Merge pull request #749 from K900/science

treewide: more vaguely related fixes

default.nix

@@ -182,36 +182,31 @@ lib.makeScope pkgs.newScope (self: {
             builtins.map
               (
                 pkgMeta:
-                if builtins.elem pkgMeta.name nixpkgsBuildSystems then {
-                  name = pkgMeta.name;
-                  value = super."${pkgMeta.name}";
-                } else rec {
-                  name = normalizePackageName pkgMeta.name;
+                let normalizedName = normalizePackageName pkgMeta.name; in
+                {
+                  name = normalizedName;
                   value = self.mkPoetryDep (
                     pkgMeta // {
                       inherit pwd preferWheels;
                       source = pkgMeta.source or null;
-                      files = lockFiles.${name};
+                      files = lockFiles.${normalizedName};
                       pythonPackages = self;
 
-                      sourceSpec =
-                        let
-                          normalizedName = normalizePackageName pkgMeta.name;
-                        in
-                        (
-                          (normalizePackageSet pyProject.tool.poetry.dependencies or { }).${normalizedName}
-                            or (normalizePackageSet pyProject.tool.poetry.dev-dependencies or { }).${normalizedName}
-                            or (normalizePackageSet pyProject.tool.poetry.group.dev.dependencies { }).${normalizedName} # Poetry 1.2.0+
-                            or { }
-                        );
+                      sourceSpec = (
+                        (normalizePackageSet pyProject.tool.poetry.dependencies or { }).${normalizedName}
+                          or (normalizePackageSet pyProject.tool.poetry.dev-dependencies or { }).${normalizedName}
+                          or (normalizePackageSet pyProject.tool.poetry.group.dev.dependencies { }).${normalizedName} # Poetry 1.2.0+
+                          or { }
+                      );
                     }
                   );
                 }
               )
               (lib.reverseList compatible)
           );
+          buildSystems = builtins.listToAttrs (builtins.map (x: { name = x; value = super.${x}; }) nixpkgsBuildSystems);
         in
-        lockPkgs // {
+        lockPkgs // buildSystems // {
           # Create a dummy null package for the current project in case any dependencies depend on the root project (issue #307)
           ${pyProject.tool.poetry.name} = null;
         };

known-build-systems.json

@@ -7,6 +7,7 @@
     "flitBuildHook",
     "cython",
     "hatchling",
+    "hatch-vcs",
     "setuptools",
     "setuptools-scm"
 ]

