From 2077aa809a815783d77afd3c2b773ff6ffe6544a Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Thu, 27 Oct 2022 16:26:25 +0200
Subject: [PATCH 01/87] use gfortran for -g77 in NVHPC

---
 easybuild/easyblocks/n/nvhpc.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/n/nvhpc.py b/easybuild/easyblocks/n/nvhpc.py
index eabb8f0600..b0216c5700 100644
--- a/easybuild/easyblocks/n/nvhpc.py
+++ b/easybuild/easyblocks/n/nvhpc.py
@@ -164,7 +164,7 @@ def install_step(self):
             line = re.sub(r"^PATH=/", r"#PATH=/", line)
             sys.stdout.write(line)
 
-        cmd = "%s -x %s -g77 /" % (makelocalrc_filename, compilers_subdir)
+        cmd = "%s -x %s -g77 gfortran" % (makelocalrc_filename, compilers_subdir)
         run_cmd(cmd, log_all=True, simple=True)
 
         # If an OS libnuma is NOT found, makelocalrc creates symbolic links to libpgnuma.so

From be5c7b421807c1b1fb1a246162e6ee9d5e257588 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Fri, 6 Jan 2023 09:47:22 +0100
Subject: [PATCH 02/87] fix TensorFlow easyblock for new versions of Bazel &
 TensorFlow

---
 easybuild/easyblocks/t/tensorflow.py | 45 ++++++++++++++++++++--------
 1 file changed, 33 insertions(+), 12 deletions(-)

diff --git a/easybuild/easyblocks/t/tensorflow.py b/easybuild/easyblocks/t/tensorflow.py
index e8912c2b2c..16f8079c33 100644
--- a/easybuild/easyblocks/t/tensorflow.py
+++ b/easybuild/easyblocks/t/tensorflow.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2017-2023 Ghent University
+# Copyright 2017-2022 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -35,14 +35,13 @@
 import re
 import stat
 import tempfile
-from distutils.version import LooseVersion
 
 import easybuild.tools.environment as env
 import easybuild.tools.toolchain as toolchain
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage, det_python_version
 from easybuild.easyblocks.python import EXTS_FILTER_PYTHON_PACKAGES
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools import run
+from easybuild.tools import run, LooseVersion
 from easybuild.tools.build_log import EasyBuildError, print_warning
 from easybuild.tools.config import build_option, IGNORE
 from easybuild.tools.filetools import adjust_permissions, apply_regex_substitutions, copy_file, mkdir, resolve_path
@@ -760,6 +759,11 @@ def build_step(self):
         self.bazel_opts = [
             '--output_user_root=%s' % self.output_user_root_dir,
         ]
+        # Environment variables and values needed for Bazel actions.
+        action_env = {}
+        # A value of None is interpreted as using the invoking environments value
+        INHERIT = None  # For better readability
+
         jvm_max_memory = self.cfg['jvm_max_memory']
         if jvm_max_memory:
             jvm_startup_memory = min(512, int(jvm_max_memory))
@@ -801,21 +805,17 @@ def build_step(self):
         # Make TF find our modules. LD_LIBRARY_PATH gets automatically added by configure.py
         cpaths, libpaths = self.system_libs_info[1:]
         if cpaths:
-            self.target_opts.append("--action_env=CPATH='%s'" % ':'.join(cpaths))
+            action_env['CPATH'] = ':'.join(cpaths)
         if libpaths:
-            self.target_opts.append("--action_env=LIBRARY_PATH='%s'" % ':'.join(libpaths))
-        self.target_opts.append('--action_env=PYTHONPATH')
+            action_env['LIBRARY_PATH'] = ':'.join(libpaths)
+        action_env['PYTHONPATH'] = INHERIT
         # Also export $EBPYTHONPREFIXES to handle the multi-deps python setup
         # See https://github.com/easybuilders/easybuild-easyblocks/pull/1664
         if 'EBPYTHONPREFIXES' in os.environ:
-            self.target_opts.append('--action_env=EBPYTHONPREFIXES')
+            action_env['EBPYTHONPREFIXES'] = INHERIT
 
         # Ignore user environment for Python
-        self.target_opts.append('--action_env=PYTHONNOUSERSITE=1')
-
-        # Use the same configuration (i.e. environment) for compiling and using host tools
-        # This means that our action_envs are always passed
-        self.target_opts.append('--distinct_host_configuration=false')
+        action_env['PYTHONNOUSERSITE'] = '1'
 
         # TF 2 (final) sets this in configure
         if LooseVersion(self.version) < LooseVersion('2.0'):
@@ -851,6 +851,26 @@ def build_step(self):
             # and download it if needed
             self.target_opts.append('--config=mkl')
 
+        bazel_version = LooseVersion(get_software_version('Bazel'))
+        if bazel_version.version is None:
+            raise EasyBuildError('Bazel version not found. Is it a dependency?')
+
+        # Use the same configuration (i.e. environment) for compiling and using host tools
+        # This means that our action_envs are (almost) always passed
+        # Fully removed in Bazel 6.0 and limitted effect after at least 3.7 (see --host_action_env)
+        if bazel_version < '6.0.0':
+            self.target_opts.append('--distinct_host_configuration=false')
+
+        for key, value in action_env.items():
+            option = key
+            if value is not None:
+                option += "='%s'" % value
+
+            self.target_opts.append('--action_env=' + option)
+            if bazel_version >= '3.7.0':
+                # See https://github.com/bazelbuild/bazel/commit/a463d9095386b22c121d20957222dbb44caef7d4
+                self.target_opts.append('--host_action_env=' + option)
+
         # Compose final command
         cmd = (
             [self.cfg['prebuildopts']]
@@ -1017,6 +1037,7 @@ def test_step(self):
                         self.log.warning('Test %s failed with output\n%s', test_name,
                                          read_file(log_path, log_error=False))
                 if failed_tests:
+                    failed_tests = sorted(set(failed_tests))  # Make unique to not count retries
                     fail_msg = 'At least %s %s tests failed:\n%s' % (
                         len(failed_tests), device, ', '.join(failed_tests))
                 self.report_test_failure(fail_msg)

From fdc069abcd9e51c8cf6e404dbc3694815fee93cb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 8 Jan 2023 15:41:30 +0100
Subject: [PATCH 03/87] make NAMD easyblock aware of (pre)testopts

---
 easybuild/easyblocks/n/namd.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/n/namd.py b/easybuild/easyblocks/n/namd.py
index 4c84f9bcfd..a0f4c82b95 100644
--- a/easybuild/easyblocks/n/namd.py
+++ b/easybuild/easyblocks/n/namd.py
@@ -201,10 +201,12 @@ def test_step(self):
             ppn = ''
             if self.toolchain.options.get('openmp', False):
                 ppn = '+ppn 2'
-            cmd = "%(namd)s %(ppn)s %(testdir)s" % {
+            cmd = "%(pretestopts)s %(namd)s %(ppn)s %(testopts)s %(testdir)s" % {
                 'namd': namdcmd,
                 'ppn': ppn,
+                'pretestopts': self.cfg['pretestopts'],
                 'testdir': os.path.join(self.cfg['start_dir'], self.namd_arch, 'src', 'alanin'),
+                'testopts': self.cfg['testopts'],
             }
             out, ec = run_cmd(cmd, simple=False)
             if ec == 0:

From 652df1dcc52e45cc92f02ef7a13ef2eab235cf2a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 10 Jan 2023 18:45:09 +0100
Subject: [PATCH 04/87] bump version to 4.7.1dev

---
 easybuild/easyblocks/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/__init__.py b/easybuild/easyblocks/__init__.py
index 94dac2bea4..9619ef8946 100644
--- a/easybuild/easyblocks/__init__.py
+++ b/easybuild/easyblocks/__init__.py
@@ -43,7 +43,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = LooseVersion('4.7.0')
+VERSION = LooseVersion('4.7.1.dev0')
 UNKNOWN = 'UNKNOWN'
 
 

From 720d392d97013ee3324698f1da10389e1d11641b Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 12 Jan 2023 16:14:36 +0100
Subject: [PATCH 05/87] Increase Bazel start/connect timeout

---
 easybuild/easyblocks/t/tensorflow.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/t/tensorflow.py b/easybuild/easyblocks/t/tensorflow.py
index 16f8079c33..719025a0a2 100644
--- a/easybuild/easyblocks/t/tensorflow.py
+++ b/easybuild/easyblocks/t/tensorflow.py
@@ -1,5 +1,5 @@
 ##
-# Copyright 2017-2022 Ghent University
+# Copyright 2017-2023 Ghent University
 #
 # This file is part of EasyBuild,
 # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
@@ -445,7 +445,7 @@ def configure_step(self):
         # and will hang forever building the TensorFlow package.
         # So limit to something high but still reasonable while allowing ECs to overwrite it
         if self.cfg['maxparallel'] is None:
-            self.cfg['parallel'] = min(self.cfg['parallel'], 64)
+            self.cfg['parallel'] = min(self.cfg['parallel'], 96)
 
         binutils_root = get_software_root('binutils')
         if not binutils_root:
@@ -758,6 +758,7 @@ def build_step(self):
         # Options passed to the bazel command
         self.bazel_opts = [
             '--output_user_root=%s' % self.output_user_root_dir,
+            '--local_startup_timeout_secs=600',  # 5min for bazel to start
         ]
         # Environment variables and values needed for Bazel actions.
         action_env = {}

From 3dddcaa15466605bd8b7a72aa75d3a5f1b27d470 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 12 Jan 2023 16:25:57 +0100
Subject: [PATCH 06/87] Make the maxparallel limitation depend on the Bazel
 version

---
 easybuild/easyblocks/t/tensorflow.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/t/tensorflow.py b/easybuild/easyblocks/t/tensorflow.py
index 719025a0a2..fbaeab509c 100644
--- a/easybuild/easyblocks/t/tensorflow.py
+++ b/easybuild/easyblocks/t/tensorflow.py
@@ -210,6 +210,14 @@ def is_version_ok(version_range):
     return result
 
 
+def get_bazel_version():
+    """Get the Bazel version as a LooseVersion. Error if not found"""
+    version = get_software_version('Bazel')
+    if version is None:
+        raise EasyBuildError('Bazel version not found. Is it a dependency?')
+    return LooseVersion(version)
+
+
 class EB_TensorFlow(PythonPackage):
     """Support for building/installing TensorFlow."""
 
