From 599f5c2c8c50caeb8e13100ceee21445ff5cd853 Mon Sep 17 00:00:00 2001 From: aleksana Date: Wed, 19 Jun 2024 15:21:45 +0800 Subject: [PATCH 1/5] python3Packages: trivial toPythonModule fixes --- pkgs/top-level/python-packages.nix | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 483cb05e6996..7d095dc78631 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -2560,7 +2560,7 @@ self: super: with self; { criticality-score = callPackage ../development/python-modules/criticality-score { }; - crocoddyl = toPythonModule (callPackage ../development/libraries/crocoddyl { + crocoddyl = toPythonModule (pkgs.crocoddyl.override { pythonSupport = true; python3Packages = self; }); @@ -4880,7 +4880,8 @@ self: super: with self; { gmpy = callPackage ../development/python-modules/gmpy { }; - gmsh = toPythonModule (callPackage ../applications/science/math/gmsh { + gmsh = toPythonModule (pkgs.gmsh.override { + inherit (self) python; enablePython = true; }); @@ -6457,6 +6458,7 @@ self: super: with self; { kmsxx = toPythonModule (pkgs.kmsxx.override { withPython = true; + python3Packages = self; }); knack = callPackage ../development/python-modules/knack { }; @@ -8802,7 +8804,7 @@ self: super: with self; { neuron-full = pkgs.neuron-full.override { python3 = python; }; - neuronpy = python.pkgs.toPythonModule neuron-full; + neuronpy = toPythonModule neuron-full; nevow = callPackage ../development/python-modules/nevow { }; @@ -9616,7 +9618,7 @@ self: super: with self; { pbs-installer = callPackage ../development/python-modules/pbs-installer { }; - pc-ble-driver-py = toPythonModule (callPackage ../development/python-modules/pc-ble-driver-py { }); + pc-ble-driver-py = callPackage ../development/python-modules/pc-ble-driver-py { }; pcapy-ng = callPackage ../development/python-modules/pcapy-ng { inherit (pkgs) libpcap; # Avoid confusion with python package of the same name @@ -15299,7 +15301,7 @@ self: super: with self; { inherit (pkgs.darwin.apple_sdk.frameworks) Security; }; - tokenize-rt = toPythonModule (callPackage ../development/python-modules/tokenize-rt { }); + tokenize-rt = callPackage ../development/python-modules/tokenize-rt { }; tokenlib = callPackage ../development/python-modules/tokenlib { }; @@ -16750,7 +16752,9 @@ self: super: with self; { vidstab = callPackage ../development/python-modules/vidstab { }; - viennarna = toPythonModule pkgs.viennarna; + viennarna = toPythonModule (pkgs.viennarna.override { + python3 = self.python; + }); viewstate = callPackage ../development/python-modules/viewstate { }; From fd531cc55c28eac6b77c7155deb12b0cde3a93ad Mon Sep 17 00:00:00 2001 From: aleksana Date: Wed, 19 Jun 2024 15:27:10 +0800 Subject: [PATCH 2/5] python3Packages.hoomd-blue: build with buildPythonPackage --- pkgs/development/python-modules/hoomd-blue/default.nix | 5 +++-- pkgs/top-level/python-packages.nix | 4 +--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/pkgs/development/python-modules/hoomd-blue/default.nix b/pkgs/development/python-modules/hoomd-blue/default.nix index ebadd5552698..28836e4854ce 100644 --- a/pkgs/development/python-modules/hoomd-blue/default.nix +++ b/pkgs/development/python-modules/hoomd-blue/default.nix @@ -1,6 +1,6 @@ { lib, - stdenv, + buildPythonPackage, fetchgit, cmake, pkgconfig, @@ -19,9 +19,10 @@ let onOffBool = b: if b then "ON" else "OFF"; withMPI = (mpi != null); in -stdenv.mkDerivation rec { +buildPythonPackage rec { version = "2.3.4"; pname = "hoomd-blue"; + pyproject = false; # Built with cmake src = fetchgit { url = "https://bitbucket.org/glotzer/hoomd-blue"; diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 7d095dc78631..ba7a9f18abc1 