{lang}[iimkl/2024a] SciPy-bundle v2024.05 WIP

easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2024.05-iimkl-2024a.eb

@@ -0,0 +1,100 @@
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2024.05'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'iimkl', 'version': '2024a'}
+toolchainopts = {'pic': True, 'lowopt': True, 'strict': True}
+
+builddependencies = [
+    ('hypothesis', '6.103.1'),
+    ('UnZip', '6.0'),
+    # scipy >= 1.9.0 uses Meson/Ninja
+    ('Meson', '1.4.0'),
+    ('meson-python', '0.16.0'),
+    ('Ninja', '1.12.1'),
+    ('pkgconf', '2.2.0'),  # required by scipy
+    ('Cython', '3.0.10'),  # required by numpy and scipy
+    ('pybind11', '2.12.0'),  # required by scipy
+]
+
+dependencies = [
+    ('Python', '3.12.3'),
+    ('Python-bundle-PyPI', '2024.06'),
+]
+
+# order is important!
+exts_list = [
+    ('numpy', '1.26.4', {
+        'patches': [
+            'numpy-1.26.4-mkl.patch',
+            'numpy-1.26.4-icx-compiler.patch',
+        ],
+        'checksums': [
+            {'numpy-1.26.4.tar.gz': '2a02aba9ed12e4ac4eb3ea9421c420301a0c6460d9830d74a9df87efa4912010'},
+            {'numpy-1.26.4-mkl.patch': '78351b21b271c37d60bf49ff55c5af15214eaa8216377936198ef03427eeffe5'},
+            {'numpy-1.26.4-icx-compiler.patch': '5e8ca296c0371d076267516aa6c1e009190e9394e1706fdd98db499a35f653fd'},
+        ],
+    }),
+    ('ply', '3.11', {
+        'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'],
+    }),
+    ('gast', '0.5.4', {
+        'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'],
+    }),
+    ('beniget', '0.4.1', {
+        'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'],
+    }),
+    ('pythran', '0.16.1', {
+        'checksums': ['861748c0f9c7d422b32724b114b3817d818ed4eab86c09781aa0a3f7ceabb7f9'],
+    }),
+    ('versioneer', '0.29', {
+        'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'],
+    }),
+    ('scipy', '1.13.1', {
+        'enable_slow_tests': True,
+        'ignore_test_result': False,
+        'patches': [
+            'scipy-1.11.1_disable-tests.patch',
+            'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch',
+            'scipy-1.13.1_TestLinprogIPSparse.patch',
+        ],
+        'checksums': [
+            {'scipy-1.13.1.tar.gz': '095a87a0312b08dfd6a6155cbbd310a8c51800fc931b8c0b84003014b874ed3c'},
+            {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'},
+            {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch':
+             '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'},
+            {'scipy-1.13.1_TestLinprogIPSparse.patch':
+             '7213c2690b76c69f7e7103529cea3fa2098c05fbea556f04325fab9ca8c065f5'},
+        ],
+    }),
+    ('numexpr', '2.10.0', {
+        'patches': ['numexpr-2.10.0_fix-numpy-1.x.patch'],
+        'checksums': [
+            {'numexpr-2.10.0.tar.gz': 'c89e930752639df040539160326d8f99a84159bbea41943ab8e960591edaaef0'},
+            {'numexpr-2.10.0_fix-numpy-1.x.patch': '8d70b2e95579e6f0adc07bc615144f7657b3b607f9210ec328b6622458ca726d'},
+        ],
+    }),
+    ('Bottleneck', '1.3.8', {
+        'checksums': ['6780d896969ba7f53c8995ba90c87c548beb3db435dc90c60b9a10ed1ab4d868'],
+    }),
+    ('tzdata', '2024.1', {
+        'checksums': ['2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd'],
+    }),
+    ('pandas', '2.2.2', {
+        'preinstallopts': "export PANDAS_CI=0 && ",
+        'checksums': ['9e79019aba43cb4fda9e4d983f8e88ca0373adbb697ae9c6c43093218de28b54'],
+    }),
+    ('mpmath', '1.3.0', {
+        'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'],
+    }),
+    ('deap', '1.4.1', {
+        'modulename': 'deap.base',
+        'checksums': ['cc01de9892dfa7d1bc9803dab28892fead177f0182c81db47360a240ead778ff'],
+    }),
+]
+
+moduleclass = 'lang'

easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4-icx-compiler.patch

@@ -0,0 +1,198 @@
+Makes sure the new icx compiler is being picked up, and not the icc one. 
