feat(uv): init uv workspace for rapid dev cycles

broadinstitute · Jan 6, 2025 · 2699b0b · 2699b0b
1 parent 3464c53
commit 2699b0b
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Showing 10 changed files with 67 additions and 1,084 deletions.
diff --git a/conductor/pyproject.toml b/conductor/pyproject.toml
@@ -13,13 +13,16 @@ dependencies = [
   "alembic~=1.13",
   "pydantic~=2.8",
   "pydantic-settings~=2.4",
-  "starrynight @ file:///${PROJECT_ROOT}/../starrynight",
   "joblib~=1.3",
-  # "cloudpahtlib[all]>0.18,<1.0",
+  "cloudpahtlib[all]>0.18,<1.0",
+  "starrynight",
 ]
 
 [project.optional-dependencies]
-dev = ["pytest~=8.2", "ruff~=0.5", "build~=1.2", "twine~=5.1"]
+dev = ["pytest", "ruff", "build", "twine"]
+
+[tools.uv.sources]
+starrynight = { path = true }
 
 [project.scripts]
 conductor = "conductor.cli.main:main"
@@ -38,6 +41,5 @@ exclude = ["vendor"]
 ignore = ["ANN101"]
 per-file-ignores = { "tests/*" = ["D103"] }
 
-
 [tool.basedpyright]
 typeCheckingMode = "basic"
diff --git a/flake.lock b/flake.lock
diff --git a/flake.nix b/flake.nix
@@ -1,11 +1,10 @@
 {
   inputs = {
-    nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.05";
-    nixpkgs_master.url = "github:NixOS/nixpkgs/master";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.11";
     systems.url = "github:nix-systems/default";
     flake-utils.url = "github:numtide/flake-utils";
     flake-utils.inputs.systems.follows = "systems";
-    cp-flake.url = "github:leoank/CellProfiler/refactor/nix";
+    cp-flake.url = "github:CellProfiler/CellProfiler";
     cp-flake.inputs.nixpkgs.follows = "nixpkgs";
   };
 
@@ -20,33 +19,27 @@
     flake-utils.lib.eachDefaultSystem (
       system:
       let
+        inherit (self) outputs;
         pkgs = import nixpkgs {
           system = system;
           config.allowUnfree = true;
         };
 
       in
-      # mpkgs = import inputs.nixpkgs_m
-      #   system = system;
-      #   config.allowUnfree = true;
-      # };
       with pkgs;
-      rec {
-        packages = import ./nix { inherit pkgs; };
-        apps = {
-          cellprofiler = {
-            type = "app";
-            program = "${packages.cellprofiler-nightly}/bin/cellprofiler";
-          };
+      {
+        packages = pkgs.callPackage ./nix {
+          inherit inputs outputs;
+          python3Packages = pkgs.python311Packages;
         };
         devShells = {
           default =
             let
               python_with_pkgs = (
                 pkgs.python311.withPackages (pp: [
-                  inputs.cp-flake.packages.${system}.cellprofiler
-                  inputs.cp-flake.packages.${system}.cellprofiler-core
-                  inputs.cp-flake.packages.${system}.cellprofiler-library
+                  (inputs.cp-flake.packages.${system}.override {
+                    python3Packages = pkgs.python311Packages;
+                  }).cellprofiler
                   pp.mysqlclient
                   pp.packaging
                   pp.snakemake
@@ -71,7 +64,7 @@
               ];
               packages = [
                 python_with_pkgs
-                python3Packages.venvShellHook
+                python311Packages.venvShellHook
                 git
                 gtk3
                 glib