[logseq] chore!: Remove flake

Resolves: tdpeuter/sisyphus#16

logseq/flake.lock

@@ -1,61 +0,0 @@
-{
-  "nodes": {
-    "flake-utils": {
-      "inputs": {
-        "systems": "systems"
-      },
-      "locked": {
-        "lastModified": 1705309234,
-        "narHash": "sha256-uNRRNRKmJyCRC/8y1RqBkqWBLM034y4qN7EprSdmgyA=",
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "rev": "1ef2e671c3b0c19053962c07dbda38332dcebf26",
-        "type": "github"
-      },
-      "original": {
-        "owner": "numtide",
-        "repo": "flake-utils",
-        "type": "github"
-      }
-    },
-    "nixpkgs": {
-      "locked": {
-        "lastModified": 1708093448,
-        "narHash": "sha256-gohEm3/NVyu7WINFhRf83yJH8UM2ie/KY9Iw3VN6fiE=",
-        "owner": "NixOS",
-        "repo": "nixpkgs",
-        "rev": "c7763249f02b7786b4ca36e13a4d7365cfba162f",
-        "type": "github"
-      },
-      "original": {
-        "owner": "NixOS",
-        "ref": "nixpkgs-unstable",
-        "repo": "nixpkgs",
-        "type": "github"
-      }
-    },
-    "root": {
-      "inputs": {
-        "flake-utils": "flake-utils",
-        "nixpkgs": "nixpkgs"
-      }
-    },
-    "systems": {
-      "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
-}

logseq/flake.nix

@@ -1,21 +0,0 @@
-{
-  description = "Logseq";
-
-  inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable";
-  inputs.flake-utils.url = "github:numtide/flake-utils";
-
-  outputs = { self, nixpkgs, flake-utils }:
-  flake-utils.lib.eachDefaultSystem
-  ( system:
-  let
-    pkgs = import nixpkgs {
-      inherit system;
-    };
-  in {
-    devShells.default = pkgs.mkShell {
-      packages = with pkgs; [
-        logseq
-      ];
-    };
-  });
-}

python/conda/flake.lock

@@ -5,11 +5,11 @@
         "systems": "systems"
       },
       "locked": {
-        "lastModified": 1694529238,
+        "lastModified": 1710146030,
-        "narHash": "sha256-zsNZZGTGnMOf9YpHKJqMSsa0dXbfmxeoJ7xHlrt+xmY=",
+        "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=",
         "owner": "numtide",
         "repo": "flake-utils",
-        "rev": "ff7b65b44d01cf9ba6a71320833626af21126384",
+        "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a",
         "type": "github"
       },
       "original": {
@@ -20,11 +20,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1695360818,
+        "lastModified": 1712608508,
-        "narHash": "sha256-JlkN3R/SSoMTa+CasbxS1gq+GpGxXQlNZRUh9+LIy/0=",
+        "narHash": "sha256-vMZ5603yU0wxgyQeHJryOI+O61yrX2AHwY6LOFyV1gM=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "e35dcc04a3853da485a396bdd332217d0ac9054f",
+        "rev": "4cba8b53da471aea2ab2b0c1f30a81e7c451f4b6",
         "type": "github"
       },
       "original": {

python/conda/flake.nix

@@ -2,8 +2,26 @@
   description = ''
     Python flake for use with conda environments.
 
-    This will create a directory `~/.conda`, which might be rather large,
+    This will create a directory ~/.conda, which might become rather large,
     depending on your required packages.
+
+    ### Usage: ###
+
+    You can enter the environment in your CLI with:
+
+    $ nix-develop -c bash -c "conda-shell -c 'conda activate <environment-name> && sh'"
+
+    If you are using Pycharm, you can start up quickly by running:
+
+    $ nix develop -c bash -c "conda-shell -c pycharm-professonial && exit"
+
+    ### Setup: ###
+
+    On your first run, enter conda using
+
+    $ nix-develop -c bash -c "conda-shell -c 'conda-install'"
+    (conda-shell)$ conda env create --name <environment-name> --file /path/to/environment.yaml
+
   '';
 
   inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
@@ -16,28 +34,14 @@
       inherit system;
       config.allowUnfree = true;
     };
-
-    installation-steps = ''
-      conda-shell -c 'conda-install'
-      printf 'Run `conda env create --name ai-practica --file environment.yaml` and exit.\n'
-      conda-shell && exit
-    '';
-    IDE-steps = ''
-      conda-shell -c pycharm-professional && exit
-    '';
-    CLI-steps = ''
-      printf 'Enter your enviroment by running `conda activate ai-practica`.\n'
-      conda-shell && exit
-    '';
   in {
     devShells.default = pkgs.mkShell {
       packages = with pkgs; [
         conda
 
         # You might want to add an IDE of your choice;
-        jetbrains.pycharm-professional
+        # (jetbrains.plugins.addPlugins jetbrains.pycharm-professional [ "github-copilot" ])
       ];
-      shellHook = IDE-steps;
     };
   });
 }

python/native/flake.lock

@@ -20,11 +20,11 @@
     },
     "nixpkgs": {
       "locked": {
-        "lastModified": 1711124224,
+        "lastModified": 1712588820,
-        "narHash": "sha256-l0zlN/3CiodvWDtfBOVxeTwYSRz93muVbXWSpaMjXxM=",
+        "narHash": "sha256-y31s5idk3jMJMAVE4Ud9AdI7HT3CgTAeMTJ0StqKN7Y=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "56528ee42526794d413d6f244648aaee4a7b56c0",
+        "rev": "d272ca50d1f7424fbfcd1e6f1c9e01d92f6da167",
         "type": "github"
       },
       "original": {
@@ -36,11 +36,11 @@
     },
     "nixpkgs-unstable": {
       "locked": {
-        "lastModified": 1711163522,
+        "lastModified": 1712608508,
-        "narHash": "sha256-YN/Ciidm+A0fmJPWlHBGvVkcarYWSC+s3NTPk/P+q3c=",
+        "narHash": "sha256-vMZ5603yU0wxgyQeHJryOI+O61yrX2AHwY6LOFyV1gM=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "44d0940ea560dee511026a53f0e2e2cde489b4d4",
+        "rev": "4cba8b53da471aea2ab2b0c1f30a81e7c451f4b6",
         "type": "github"
       },
       "original": {

python/native/flake.nix

@@ -21,6 +21,7 @@
       biopython
       numpy
       dask
+      numba
     ];
   in {
     devShells.default = pkgs.mkShell {
@@ -32,7 +33,7 @@
         memray
 
         # Editor of your choice
-        # jetbrains.pycharm-professional
+        # (jetbrains.plugins.addPlugins jetbrains.pycharm-professional [ "github-copilot" ])
         # vscodium
       ]);
     };