+Author: J. Sassmannshausen (Imperial College London/UK)
+diff --git a/numpy-1.26.4.orig/numpy/distutils/ccompiler_opt.py b/numpy-1.26.4/numpy/distutils/ccompiler_opt.py
+index 37a5368..5af425d 100644
+--- a/numpy-1.26.4.orig/numpy/distutils/ccompiler_opt.py
++++ b/numpy-1.26.4/numpy/distutils/ccompiler_opt.py
+@@ -211,6 +211,11 @@ class _Config:
+             opt = '-O3',
+             werror = '-Werror',
+         ),
++        icx = dict(
++            native = '-xHost',
++            opt = '-O3',
++            werror = '-Werror',
++        ),
+         iccw = dict(
+             native = '/QxHost',
+             opt = '/O3',
+@@ -369,7 +374,7 @@ class _Config:
+             ),
+             AVX512_SPR = dict(flags="-mavx512fp16"),
+         )
+-        if on_x86 and self.cc_is_icc: return dict(
++        if on_x86 and self.cc_is_icx: return dict(
+             SSE    = dict(flags="-msse"),
+             SSE2   = dict(flags="-msse2"),
+             SSE3   = dict(flags="-msse3"),
+@@ -937,7 +942,7 @@ class _CCompiler:
+         if the compiler is unknown
+     cc_is_clang : bool
+         True if the compiler is Clang
+-    cc_is_icc : bool
++    cc_is_icx : bool
+         True if the compiler is Intel compiler (unix like)
+     cc_is_iccw : bool
+         True if the compiler is Intel compiler (msvc like)
+@@ -984,7 +989,8 @@ class _CCompiler:
+             ("cc_is_clang",    ".*clang.*", ""),
+             # intel msvc like
+             ("cc_is_iccw",     ".*(intelw|intelemw|iccw).*", ""),
+-            ("cc_is_icc",      ".*(intel|icc).*", ""),  # intel unix like
++            ("cc_is_icc",      ".*(intel|icc|icx).*", ""),  # intel unix like
++            ("cc_is_icx",      ".*(intel|icx).*", ""),  # intel unix like
+             ("cc_is_msvc",     ".*msvc.*", ""),
+             ("cc_is_fcc",     ".*fcc.*", ""),
+             # undefined compiler will be treat it as gcc
+@@ -1054,7 +1060,7 @@ class _CCompiler:
+                 break
+
+         self.cc_name = "unknown"
+-        for name in ("gcc", "clang", "iccw", "icc", "msvc", "fcc"):
++        for name in ("gcc", "clang", "iccw", "icc", "icx", "msvc", "fcc"):
+             if getattr(self, "cc_is_" + name):
+                 self.cc_name = name
+                 break
+@@ -1133,7 +1139,7 @@ class _CCompiler:
+         ['-march=core-avx2']
+         """
+         assert(isinstance(flags, list))
+-        if self.cc_is_gcc or self.cc_is_clang or self.cc_is_icc:
++        if self.cc_is_gcc or self.cc_is_clang or self.cc_is_icx:
+             return self._cc_normalize_unix(flags)
+
+         if self.cc_is_msvc or self.cc_is_iccw:
+diff --git a/numpy-1.26.4.orig/numpy/distutils/tests/test_ccompiler_opt.py b/numpy-1.26.4/numpy/distutils/tests/test_ccompiler_opt.py
+index 3714aea..37968f9 100644
+--- a/numpy-1.26.4.orig/numpy/distutils/tests/test_ccompiler_opt.py
++++ b/numpy-1.26.4/numpy/distutils/tests/test_ccompiler_opt.py
+@@ -26,8 +26,8 @@ else:
+
+ # architectures and compilers to test
+ arch_compilers = dict(
+-    x86 = ("gcc", "clang", "icc", "iccw", "msvc"),
+-    x64 = ("gcc", "clang", "icc", "iccw", "msvc"),
++    x86 = ("gcc", "clang", "icc", "icx", "iccw", "msvc"),
++    x64 = ("gcc", "clang", "icc", "icx", "iccw", "msvc"),
+     ppc64 = ("gcc", "clang"),
+     ppc64le = ("gcc", "clang"),
+     armhf = ("gcc", "clang"),
+@@ -277,7 +277,7 @@ class _Test_CCompilerOpt:
+
+     def test_interface(self):
+         wrong_arch = "ppc64" if self.arch != "ppc64" else "x86"
+-        wrong_cc   = "clang" if self.cc   != "clang" else "icc"
++        wrong_cc   = "clang" if self.cc   != "clang" else "icx"
+         opt = self.opt()
+         assert_(getattr(opt, "cc_on_" + self.arch))
+         assert_(not getattr(opt, "cc_on_" + wrong_arch))