@@ -445,7 +453,9 @@ def configure_step(self):
         # and will hang forever building the TensorFlow package.
         # So limit to something high but still reasonable while allowing ECs to overwrite it
         if self.cfg['maxparallel'] is None:
-            self.cfg['parallel'] = min(self.cfg['parallel'], 96)
+            # Seemingly Bazel around 3.x got better, so double the max there
+            bazel_max = 64 if get_bazel_version() < '3.0.0' else 128
+            self.cfg['parallel'] = min(self.cfg['parallel'], bazel_max)
 
         binutils_root = get_software_root('binutils')
         if not binutils_root:
@@ -852,9 +862,7 @@ def build_step(self):
             # and download it if needed
             self.target_opts.append('--config=mkl')
 
-        bazel_version = LooseVersion(get_software_version('Bazel'))
-        if bazel_version.version is None:
-            raise EasyBuildError('Bazel version not found. Is it a dependency?')
+        bazel_version = get_bazel_version()
 
         # Use the same configuration (i.e. environment) for compiling and using host tools
         # This means that our action_envs are (almost) always passed

From 8c88c719df95614896958bf5e93b9d7800a1ad8a Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Fri, 13 Jan 2023 18:03:31 +0100
Subject: [PATCH 07/87] Fix cmdline for Bazel < 4.0

---
 easybuild/easyblocks/t/tensorflow.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/t/tensorflow.py b/easybuild/easyblocks/t/tensorflow.py
index fbaeab509c..47c8a48f71 100644
--- a/easybuild/easyblocks/t/tensorflow.py
+++ b/easybuild/easyblocks/t/tensorflow.py
@@ -758,6 +758,8 @@ def patch_crosstool_files(self):
     def build_step(self):
         """Custom build procedure for TensorFlow."""
 
+        bazel_version = get_bazel_version()
+
         # pre-create target installation directory
         mkdir(os.path.join(self.installdir, self.pylibdir), parents=True)
 
@@ -768,8 +770,10 @@ def build_step(self):
         # Options passed to the bazel command
         self.bazel_opts = [
             '--output_user_root=%s' % self.output_user_root_dir,
-            '--local_startup_timeout_secs=600',  # 5min for bazel to start
         ]
+        if bazel_version >= '4.0.0':
+            self.bazel_opts.append('--local_startup_timeout_secs=600')  # 5min for bazel to start
+
         # Environment variables and values needed for Bazel actions.
         action_env = {}
         # A value of None is interpreted as using the invoking environments value
@@ -862,8 +866,6 @@ def build_step(self):
             # and download it if needed
             self.target_opts.append('--config=mkl')
 
-        bazel_version = get_bazel_version()
-
         # Use the same configuration (i.e. environment) for compiling and using host tools
         # This means that our action_envs are (almost) always passed
         # Fully removed in Bazel 6.0 and limitted effect after at least 3.7 (see --host_action_env)

From 4520a34ba9fc42023dc94e8cb7d3006f9f8c92a9 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Tue, 17 Jan 2023 10:26:11 +0000
Subject: [PATCH 08/87] update MesonNinja easyblock for Meson >=0.64.0

---
 easybuild/easyblocks/generic/mesonninja.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/mesonninja.py b/easybuild/easyblocks/generic/mesonninja.py
index fab1a79296..601dbe5210 100644
--- a/easybuild/easyblocks/generic/mesonninja.py
+++ b/easybuild/easyblocks/generic/mesonninja.py
@@ -28,12 +28,16 @@
 @author: Kenneth Hoste (Ghent University)
 """
 
+from distutils.version import LooseVersion
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import change_dir, create_unused_dir, which
+from easybuild.tools.modules import get_software_version
 from easybuild.tools.run import run_cmd
 
+DEFAULT_CONFIGURE_CMD = 'meson'
+
 
 class MesonNinja(EasyBlock):
     """
@@ -45,6 +49,7 @@ def extra_options(extra_vars=None):
         """Define extra easyconfig parameters specific to MesonNinja."""
         extra_vars = EasyBlock.extra_options(extra_vars)
         extra_vars.update({
+            'configure_cmd': [DEFAULT_CONFIGURE_CMD, "Configure command to use", CUSTOM],
             'separate_build_dir': [True, "Perform build in a separate directory", CUSTOM],
         })
         return extra_vars
@@ -73,8 +78,16 @@ def configure_step(self, cmd_prefix=''):
         if no_Dlibdir and no_libdir:
             self.cfg.update('configopts', '-Dlibdir=lib')
 
-        cmd = "%(preconfigopts)s meson --prefix %(installdir)s %(configopts)s %(sourcedir)s" % {
+        configure_cmd = self.cfg.get('configure_cmd') or DEFAULT_CONFIGURE_CMD
+        # Meson >= 0.64.0 has a deprecatation warning for running `meson [options]`
+        # instead of `meson setup [options]`
+        if (LooseVersion(get_software_version('Meson')) >= LooseVersion('0.64.0')
+            and configure_cmd == DEFAULT_CONFIGURE_CMD):
+                configure_cmd += ' setup' 
+
+        cmd = "%(preconfigopts)s %(configure_cmd)s --prefix %(installdir)s %(configopts)s %(sourcedir)s" % {
             'configopts': self.cfg['configopts'],
+            'configure_cmd': configure_cmd,
             'installdir': self.installdir,
             'preconfigopts': self.cfg['preconfigopts'],
             'sourcedir': self.start_dir,

From fec5e3b8c3c9d73c186dcc49e56a3adfdbfc6c47 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Tue, 17 Jan 2023 10:31:46 +0000
Subject: [PATCH 09/87] linting

---
 easybuild/easyblocks/generic/mesonninja.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/generic/mesonninja.py b/easybuild/easyblocks/generic/mesonninja.py
index 601dbe5210..c8ad0af51b 100644
--- a/easybuild/easyblocks/generic/mesonninja.py
+++ b/easybuild/easyblocks/generic/mesonninja.py
@@ -81,9 +81,9 @@ def configure_step(self, cmd_prefix=''):
         configure_cmd = self.cfg.get('configure_cmd') or DEFAULT_CONFIGURE_CMD
         # Meson >= 0.64.0 has a deprecatation warning for running `meson [options]`
         # instead of `meson setup [options]`
-        if (LooseVersion(get_software_version('Meson')) >= LooseVersion('0.64.0')
-            and configure_cmd == DEFAULT_CONFIGURE_CMD):
-                configure_cmd += ' setup' 
+        if (LooseVersion(get_software_version('Meson')) >= LooseVersion('0.64.0') and
+                configure_cmd == DEFAULT_CONFIGURE_CMD):
+            configure_cmd += ' setup'
 
         cmd = "%(preconfigopts)s %(configure_cmd)s --prefix %(installdir)s %(configopts)s %(sourcedir)s" % {
             'configopts': self.cfg['configopts'],

From 182704176f49880be9f0e686dd4636e9e652fb82 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Tue, 17 Jan 2023 15:48:16 +0000
Subject: [PATCH 10/87] update scipy easyblock for scipy >= 1.9.0 to use
 meson/ninja

---
 easybuild/easyblocks/s/scipy.py | 79 +++++++++++++++++++++++++++++----
 1 file changed, 71 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index c4ebd92ed9..79acdb95fe 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -30,33 +30,96 @@
 @author: Kenneth Hoste (Ghent University)
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
+@author: Jasper Grimm (University of York)
 """
+import os
 from distutils.version import LooseVersion
 
+import easybuild.tools.environment as env
+import easybuild.tools.toolchain as toolchain
 from easybuild.easyblocks.generic.fortranpythonpackage import FortranPythonPackage
+from easybuild.easyblocks.generic.mesonninja import MesonNinja
 from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
-import easybuild.tools.toolchain as toolchain
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.modules import get_software_root
+from easybuild.tools.run import run_cmd
 
 
-class EB_scipy(FortranPythonPackage):
+class EB_scipy(FortranPythonPackage, MesonNinja):
     """Support for installing the scipy Python package as part of a Python installation."""
 
     def __init__(self, *args, **kwargs):
         """Set scipy-specific test command."""
         super(EB_scipy, self).__init__(*args, **kwargs)
 
+        self.use_meson = LooseVersion(self.version) >= LooseVersion('1.9')
+        self.pylibdir = None
         self.testinstall = True
         self.testcmd = "cd .. && %(python)s -c 'import numpy; import scipy; scipy.test(verbose=2)'"
 
     def configure_step(self):
         """Custom configure step for scipy: set extra installation options when needed."""
-        super(EB_scipy, self).configure_step()
+        self.pylibdir = det_pylibdir()
+        
+        # scipy >= 1.9.0 uses Meson/Ninja
+        if self.use_meson:
+            # configure BLAS/LAPACK library to use with Meson for scipy >= 1.9.0
+            lapack_lib = self.toolchain.lapack_family()
+            if lapack_lib == toolchain.FLEXIBLAS:
+                blas_lapack = 'flexiblas'
+            elif lapack_lib == toolchain.INTELMKL:
+                blas_lapack = 'mkl'
+            elif lapack_lib == toolchain.OPENBLAS:
+                blas_lapack = 'openblas'
+            else:
+                raise EasyBuildError("Unknown BLAS/LAPACK library used: %s", lapack_lib) 
+            
+            configopts = '-Dblas=%(blas_lapack)s -Dlapack=%(blas_lapack)s' % {'blas_lapack': blas_lapack}
+            self.cfg.update('configopts', configopts)
+            
+            pythonpath = os.getenv('PYTHONPATH')
+            env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, self.pylibdir), pythonpath]))
+            
+            path = os.getenv('PATH')
+            env.setvar('PATH', os.pathsep.join([os.path.join(self.installdir, 'bin'), path]))
+
+            MesonNinja.configure_step(self)
+        else:
+            super(EB_scipy, self).configure_step()
+
+            if LooseVersion(self.version) >= LooseVersion('0.13'):
+                # in recent scipy versions, additional compilation is done in the install step,
+                # which requires unsetting $LDFLAGS
+                if self.toolchain.comp_family() in [toolchain.GCC, toolchain.CLANGGCC]:  # @UndefinedVariable
+                    self.cfg.update('preinstallopts', "unset LDFLAGS && ")
+
+    def build_step(self):
+        """Custom build step for scipy: use ninja for scipy >= 1.9.0"""
+        if self.use_meson:
+            MesonNinja.build_step(self)
+        else:
+            super(EB_scipy, self).build_step()
+
+    def test_step(self):
+        """Custom test step for scipy: skip if scipy >= 1.9.0"""
+        if self.use_meson:
+            # need to run `ninja install` before we can run the test
+            pass
+        else:
+            super(EB_scipy, self).build_step()
 
-        if LooseVersion(self.version) >= LooseVersion('0.13'):
-            # in recent scipy versions, additional compilation is done in the install step,
-            # which requires unsetting $LDFLAGS
-            if self.toolchain.comp_family() in [toolchain.GCC, toolchain.CLANGGCC]:  # @UndefinedVariable
-                self.cfg.update('preinstallopts', "unset LDFLAGS && ")
+    def install_step(self):
+        """Custom install step for scipy: use ninja for scipy >= 1.9.0"""
+        if self.use_meson:
+            self.cfg['installopts'] = ""
+            MesonNinja.install_step(self)
+           
+           # also run the test
+            python_root = get_software_root('Python')
+            python_bin = os.path.join(python_root, 'bin', 'python')
+            run_cmd(self.testcmd % {'python': python_bin}, log_all=True, simple=True)
+        else:
+            super(EB_scipy, self).install_step()
 
     def sanity_check_step(self, *args, **kwargs):
         """Custom sanity check for scipy."""

