From 23e62a705d3b8d2ad28cb93f3f90ca91d9785b6c Mon Sep 17 00:00:00 2001 From: "R. Ryantm" Date: Thu, 28 Aug 2025 03:20:02 +0000 Subject: [PATCH 1/5] python3Packages.rowan: 1.3.0 -> 1.3.2 --- pkgs/development/python-modules/rowan/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/rowan/default.nix b/pkgs/development/python-modules/rowan/default.nix index 84b872d871a7..003582e9ea8b 100644 --- a/pkgs/development/python-modules/rowan/default.nix +++ b/pkgs/development/python-modules/rowan/default.nix @@ -10,14 +10,14 @@ buildPythonPackage rec { pname = "rowan"; - version = "1.3.0"; + version = "1.3.2"; pyproject = true; src = fetchFromGitHub { owner = "glotzerlab"; repo = "rowan"; rev = "v${version}"; - hash = "sha256-klIqyX04w1xYmYtAbLF5jwpcJ83oKOaENboxyCL70EY="; + hash = "sha256-fcxVpzLhbLjPIifNBx0olq1dUTmNM9IH38MQybkWZSg="; }; nativeBuildInputs = [ From 26a0a4ab753bebb4b471612b5a127b85e620a041 Mon Sep 17 00:00:00 2001 From: Doron Behar Date: Sun, 14 Sep 2025 01:01:47 +0300 Subject: [PATCH 2/5] python312Packages.freud: remove unused stdenv argument --- pkgs/development/python-modules/freud/default.nix | 1 - 1 file changed, 1 deletion(-) diff --git a/pkgs/development/python-modules/freud/default.nix b/pkgs/development/python-modules/freud/default.nix index b7f7646f18bd..711bb3d025c7 100644 --- a/pkgs/development/python-modules/freud/default.nix +++ b/pkgs/development/python-modules/freud/default.nix @@ -1,6 +1,5 @@ { lib, - stdenv, buildPythonPackage, fetchFromGitHub, fetchpatch, From 0cd00aa2e4d2a4a36eb2316b59bad197e0d73b58 Mon Sep 17 00:00:00 2001 From: Doron Behar Date: Sun, 14 Sep 2025 01:03:17 +0300 Subject: [PATCH 3/5] python312Packages.freud: small formatting changes --- .../development/python-modules/freud/default.nix | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/pkgs/development/python-modules/freud/default.nix b/pkgs/development/python-modules/freud/default.nix index 711bb3d025c7..31d68996bfbf 100644 --- a/pkgs/development/python-modules/freud/default.nix +++ b/pkgs/development/python-modules/freud/default.nix @@ -3,15 +3,23 @@ buildPythonPackage, fetchFromGitHub, fetchpatch, + + # build-system cmake, cython, oldest-supported-numpy, scikit-build, setuptools, + + # buildInputs tbb, + + # dependencies numpy, rowan, scipy, + + # tests pytestCheckHook, python, gsd, @@ -50,7 +58,7 @@ buildPythonPackage rec { touch extern/{voro++,fsph,Eigen}/.git ''; - nativeBuildInputs = [ + build-system = [ cmake cython oldest-supported-numpy @@ -58,9 +66,11 @@ buildPythonPackage rec { setuptools ]; dontUseCmakeConfigure = true; - buildInputs = [ tbb ]; + buildInputs = [ + tbb + ]; - propagatedBuildInputs = [ + dependencies = [ numpy rowan scipy From f1f6b55f192152809a8a0e991cc63c5871f49cc0 Mon Sep 17 00:00:00 2001 From: Doron Behar Date: Sun, 14 Sep 2025 01:18:29 +0300 Subject: [PATCH 4/5] python3.pkgs.parsnip: init at 0.4.0 --- .../python-modules/parsnip/default.nix | 44 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 46 insertions(+) create mode 100644 pkgs/development/python-modules/parsnip/default.nix diff --git a/pkgs/development/python-modules/parsnip/default.nix b/pkgs/development/python-modules/parsnip/default.nix new file mode 100644 index 000000000000..e9dcf670fbeb --- /dev/null +++ b/pkgs/development/python-modules/parsnip/default.nix @@ -0,0 +1,44 @@ +{ + lib, + buildPythonPackage, + fetchFromGitHub, + setuptools, + wheel, + more-itertools, + numpy, +}: + +buildPythonPackage rec { + pname = "parsnip"; + version = "0.4.0"; + pyproject = true; + + src = fetchFromGitHub { + owner = "glotzerlab"; + repo = "parsnip"; + rev = "v${version}"; + hash = "sha256-Nac0afep7+HkpSBpqClHpPFSc8H3g8l4q067RQe5K54="; + }; + + build-system = [ + setuptools + wheel + ]; + + dependencies = [ + more-itertools + numpy + ]; + + pythonImportsCheck = [ + "parsnip" + ]; + + meta = { + description = "Lightweight, performant library for parsing CIF files in Python"; + homepage = "https://github.com/glotzerlab/parsnip"; + changelog = "https://github.com/glotzerlab/parsnip/blob/${src.rev}/changelog.rst"; + license = lib.licenses.bsd3; + maintainers = with lib.maintainers; [ doronbehar ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 9ebff811a85c..a33c0c0c43a4 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -11320,6 +11320,8 @@ self: super: with self; { parsley = callPackage ../development/python-modules/parsley { }; + parsnip = callPackage ../development/python-modules/parsnip { }; + parso = callPackage ../development/python-modules/parso { }; parsy = callPackage ../development/python-modules/parsy { }; From d01163e51d693a548f13a8d3a6e5657fd77c8f0c Mon Sep 17 00:00:00 2001 From: Doron Behar Date: Sun, 14 Sep 2025 01:00:07 +0300 Subject: [PATCH 5/5] python313Packages.freud: 3.3.1 -> 3.4.0 Diff: https://github.com/glotzerlab/freud/compare/v3.3.1...v3.4.0 Changelog: https://github.com/glotzerlab/freud/blob/v3.4.0/ChangeLog.md --- .../python-modules/freud/default.nix | 46 ++++++++----------- 1 file changed, 19 insertions(+), 27 deletions(-) diff --git a/pkgs/development/python-modules/freud/default.nix b/pkgs/development/python-modules/freud/default.nix index 31d68996bfbf..3735dab43ff8 100644 --- a/pkgs/development/python-modules/freud/default.nix +++ b/pkgs/development/python-modules/freud/default.nix @@ -2,22 +2,25 @@ lib, buildPythonPackage, fetchFromGitHub, - fetchpatch, # build-system - cmake, + scikit-build-core, cython, oldest-supported-numpy, - scikit-build, - setuptools, + + # nativeBuildInputs + cmake, + ninja, # buildInputs - tbb, + tbb_2022, + nanobind, # dependencies numpy, rowan, scipy, + parsnip, # tests pytestCheckHook, @@ -29,25 +32,17 @@ buildPythonPackage rec { pname = "freud"; - version = "3.3.1"; + version = "3.4.0"; pyproject = true; src = fetchFromGitHub { owner = "glotzerlab"; repo = "freud"; tag = "v${version}"; - hash = "sha256-3THoGPjfaDy2s96+Oaf1f2SDzxTaqRDQlNa3gZ/ytUU="; + hash = "sha256-JX3pbzNTj85UTAtWYnDRvtJSjS27qgY/vitaAjmXbjA="; fetchSubmodules = true; }; - patches = [ - # https://github.com/glotzerlab/freud/issues/1269 - (fetchpatch { - url = "https://github.com/glotzerlab/freud/commit/8f636e3815737945e45da5b9996b5f69df07c9a5.patch"; - hash = "sha256-PLorRrYj16oBWHYzXDq62kECzVTtyr+1Z20DJqTkXxg="; - }) - ]; - # Because we prefer to not `leaveDotGit`, we need to fool upstream into # thinking we left the .git files in the submodules, so cmake won't think we # didn't initialize them. Upstream doesn't support using the system wide @@ -59,21 +54,26 @@ buildPythonPackage rec { ''; build-system = [ - cmake + scikit-build-core cython oldest-supported-numpy - scikit-build - setuptools + ]; + + nativeBuildInputs = [ + cmake + ninja ]; dontUseCmakeConfigure = true; buildInputs = [ - tbb + tbb_2022 + nanobind ]; dependencies = [ numpy rowan scipy + parsnip ]; nativeCheckInputs = [ @@ -82,14 +82,6 @@ buildPythonPackage rec { matplotlib sympy ]; - disabledTests = [ - # https://github.com/glotzerlab/freud/issues/961 - # - # For x86_64-linux, see: - # - # https://github.com/glotzerlab/freud/issues/961#issuecomment-2553344968 - "test_docstring" - ]; # On top of cd $out due to https://github.com/NixOS/nixpkgs/issues/255262 , # we need to also copy the tests because otherwise pytest won't find them. preCheck = ''