overrides/build-systems.json

@@ -790,6 +790,7 @@
     "setuptools"
   ],
   "apipkg": [
+    "hatch-vcs",
     "hatchling",
     "setuptools"
   ],
@@ -1918,8 +1919,12 @@
   ],
   "black": [
     {
-      "buildSystem": "hatch-fancy-pypi-readme",
-      "from": "22.10.0"
+      "buildSystem": "setuptools",
+      "until": "22.10.0"
+    },
+    {
+      "buildSystem": "setuptools-scm",
+      "until": "22.10.0"
     },
     {
       "buildSystem": "hatchling",
@@ -1929,8 +1934,10 @@
       "buildSystem": "hatch-vcs",
       "from": "22.10.0"
     },
-    "setuptools",
-    "setuptools-scm"
+    {
+      "buildSystem": "hatch-fancy-pypi-readme",
+      "from": "22.10.0"
+    }
   ],
   "black-macchiato": [
     "setuptools"
@@ -3367,7 +3374,8 @@
     "setuptools"
   ],
   "dbus-fast": [
-    "poetry-core"
+    "poetry-core",
+    "setuptools"
   ],
   "dbus-next": [
     "setuptools"
@@ -7206,7 +7214,10 @@
       "buildSystem": "hatchling",
       "from": "4.11.0"
     },
-    "setuptools"
+    {
+      "buildSystem": "setuptools",
+      "until": "4.11.0"
+    }
   ],
   "jupyter-lsp": [
     "setuptools"
@@ -8681,6 +8692,9 @@
     "poetry-core",
     "setuptools"
   ],
+  "mypy-boto3-cognito": [
+    "setuptools"
+  ],
   "mypy-boto3-cognito-idp": [
     "setuptools"
   ],
@@ -8794,15 +8808,37 @@
     "setuptools"
   ],
   "nbconvert": [
-    "setuptools"
+    {
+      "buildSystem": "setuptools",
+      "until": "7.0.0"
+    },
+    {
+      "buildSystem": "hatchling",
+      "from": "7.0.0"
+    }
   ],
   "nbdime": [
     "setuptools",
     "setuptools-scm"
   ],
   "nbformat": [
-    "flit-core",
-    "setuptools"
+    {
+      "buildSystem": "setuptools",
+      "until": "5.4.0"
+    },
+    {
+      "buildSystem": "flit-core",
+      "from": "5.4.0",
+      "until": "5.6.0"
+    },
+    {
+      "buildSystem": "hatchling",
+      "from": "5.6.0"
+    },
+    {
+      "buildSystem": "hatch-nodejs-version",
+      "from": "5.6.0"
+    }
   ],
   "nbmerge": [
     "setuptools"
@@ -10104,6 +10140,7 @@
     "setuptools"
   ],
   "pipdeptree": [
+    "hatch-vcs",
     "hatchling",
     "setuptools"
   ],
@@ -10383,6 +10420,9 @@
   "prayer-times-calculator": [
     "setuptools"
   ],
+  "pre-commit": [
+    "setuptools"
+  ],
   "pre-commit-hooks": [
     "setuptools"
   ],
@@ -11409,6 +11449,7 @@
     "setuptools"
   ],
   "pyhamcrest": [
+    "hatch-vcs",
     "hatchling",
     "setuptools"
   ],
@@ -14697,8 +14738,14 @@
     "setuptools"
   ],
   "seaborn": [
-    "flit-core",
-    "setuptools"
+    {
+      "buildSystem": "setuptools",
+      "until": "0.12.0"
+    },
+    {
+      "buildSystem": "flit-core",
+      "from": "0.12.0"
+    }
   ],
   "seabreeze": [
     "cython",
@@ -17069,6 +17116,7 @@
     "setuptools-scm"
   ],
   "vector": [
+    "hatch-vcs",
     "hatchling"
   ],
   "vega": [

overrides/default.nix

@@ -194,7 +194,6 @@ lib.composeManyExtensions [
           }.${version} or (
             lib.warn "Unknown bcrypt version: '${version}'. Please update getCargoHash." lib.fakeHash
           );
-          sha256 = getCargoHash super.bcrypt.version;
         in
         super.bcrypt.overridePythonAttrs (
           old: {
@@ -206,7 +205,7 @@ lib.composeManyExtensions [
               (old.nativeBuildInputs or [ ])
                 ++ lib.optionals (lib.versionAtLeast old.version "4")
                 (with pkgs.rustPlatform; [ rust.rustc rust.cargo cargoSetupHook self.setuptools-rust ]);
-          } // lib.optionalAttrs (lib.versionAtLeast old.version "4") rec {
+          } // lib.optionalAttrs (lib.versionAtLeast old.version "4") {
             cargoDeps =
               pkgs.rustPlatform.fetchCargoTarball
                 {
@@ -269,6 +268,10 @@ lib.composeManyExtensions [
         propagatedBuildInputs = (old.propagatedBuildInputs or [ ]) ++ [ self.setuptools ];
       });
 
+      cerberus = super.cerberus.overridePythonAttrs (old: {
+        propagatedBuildInputs = (old.propagatedBuildInputs or [ ]) ++ [ self.setuptools ];
+      });
+
       cssselect2 = super.cssselect2.overridePythonAttrs (
         old: {
           buildInputs = (old.buildInputs or [ ]) ++ [ self.pytest-runner ];
@@ -806,6 +809,12 @@ lib.composeManyExtensions [
         }
       );
 