From 57d52d990dca8f653e662739f1c4adac9a365670 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Tue, 17 Jan 2023 15:54:38 +0000
Subject: [PATCH 11/87] linting

---
 easybuild/easyblocks/s/scipy.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 79acdb95fe..826ed358d1 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -60,7 +60,7 @@ def __init__(self, *args, **kwargs):
     def configure_step(self):
         """Custom configure step for scipy: set extra installation options when needed."""
         self.pylibdir = det_pylibdir()
-        
+
         # scipy >= 1.9.0 uses Meson/Ninja
         if self.use_meson:
             # configure BLAS/LAPACK library to use with Meson for scipy >= 1.9.0
@@ -72,14 +72,14 @@ def configure_step(self):
             elif lapack_lib == toolchain.OPENBLAS:
                 blas_lapack = 'openblas'
             else:
-                raise EasyBuildError("Unknown BLAS/LAPACK library used: %s", lapack_lib) 
-            
+                raise EasyBuildError("Unknown BLAS/LAPACK library used: %s", lapack_lib)
+
             configopts = '-Dblas=%(blas_lapack)s -Dlapack=%(blas_lapack)s' % {'blas_lapack': blas_lapack}
             self.cfg.update('configopts', configopts)
-            
+
             pythonpath = os.getenv('PYTHONPATH')
             env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, self.pylibdir), pythonpath]))
-            
+
             path = os.getenv('PATH')
             env.setvar('PATH', os.pathsep.join([os.path.join(self.installdir, 'bin'), path]))
 
@@ -113,8 +113,8 @@ def install_step(self):
         if self.use_meson:
             self.cfg['installopts'] = ""
             MesonNinja.install_step(self)
-           
-           # also run the test
+
+            # also run the test
             python_root = get_software_root('Python')
             python_bin = os.path.join(python_root, 'bin', 'python')
             run_cmd(self.testcmd % {'python': python_bin}, log_all=True, simple=True)

From cf9f565d89ee60642c0515665349be1aff9b339c Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Tue, 17 Jan 2023 20:37:03 +0100
Subject: [PATCH 12/87] do not use -g77 option when installing NVHPC 22.9+

---
 easybuild/easyblocks/n/nvhpc.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/n/nvhpc.py b/easybuild/easyblocks/n/nvhpc.py
index 761fb1e468..b9b27cb009 100644
--- a/easybuild/easyblocks/n/nvhpc.py
+++ b/easybuild/easyblocks/n/nvhpc.py
@@ -164,7 +164,10 @@ def install_step(self):
             line = re.sub(r"^PATH=/", r"#PATH=/", line)
             sys.stdout.write(line)
 
-        cmd = "%s -x %s -g77 gfortran" % (makelocalrc_filename, compilers_subdir)
+        if LooseVersion(self.version) >= LooseVersion('22.9'):
+            cmd = "%s -x %s" % (makelocalrc_filename, compilers_subdir)
+        else:
+            cmd = "%s -x %s -g77 /" % (makelocalrc_filename, compilers_subdir)
         run_cmd(cmd, log_all=True, simple=True)
 
         # If an OS libnuma is NOT found, makelocalrc creates symbolic links to libpgnuma.so

From 7f9bf4fb8544c3693d17db2dd197e6d44889bd1f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 18 Jan 2023 09:52:43 +0100
Subject: [PATCH 13/87] only give read permissions in GitHub Actions workflows

---
 .github/workflows/linting.yml    | 3 +++
 .github/workflows/unit_tests.yml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index d7482ec3f7..bfa19cc1a8 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -1,6 +1,9 @@
 name: Static Analysis
 on: [push, pull_request]
 
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
 concurrency:
   group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
   cancel-in-progress: true
diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
index c6b163cac3..b5164b143b 100644
--- a/.github/workflows/unit_tests.yml
+++ b/.github/workflows/unit_tests.yml
@@ -1,6 +1,9 @@
 name: easyblocks unit tests
 on: [push, pull_request]
 
+permissions:
+  contents: read # to fetch code (actions/checkout)
+
 concurrency:
   group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}}
   cancel-in-progress: true

From 795e8b66356edf44fea52f0e7f1baa642dcb6f4b Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 19 Jan 2023 09:46:44 +0100
Subject: [PATCH 14/87] Improve readability

---
 easybuild/easyblocks/t/tensorflow.py | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/t/tensorflow.py b/easybuild/easyblocks/t/tensorflow.py
index 47c8a48f71..229cc72c1d 100644
--- a/easybuild/easyblocks/t/tensorflow.py
+++ b/easybuild/easyblocks/t/tensorflow.py
@@ -771,8 +771,9 @@ def build_step(self):
         self.bazel_opts = [
             '--output_user_root=%s' % self.output_user_root_dir,
         ]
+        # Increase time to wait for bazel to start, available since 4.0+
         if bazel_version >= '4.0.0':
-            self.bazel_opts.append('--local_startup_timeout_secs=600')  # 5min for bazel to start
+            self.bazel_opts.append('--local_startup_timeout_secs=300')  # 5min
 
         # Environment variables and values needed for Bazel actions.
         action_env = {}
@@ -868,17 +869,19 @@ def build_step(self):
 
         # Use the same configuration (i.e. environment) for compiling and using host tools
         # This means that our action_envs are (almost) always passed
-        # Fully removed in Bazel 6.0 and limitted effect after at least 3.7 (see --host_action_env)
+        # Fully removed in Bazel 6.0 and limited effect after at least 3.7 (see --host_action_env)
         if bazel_version < '6.0.0':
             self.target_opts.append('--distinct_host_configuration=false')
 
-        for key, value in action_env.items():
+        for key, value in sorted(action_env.items()):
             option = key
             if value is not None:
                 option += "='%s'" % value
 
             self.target_opts.append('--action_env=' + option)
             if bazel_version >= '3.7.0':
+                # Since Bazel 3.7 action_env only applies to the "target" environment, not the "host" environment
+                # As we are not cross-compiling we need both be the same -> Duplicate the setting to host_action_env
                 # See https://github.com/bazelbuild/bazel/commit/a463d9095386b22c121d20957222dbb44caef7d4
                 self.target_opts.append('--host_action_env=' + option)
 

From 5f93ffc9fd61243d2c0068e0f08bbe6059f135c8 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 19 Jan 2023 09:52:39 +0100
Subject: [PATCH 15/87] Improve bazel error msg

---
 easybuild/easyblocks/t/tensorflow.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/t/tensorflow.py b/easybuild/easyblocks/t/tensorflow.py
index 229cc72c1d..d63a4bc3f6 100644
--- a/easybuild/easyblocks/t/tensorflow.py
+++ b/easybuild/easyblocks/t/tensorflow.py
@@ -214,7 +214,7 @@ def get_bazel_version():
     """Get the Bazel version as a LooseVersion. Error if not found"""
     version = get_software_version('Bazel')
     if version is None:
-        raise EasyBuildError('Bazel version not found. Is it a dependency?')
+        raise EasyBuildError('Failed to determine Bazel version - is it listed as a (build) dependency?')
     return LooseVersion(version)
 
 

From 1fec03336db8b93285c9ba2acf823e7b9c3d5cfa Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Thu, 19 Jan 2023 15:21:36 +0000
Subject: [PATCH 16/87] improve scipy testing

---
 easybuild/easyblocks/s/scipy.py | 84 ++++++++++++++++++++++++++-------
 1 file changed, 67 insertions(+), 17 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 826ed358d1..ecfa42b8ff 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -33,6 +33,7 @@
 @author: Jasper Grimm (University of York)
 """
 import os
+import tempfile
 from distutils.version import LooseVersion
 
 import easybuild.tools.environment as env
@@ -41,6 +42,7 @@
 from easybuild.easyblocks.generic.mesonninja import MesonNinja
 from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.filetools import change_dir, mkdir, remove_dir
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd
 
@@ -53,13 +55,16 @@ def __init__(self, *args, **kwargs):
         super(EB_scipy, self).__init__(*args, **kwargs)
 
         self.use_meson = LooseVersion(self.version) >= LooseVersion('1.9')
-        self.pylibdir = None
         self.testinstall = True
-        self.testcmd = "cd .. && %(python)s -c 'import numpy; import scipy; scipy.test(verbose=2)'"
+        self.testcmd = " && ".join([
+            "cd ..",
+            "touch %(srcdir)s/.coveragerc",
+            "%(python)s %(srcdir)s/runtests.py -v --no-build --parallel %(parallel)s",
+        ])
 
     def configure_step(self):
         """Custom configure step for scipy: set extra installation options when needed."""
-        self.pylibdir = det_pylibdir()
+        pylibdir = det_pylibdir()
 
         # scipy >= 1.9.0 uses Meson/Ninja
         if self.use_meson:
@@ -77,21 +82,23 @@ def configure_step(self):
             configopts = '-Dblas=%(blas_lapack)s -Dlapack=%(blas_lapack)s' % {'blas_lapack': blas_lapack}
             self.cfg.update('configopts', configopts)
 
+            # need to have already installed extensions in PATH, PYTHONPATH for configure/build/install steps
             pythonpath = os.getenv('PYTHONPATH')
-            env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, self.pylibdir), pythonpath]))
+            env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, pylibdir), pythonpath]))
 
             path = os.getenv('PATH')
             env.setvar('PATH', os.pathsep.join([os.path.join(self.installdir, 'bin'), path]))
 
             MesonNinja.configure_step(self)
+
         else:
             super(EB_scipy, self).configure_step()
 
-            if LooseVersion(self.version) >= LooseVersion('0.13'):
-                # in recent scipy versions, additional compilation is done in the install step,
-                # which requires unsetting $LDFLAGS
-                if self.toolchain.comp_family() in [toolchain.GCC, toolchain.CLANGGCC]:  # @UndefinedVariable
-                    self.cfg.update('preinstallopts', "unset LDFLAGS && ")
+        if LooseVersion(self.version) >= LooseVersion('0.13'):
+            # in recent scipy versions, additional compilation is done in the install step,
+            # which requires unsetting $LDFLAGS
+            if self.toolchain.comp_family() in [toolchain.GCC, toolchain.CLANGGCC]:  # @UndefinedVariable
+                self.cfg.update('preinstallopts', "unset LDFLAGS && ")
 
     def build_step(self):
         """Custom build step for scipy: use ninja for scipy >= 1.9.0"""
@@ -101,23 +108,66 @@ def build_step(self):
             super(EB_scipy, self).build_step()
 