+@@ -349,7 +349,7 @@ class _Test_CCompilerOpt:
+         """
+         special cases
+         """
+-        # in icc and msvc, FMA3 and AVX2 can't be separated
++        # in icc/icx and msvc, FMA3 and AVX2 can't be separated
+         # both need to implies each other, same for avx512f & cd
+         for f0, f1 in (
+             ("fma3",    "avx2"),
+@@ -358,11 +358,11 @@ class _Test_CCompilerOpt:
+             diff = ".* sse42 .* %s .*%s$" % (f0, f1)
+             self.expect_baseline(f0,
+                 x86_gcc=".* sse42 .* %s$" % f0,
+-                x86_icc=diff, x86_iccw=diff
++                x86_icx=diff, x86_iccw=diff
+             )
+             self.expect_baseline(f1,
+                 x86_gcc=".* avx .* %s$" % f1,
+-                x86_icc=diff, x86_iccw=diff
++                x86_icx=diff, x86_iccw=diff
+             )
+         # in msvc, following features can't be separated too
+         for f in (("fma3", "avx2"), ("avx512f", "avx512cd", "avx512_skx")):
+@@ -400,7 +400,7 @@ class _Test_CCompilerOpt:
+             self.expect(o,
+                 x86_gcc=".* xop fma4 .* avx512f .* avx512_knl avx512_knm avx512_skx .*",
+                 # in icc, xop and fam4 aren't supported
+-                x86_icc=".* avx512f .* avx512_knl avx512_knm avx512_skx .*",
++                x86_icx=".* avx512f .* avx512_knl avx512_knm avx512_skx .*",
+                 x86_iccw=".* avx512f .* avx512_knl avx512_knm avx512_skx .*",
+                 # in msvc, avx512_knl avx512_knm aren't supported
+                 x86_msvc=".* xop fma4 .* avx512f .* avx512_skx .*",
+@@ -436,7 +436,7 @@ class _Test_CCompilerOpt:
+     def test_flags(self):
+         self.expect_flags(
+             "sse sse2 vsx vsx2 neon neon_fp16 vx vxe",
+-            x86_gcc="-msse -msse2", x86_icc="-msse -msse2",
++            x86_gcc="-msse -msse2", x86_icx="-msse -msse2",
+             x86_iccw="/arch:SSE2",
+             x86_msvc="/arch:SSE2" if self.march() == "x86" else "",
+             ppc64_gcc= "-mcpu=power8",
+@@ -594,7 +594,7 @@ class _Test_CCompilerOpt:
+             baseline="",
+             x86_gcc="avx512cd avx512f avx2 fma3 avx sse2",
+             x86_msvc="avx512cd avx2 avx sse2",
+-            x86_icc="avx512cd avx2 avx sse2",
++            x86_icx="avx512cd avx2 avx sse2",
+             x86_iccw="avx512cd avx2 avx sse2",
+             ppc64="vsx3 vsx2 vsx",
+             ppc64le="vsx3 vsx2",
+@@ -652,7 +652,7 @@ class _Test_CCompilerOpt:
+             */
+             """,
+             x86_gcc="avx512f avx2 sse42 sse41 sse2",
+-            x86_icc="avx512f avx2 sse42 sse41 sse2",
++            x86_icx="avx512f avx2 sse42 sse41 sse2",
+             x86_iccw="avx512f avx2 sse42 sse41 sse2",
+             x86_msvc="avx512f avx2 sse2"
+                      if self.march() == 'x86' else "avx512f avx2",
+@@ -665,7 +665,7 @@ class _Test_CCompilerOpt:
+             # 'maxopt' and autovec set the max acceptable optimization flags
+             self.expect_target_flags(
+                 "/*@targets baseline %s */" % policy,
+-                gcc={"baseline":".*-O3.*"}, icc={"baseline":".*-O3.*"},
++                gcc={"baseline":".*-O3.*"}, icx={"baseline":".*-O3.*"},
+                 iccw={"baseline":".*/O3.*"}, msvc={"baseline":".*/O2.*"},
+                 unknown={"baseline":".*"}
+             )
+@@ -673,7 +673,7 @@ class _Test_CCompilerOpt:
+         # 'werror', force compilers to treat warnings as errors
+         self.expect_target_flags(
+             "/*@targets baseline $werror */",
+-            gcc={"baseline":".*-Werror.*"}, icc={"baseline":".*-Werror.*"},
++            gcc={"baseline":".*-Werror.*"}, icx={"baseline":".*-Werror.*"},
+             iccw={"baseline":".*/Werror.*"}, msvc={"baseline":".*/WX.*"},