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -5465,9 +5465,7 @@ self: super: with self; { homepluscontrol = callPackage ../development/python-modules/homepluscontrol { }; - hoomd-blue = toPythonModule (callPackage ../development/python-modules/hoomd-blue { - inherit python; - }); + hoomd-blue = callPackage ../development/python-modules/hoomd-blue { }; hopcroftkarp = callPackage ../development/python-modules/hopcroftkarp { }; From 01ef5abcfa26d719b85fcc2cf6bb845556223d71 Mon Sep 17 00:00:00 2001 From: aleksana Date: Wed, 19 Jun 2024 15:41:11 +0800 Subject: [PATCH 3/5] python3Packages.py3buddy: build with buildPythonPackage --- pkgs/development/python-modules/py3buddy/default.nix | 11 ++++++----- pkgs/top-level/python-packages.nix | 2 +- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/pkgs/development/python-modules/py3buddy/default.nix b/pkgs/development/python-modules/py3buddy/default.nix index 33a5cfc593a3..e076aa3b667e 100644 --- a/pkgs/development/python-modules/py3buddy/default.nix +++ b/pkgs/development/python-modules/py3buddy/default.nix @@ -1,23 +1,24 @@ { lib, - stdenv, + buildPythonPackage, fetchFromGitHub, python, pyusb, }: -stdenv.mkDerivation (finalAttrs: { +buildPythonPackage rec { pname = "py3buddy"; version = "1.0"; + pyproject = false; # manually installed src = fetchFromGitHub { owner = "armijnhemel"; repo = "py3buddy"; - rev = finalAttrs.version; + rev = version; hash = "sha256-KJ0xGEXHY6o2074WFZ0u7gATS+wrrjyzanYretckWYk="; }; - propagatedBuildInputs = [ pyusb ]; + dependencies = [ pyusb ]; dontConfigure = true; dontBuild = true; @@ -40,4 +41,4 @@ stdenv.mkDerivation (finalAttrs: { license = lib.licenses.mit; maintainers = with lib.maintainers; [ prusnak ]; }; -}) +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index ba7a9f18abc1..cec492852b2a 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -10640,7 +10640,7 @@ self: super: with self; { py2bit = callPackage ../development/python-modules/py2bit { }; - py3buddy = toPythonModule (callPackage ../development/python-modules/py3buddy { }); + py3buddy = callPackage ../development/python-modules/py3buddy { }; py3exiv2 = callPackage ../development/python-modules/py3exiv2 { }; From 1fef68b065403f0b7db29016e52a164dd4552863 Mon Sep 17 00:00:00 2001 From: aleksana Date: Wed, 19 Jun 2024 16:00:15 +0800 Subject: [PATCH 4/5] python3Packages.pyunbound: migrate to python-modules and build with buildPythonPackage --- .../python-modules/pyunbound/default.nix} | 9 ++++----- pkgs/top-level/python-packages.nix | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-) rename pkgs/{tools/networking/unbound/python.nix => development/python-modules/pyunbound/default.nix} (92%) diff --git a/pkgs/tools/networking/unbound/python.nix b/pkgs/development/python-modules/pyunbound/default.nix similarity index 92% rename from pkgs/tools/networking/unbound/python.nix rename to pkgs/development/python-modules/pyunbound/default.nix index 94f2374d904d..a5d33cbfa440 100644 --- a/pkgs/tools/networking/unbound/python.nix +++ b/pkgs/development/python-modules/pyunbound/default.nix @@ -1,11 +1,10 @@ -{ lib, stdenv, unbound, openssl, expat, libevent, swig, pythonPackages }: +{ lib, buildPythonPackage, unbound, openssl, expat, libevent, swig, python, stdenv }: -let - inherit (pythonPackages) python; -in -stdenv.mkDerivation rec { +buildPythonPackage rec { pname = "pyunbound"; inherit (unbound) version src; + pyproject = false; # Built with configure script + patches = unbound.patches or null; nativeBuildInputs = [ swig ]; diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index cec492852b2a..85ff6f7116b6 