     def test_step(self):
-        """Custom test step for scipy: skip if scipy >= 1.9.0"""
+        """Run available scipy unit tests. Adapted from numpy easyblock"""
+
         if self.use_meson:
-            # need to run `ninja install` before we can run the test
-            pass
+
+            # temporarily install scipy so we can run the test suite
+            tmpdir = tempfile.mkdtemp()
+            cwd = os.getcwd()
+
+            cmd = " && ".join([
+                # reconfigure meson to use temp dir
+                'meson configure --prefix=%s' % tmpdir,
+                'ninja -j %s install' % self.cfg['parallel'],
+            ])
+            run_cmd(cmd, log_all=True, simple=True, verbose=False)
+
+            abs_pylibdirs = [os.path.join(tmpdir, pylibdir) for pylibdir in self.all_pylibdirs]
+            for pylibdir in abs_pylibdirs:
+                mkdir(pylibdir, parents=True)
+            python_root = get_software_root('Python')
+            python_bin = os.path.join(python_root, 'bin', 'python')
+
+            self.cfg['pretestopts'] = " && ".join([
+                # LDFLAGS should not be set when testing numpy/scipy, because it overwrites whatever numpy/scipy sets
+                # see http://projects.scipy.org/numpy/ticket/182
+                "unset LDFLAGS",
+                "export PYTHONPATH=%s:$PYTHONPATH" % os.pathsep.join(abs_pylibdirs),
+                "",
+            ])
+            self.cfg['runtest'] = self.testcmd % {
+                'python': python_bin,
+                'srcdir': self.cfg['start_dir'],
+                'parallel': self.cfg['parallel'],
+            }
+
+            MesonNinja.test_step(self)
+
+            # reconfigure meson to use real install dir
+            os.chdir(cwd)
+            cmd = 'meson configure --prefix=%s' % self.installdir
+            run_cmd(cmd, log_all=True, simple=True, verbose=False)
+
+            try:
+                remove_dir(tmpdir)
+            except OSError as err:
+                raise EasyBuildError("Failed to remove directory %s: %s", tmpdir, err)
+
         else:
-            super(EB_scipy, self).build_step()
+            self.testcmd = self.testcmd % {
+                'srcdir': self.cfg['start_dir'],
+                'parallel': self.cfg['parallel']
+            }
+            super(EB_scipy, self).test_step()
 
     def install_step(self):
         """Custom install step for scipy: use ninja for scipy >= 1.9.0"""
         if self.use_meson:
+            # ignore installopts inherited from FortranPythonPackage
             self.cfg['installopts'] = ""
             MesonNinja.install_step(self)
 
-            # also run the test
-            python_root = get_software_root('Python')
-            python_bin = os.path.join(python_root, 'bin', 'python')
-            run_cmd(self.testcmd % {'python': python_bin}, log_all=True, simple=True)
         else:
             super(EB_scipy, self).install_step()
 

From 4e8e47ffb95107c711c6bde33405c4160f5dc510 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Thu, 19 Jan 2023 15:22:44 +0000
Subject: [PATCH 17/87] use change_dir

---
 easybuild/easyblocks/s/scipy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index ecfa42b8ff..06efba71d3 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -145,7 +145,7 @@ def test_step(self):
             MesonNinja.test_step(self)
 
             # reconfigure meson to use real install dir
-            os.chdir(cwd)
+            change_dir(cwd)
             cmd = 'meson configure --prefix=%s' % self.installdir
             run_cmd(cmd, log_all=True, simple=True, verbose=False)
 

From b71ca1bff3ae520b3dacda217f3883e114f0451e Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Thu, 19 Jan 2023 18:11:06 +0000
Subject: [PATCH 18/87] fix tests for non-meson builds

---
 easybuild/easyblocks/s/scipy.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 06efba71d3..de8a30f847 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -156,8 +156,9 @@ def test_step(self):
 
         else:
             self.testcmd = self.testcmd % {
+                'python': '%(python)s',
                 'srcdir': self.cfg['start_dir'],
-                'parallel': self.cfg['parallel']
+                'parallel': self.cfg['parallel'],
             }
             super(EB_scipy, self).test_step()
 

From 34ba9b8be384c1249c2c0ef60f7e6f328f4776cd Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 20 Jan 2023 11:02:58 +0100
Subject: [PATCH 19/87] check that sanity_check_module_loaded attribute exists
 before querying it in PythonPackage easyblock (fixes #2864)

---
 easybuild/easyblocks/generic/pythonpackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/pythonpackage.py b/easybuild/easyblocks/generic/pythonpackage.py
index 449f699792..d89e495122 100644
--- a/easybuild/easyblocks/generic/pythonpackage.py
+++ b/easybuild/easyblocks/generic/pythonpackage.py
@@ -793,7 +793,7 @@ def sanity_check_step(self, *args, **kwargs):
         # load module early ourselves rather than letting parent sanity_check_step method do so,
         # since custom actions taken below require that environment is set up properly already
         # (especially when using --sanity-check-only)
-        if not self.sanity_check_module_loaded:
+        if hasattr(self, 'sanity_check_module_loaded') and not self.sanity_check_module_loaded:
             extension = self.is_extension or kwargs.get('extension', False)
             extra_modules = kwargs.get('extra_modules', None)
             self.fake_mod_data = self.sanity_check_load_module(extension=extension, extra_modules=extra_modules)

From b18e343b17597ce673c58c0dac1e3374ead18577 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Fri, 20 Jan 2023 11:10:36 +0000
Subject: [PATCH 20/87] add extra variable to enable/disable running of slow
 scipy tests

---
 easybuild/easyblocks/s/scipy.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index de8a30f847..895a19cab3 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -41,6 +41,7 @@
 from easybuild.easyblocks.generic.fortranpythonpackage import FortranPythonPackage
 from easybuild.easyblocks.generic.mesonninja import MesonNinja
 from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
+from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import change_dir, mkdir, remove_dir
 from easybuild.tools.modules import get_software_root
@@ -50,6 +51,15 @@
 class EB_scipy(FortranPythonPackage, MesonNinja):
     """Support for installing the scipy Python package as part of a Python installation."""
 
+    @staticmethod
+    def extra_options():
+        """Easyconfig parameters specific to scipy."""
+        extra_vars = ({
+            'enable_slow_tests': [False, "Run scipy test suite, including tests marked as slow", CUSTOM],
+        })
+
+        return FortranPythonPackage.extra_options(extra_vars=extra_vars)
+
     def __init__(self, *args, **kwargs):
         """Set scipy-specific test command."""
         super(EB_scipy, self).__init__(*args, **kwargs)
@@ -61,6 +71,8 @@ def __init__(self, *args, **kwargs):
             "touch %(srcdir)s/.coveragerc",
             "%(python)s %(srcdir)s/runtests.py -v --no-build --parallel %(parallel)s",
         ])
+        if self.cfg['enable_slow_tests'] is True:
+            self.testcmd += " -m full "
 
     def configure_step(self):
         """Custom configure step for scipy: set extra installation options when needed."""

From 0060fa23574695a804b42e5af64c048d7c0f0139 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Fri, 20 Jan 2023 11:44:25 +0000
Subject: [PATCH 21/87] add option to ignore scipy test results

---
 easybuild/easyblocks/s/scipy.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 895a19cab3..d42c6d92e2 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -56,6 +56,7 @@ def extra_options():
         """Easyconfig parameters specific to scipy."""
         extra_vars = ({
             'enable_slow_tests': [False, "Run scipy test suite, including tests marked as slow", CUSTOM],
+            'ignore_test_result': [False, "Run scipy test suite, but ignore result (only log)", CUSTOM],
         })
 
         return FortranPythonPackage.extra_options(extra_vars=extra_vars)
@@ -66,13 +67,17 @@ def __init__(self, *args, **kwargs):
 
         self.use_meson = LooseVersion(self.version) >= LooseVersion('1.9')
         self.testinstall = True
-        self.testcmd = " && ".join([
-            "cd ..",
-            "touch %(srcdir)s/.coveragerc",
-            "%(python)s %(srcdir)s/runtests.py -v --no-build --parallel %(parallel)s",
-        ])
-        if self.cfg['enable_slow_tests'] is True:
-            self.testcmd += " -m full "
+        if self.cfg['ignore_test_result']:
+            # running tests this way exits with 0 regardless
+            self.testcmd = "cd .. && %(python)s -c 'import numpy; import scipy; scipy.test(verbose=2)'"
+        else:
+            self.testcmd = " && ".join([
+                "cd ..",
+                "touch %(srcdir)s/.coveragerc",
+                "%(python)s %(srcdir)s/runtests.py -v --no-build --parallel %(parallel)s",
+            ])
+            if self.cfg['enable_slow_tests'] is True:
+                self.testcmd += " -m full "
 
     def configure_step(self):
         """Custom configure step for scipy: set extra installation options when needed."""

From 40deb9f83814fe5e68e67847592ea0c82fe69475 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Fri, 20 Jan 2023 11:56:39 +0000
Subject: [PATCH 22/87] ignore test results by default to maintain current
 behaviour for older easyconfigs

---
 easybuild/easyblocks/s/scipy.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index d42c6d92e2..13e87d0937 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -56,7 +56,8 @@ def extra_options():
         """Easyconfig parameters specific to scipy."""
         extra_vars = ({
             'enable_slow_tests': [False, "Run scipy test suite, including tests marked as slow", CUSTOM],
-            'ignore_test_result': [False, "Run scipy test suite, but ignore result (only log)", CUSTOM],
+            # ignore tests by default to maintain behaviour in older easyconfigs
+            'ignore_test_result': [True, "Run scipy test suite, but ignore result (only log)", CUSTOM],
         })
 
         return FortranPythonPackage.extra_options(extra_vars=extra_vars)

From f2808b01201ec407f63790b6516cc1bfcd739661 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Mon, 23 Jan 2023 15:50:46 +0000
Subject: [PATCH 23/87] make changes suggested in review

---
 easybuild/easyblocks/s/scipy.py | 84 ++++++++++++++++-----------------
 1 file changed, 42 insertions(+), 42 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 13e87d0937..22a7e1cc40 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -40,15 +40,15 @@
 import easybuild.tools.toolchain as toolchain
 from easybuild.easyblocks.generic.fortranpythonpackage import FortranPythonPackage
 from easybuild.easyblocks.generic.mesonninja import MesonNinja
-from easybuild.easyblocks.generic.pythonpackage import det_pylibdir
+from easybuild.easyblocks.generic.pythonpackage import PythonPackage, det_pylibdir
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import change_dir, mkdir, remove_dir
+from easybuild.tools.filetools import change_dir, copy_dir, mkdir
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd
 
 
-class EB_scipy(FortranPythonPackage, MesonNinja):
+class EB_scipy(FortranPythonPackage, PythonPackage, MesonNinja):
     """Support for installing the scipy Python package as part of a Python installation."""
 