+             unknown={"baseline":".*"}
+         )
+@@ -769,7 +769,7 @@ class _Test_CCompilerOpt:
+             */
+             """,
+             x86_gcc=r"fma3 avx2 \(fma3 avx2\)",
+-            x86_icc="avx2", x86_iccw="avx2",
++            x86_icx="avx2", x86_iccw="avx2",
+             x86_msvc="avx2"
+         )
+
+@@ -793,7 +793,7 @@ def new_test(arch, cc):
+     )
+ """
+ if 1 and is_standalone:
+-    FakeCCompilerOpt.fake_info = "x86_icc"
++    FakeCCompilerOpt.fake_info = "x86_icx"
+     cco = FakeCCompilerOpt(None, cpu_baseline="avx2")
+     print(' '.join(cco.cpu_baseline_names()))
+     print(cco.cpu_baseline_flags())
+diff --git a/numpy-1.26.4.orig/numpy/distutils/tests/test_ccompiler_opt_conf.py b/numpy-1.26.4/numpy/distutils/tests/test_ccompiler_opt_conf.py
+index d9e8b2b..44dd441 100644
+--- a/numpy-1.26.4.orig/numpy/distutils/tests/test_ccompiler_opt_conf.py
++++ b/numpy-1.26.4/numpy/distutils/tests/test_ccompiler_opt_conf.py
+@@ -9,8 +9,8 @@ else:
+     from numpy.distutils.ccompiler_opt import CCompilerOpt
+
+ arch_compilers = dict(
+-    x86 = ("gcc", "clang", "icc", "iccw", "msvc"),
+-    x64 = ("gcc", "clang", "icc", "iccw", "msvc"),
++    x86 = ("gcc", "clang", "icc", "icx", "iccw", "msvc"),
++    x64 = ("gcc", "clang", "icc", "icx", "iccw", "msvc"),
+     ppc64 = ("gcc", "clang"),
+     ppc64le = ("gcc", "clang"),
+     armhf = ("gcc", "clang"),

easybuild/easyconfigs/s/SciPy-bundle/numpy-1.26.4-mkl.patch

@@ -0,0 +1,57 @@
+Based on numpy-1.18.2-mkl.patch
+Author: J. Sassmannshause (Imperial College London/UK)
+--- a/numpy-1.26.4.orig/numpy/distutils/fcompiler/__init__.py
++++ b/numpy-1.26.4/numpy/distutils/fcompiler/__init__.py
+@@ -643,7 +643,10 @@ class FCompiler(CCompiler):
+         return options
+
+     def library_option(self, lib):
+-        return "-l" + lib
++        if lib[0]=='-':
++            return lib
++        else:
++            return "-l" + lib
+     def library_dir_option(self, dir):
+         return "-L" + dir
+
+diff --git a/numpy-1.26.4.orig/numpy/distutils/system_info.py b/numpy-1.26.4/numpy/distutils/system_info.py
+index feb28f6..7f6f937 100644
+--- a/numpy-1.26.4.orig/numpy/distutils/system_info.py
++++ b/numpy-1.26.4/numpy/distutils/system_info.py
+@@ -956,7 +956,7 @@ class system_info:
+             if is_string(default):
+                 return [default]
+             return default
+-        return [b for b in [a.strip() for a in libs.split(',')] if b]
++        return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b]
+
+     def get_libraries(self, key='libraries'):
+         if hasattr(self, '_lib_names'):
+@@ -1043,6 +1043,9 @@ class system_info:
+         # make sure we preserve the order of libs, as it can be important
+         found_dirs, found_libs = [], []
+         for lib in libs:
++            if lib[0] == '-':
++                found_libs.append(lib)
++                continue
+             for lib_dir in lib_dirs:
+                 found_lib = self._find_lib(lib_dir, lib, exts)
+                 if found_lib:
+diff --git a/numpy-1.26.4.orig/numpy/distutils/unixccompiler.py b/numpy-1.26.4/numpy/distutils/unixccompiler.py
+index 4884960..6fdcdc4 100644
+--- a/numpy-1.26.4.orig/numpy/distutils/unixccompiler.py
++++ b/numpy-1.26.4/numpy/distutils/unixccompiler.py
+@@ -139,3 +139,13 @@ def UnixCCompiler_create_static_lib(self, objects, output_libname,
+
+ replace_method(UnixCCompiler, 'create_static_lib',
+                UnixCCompiler_create_static_lib)
++
++def UnixCCompiler_library_option(self, lib):
++    if lib[0]=='-':
++        return lib
++    else:
++        return "-l" + lib
++
++replace_method(UnixCCompiler, 'library_option',
++               UnixCCompiler_library_option)
++