From 5bfacde24ba22c8dae9c28542232c68b26c3c321 Mon Sep 17 00:00:00 2001 From: natsukium Date: Tue, 29 Oct 2024 22:33:19 +0900 Subject: [PATCH] python312Packages.numpy: 1.26.4 -> 2.1.2 --- .../python-modules/astropy-healpix/default.nix | 4 ---- pkgs/development/python-modules/astropy/default.nix | 5 ----- pkgs/development/python-modules/blis/default.nix | 12 +++--------- pkgs/development/python-modules/blosc2/default.nix | 2 -- pkgs/development/python-modules/cartopy/default.nix | 5 ----- .../python-modules/fastparquet/default.nix | 8 +------- pkgs/development/python-modules/freud/default.nix | 7 ------- pkgs/development/python-modules/gsd/default.nix | 3 +-- pkgs/development/python-modules/gstools/default.nix | 7 ------- .../python-modules/matplotlib/default.nix | 2 -- pkgs/development/python-modules/netcdf4/default.nix | 4 ---- pkgs/development/python-modules/nitime/default.nix | 7 ------- pkgs/development/python-modules/numba/default.nix | 6 +++--- pkgs/development/python-modules/numexpr/default.nix | 9 --------- pkgs/development/python-modules/pandas/default.nix | 1 - .../development/python-modules/photutils/default.nix | 5 ----- pkgs/development/python-modules/pot/default.nix | 3 --- pkgs/development/python-modules/pyerfa/default.nix | 5 ----- pkgs/development/python-modules/pykdtree/default.nix | 5 ----- pkgs/development/python-modules/pymatgen/default.nix | 5 ----- .../python-modules/pywavelets/default.nix | 5 ----- pkgs/development/python-modules/rasterio/default.nix | 6 ------ .../development/python-modules/reproject/default.nix | 3 +-- .../python-modules/scikit-image/default.nix | 3 --- .../python-modules/scikit-learn/default.nix | 3 --- pkgs/development/python-modules/scipy/default.nix | 5 ----- pkgs/development/python-modules/spacy/default.nix | 6 ------ .../python-modules/statsmodels/default.nix | 5 ----- pkgs/development/python-modules/vispy/default.nix | 7 ------- pkgs/top-level/python-packages.nix | 2 +- 30 files changed, 10 insertions(+), 140 deletions(-) diff --git a/pkgs/development/python-modules/astropy-healpix/default.nix b/pkgs/development/python-modules/astropy-healpix/default.nix index e65d0d222285..fce3ab8e11e9 100644 --- a/pkgs/development/python-modules/astropy-healpix/default.nix +++ b/pkgs/development/python-modules/astropy-healpix/default.nix @@ -24,10 +24,6 @@ buildPythonPackage rec { hash = "sha256-3l0qfsl7FnBFBmlx8loVDR5AYfBxWb4jZJY02zbnl0Y="; }; - postPatch = '' - substituteInPlace pyproject.toml --replace "numpy>=2.0.0rc1" "numpy" - ''; - nativeBuildInputs = [ astropy-extension-helpers numpy diff --git a/pkgs/development/python-modules/astropy/default.nix b/pkgs/development/python-modules/astropy/default.nix index 8315d4454280..956d39cfdc3a 100644 --- a/pkgs/development/python-modules/astropy/default.nix +++ b/pkgs/development/python-modules/astropy/default.nix @@ -36,11 +36,6 @@ buildPythonPackage rec { hash = "sha256-NhVY4rCTqZvr5p8f1H+shqGSYHpMFu05ugqACyq2DDQ="; }; - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0" "numpy" - ''; - build-system = [ astropy-extension-helpers cython diff --git a/pkgs/development/python-modules/blis/default.nix b/pkgs/development/python-modules/blis/default.nix index 26cb315a62e0..00d40e461c09 100644 --- a/pkgs/development/python-modules/blis/default.nix +++ b/pkgs/development/python-modules/blis/default.nix @@ -9,7 +9,7 @@ pytestCheckHook, pythonOlder, blis, - numpy_2, + numpy_1, gitUpdater, }: @@ -28,12 +28,6 @@ buildPythonPackage rec { }; postPatch = '' - # The commit pinning numpy to version 2 doesn't have any functional changes: - # https://github.com/explosion/cython-blis/pull/108 - # BLIS should thus work with numpy and numpy_2. - substituteInPlace pyproject.toml setup.py \ - --replace-fail "numpy>=2.0.0,<3.0.0" numpy - # See https://github.com/numpy/numpy/issues/21079 # has no functional difference as the name is only used in log output