",
+        "rev": "614b4613980a522ba49f0d194531beddbb7220d3",

         "type": "github"
       },
       "original": {
         "type": "github"
       },
       "original": {

-        "id": "nixpkgs",
-        "type": "indirect"
+        "owner": "NixOS",
+        "ref": "nixos-23.11",
+        "repo": "nixpkgs",
+        "type": "github"

       }
     },
       }
     },

-    "nixpkgs_3": {
+    "nixpkgs_2": {

       "locked": {
       "locked": {

-        "lastModified": 1727264057,
-        "narHash": "sha256-KQPI8CTTnB9CrJ7LrmLC4VWbKZfljEPBXOFGZFRpxao=",
+        "lastModified": 1755704039,
+        "narHash": "sha256-gKlP0LbyJ3qX0KObfIWcp5nbuHSb5EHwIvU6UcNBg2A=",

         "owner": "NixOS",
         "repo": "nixpkgs",
         "owner": "NixOS",
         "repo": "nixpkgs",

-        "rev": "759537f06e6999e141588ff1c9be7f3a5c060106",
+        "rev": "9cb344e96d5b6918e94e1bca2d9f3ea1e9615545",

         "type": "github"
       },
       "original": {
         "type": "github"
       },
       "original": {


@@ -280,7 +386,8 @@
     "root": {
       "inputs": {
         "literate-phylomemy": "literate-phylomemy",
     "root": {
       "inputs": {
         "literate-phylomemy": "literate-phylomemy",

-        "nixpkgs": "nixpkgs_3"
+        "logic": "logic_2",
+        "nixpkgs": "nixpkgs_2"

       }
     },
     "systems": {
       }
     },
     "systems": {


@@ -312,6 +419,21 @@
         "repo": "default",
         "type": "github"
       }
         "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",
     }
   },
   "root": "root",

diff --git a/flake.nix b/flake.nix
index a87037a45f5b7b8a0afbb78b091047ff4fb55ff6..e8f67f24f6f43d9ba839a2724941429fe2fd0896 100644 (file)
--- 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";
     # 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:
   };
   outputs =
     inputs:


@@ -35,6 +40,7 @@
             haskellPackages: [
               # Extra Haskell packages available
               inputs.literate-phylomemy.packages.${system}.default
             haskellPackages: [
               # Extra Haskell packages available
               inputs.literate-phylomemy.packages.${system}.default

+              inputs.logic.packages.${system}.default

               haskellPackages.bytestring
               haskellPackages.turtle
               haskellPackages.pretty-show
               haskellPackages.bytestring
               haskellPackages.turtle
               haskellPackages.pretty-show

diff --git a/script.hs b/script.hs
index 079b8df5b8b53bed23c2d75d933f3b3a162c6b42..82da06685b2d0aec791e17eb11fbc8313d867fd5 100755 (executable)
--- 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 ->
             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)
 
             pPrint ("Number of maximal spanning trees", length phylomemy)
             Sys.withFile "phylomemy.dot" Sys.WriteMode (`BS.hPutBuilder` dot)