feat(nix): setup to move towards uv workspace

broadinstitute · Jan 5, 2025 · d985062 · d985062
1 parent e48c63d
commit d985062
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Showing 7 changed files with 52 additions and 65 deletions.
diff --git a/nix/containers/default.nix b/nix/containers/default.nix
diff --git a/nix/containers/illum-calculate.nix b/nix/containers/illum-calculate.nix
@@ -1,16 +1,16 @@
 {
-  inputs,
+  pkgs,
+  nix2container,
   outputs,
   ...
 }:
-{
-  illum_calculate = inputs.nix2container.buildImage {
-    name = "starrynight-illum-calculate";
-    config = {
-      entrypoint = [
-        "${outputs.packages.starrynight}/bin/starrynight"
-        "illum"
-      ];
-    };
+pkgs.dockerTools.buildImage {
+  name = "ghcr.io/broadinstitute/starrynight-illum-calculate";
+  tag = "dev";
+  config = {
+    Cmd = [
+      "${outputs.packages.${pkgs.system}.starrynight}/bin/starrynight"
+      "illum"
+    ];
   };
 }
diff --git a/nix/cpgdata.nix b/nix/cpgdata.nix
@@ -2,6 +2,7 @@
   lib,
   buildPythonPackage,
   fetchPypi,
+  poetry-core,
   pytest,
   cython,
   setuptools,
@@ -15,28 +16,29 @@
   tqdm,
   lark,
 }:
-buildPythonPackage {
+buildPythonPackage rec {
   pname = "cpgdata";
   version = "0.4.0";
   src = fetchPypi {
     inherit pname version;
-    sha256 = "";
+    sha256 = "sha256-nCDzjnEXD0Hs4lfS9NP9DbG0ly84Y8NDICbvpuMD1cU=";
 
   };
   pyproject = true;
 
   # Relax deps constraints
-  # postPatch = ''
-  #   substituteInPlace setup.py \
-  #     --replace "scipy>=1.4.1,<1.11" "scipy>=1.4.1" \
-  #     --replace "matplotlib>=3.1.3,<3.8" "matplotlib>=3.1.3"
-  # '';
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace-warn 'polars = "^0.19"' 'polars = ">=0.19"' \
+      --replace-warn 'pyarrow = "^13.0"' 'pyarrow = ">=13.0"'
+  '';
 
   buildInputs = [
     pytest
     cython
     setuptools
     setuptools-scm
+    poetry-core
   ];
 
   propagatedBuildInputs = [

diff --git a/nix/cpgparser.nix b/nix/cpgparser.nix
@@ -2,39 +2,30 @@
   lib,
   buildPythonPackage,
   fetchPypi,
-  pytest,
-  cython,
-  setuptools,
-  setuptools-scm,
-  maturin,
+  rustPlatform,
 }:
-buildPythonPackage {
+buildPythonPackage rec {
   pname = "cpgparser";
   version = "0.2.0";
+  pyproject = true;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "";
+    sha256 = "sha256-5k3u873kKKFyP2qps1Buq+SmIuU0BPUfa23+FaAoomE=";
 
   };
-  pyproject = true;
-
-  # Relax deps constraints
-  # postPatch = ''
-  #   substituteInPlace setup.py \
-  #     --replace "scipy>=1.4.1,<1.11" "scipy>=1.4.1" \
-  #     --replace "matplotlib>=3.1.3,<3.8" "matplotlib>=3.1.3"
-  # '';
 
-  buildInputs = [
-    pytest
-    cython
-    setuptools
-    setuptools-scm
-    maturin
+  nativeBuildInputs = with rustPlatform; [
+    maturinBuildHook
+    cargoSetupHook
   ];
 
-  propagatedBuildInputs = [
+  cargoDeps = rustPlatform.fetchCargoTarball {
+    inherit pname version src;
+    hash = "sha256-uz/q3cnWNf9k8bNeUIh1gzJGCWWOnPSwSoAgvlwAdlo=";
+  };
+
+  dependencies = [
   ];
   pythonImportsCheck = [ "cpgparser" ];
 

diff --git a/nix/default.nix b/nix/default.nix
@@ -8,15 +8,24 @@
 }:
 
 let
+  # tools
+  inherit (inputs.nix2container.packages.${pkgs.system}) nix2container;
   # Apps
   packages = rec {
+    cp-pkgs = inputs.cp-flake.packages.${pkgs.system};
     pipecraft = python3Packages.callPackage ./pipecraft.nix { };
     cpgparser = python3Packages.callPackage ./cpgparser.nix { };
-    # cpgdata = python3Packages.callPackage ./cpgdata.nix { };
-    # starrynight = python3Packages.callPackage ./starrynight.nix { inherit pipecraft cpgdata; };
+    cpgdata = python3Packages.callPackage ./cpgdata.nix { inherit cpgparser; };
+    starrynight = python3Packages.callPackage ./starrynight.nix {
+      inherit cpgdata pipecraft;
+      inherit (cp-pkgs) cellprofiler cellprofiler-core cellprofiler-library;
+    };
+
+    # Containers
+    container_illum_calculate = pkgs.callPackage ./containers/illum-calculate.nix {
+      inherit nix2container outputs;
+    };
   };
 
 in
-# Containers
-# containers = import pkgs.callPackage ./containers { };
 packages
diff --git a/nix/pipecraft.nix b/nix/pipecraft.nix
@@ -18,13 +18,6 @@ buildPythonPackage {
   src = ./../pipecraft;
   pyproject = true;
 
-  # Relax deps constraints
-  # postPatch = ''
-  #   substituteInPlace setup.py \
-  #     --replace "scipy>=1.4.1,<1.11" "scipy>=1.4.1" \
-  #     --replace "matplotlib>=3.1.3,<3.8" "matplotlib>=3.1.3"
-  # '';
-
   buildInputs = [
     pytest
     cython
@@ -42,8 +35,8 @@ buildPythonPackage {
   pythonImportsCheck = [ "pipecraft" ];
 
   meta = {
-    description = "Centrosome";
-    homepage = "https://cellprofiler.org";
+    description = "Pipecraft library for crafting data pipelines in python";
+    homepage = "https://github.com/broadinstitute/starrynight";
     license = lib.licenses.mit;
   };
 

diff --git a/nix/starrynight.nix b/nix/starrynight.nix
@@ -6,6 +6,7 @@
   setuptools,
   setuptools-scm,
   pipecraft,
+  cpgdata,
   lark,
   numpy,
   contourpy,
@@ -18,6 +19,7 @@
 buildPythonPackage {
   pname = "starrynight";
   version = "0.1.0";
+  pyproject = true;
 
   src = ./../starrynight;
 
@@ -37,6 +39,7 @@ buildPythonPackage {
 
   propagatedBuildInputs = [
     pipecraft
+    cpgdata
     lark
     numpy
     contourpy
@@ -49,8 +52,8 @@ buildPythonPackage {
   pythonImportsCheck = [ "starrynight" ];
 
   meta = {
-    description = "Centrosome";
-    homepage = "https://cellprofiler.org";
+    description = "Starrynight";
+    homepage = "https://github.com/broadinstitute/bin/starrynight";
     license = lib.licenses.mit;
   };