diff --git a/pkgs/development/python-modules/segyio/add_missing_cstdint.patch b/pkgs/development/python-modules/segyio/add_missing_cstdint.patch deleted file mode 100644 index 2c26d6e454b1..000000000000 --- a/pkgs/development/python-modules/segyio/add_missing_cstdint.patch +++ /dev/null @@ -1,47 +0,0 @@ -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 1346623c9807..ed8276efe92f 100644 --- a/pkgs/development/python-modules/segyio/default.nix +++ b/pkgs/development/python-modules/segyio/default.nix @@ -2,6 +2,7 @@ lib, buildPythonPackage, fetchFromGitHub, + fetchpatch, cmake, ninja, scikit-build, @@ -15,12 +16,11 @@ buildPythonPackage rec { pyproject = false; # Built with cmake patches = [ - # https://github.com/equinor/segyio/pull/570 - ./add_missing_cstdint.patch - # https://github.com/equinor/segyio/pull/576/ - ./fix-setuptools.patch - ./explicitly-cast.patch - ./numpy-2.patch + # Bump minimum CMake version to 3.11 + (fetchpatch { + url = "https://github.com/equinor/segyio/commit/3e2cbe6ca6d4bc7d4f4d95666f5d2983836e8461.patch?full_index=1"; + hash = "sha256-sOBHi8meMSkxEZy0AXwebAnIVPatpwQHd+4Co5zIhLQ="; + }) ]; postPatch = '' diff --git a/pkgs/development/python-modules/segyio/explicitly-cast.patch b/pkgs/development/python-modules/segyio/explicitly-cast.patch deleted file mode 100644 index 7030f07e5f72..000000000000 --- a/pkgs/development/python-modules/segyio/explicitly-cast.patch +++ /dev/null @@ -1,32 +0,0 @@ -From eafe8476566e1d8e8b9a486ca808685cb439a767 Mon Sep 17 00:00:00 2001 -From: Sveinung Rundhovde -Date: Mon, 29 Jul 2024 10:46:35 +0200 -Subject: [PATCH] Explicitly cast from BinField to int - -Parsing segyio.BinField type as int in PyArg_ParseTuple is no longer -possible. ---- - python/segyio/open.py | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/python/segyio/open.py b/python/segyio/open.py -index cd902c15..80bc3a5b 100644 ---- a/python/segyio/open.py -+++ b/python/segyio/open.py -@@ -166,8 +166,8 @@ def open(filename, mode="r", iline = 189, - f = segyio.SegyFile(fd, - filename = str(filename), - mode = mode, -- iline = iline, -- xline = xline, -+ iline = int(iline), -+ xline = int(xline), - endian = endian, - ) - -@@ -189,4 +189,4 @@ def open(filename, mode="r", iline = 189, - if ignore_geometry: - return f - -- return infer_geometry(f, metrics, iline, xline, strict) -+ return infer_geometry(f, metrics, int(iline), int(xline), strict) diff --git a/pkgs/development/python-modules/segyio/fix-setuptools.patch b/pkgs/development/python-modules/segyio/fix-setuptools.patch deleted file mode 100644 index 42b4260434ad..000000000000 --- a/pkgs/development/python-modules/segyio/fix-setuptools.patch +++ /dev/null @@ -1,32 +0,0 @@ -From 6df089258c2ef4356427263f652cff0c053c6173 Mon Sep 17 00:00:00 2001 -From: Sveinung Rundhovde -Date: Fri, 26 Jul 2024 15:03:33 +0200 -Subject: [PATCH] Fix attribute error in setup.py - -This line was causing a error due to an update to scikit-build. The -issue was that the setuptools.command.test module is not put into the -symbol table by the setuptools import, but it was put there during the -skbuild import causing it to be available. Due to changes in -scikit-build this is no longer the case and the line gives an -AttributError. - -The rationale for this line was that scikit-builds test command implied -develop (this was obnoxious), something that is no longer true. There is -thus no longer any reason to keep this line, so we can fix this issue by -simply removing it. ---- - python/setup.py | 1 - - 1 file changed, 1 deletion(-) - -diff --git a/python/setup.py b/python/setup.py -index 6c6553bc..6bae62f0 100644 ---- a/python/setup.py -+++ b/python/setup.py -@@ -95,7 +95,6 @@ def src(x): - # supported OS X release 10.9 - '-DCMAKE_OSX_DEPLOYMENT_TARGET=10.9', - ], -- cmdclass = { 'test': setuptools.command.test.test }, - classifiers = [ - 'Development Status :: 5 - Production/Stable', - 'Environment :: Other Environment', diff --git a/pkgs/development/python-modules/segyio/numpy-2.patch b/pkgs/development/python-modules/segyio/numpy-2.patch deleted file mode 100644 index fa8b1d41002c..000000000000 --- a/pkgs/development/python-modules/segyio/numpy-2.patch +++ /dev/null @@ -1,34 +0,0 @@ -From 75b2156a6414e2464eb15663004b8ab928374135 Mon Sep 17 00:00:00 2001 -From: Sveinung Rundhovde -Date: Tue, 30 Jul 2024 08:32:56 +0200 -Subject: [PATCH] Fix test failing due to Numpy 2.0 promotion rules - -From Numpy 2.0 adding a numpy.float32 and a Python numeric type returns -a numy.float32 when it previously returned a numpy.float64. This changes -the behavior when using the Python builtin sum function on a -numpy.float32 array as the internal computations now will be performed -as numpy.float32 additions when it used to be numpy.float64. - -Passing a numpy.double(0) as a start value to the innermost sum forces -the old behavior and provides consistent results for Numpy 1 and 2. ---- - python/test/segyio_c.py | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/python/test/segyio_c.py b/python/test/segyio_c.py -index 45fe95d89..b1e144d9d 100644 ---- a/python/test/segyio_c.py -+++ b/python/test/segyio_c.py -@@ -540,10 +540,10 @@ def read_line(f, metrics, iline_idx, xline_idx): - buf = numpy.zeros((len(iline_idx), samples), dtype=numpy.single) - - f.getline(xline_trace0, len(iline_idx), xline_stride, offsets, buf) -- assert sum(sum(buf)) == approx(800.061169624, abs=1e-6) -+ assert sum(sum(buf), numpy.double(0)) == approx(800.061169624, abs=1e-6) - - f.getline(iline_trace0, len(xline_idx), iline_stride, offsets, buf) -- assert sum(sum(buf)) == approx(305.061146736, abs=1e-6) -+ assert sum(sum(buf), numpy.double(0)) == approx(305.061146736, abs=1e-6) - - f.close() -