+      ipython = super.ipython.overridePythonAttrs (
+        old: {
+          propagatedBuildInputs = (old.propagatedBuildInputs or [ ]) ++ [ self.setuptools ];
+        }
+      );
+
       isort = super.isort.overridePythonAttrs (
         old: {
           propagatedBuildInputs = (old.propagatedBuildInputs or [ ]) ++ [ self.setuptools ];
@@ -884,7 +893,7 @@ lib.composeManyExtensions [
       );
 
       jupyter-packaging = super.jupyter-packaging.overridePythonAttrs (old: {
-        propagatedBuildInputs = (old.propagatedBuildInputs or [ ]) ++ [ self.wheel ];
+        propagatedBuildInputs = (old.propagatedBuildInputs or [ ]) ++ [ self.setuptools self.wheel ];
       });
 
       jupyterlab-widgets = super.jupyterlab-widgets.overridePythonAttrs (
@@ -1059,6 +1068,9 @@ lib.composeManyExtensions [
             self.setuptools-scm-git-archive
           ];
 
+          # Clang doesn't understand -fno-strict-overflow, and matplotlib builds with -Werror
+          hardeningDisable = if stdenv.isDarwin then [ "strictoverflow" ] else [ ];
+
           passthru = old.passthru or { } // passthru;
 
           MPLSETUPCFG = pkgs.writeText "mplsetup.cfg" (lib.generators.toINI { } passthru.config);
@@ -1251,6 +1263,8 @@ lib.composeManyExtensions [
           };
         in
         {
+          # fails to build with format=pyproject and setuptools >= 65
+          format = if (old.format == "poetry2nix") then "setuptools" else old.format;
           nativeBuildInputs = (old.nativeBuildInputs or [ ]) ++ [ pkgs.gfortran ];
           buildInputs = (old.buildInputs or [ ]) ++ [ blas ];
           enableParallelBuilding = true;

plugins.nix

@@ -19,7 +19,7 @@ let
       inherit (drv) src version meta;
 
       buildInputs = drv.buildInputs ++ drv.propagatedBuildInputs ++ buildInputs;
-      nativeBuildInputs = drv.nativeBuildInputs ++ nativeBuildInputs;
+      nativeBuildInputs = builtins.filter (x: x.name != "python-output-dist-hook") (drv.nativeBuildInputs ++ nativeBuildInputs);
 
       dontConfigure = true;
       dontBuild = true;

tests/default.nix

@@ -123,5 +123,7 @@ builtins.removeAttrs
   manylinux = callTest ./manylinux { };
   shapely = callTest ./shapely { };
   setuptools = callTest ./setuptools { };
+
+  scientific = callTest ./scientific { };
 }
   skipTests

tests/path-deps-develop/default.nix

@@ -7,6 +7,12 @@ let
     editablePackageSources = {
       dep1 = null;
     };
+
+    overrides = poetry2nix.overrides.withDefaults (self: super: {
+      dep1 = super.dep1.overridePythonAttrs (old: {
+        buildInputs = (old.buildInputs or [ ]) ++ [ self.setuptools ];
+      });
+    });
   };
 
 in

tests/scientific/default.nix

@@ -0,0 +1,8 @@
+{ lib, poetry2nix, python3 }:
+
+poetry2nix.mkPoetryApplication {
+  python = python3;
+  pyproject = ./pyproject.toml;
+  poetrylock = ./poetry.lock;
+  src = lib.cleanSource ./.;
+}

tests/scientific/pyproject.toml

@@ -0,0 +1,22 @@
+[tool.poetry]
+name = "scientific_test"
+version = "0.1.0"
+description = ""
+authors = ["Your Name <you@example.com>"]
+
+[tool.poetry.dependencies]
+python = "^3.10"
+numpy = "*"
+scipy = "*"
+scikit-learn = "*"
+matplotlib = "*"
+seaborn = "*"
+pandas = "*"
+jupyter = "*"
+
+# FIXME: pin a lower version until we figure out how to build newer ones
+nbconvert = "<7"
+
+[build-system]
+requires = ["poetry-core>=1.1"]
+build-backend = "poetry.core.masonry.api"