     @staticmethod
@@ -57,19 +57,31 @@ def extra_options():
         extra_vars = ({
             'enable_slow_tests': [False, "Run scipy test suite, including tests marked as slow", CUSTOM],
             # ignore tests by default to maintain behaviour in older easyconfigs
-            'ignore_test_result': [True, "Run scipy test suite, but ignore result (only log)", CUSTOM],
+            'ignore_test_result': [None, "Run scipy test suite, but ignore result (only log)", CUSTOM],
         })
 
-        return FortranPythonPackage.extra_options(extra_vars=extra_vars)
+        return PythonPackage.extra_options(extra_vars=extra_vars)
 
     def __init__(self, *args, **kwargs):
         """Set scipy-specific test command."""
-        super(EB_scipy, self).__init__(*args, **kwargs)
-
-        self.use_meson = LooseVersion(self.version) >= LooseVersion('1.9')
+        # calling PythonPackage __init__ also lets MesonNinja work in an extension
+        PythonPackage.__init__(self, *args, **kwargs)
         self.testinstall = True
+
+        if LooseVersion(self.version) >= LooseVersion('1.9'):
+            self.use_meson = True
+            # enforce scipy test suite results if not explicitly disabled for scipy >= 1.9
+            if self.cfg['ignore_test_result'] is None:
+                self.cfg['ignore_test_result'] = True
+            # ignore installopts inherited from FortranPythonPackage
+            self.cfg['installopts'] = ""
+        else:
+            self.use_meson = False
+        
         if self.cfg['ignore_test_result']:
-            # running tests this way exits with 0 regardless
+            # maintains compatibility with easyconfigs predating scipy 1.9. Runs tests (serially) in
+            # a way that exits with code 0 regardless of test results, see:
+            # https://github.com/easybuilders/easybuild-easyblocks/issues/2237
             self.testcmd = "cd .. && %(python)s -c 'import numpy; import scipy; scipy.test(verbose=2)'"
         else:
             self.testcmd = " && ".join([
@@ -77,12 +89,11 @@ def __init__(self, *args, **kwargs):
                 "touch %(srcdir)s/.coveragerc",
                 "%(python)s %(srcdir)s/runtests.py -v --no-build --parallel %(parallel)s",
             ])
-            if self.cfg['enable_slow_tests'] is True:
+            if self.cfg['enable_slow_tests']:
                 self.testcmd += " -m full "
 
     def configure_step(self):
         """Custom configure step for scipy: set extra installation options when needed."""
-        pylibdir = det_pylibdir()
 
         # scipy >= 1.9.0 uses Meson/Ninja
         if self.use_meson:
@@ -102,6 +113,7 @@ def configure_step(self):
 
             # need to have already installed extensions in PATH, PYTHONPATH for configure/build/install steps
             pythonpath = os.getenv('PYTHONPATH')
+            pylibdir = det_pylibdir()
             env.setvar('PYTHONPATH', os.pathsep.join([os.path.join(self.installdir, pylibdir), pythonpath]))
 
             path = os.getenv('PATH')
@@ -110,7 +122,7 @@ def configure_step(self):
             MesonNinja.configure_step(self)
 
         else:
-            super(EB_scipy, self).configure_step()
+            FortranPythonPackage.configure_step(self)
 
         if LooseVersion(self.version) >= LooseVersion('0.13'):
             # in recent scipy versions, additional compilation is done in the install step,
@@ -123,72 +135,60 @@ def build_step(self):
         if self.use_meson:
             MesonNinja.build_step(self)
         else:
-            super(EB_scipy, self).build_step()
+            FortranPythonPackage.build_step(self)
 
     def test_step(self):
         """Run available scipy unit tests. Adapted from numpy easyblock"""
 
         if self.use_meson:
-
             # temporarily install scipy so we can run the test suite
             tmpdir = tempfile.mkdtemp()
             cwd = os.getcwd()
 
-            cmd = " && ".join([
-                # reconfigure meson to use temp dir
-                'meson configure --prefix=%s' % tmpdir,
-                'ninja -j %s install' % self.cfg['parallel'],
-            ])
-            run_cmd(cmd, log_all=True, simple=True, verbose=False)
+            tmp_builddir = os.path.join(tmpdir, 'build')
+            tmp_installdir = os.path.join(tmpdir, 'install')
 
-            abs_pylibdirs = [os.path.join(tmpdir, pylibdir) for pylibdir in self.all_pylibdirs]
-            for pylibdir in abs_pylibdirs:
-                mkdir(pylibdir, parents=True)
-            python_root = get_software_root('Python')
-            python_bin = os.path.join(python_root, 'bin', 'python')
+            # create a copy of the builddir
+            copy_dir(cwd, tmp_builddir)
+            change_dir(tmp_builddir)
+
+            # reconfigure (to update prefix), and install to tmpdir
+            MesonNinja.configure_step(self, cmd_prefix=tmp_installdir)
+            MesonNinja.install_step(self)
+
+            tmp_pylibdir = [os.path.join(tmp_installdir, det_pylibdir())]
+            self.prepare_python()
 
             self.cfg['pretestopts'] = " && ".join([
                 # LDFLAGS should not be set when testing numpy/scipy, because it overwrites whatever numpy/scipy sets
                 # see http://projects.scipy.org/numpy/ticket/182
                 "unset LDFLAGS",
-                "export PYTHONPATH=%s:$PYTHONPATH" % os.pathsep.join(abs_pylibdirs),
+                "export PYTHONPATH=%s:$PYTHONPATH" % tmp_pylibdir,
                 "",
             ])
             self.cfg['runtest'] = self.testcmd % {
-                'python': python_bin,
+                'python': self.python_cmd,
                 'srcdir': self.cfg['start_dir'],
                 'parallel': self.cfg['parallel'],
             }
 
             MesonNinja.test_step(self)
 
-            # reconfigure meson to use real install dir
-            change_dir(cwd)
-            cmd = 'meson configure --prefix=%s' % self.installdir
-            run_cmd(cmd, log_all=True, simple=True, verbose=False)
-
-            try:
-                remove_dir(tmpdir)
-            except OSError as err:
-                raise EasyBuildError("Failed to remove directory %s: %s", tmpdir, err)
-
         else:
             self.testcmd = self.testcmd % {
                 'python': '%(python)s',
                 'srcdir': self.cfg['start_dir'],
                 'parallel': self.cfg['parallel'],
             }
-            super(EB_scipy, self).test_step()
+            FortranPythonPackage.test_step(self)
 
     def install_step(self):
         """Custom install step for scipy: use ninja for scipy >= 1.9.0"""
         if self.use_meson:
-            # ignore installopts inherited from FortranPythonPackage
-            self.cfg['installopts'] = ""
             MesonNinja.install_step(self)
 
         else:
-            super(EB_scipy, self).install_step()
+            FortranPythonPackage.install_step(self)
 
     def sanity_check_step(self, *args, **kwargs):
         """Custom sanity check for scipy."""
@@ -200,4 +200,4 @@ def sanity_check_step(self, *args, **kwargs):
             'dirs': [det_pylibdir()],
         }
 
-        return super(EB_scipy, self).sanity_check_step(custom_paths=custom_paths)
+        return PythonPackage.sanity_check_step(self, custom_paths=custom_paths)

From 8d44a255b7f44b5019fbc62547d44867b8322f99 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Mon, 23 Jan 2023 15:53:07 +0000
Subject: [PATCH 24/87] appease the hound

---
 easybuild/easyblocks/s/scipy.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 22a7e1cc40..1df30766b9 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -43,9 +43,7 @@
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage, det_pylibdir
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import change_dir, copy_dir, mkdir
-from easybuild.tools.modules import get_software_root
-from easybuild.tools.run import run_cmd
+from easybuild.tools.filetools import change_dir, copy_dir
 
 
 class EB_scipy(FortranPythonPackage, PythonPackage, MesonNinja):
@@ -77,7 +75,7 @@ def __init__(self, *args, **kwargs):
             self.cfg['installopts'] = ""
         else:
             self.use_meson = False
-        
+
         if self.cfg['ignore_test_result']:
             # maintains compatibility with easyconfigs predating scipy 1.9. Runs tests (serially) in
             # a way that exits with code 0 regardless of test results, see:

From b1fc372617ed6b20dbce563a67f0220fbd4e3990 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Thu, 26 Jan 2023 15:27:51 +0100
Subject: [PATCH 25/87] use start dir of extension to install R packages

---
 easybuild/easyblocks/generic/rpackage.py | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/easybuild/easyblocks/generic/rpackage.py b/easybuild/easyblocks/generic/rpackage.py
index 572dab6935..190e416db0 100644
--- a/easybuild/easyblocks/generic/rpackage.py
+++ b/easybuild/easyblocks/generic/rpackage.py
@@ -134,15 +134,10 @@ def make_cmdline_cmd(self, prefix=None):
         else:
             prefix = ''
 
-        if self.start_dir:
-            loc = os.path.join(self.ext_dir or os.path.sep, self.start_dir)
-        else:
-            loc = self.ext_dir or self.ext_src
-
         cmd = ' '.join([
             self.cfg['preinstallopts'],
             "R CMD INSTALL",
-            loc,
+            self.start_dir,
             confargs,
             confvars,
             prefix,

From e357a408feb3b78f4e9a506f826dab2a20629545 Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Thu, 26 Jan 2023 15:03:05 +0000
Subject: [PATCH 26/87] modified the logic to find the PyQt5 sipdir in more
 places

---
 easybuild/easyblocks/q/qscintilla.py | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/q/qscintilla.py b/easybuild/easyblocks/q/qscintilla.py
index a712222c48..c4dd6bc3ef 100644
--- a/easybuild/easyblocks/q/qscintilla.py
+++ b/easybuild/easyblocks/q/qscintilla.py
@@ -118,16 +118,23 @@ def install_step(self):
             pyshortver = '.'.join(get_software_version('Python').split('.')[:2])
 
             sip_incdir = find_glob_pattern(os.path.join(self.pyqt_root, 'include', 'python%s*' % pyshortver), False)
-            # in case PyQt5's sip was installed in directories that are specific to each version of python
-            # as could happen with multi_deps
-            pyqt_sipdir = find_glob_pattern(os.path.join(self.pyqt_root, 'share', 'python%s*' % pyshortver,
-                                                         'site-packages', 'sip', self.pyqt_pkg_name), False)
-            # fall back to a single sipdir
+            # depending on PyQt5 versions and how it was installed, the sip directory could be in various places
+            # test them and figure out the first one that matches
+            pyqt_sip_subidr = [os.path.join('share', 'python%s*' % pyshortver, 'site-packages', 'sip',
+                                            self.pyqt_pkg_name),
+                               os.path.join('share', 'sip', self.pyqt_pkg_name),
+                               os.path.join('share', 'sip'),
+                               os.path.join('lib', 'python%s*' % pyshortver, 'site-packages', self.pyqt_pkg_name,
+                                            'bindings')
+                              ]
+            pyqt_sipdir_options = [os.path.join(self.pyqt_root, subdir) for subdir in pyqt_sip_subidr]
+            for pyqt_sipdir_option in pyqt_sipdir_options:
+                pyqt_sipdir = find_glob_pattern(pyqt_sipdir_option, False)
+                if pyqt_sipdir:
+                    break
+
             if not pyqt_sipdir:
-                if LooseVersion(get_software_version(self.pyqt_pkg_name)) >= LooseVersion('5.15'):
-                    pyqt_sipdir = os.path.join(self.pyqt_root, 'share', 'sip')
-                else:
-                    pyqt_sipdir = os.path.join(self.pyqt_root, 'share', 'sip', self.pyqt_pkg_name)
+                raise EasyBuildError("Failed to find PyQt5 sip directory")
 
             cfgopts = [
                 '--destdir %s' % os.path.join(self.installdir, pylibdir),

From a90d61708a214cd7c72e2767c729c787619a2927 Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Thu, 26 Jan 2023 15:07:11 +0000
Subject: [PATCH 27/87] appeasing hound