substituteInPlace blis/benchmark.py \ @@ -62,8 +56,8 @@ buildPythonPackage rec { passthru = { tests = { - numpy_2 = blis.overridePythonAttrs (old: { - numpy = numpy_2; + numpy_1 = blis.overridePythonAttrs (old: { + numpy = numpy_1; }); }; updateScript = gitUpdater { diff --git a/pkgs/development/python-modules/blosc2/default.nix b/pkgs/development/python-modules/blosc2/default.nix index f72a50eb26d3..51163f0689be 100644 --- a/pkgs/development/python-modules/blosc2/default.nix +++ b/pkgs/development/python-modules/blosc2/default.nix @@ -43,8 +43,6 @@ buildPythonPackage rec { }; postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0" "numpy" substituteInPlace requirements-runtime.txt \ --replace "pytest" "" ''; diff --git a/pkgs/development/python-modules/cartopy/default.nix b/pkgs/development/python-modules/cartopy/default.nix index 79059c7d53f5..104adf729968 100644 --- a/pkgs/development/python-modules/cartopy/default.nix +++ b/pkgs/development/python-modules/cartopy/default.nix @@ -34,11 +34,6 @@ buildPythonPackage rec { hash = "sha256-AckQ1WNMaafv3sRuChfUc9Iyh2fwAdTcC1xLSOWFyL0="; }; - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0rc1" "numpy" - ''; - build-system = [ setuptools-scm ]; nativeBuildInputs = [ diff --git a/pkgs/development/python-modules/fastparquet/default.nix b/pkgs/development/python-modules/fastparquet/default.nix index 5beafcea7a1c..79185e3a3c2f 100644 --- a/pkgs/development/python-modules/fastparquet/default.nix +++ b/pkgs/development/python-modules/fastparquet/default.nix @@ -7,7 +7,6 @@ fsspec, git, numpy, - oldest-supported-numpy, packaging, pandas, pytestCheckHook, @@ -33,11 +32,6 @@ buildPythonPackage rec { hash = "sha256-YiaVkpPzH8ZmTiEtCom9xLbKzByIt7Ilig/WlmGrYH4="; }; - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0rc1" "oldest-supported-numpy" - ''; - build-system = [ setuptools setuptools-scm @@ -47,7 +41,7 @@ buildPythonPackage rec { nativeBuildInputs = [ cython git - oldest-supported-numpy + numpy ]; dependencies = [ diff --git a/pkgs/development/python-modules/freud/default.nix b/pkgs/development/python-modules/freud/default.nix index 9fa555e28170..da4d966c8129 100644 --- a/pkgs/development/python-modules/freud/default.nix +++ b/pkgs/development/python-modules/freud/default.nix @@ -51,13 +51,6 @@ buildPythonPackage rec { touch extern/{voro++,fsph,Eigen}/.git ''; - # Scipy still depends on numpy 1, and so we'd get 'package duplicates in - # closure' error if we'd use numpy_2 - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail 'numpy>=2.0.0rc1' 'numpy' \ - ''; - nativeBuildInputs = [ cmake cython diff --git a/pkgs/development/python-modules/gsd/default.nix b/pkgs/development/python-modules/gsd/default.nix index 28c9a5aa3d25..2ff6279b0120 100644 --- a/pkgs/development/python-modules/gsd/default.nix +++ b/pkgs/development/python-modules/gsd/default.nix @@ -4,7 +4,6 @@ cython, fetchFromGitHub, numpy, - numpy_2, pytestCheckHook, pythonOlder, setuptools, @@ -26,7 +25,7 @@ buildPythonPackage rec { build-system = [ cython - numpy_2 + numpy setuptools ]; diff --git a/pkgs/development/python-modules/gstools/default.nix b/pkgs/development/python-modules/gstools/default.nix index e11048953986..136c79b2d67e 100644 --- a/pkgs/development/python-modules/gstools/default.nix +++ b/pkgs/development/python-modules/gstools/default.nix @@ -44,13 +44,6 @@ buildPythonPackage rec { scipy ]; - # scipy derivation dont support numpy_2 and is patched to use version 1 - # Using numpy_2 in the derivation will cause a clojure duplicate error - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail 'numpy>=2.0.0rc1,' 'numpy' \ - ''; - pythonImportsCheck = [ "gstools" ]; nativeCheckInputs = [ pytestCheckHook ]; diff --git a/pkgs/development/python-modules/matplotlib/default.nix b/pkgs/development/python-modules/matplotlib/default.nix index f07acb53dc69..437bd302e3e2 100644 --- a/pkgs/development/python-modules/matplotlib/default.nix +++ b/pkgs/development/python-modules/matplotlib/default.nix @@ -110,8 +110,6 @@ buildPythonPackage rec { # script. postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail '"numpy>=2.0.0rc1,<2.3",' "" patchShebangs tools '' + lib.optionalString (stdenv.hostPlatform.isLinux && interactive) '' diff --git a/pkgs/development/python-modules/netcdf4/default.nix b/pkgs/development/python-modules/netcdf4/default.nix index 056949ef2f97..7f49fed39528 100644 --- a/pkgs/development/python-modules/netcdf4/default.nix +++ b/pkgs/development/python-modules/netcdf4/default.nix @@ -32,10 +32,6 @@ buildPythonPackage rec { hash = "sha256-N9VX42ZUiJ1wIBkr+1b51fk4lMsymX64N65YbFOP17Y="; }; - postPatch = '' - sed -i "/numpy>=/d" pyproject.toml - ''; - build-system = [ cython oldest-supported-numpy diff --git a/pkgs/development/python-modules/nitime/default.nix b/pkgs/development/python-modules/nitime/default.nix index 35b8eb4c46fc..d6295005e693 100644 --- a/pkgs/development/python-modules/nitime/default.nix +++ b/pkgs/development/python-modules/nitime/default.nix @@ -27,13 +27,6 @@ buildPythonPackage rec { hash = "sha256-4Ie8fuk9CKdn/64TsCfN2No2dU16ICpBRWYerqqF0/0="; }; - # Upstream wants to build against the newest version of numpy possible, but - # we only want to build against our default numpy. - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0rc1,<3" "numpy" - ''; - nativeBuildInputs = [ cython setuptools diff --git a/pkgs/development/python-modules/numba/default.nix b/pkgs/development/python-modules/numba/default.nix index 18bd264c5d76..b9a3e734a580 100644 --- a/pkgs/development/python-modules/numba/default.nix +++ b/pkgs/development/python-modules/numba/default.nix @@ -8,7 +8,7 @@ buildPythonPackage, setuptools, numpy, - numpy_2, + numpy_1, llvmlite, libcxx, importlib-metadata, @@ -161,8 +161,8 @@ buildPythonPackage rec { doFullCheck = true; testsWithoutSandbox = false; }; - numpy_2 = numba.override { - numpy = numpy_2; + numpy_1 = numba.override { + numpy = numpy_1; }; }; diff --git a/pkgs/development/python-modules/numexpr/default.nix b/pkgs/development/python-modules/numexpr/default.nix index 3681e0d9c73a..bda5304a69c0 100644 --- a/pkgs/development/python-modules/numexpr/default.nix +++ b/pkgs/development/python-modules/numexpr/default.nix @@ -32,15 +32,6 @@ buildPythonPackage rec { dos2unix numexpr/tests/test_numexpr.py ''; - # patch for compatibility with numpy < 2.0 - # see more details, https://numpy.org/devdocs/numpy_2_0_migration_guide.html#c-api-changes - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0" "numpy" - sed -i "1i#define PyDataType_SET_ELSIZE(descr, elsize)" numexpr/interpreter.cpp - sed -i "1i#define PyDataType_ELSIZE(descr) ((descr)->elsize)" numexpr/interpreter.cpp - ''; - nativeBuildInputs = [ dos2unix ]; build-system = [ diff --git a/pkgs/development/python-modules/pandas/default.nix b/pkgs/development/python-modules/pandas/default.nix index 9c707351f209..1e2d51af3627 100644 --- a/pkgs/development/python-modules/pandas/default.nix +++ b/pkgs/development/python-modules/pandas/default.nix @@ -80,7 +80,6 @@ let substituteInPlace pyproject.toml \ --replace-fail "meson-python==0.13.1" "meson-python>=0.13.1" \ --replace-fail "meson==1.2.1" "meson>=1.2.1" \ - --replace-fail "numpy>=2.0" "numpy" ''; nativeBuildInputs = [ diff --git a/pkgs/development/python-modules/photutils/default.nix b/pkgs/development/python-modules/photutils/default.nix index f81ba4f5ec4d..bfe057b3796f 100644 --- a/pkgs/development/python-modules/photutils/default.nix +++ b/pkgs/development/python-modules/photutils/default.nix @@ -35,11 +35,6 @@ buildPythonPackage rec { hash = "sha256-gXtC6O8rXBBa8VMuqxshnJieAahv3bCY2C1BXNmJxb4="; }; - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "'numpy>=2.0.0'," "" - ''; - build-system = [ setuptools setuptools-scm diff --git a/pkgs/development/python-modules/pot/default.nix