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -12754,7 +12754,7 @@ self: super: with self; { inherit (pkgs) udev; }; - pyunbound = toPythonModule (callPackage ../tools/networking/unbound/python.nix { }); + pyunbound = callPackage ../development/python-modules/pyunbound { }; pyunifi = callPackage ../development/python-modules/pyunifi { }; From 1fec67710971470546fe862071cf9fba723a77c2 Mon Sep 17 00:00:00 2001 From: aleksana Date: Wed, 19 Jun 2024 16:14:10 +0800 Subject: [PATCH 5/5] python3Packages.segyio: build with buildPythonPackage, fix build --- .../segyio/add_missing_cstdint.patch | 47 +++++++++++++++++++ .../python-modules/segyio/default.nix | 12 +++-- pkgs/top-level/python-packages.nix | 4 +- 3 files changed, 57 insertions(+), 6 deletions(-) create mode 100644 pkgs/development/python-modules/segyio/add_missing_cstdint.patch diff --git a/pkgs/development/python-modules/segyio/add_missing_cstdint.patch b/pkgs/development/python-modules/segyio/add_missing_cstdint.patch new file mode 100644 index 000000000000..2c26d6e454b1 --- /dev/null +++ b/pkgs/development/python-modules/segyio/add_missing_cstdint.patch @@ -0,0 +1,47 @@ +From 64f06c0643f1f8691a8f2757496b60f1ab98c866 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Sa=C3=AFd=20Benaissa?= +Date: Fri, 8 Dec 2023 21:51:32 +0100 +Subject: [PATCH] Add include for cstdint, fix segyio build on fedora + +--- + lib/experimental/segyio/segyio.hpp | 1 + + python/segyio/segyio.cpp | 1 + + python/setup.py | 2 +- + 3 files changed, 3 insertions(+), 1 deletion(-) + +diff --git a/lib/experimental/segyio/segyio.hpp b/lib/experimental/segyio/segyio.hpp +index 706f07ff5..7ba3ffb99 100644 +--- a/lib/experimental/segyio/segyio.hpp ++++ b/lib/experimental/segyio/segyio.hpp +@@ -13,6 +13,7 @@ + #include + + #include ++#include + + /* + * KNOWN ISSUES AND TODOs: +diff --git a/python/segyio/segyio.cpp b/python/segyio/segyio.cpp +index 76da965c3..bd8a8622e 100644 +--- a/python/segyio/segyio.cpp ++++ b/python/segyio/segyio.cpp +@@ -16,6 +16,7 @@ + #include + #include + #include ++#include + + #if PY_MAJOR_VERSION >= 3 + #define IS_PY3K +diff --git a/python/setup.py b/python/setup.py +index 6c6553bc7..654075be9 100644 +--- a/python/setup.py ++++ b/python/setup.py +@@ -1,6 +1,6 @@ + import os + import sys +-import skbuild ++import skbuild # pip install scikit-build + import setuptools + + long_description = """ diff --git a/pkgs/development/python-modules/segyio/default.nix b/pkgs/development/python-modules/segyio/default.nix index aba2d06a5e2a..9e221db8cfe7 100644 --- a/pkgs/development/python-modules/segyio/default.nix +++ b/pkgs/development/python-modules/segyio/default.nix @@ -1,18 +1,23 @@ { lib, - stdenv, + buildPythonPackage, fetchFromGitHub, cmake, ninja, - python, scikit-build, pytest, numpy, }: -stdenv.mkDerivation rec { +buildPythonPackage rec { pname = "segyio"; version = "1.9.12"; + pyproject = false; # Built with cmake + + patches = [ + # https://github.com/equinor/segyio/pull/570 + ./add_missing_cstdint.patch + ]; postPatch = '' # Removing unecessary build dependency @@ -34,7 +39,6 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ninja - python scikit-build ]; diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 85ff6f7116b6..275f8b73ba8b 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -13792,9 +13792,9 @@ self: super: with self; { segno = callPackage ../development/python-modules/segno { }; - segyio = toPythonModule (callPackage ../development/python-modules/segyio { + segyio = callPackage ../development/python-modules/segyio { inherit (pkgs) cmake ninja; - }); + }; selectors2 = callPackage ../development/python-modules/selectors2 { };