---
 easybuild/easyblocks/q/qscintilla.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/q/qscintilla.py b/easybuild/easyblocks/q/qscintilla.py
index c4dd6bc3ef..ac7a2bbeeb 100644
--- a/easybuild/easyblocks/q/qscintilla.py
+++ b/easybuild/easyblocks/q/qscintilla.py
@@ -126,7 +126,7 @@ def install_step(self):
                                os.path.join('share', 'sip'),
                                os.path.join('lib', 'python%s*' % pyshortver, 'site-packages', self.pyqt_pkg_name,
                                             'bindings')
-                              ]
+                               ]
             pyqt_sipdir_options = [os.path.join(self.pyqt_root, subdir) for subdir in pyqt_sip_subidr]
             for pyqt_sipdir_option in pyqt_sipdir_options:
                 pyqt_sipdir = find_glob_pattern(pyqt_sipdir_option, False)

From 3e491c0b28a8692d422d45685885ee4c74b0b91f Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Thu, 26 Jan 2023 15:14:26 +0000
Subject: [PATCH 28/87] fixed typos

---
 easybuild/easyblocks/q/qscintilla.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/q/qscintilla.py b/easybuild/easyblocks/q/qscintilla.py
index ac7a2bbeeb..3a64d6c607 100644
--- a/easybuild/easyblocks/q/qscintilla.py
+++ b/easybuild/easyblocks/q/qscintilla.py
@@ -120,14 +120,14 @@ def install_step(self):
             sip_incdir = find_glob_pattern(os.path.join(self.pyqt_root, 'include', 'python%s*' % pyshortver), False)
             # depending on PyQt5 versions and how it was installed, the sip directory could be in various places
             # test them and figure out the first one that matches
-            pyqt_sip_subidr = [os.path.join('share', 'python%s*' % pyshortver, 'site-packages', 'sip',
+            pyqt_sip_subdir = [os.path.join('share', 'python%s*' % pyshortver, 'site-packages', 'sip',
                                             self.pyqt_pkg_name),
                                os.path.join('share', 'sip', self.pyqt_pkg_name),
                                os.path.join('share', 'sip'),
                                os.path.join('lib', 'python%s*' % pyshortver, 'site-packages', self.pyqt_pkg_name,
                                             'bindings')
                                ]
-            pyqt_sipdir_options = [os.path.join(self.pyqt_root, subdir) for subdir in pyqt_sip_subidr]
+            pyqt_sipdir_options = [os.path.join(self.pyqt_root, subdir) for subdir in pyqt_sip_subdir]
             for pyqt_sipdir_option in pyqt_sipdir_options:
                 pyqt_sipdir = find_glob_pattern(pyqt_sipdir_option, False)
                 if pyqt_sipdir:

From 8f5534a80e5b07f16e44af8e47d29de1354af845 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Thu, 26 Jan 2023 16:31:06 +0100
Subject: [PATCH 29/87] fix JULIA_DEPOT_PATH in installation of multiple
 JuliaPackage extensions

---
 easybuild/easyblocks/generic/juliapackage.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/generic/juliapackage.py b/easybuild/easyblocks/generic/juliapackage.py
index 239ed5f5d3..2490bc2823 100644
--- a/easybuild/easyblocks/generic/juliapackage.py
+++ b/easybuild/easyblocks/generic/juliapackage.py
@@ -96,11 +96,12 @@ def install_step(self):
         """Install Julia package with Pkg"""
 
         # prepend installation directory to Julia DEPOT_PATH
+        # extensions in a bundle can share their DEPOT_PATH
         # see https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
-        depot_path = os.getenv('JULIA_DEPOT_PATH')
-        if depot_path is not None:
-            depot_path = ':'.join([self.installdir, depot_path])
-        env.setvar('JULIA_DEPOT_PATH', depot_path)
+        depot_path = os.getenv('JULIA_DEPOT_PATH', '')
+        if self.installdir not in depot_path:
+            depot_path = ':'.join([depot for depot in (self.installdir, depot_path) if depot])
+            env.setvar('JULIA_DEPOT_PATH', depot_path)
 
         # command sequence for Julia.Pkg
         julia_pkg_cmd = ['using Pkg']

From e30d17fde03fd13a40157dfb0a9808452a5ae89a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 29 Jan 2023 12:12:20 +0100
Subject: [PATCH 30/87] fix website/docs links in README

---
 README.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index b651c614a6..fd11b4fe04 100644
--- a/README.rst
+++ b/README.rst
@@ -4,7 +4,7 @@
 
 .. image:: https://github.com/easybuilders/easybuild-easyblocks/workflows/easyblocks%20unit%20tests/badge.svg?branch=develop
 
-`EasyBuild <https://easybuilders.github.io/easybuild>`_ is a software build
+`EasyBuild <https://easybuild.io>`_ is a software build
 and installation framework that allows you to manage (scientific) software
 on High Performance Computing (HPC) systems in an efficient way.
 
@@ -13,7 +13,7 @@ EasyBuild. Easyblocks are Python modules that implement the install procedure fo
 (group of) software package(s). Together with the EasyBuild framework,
 they allow to easily build and install supported software packages.
 
-The EasyBuild documentation is available at http://easybuild.readthedocs.org/.
+The EasyBuild documentation is available at http://docs.easybuild.io/.
 
 The easybuild-easyblocks source code is hosted on GitHub, along
 with an issue tracker for bug reports and feature requests, see

From 2d3de771df47fa0cb63c05cb29c875c7b6abe092 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Mon, 30 Jan 2023 14:25:34 +0100
Subject: [PATCH 31/87] Add `testinstall` EC option to PythonPackage

---
 easybuild/easyblocks/generic/pythonpackage.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/pythonpackage.py b/easybuild/easyblocks/generic/pythonpackage.py
index d89e495122..00ea6183a0 100644
--- a/easybuild/easyblocks/generic/pythonpackage.py
+++ b/easybuild/easyblocks/generic/pythonpackage.py
@@ -250,6 +250,7 @@ def extra_options(extra_vars=None):
             'sanity_pip_check': [False, "Run 'python -m pip check' to ensure all required Python packages are "
                                         "installed and check for any package with an invalid (0.0.0) version.", CUSTOM],
             'runtest': [True, "Run unit tests.", CUSTOM],  # overrides default
+            'testinstall': [False, "Install into temporary directory prior to running the tests.", CUSTOM],
             'unpack_sources': [None, "Unpack sources prior to build/install. Defaults to 'True' except for whl files",
                                CUSTOM],
             # A version of 0.0.0 is usually an error on installation unless the package does really not provide a
@@ -283,7 +284,7 @@ def __init__(self, *args, **kwargs):
         self.sitecfgfn = 'site.cfg'
         self.sitecfglibdir = None
         self.sitecfgincdir = None
-        self.testinstall = False
+        self.testinstall = self.cfg['testinstall']
         self.testcmd = None
         self.unpack_options = self.cfg['unpack_options']
 

From 6f10887b1634025fc91ace2c67b5666f5e813119 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 30 Jan 2023 14:57:29 +0100
Subject: [PATCH 32/87] fix checking of CUDA/ROCR-Runtime dependencies for
 Clang to determine default build targets (fixes #2871)

---
 easybuild/easyblocks/c/clang.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/c/clang.py b/easybuild/easyblocks/c/clang.py
index 4f1344187a..e9f195b275 100644
--- a/easybuild/easyblocks/c/clang.py
+++ b/easybuild/easyblocks/c/clang.py
@@ -177,18 +177,19 @@ def __init__(self, *args, **kwargs):
         build_targets = self.cfg['build_targets']
         # define build_targets if not set
         if build_targets is None:
+            deps = [dep['name'].lower() for dep in self.cfg.dependencies()]
             arch = get_cpu_architecture()
             try:
                 default_targets = DEFAULT_TARGETS_MAP[arch][:]
                 # If CUDA is included as a dep, add NVPTX as a target
-                if get_software_root("CUDA"):
-                    default_targets += ["NVPTX"]
+                if 'cuda' in deps:
+                    default_targets += ['NVPTX']
                 # For AMDGPU support we need ROCR-Runtime and
                 # ROCT-Thunk-Interface, however, since ROCT is a dependency of
                 # ROCR we only check for the ROCR-Runtime here
                 # https://openmp.llvm.org/SupportAndFAQ.html#q-how-to-build-an-openmp-amdgpu-offload-capable-compiler
-                if get_software_root("ROCR-Runtime"):
-                    default_targets += ["AMDGPU"]
+                if 'rocr-runtime' in deps:
+                    default_targets += ['AMDGPU']
                 self.cfg['build_targets'] = build_targets = default_targets
                 self.log.debug("Using %s as default build targets for CPU/GPU architecture %s.", default_targets, arch)
             except KeyError:

From 4f30aab3822002794251fdc94e9b69ff8afed9ed Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 30 Jan 2023 16:08:22 +0100
Subject: [PATCH 33/87] take into account that CUDA may be an indirect
 dependency via the toolchain

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 easybuild/easyblocks/c/clang.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/c/clang.py b/easybuild/easyblocks/c/clang.py
index e9f195b275..172811566d 100644
--- a/easybuild/easyblocks/c/clang.py
+++ b/easybuild/easyblocks/c/clang.py
@@ -182,7 +182,9 @@ def __init__(self, *args, **kwargs):
             try:
                 default_targets = DEFAULT_TARGETS_MAP[arch][:]
                 # If CUDA is included as a dep, add NVPTX as a target
-                if 'cuda' in deps:
+                # There are (old) toolchains with CUDA as part of the toolchain
+                cuda_toolchain = hasattr(self.toolchain, 'COMPILER_CUDA_FAMILY')
+                if 'cuda' in deps or cuda_toolchain:
                     default_targets += ['NVPTX']
                 # For AMDGPU support we need ROCR-Runtime and
                 # ROCT-Thunk-Interface, however, since ROCT is a dependency of

From e98c8ea693907979ef23c5d0bcb83addd744e990 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 2 Feb 2023 13:42:31 +0100
Subject: [PATCH 34/87] Show template values of exts_default_options in
 PythonBundle

---
 easybuild/easyblocks/generic/pythonbundle.py | 22 ++++++++------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/easybuild/easyblocks/generic/pythonbundle.py b/easybuild/easyblocks/generic/pythonbundle.py
index 8e38e0cfa5..292cc275aa 100644
--- a/easybuild/easyblocks/generic/pythonbundle.py
+++ b/easybuild/easyblocks/generic/pythonbundle.py
@@ -62,21 +62,17 @@ def __init__(self, *args, **kwargs):
         self.cfg['exts_filter'] = EXTS_FILTER_PYTHON_PACKAGES
 
         # need to disable templating to ensure that actual value for exts_default_options is updated...
-        prev_enable_templating = self.cfg.enable_templating
-        self.cfg.enable_templating = False
+        with self.cfg.disable_templating():
+            # set default options for extensions according to relevant top-level easyconfig parameters
+            pypkg_keys = PythonPackage.extra_options().keys()
+            for key in pypkg_keys:
+                if key not in self.cfg['exts_default_options']:
+                    self.cfg['exts_default_options'][key] = self.cfg[key]
 