b/pkgs/development/python-modules/pot/default.nix index 9d361a3ff11c..196b93dc224a 100644 --- a/pkgs/development/python-modules/pot/default.nix +++ b/pkgs/development/python-modules/pot/default.nix @@ -87,9 +87,6 @@ buildPythonPackage rec { --replace " --durations=20" "" \ --replace " --junit-xml=junit-results.xml" "" - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0" "numpy" - # we don't need setup.py to find the macos sdk for us sed -i '/sdk_path/d' setup.py ''; diff --git a/pkgs/development/python-modules/pyerfa/default.nix b/pkgs/development/python-modules/pyerfa/default.nix index 68e5f7d97496..e5bd3e20e5be 100644 --- a/pkgs/development/python-modules/pyerfa/default.nix +++ b/pkgs/development/python-modules/pyerfa/default.nix @@ -22,11 +22,6 @@ buildPythonPackage rec { hash = "sha256-rLimcTIy6jXAS8bkCsTkYd/MgX05XvKjyAUcGjMkndM="; }; - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0rc1" "numpy" - ''; - build-system = [ jinja2 packaging diff --git a/pkgs/development/python-modules/pykdtree/default.nix b/pkgs/development/python-modules/pykdtree/default.nix index f169201b2cc5..db1452a61451 100644 --- a/pkgs/development/python-modules/pykdtree/default.nix +++ b/pkgs/development/python-modules/pykdtree/default.nix @@ -25,11 +25,6 @@ buildPythonPackage rec { hash = "sha256-Osz4UulGZT45nD1Nu+EZ28bT9yz9LVqVyr8L8Mf5JP4="; }; - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-warn "numpy>=2.0.0rc1,<3" "numpy" - ''; - nativeBuildInputs = [ cython numpy diff --git a/pkgs/development/python-modules/pymatgen/default.nix b/pkgs/development/python-modules/pymatgen/default.nix index 2b133f061bf3..6074b06b0bdc 100644 --- a/pkgs/development/python-modules/pymatgen/default.nix +++ b/pkgs/development/python-modules/pymatgen/default.nix @@ -43,11 +43,6 @@ buildPythonPackage rec { hash = "sha256-o76bGItldcLfgZ5KDw2uL0GJvyljQJEwISR0topVR44="; }; - prePatch = '' - # Upstream switched to building against numpy2 but should still be compatible with numpy1 - substituteInPlace pyproject.toml --replace-fail "numpy>=2.1.0" "numpy>=1.26.0" - ''; - build-system = [ setuptools ]; nativeBuildInputs = [ diff --git a/pkgs/development/python-modules/pywavelets/default.nix b/pkgs/development/python-modules/pywavelets/default.nix index e3350c4e624d..ba81da659d5a 100644 --- a/pkgs/development/python-modules/pywavelets/default.nix +++ b/pkgs/development/python-modules/pywavelets/default.nix @@ -23,11 +23,6 @@ buildPythonPackage rec { hash = "sha256-oWAF8YDvb0SdlRzSjG2BNEekBkvR3U6KQ+e2FoIs+tw="; }; - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0" "numpy" - ''; - build-system = [ meson-python cython diff --git a/pkgs/development/python-modules/rasterio/default.nix b/pkgs/development/python-modules/rasterio/default.nix index 30dd05cffbdd..4b3650119007 100644 --- a/pkgs/development/python-modules/rasterio/default.nix +++ b/pkgs/development/python-modules/rasterio/default.nix @@ -45,12 +45,6 @@ buildPythonPackage rec { hash = "sha256-A8o8FYuhlzL6Wl6sfB7D2KRAKZl28E6K2AdUik9zmgs="; }; - postPatch = '' - # relax numpy dependency - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2" "numpy" - ''; - nativeBuildInputs = [ cython gdal diff --git a/pkgs/development/python-modules/reproject/default.nix b/pkgs/development/python-modules/reproject/default.nix index 48fec33e8cd1..c4fca7a1fa8a 100644 --- a/pkgs/development/python-modules/reproject/default.nix +++ b/pkgs/development/python-modules/reproject/default.nix @@ -32,8 +32,7 @@ buildPythonPackage rec { postPatch = '' substituteInPlace pyproject.toml \ - --replace "cython==" "cython>=" \ - --replace "numpy>=2.0.0rc1" "numpy" + --replace "cython==" "cython>=" ''; nativeBuildInputs = [ diff --git a/pkgs/development/python-modules/scikit-image/default.nix b/pkgs/development/python-modules/scikit-image/default.nix index b04e02faa6e3..a125aced5a35 100644 --- a/pkgs/development/python-modules/scikit-image/default.nix +++ b/pkgs/development/python-modules/scikit-image/default.nix @@ -49,9 +49,6 @@ let postPatch = '' patchShebangs skimage/_build_utils/{version,cythoner}.py - - substituteInPlace pyproject.toml \ - --replace "numpy>=2.0.0rc1" "numpy" ''; nativeBuildInputs = [ diff --git a/pkgs/development/python-modules/scikit-learn/default.nix b/pkgs/development/python-modules/scikit-learn/default.nix index 6766ceca847e..99e57dabee14 100644 --- a/pkgs/development/python-modules/scikit-learn/default.nix +++ b/pkgs/development/python-modules/scikit-learn/default.nix @@ -36,9 +36,6 @@ buildPythonPackage rec { }; postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2" "numpy" - substituteInPlace meson.build --replace-fail \ "run_command('sklearn/_build_utils/version.py', check: true).stdout().strip()," \ "'${version}'," diff --git a/pkgs/development/python-modules/scipy/default.nix b/pkgs/development/python-modules/scipy/default.nix index e5b2db20a1c0..31a9010c3b29 100644 --- a/pkgs/development/python-modules/scipy/default.nix +++ b/pkgs/development/python-modules/scipy/default.nix @@ -92,13 +92,8 @@ buildPythonPackage { }) ]; - # Upstream says in a comment in their pyproject.toml that building against - # both numpy 2 and numpy 1 should work, but they seem to worry about numpy - # incompatibilities that we here with Nixpkgs' Python ecosystem, shouldn't - # experience. postPatch = '' substituteInPlace pyproject.toml \ - --replace-fail 'numpy>=2.0.0rc1,' 'numpy' \ --replace-fail "pybind11>=2.12.0,<2.13.0" "pybind11>=2.12.0" \ ''; diff --git a/pkgs/development/python-modules/spacy/default.nix b/pkgs/development/python-modules/spacy/default.nix index df9004d483ff..9f6dd8f79a59 100644 --- a/pkgs/development/python-modules/spacy/default.nix +++ b/pkgs/development/python-modules/spacy/default.nix @@ -46,12 +46,6 @@ buildPythonPackage rec { hash = "sha256-Szfr0lraQFmw3J4Ik+cN3l34NIUymgaO8EWA5wiSpl0="; }; - postPatch = '' - # spaCy is compatible with NumPy v1 and v2 - substituteInPlace pyproject.toml setup.cfg \ - --replace-fail "numpy>=2.0.0,<2.1.0" numpy - ''; - build-system = [ cymem cython_0 diff --git a/pkgs/development/python-modules/statsmodels/default.nix b/pkgs/development/python-modules/statsmodels/default.nix index f08c9613fc34..07cb6fe42278 100644 --- a/pkgs/development/python-modules/statsmodels/default.nix +++ b/pkgs/development/python-modules/statsmodels/default.nix @@ -26,11 +26,6 @@ buildPythonPackage rec { hash = "sha256-7PNQJkP6k6q+XwvfI477WWCVF8TWCoEWMtMfzc6GwtI="; }; - postPatch = '' - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0,<3" "numpy" - ''; - build-system = [ cython numpy diff --git a/pkgs/development/python-modules/vispy/default.nix b/pkgs/development/python-modules/vispy/default.nix index dd74e0212bc5..eb3b16c0a3ea 100644 --- a/pkgs/development/python-modules/vispy/default.nix +++ b/pkgs/development/python-modules/vispy/default.nix @@ -31,13 +31,6 @@ buildPythonPackage rec { hash = "sha256-77u4R6kIuvfnFpq5vylhOKOTZPNn5ssKjsA61xaZ0x0="; }; - postPatch = '' - # https://numpy.org/devdocs/dev/depending_on_numpy.html#numpy-2-0-specific-advice - # upstream enforce builds with numpy 2+, which is backward compat with 1.xx - substituteInPlace pyproject.toml \ - --replace-fail "numpy>=2.0.0rc2" "numpy" - ''; - patches = lib.optionals (!stdenv.hostPlatform.isDarwin) [ (substituteAll { src = ./library-paths.patch; diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index a2d65b97846a..757e598e1717 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -9257,7 +9257,7 @@ self: super: with self; { numpy_1 = callPackage ../development/python-modules/numpy/1.nix { }; numpy_2 = callPackage ../development/python-modules/numpy/2.nix { }; - numpy = if self.pythonOlder "3.13" then numpy_1 else numpy_2; + numpy = numpy_2; numpy-groupies = callPackage ../development/python-modules/numpy-groupies { };