-        # set default options for extensions according to relevant top-level easyconfig parameters
-        pypkg_keys = PythonPackage.extra_options().keys()
-        for key in pypkg_keys:
-            if key not in self.cfg['exts_default_options']:
-                self.cfg['exts_default_options'][key] = self.cfg[key]
+            self.cfg['exts_default_options']['download_dep_fail'] = True
+            self.log.info("Detection of downloaded extension dependencies is enabled")
 
-        self.cfg['exts_default_options']['download_dep_fail'] = True
-        self.log.info("Detection of downloaded extension dependencies is enabled")
-
-        self.cfg.enable_templating = prev_enable_templating
-
-        self.log.info("exts_default_options: %s", self.cfg['exts_default_options'])
+            self.log.info("exts_default_options: %s", self.cfg['exts_default_options'])
 
         self.pylibdir = None
         self.all_pylibdirs = []

From 46c81b79c51c8ba32cdcf3ab54b95049f1a70d3a Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Fri, 3 Feb 2023 15:03:23 +0100
Subject: [PATCH 35/87] Fix missing initialization of CMakeMake in
 CMakePythonPackage

---
 easybuild/easyblocks/generic/cmakepythonpackage.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/easybuild/easyblocks/generic/cmakepythonpackage.py b/easybuild/easyblocks/generic/cmakepythonpackage.py
index f70fd83340..fac9aeced4 100644
--- a/easybuild/easyblocks/generic/cmakepythonpackage.py
+++ b/easybuild/easyblocks/generic/cmakepythonpackage.py
@@ -53,11 +53,6 @@ def extra_options(extra_vars=None):
         extra_vars['runtest'][0] = None
         return extra_vars
 
-    def __init__(self, *args, **kwargs):
-        """Initialize with PythonPackage."""
-        PythonPackage.__init__(self, *args, **kwargs)
-        self._lib_ext = None  # From CMakeMake.__init__
-
     def configure_step(self, *args, **kwargs):
         """Main configuration using cmake"""
 

From ebd73924ec5f68b04dbbe8ea7fb9dc69c2877fa7 Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Mon, 6 Feb 2023 12:35:34 +0100
Subject: [PATCH 36/87] Fix error when failing PIP version check during
 PythonPackage sanity check.

The arguments must be passed individually not as a tuple, else you get:
>   File "/easybuild-easyblocks/easybuild/easyblocks/generic/pythonpackage.py", line 921, in sanity_check_step
>     pip_version))
>   File "/easybuild-framework/easybuild/tools/build_log.py", line 81, in __init__
>     msg = msg % args
> TypeError: not enough arguments for format string
---
 easybuild/easyblocks/generic/pythonpackage.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/generic/pythonpackage.py b/easybuild/easyblocks/generic/pythonpackage.py
index 00ea6183a0..3e5e5e3a02 100644
--- a/easybuild/easyblocks/generic/pythonpackage.py
+++ b/easybuild/easyblocks/generic/pythonpackage.py
@@ -917,8 +917,9 @@ def sanity_check_step(self, *args, **kwargs):
                     if pip_check_errors:
                         raise EasyBuildError('\n'.join(pip_check_errors))
                 else:
-                    raise EasyBuildError("pip >= 9.0.0 is required for running '%s', found %s", (pip_check_command,
-                                                                                                 pip_version))
+                    raise EasyBuildError("pip >= 9.0.0 is required for running '%s', found %s",
+                                         pip_check_command,
+                                         pip_version)
             else:
                 raise EasyBuildError("Failed to determine pip version!")
 

From 844a3a3e95767b03324a889d9f001fe6c2ff4d9c Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Tue, 7 Feb 2023 10:38:23 +0100
Subject: [PATCH 37/87] add debug flag to gopackage easyblock

---
 easybuild/easyblocks/generic/gopackage.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easybuild/easyblocks/generic/gopackage.py b/easybuild/easyblocks/generic/gopackage.py
index d6f00f51a0..b94845b8cd 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -34,6 +34,7 @@
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.config import build_option
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
 
@@ -126,6 +127,9 @@ def build_step(self):
     def install_step(self):
         """Install Go package to a custom path"""
 
+        if build_option('debug'):
+            self.cfg['installopts'] = '-x ' + self.cfg['installopts']
+
         # actually install Go package
         cmd = ' '.join([
             self.cfg['preinstallopts'],

From 0194c09906ac8fa7565bb4acf0381bd2eb0ec638 Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Wed, 8 Feb 2023 20:55:50 +0000
Subject: [PATCH 38/87] handle templating correctly when playing with
 configopts

---
 easybuild/easyblocks/generic/cmakemake.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyblocks/generic/cmakemake.py b/easybuild/easyblocks/generic/cmakemake.py
index f747702fc9..d9ee0d53af 100644
--- a/easybuild/easyblocks/generic/cmakemake.py
+++ b/easybuild/easyblocks/generic/cmakemake.py
@@ -141,12 +141,18 @@ def build_type(self):
 
     def prepend_config_opts(self, config_opts):
         """Prepends configure options (-Dkey=value) to configopts ignoring those already set"""
+        # need to disable template resolution or it will remain the same for all runs
+        self.cfg.enable_templating = False
+
         cfg_configopts = self.cfg['configopts']
         # All options are of the form '-D<key>=<value>'
         new_opts = ' '.join('-D%s=%s' % (key, value) for key, value in config_opts.items()
                             if '-D%s=' % key not in cfg_configopts)
         self.cfg['configopts'] = ' '.join([new_opts, cfg_configopts])
 
+        #re-enable template resolution
+        self.cfg.enable_templating = True
+
     def configure_step(self, srcdir=None, builddir=None):
         """Configure build using cmake"""
 

From 950582fb37a684cf5e20908d8d14d9b491ad2a6e Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Wed, 8 Feb 2023 20:58:28 +0000
Subject: [PATCH 39/87] appeasing hound

---
 easybuild/easyblocks/generic/cmakemake.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/cmakemake.py b/easybuild/easyblocks/generic/cmakemake.py
index d9ee0d53af..8bf841f313 100644
--- a/easybuild/easyblocks/generic/cmakemake.py
+++ b/easybuild/easyblocks/generic/cmakemake.py
@@ -150,7 +150,7 @@ def prepend_config_opts(self, config_opts):
                             if '-D%s=' % key not in cfg_configopts)
         self.cfg['configopts'] = ' '.join([new_opts, cfg_configopts])
 
-        #re-enable template resolution
+        # re-enable template resolution
         self.cfg.enable_templating = True
 
     def configure_step(self, srcdir=None, builddir=None):

From 84c56102051048f339568fd736afb69afa136582 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Thu, 9 Feb 2023 08:41:22 +0100
Subject: [PATCH 40/87] void pytorch test_step crashing if runtest is not a
 command

---
 easybuild/easyblocks/p/pytorch.py | 264 +++++++++++++++---------------
 1 file changed, 135 insertions(+), 129 deletions(-)

diff --git a/easybuild/easyblocks/p/pytorch.py b/easybuild/easyblocks/p/pytorch.py
index 9a7637fed1..53dca5176b 100644
--- a/easybuild/easyblocks/p/pytorch.py
+++ b/easybuild/easyblocks/p/pytorch.py
@@ -248,137 +248,143 @@ def _set_cache_dir(self):
 
     def test_step(self):
         """Run unit tests"""
-        self._set_cache_dir()
-        # Pretend to be on FB CI which disables some tests, especially those which download stuff
-        env.setvar('SANDCASTLE', '1')
-        # Skip this test(s) which is very flaky
-        env.setvar('SKIP_TEST_BOTTLENECK', '1')
-        # Parse excluded_tests and flatten into space separated string
-        excluded_tests = []
-        for arch, tests in self.cfg['excluded_tests'].items():
-            if not arch or arch == get_cpu_architecture():
-                excluded_tests.extend(tests)
-        # -x should not be used if there are no excluded tests
-        if excluded_tests:
-            excluded_tests = ['-x'] + excluded_tests
-        self.cfg.template_values.update({
-            'python': self.python_cmd,
-            'excluded_tests': ' '.join(excluded_tests)
-        })
 
-        tests_out, tests_ec = super(EB_PyTorch, self).test_step(return_output_ec=True)
-
-        def get_count_for_pattern(regex, text):
-            """Match the regexp containing a single group and return the integer value of the matched group.
-               Return zero if no or more than 1 match was found and warn for the latter case
-            """
-            match = re.findall(regex, text)
-            if len(match) == 1:
-                return int(match[0])
-            elif len(match) > 1:
-                # Shouldn't happen, but means something went wrong with the regular expressions.
-                # Throw warning, as the build might be fine, no need to error on this.
-                warn_msg = "Error in counting the number of test failures in the output of the PyTorch test suite.\n"
-                warn_msg += "Please check the EasyBuild log to verify the number of failures (if any) was acceptable."
-                print_warning(warn_msg)
-            return 0
-
-        # Create clear summary report
-        failure_report = ""
-        failure_cnt = 0
-        error_cnt = 0
-        failed_test_suites = []
-
-        # Grep for patterns like:
-        # Ran 219 tests in 67.325s
-        #
-        # FAILED (errors=10, skipped=190, expected failures=6)
-        # test_fx failed!
-        regex = (r"^Ran (?P<test_cnt>[0-9]+) tests.*$\n\n"
-                 r"FAILED \((?P<failure_summary>.*)\)$\n"
-                 r"(?:^(?:(?!failed!).)*$\n)*"
-                 r"(?P<failed_test_suite_name>.*) failed!(?: Received signal: \w+)?\s*$")
-
-        for m in re.finditer(regex, tests_out, re.M):
-            # E.g. 'failures=3, errors=10, skipped=190, expected failures=6'
-            failure_summary = m.group('failure_summary')
-            total, test_suite = m.group('test_cnt', 'failed_test_suite_name')
-            failure_report += "{test_suite} ({total} total tests, {failure_summary})\n".format(
-                    test_suite=test_suite, total=total, failure_summary=failure_summary
+        # Must not run this unless runtest is actually set to a command,
+        # otherwise PythonPackage.test_step doesn't return the expected "out, ec" values which makes the code crash
+        if isinstance(self.cfg['runtest'], string_type):
+            cmd = self.cfg['runtest']
+        if self.cfg['runtest'] and cmd is not None:
+            self._set_cache_dir()
+            # Pretend to be on FB CI which disables some tests, especially those which download stuff
+            env.setvar('SANDCASTLE', '1')
+            # Skip this test(s) which is very flaky
+            env.setvar('SKIP_TEST_BOTTLENECK', '1')
+            # Parse excluded_tests and flatten into space separated string
+            excluded_tests = []
+            for arch, tests in self.cfg['excluded_tests'].items():
+                if not arch or arch == get_cpu_architecture():
+                    excluded_tests.extend(tests)
+            # -x should not be used if there are no excluded tests
+            if excluded_tests:
+                excluded_tests = ['-x'] + excluded_tests
+            self.cfg.template_values.update({
+                'python': self.python_cmd,
+                'excluded_tests': ' '.join(excluded_tests)
+            })
+
+            tests_out, tests_ec = super(EB_PyTorch, self).test_step(return_output_ec=True)
+
+            def get_count_for_pattern(regex, text):
+                """Match the regexp containing a single group and return the integer value of the matched group.
+                   Return zero if no or more than 1 match was found and warn for the latter case
+                """
+                match = re.findall(regex, text)
+                if len(match) == 1:
+                    return int(match[0])
+                elif len(match) > 1:
+                    # Shouldn't happen, but means something went wrong with the regular expressions.
+                    # Throw warning, as the build might be fine, no need to error on this.
+                    warn_msg = "Error in counting the number of test failures in the output of the PyTorch test suite.\n"
+                    warn_msg += "Please check the EasyBuild log to verify the number of failures (if any) was acceptable."
+                    print_warning(warn_msg)
+                return 0
+
+            # Create clear summary report
+            failure_report = ""
+            failure_cnt = 0
+            error_cnt = 0
+            failed_test_suites = []
+
+            # Grep for patterns like:
+            # Ran 219 tests in 67.325s
+            #
+            # FAILED (errors=10, skipped=190, expected failures=6)
+            # test_fx failed!
+            regex = (r"^Ran (?P<test_cnt>[0-9]+) tests.*$\n\n"
+                     r"FAILED \((?P<failure_summary>.*)\)$\n"
+                     r"(?:^(?:(?!failed!).)*$\n)*"
+                     r"(?P<failed_test_suite_name>.*) failed!(?: Received signal: \w+)?\s*$")
+
+            for m in re.finditer(regex, tests_out, re.M):
+                # E.g. 'failures=3, errors=10, skipped=190, expected failures=6'
+                failure_summary = m.group('failure_summary')
+                total, test_suite = m.group('test_cnt', 'failed_test_suite_name')
+                failure_report += "{test_suite} ({total} total tests, {failure_summary})\n".format(
+                        test_suite=test_suite, total=total, failure_summary=failure_summary
+                    )
+                failure_cnt += get_count_for_pattern(r"(?<!expected )failures=([0-9]+)", failure_summary)
+                error_cnt += get_count_for_pattern(r"errors=([0-9]+)", failure_summary)
+                failed_test_suites.append(test_suite)
+
+            # Grep for patterns like:
+            # ===================== 2 failed, 128 passed, 2 skipped, 2 warnings in 3.43s =====================
+            regex = r"^=+ (?P<failure_summary>.*) in [0-9]+\.*[0-9]*[a-zA-Z]* =+$\n(?P<failed_test_suite_name>.*) failed!$"
+
+            for m in re.finditer(regex, tests_out, re.M):
+                # E.g. '2 failed, 128 passed, 2 skipped, 2 warnings'
+                failure_summary = m.group('failure_summary')
+                test_suite = m.group('failed_test_suite_name')
+                failure_report += "{test_suite} ({failure_summary})\n".format(
+                        test_suite=test_suite, failure_summary=failure_summary
+                    )
+                failure_cnt += get_count_for_pattern(r"([0-9]+) failed", failure_summary)
+                error_cnt += get_count_for_pattern(r"([0-9]+) error", failure_summary)
+                failed_test_suites.append(test_suite)
+
+            # Make the names unique and sorted
+            failed_test_suites = sorted(set(failed_test_suites))
+            # Gather all failed tests suites in case we missed any (e.g. when it exited due to syntax errors)
+            # Also unique and sorted to be able to compare the lists below
+            all_failed_test_suites = sorted(set(
+                re.findall(r"^(?P<test_name>.*) failed!(?: Received signal: \w+)?\s*$", tests_out, re.M)
+            ))
+            # If we missed any test suites prepend a list of all failed test suites
+            if failed_test_suites != all_failed_test_suites:
+                failure_report_save = failure_report
+                failure_report = 'Failed tests (suites/files):\n'
+                failure_report += '\n'.join('* %s' % t for t in all_failed_test_suites)
+                if failure_report_save:
+                    failure_report += '\n' + failure_report_save
+
+            # Calculate total number of unsuccesful and total tests
+            failed_test_cnt = failure_cnt + error_cnt
+            test_cnt = sum(int(hit) for hit in re.findall(r"^Ran (?P<test_cnt>[0-9]+) tests in", tests_out, re.M))
+
+            if failed_test_cnt > 0:
+                max_failed_tests = self.cfg['max_failed_tests']
+
+                failure_or_failures = 'failure' if failure_cnt == 1 else 'failures'
+                error_or_errors = 'error' if error_cnt == 1 else 'errors'
+                msg = "%d test %s, %d test %s (out of %d):\n" % (
+                    failure_cnt, failure_or_failures, error_cnt, error_or_errors, test_cnt
                 )
-            failure_cnt += get_count_for_pattern(r"(?<!expected )failures=([0-9]+)", failure_summary)
-            error_cnt += get_count_for_pattern(r"errors=([0-9]+)", failure_summary)
-            failed_test_suites.append(test_suite)
-
-        # Grep for patterns like:
-        # ===================== 2 failed, 128 passed, 2 skipped, 2 warnings in 3.43s =====================
-        regex = r"^=+ (?P<failure_summary>.*) in [0-9]+\.*[0-9]*[a-zA-Z]* =+$\n(?P<failed_test_suite_name>.*) failed!$"
-
-        for m in re.finditer(regex, tests_out, re.M):
-            # E.g. '2 failed, 128 passed, 2 skipped, 2 warnings'
-            failure_summary = m.group('failure_summary')
-            test_suite = m.group('failed_test_suite_name')
-            failure_report += "{test_suite} ({failure_summary})\n".format(
-                    test_suite=test_suite, failure_summary=failure_summary
-                )
-            failure_cnt += get_count_for_pattern(r"([0-9]+) failed", failure_summary)
-            error_cnt += get_count_for_pattern(r"([0-9]+) error", failure_summary)
-            failed_test_suites.append(test_suite)
-
-        # Make the names unique and sorted
-        failed_test_suites = sorted(set(failed_test_suites))
-        # Gather all failed tests suites in case we missed any (e.g. when it exited due to syntax errors)
-        # Also unique and sorted to be able to compare the lists below
-        all_failed_test_suites = sorted(set(
-            re.findall(r"^(?P<test_name>.*) failed!(?: Received signal: \w+)?\s*$", tests_out, re.M)
-        ))
-        # If we missed any test suites prepend a list of all failed test suites
-        if failed_test_suites != all_failed_test_suites:
-            failure_report_save = failure_report
-            failure_report = 'Failed tests (suites/files):\n'
-            failure_report += '\n'.join('* %s' % t for t in all_failed_test_suites)
-            if failure_report_save:
-                failure_report += '\n' + failure_report_save
-
-        # Calculate total number of unsuccesful and total tests
-        failed_test_cnt = failure_cnt + error_cnt
-        test_cnt = sum(int(hit) for hit in re.findall(r"^Ran (?P<test_cnt>[0-9]+) tests in", tests_out, re.M))
-
-        if failed_test_cnt > 0:
-            max_failed_tests = self.cfg['max_failed_tests']
-
-            failure_or_failures = 'failure' if failure_cnt == 1 else 'failures'
-            error_or_errors = 'error' if error_cnt == 1 else 'errors'
-            msg = "%d test %s, %d test %s (out of %d):\n" % (
-                failure_cnt, failure_or_failures, error_cnt, error_or_errors, test_cnt
-            )
-            msg += failure_report
-
-            # If no tests are supposed to fail or some failed for which we were not able to count errors fail now
-            if max_failed_tests == 0 or failed_test_suites != all_failed_test_suites:
-                raise EasyBuildError(msg)
-            else:
-                msg += '\n\n' + ' '.join([
-                    "The PyTorch test suite is known to include some flaky tests,",
-                    "which may fail depending on the specifics of the system or the context in which they are run.",
-                    "For this PyTorch installation, EasyBuild allows up to %d tests to fail." % max_failed_tests,
-                    "We recommend to double check that the failing tests listed above ",
-                    "are known to be flaky, or do not affect your intended usage of PyTorch.",
-                    "In case of doubt, reach out to the EasyBuild community (via GitHub, Slack, or mailing list).",
-                ])
-                # Print to console, the user should really be aware that we are accepting failing tests here...
-                print_warning(msg)
-
-                # Also log this warning in the file log
-                self.log.warning(msg)
-
-                if failed_test_cnt > max_failed_tests:
-                    raise EasyBuildError("Too many failed tests (%d), maximum allowed is %d",
-                                         failed_test_cnt, max_failed_tests)
-        elif failure_report:
-            raise EasyBuildError("Test command had non-zero exit code (%s)!\n%s", tests_ec, failure_report)
-        elif tests_ec:
-            raise EasyBuildError("Test command had non-zero exit code (%s), but no failed tests found?!", tests_ec)
+                msg += failure_report
+
+                # If no tests are supposed to fail or some failed for which we were not able to count errors fail now
+                if max_failed_tests == 0 or failed_test_suites != all_failed_test_suites:
+                    raise EasyBuildError(msg)
+                else:
+                    msg += '\n\n' + ' '.join([
+                        "The PyTorch test suite is known to include some flaky tests,",
+                        "which may fail depending on the specifics of the system or the context in which they are run.",
+                        "For this PyTorch installation, EasyBuild allows up to %d tests to fail." % max_failed_tests,
+                        "We recommend to double check that the failing tests listed above ",
+                        "are known to be flaky, or do not affect your intended usage of PyTorch.",
+                        "In case of doubt, reach out to the EasyBuild community (via GitHub, Slack, or mailing list).",
+                    ])
+                    # Print to console, the user should really be aware that we are accepting failing tests here...
+                    print_warning(msg)
+
+                    # Also log this warning in the file log
+                    self.log.warning(msg)
+
+                    if failed_test_cnt > max_failed_tests:
+                        raise EasyBuildError("Too many failed tests (%d), maximum allowed is %d",
+                                             failed_test_cnt, max_failed_tests)
+            elif failure_report:
+                raise EasyBuildError("Test command had non-zero exit code (%s)!\n%s", tests_ec, failure_report)
+            elif tests_ec:
+                raise EasyBuildError("Test command had non-zero exit code (%s), but no failed tests found?!", tests_ec)
 
     def test_cases_step(self):
         self._set_cache_dir()

From 0a8ebd285f546cc5164c51b00dc993c95700ba80 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Thu, 9 Feb 2023 13:10:27 +0100
Subject: [PATCH 41/87] test return from super(EB_PyTorch, self).test_step and
 handle the result instead of trying to avoid the problem explicitly.

---
 easybuild/easyblocks/p/pytorch.py | 272 +++++++++++++++---------------
 1 file changed, 137 insertions(+), 135 deletions(-)

diff --git a/easybuild/easyblocks/p/pytorch.py b/easybuild/easyblocks/p/pytorch.py
index 53dca5176b..f4fd1e80f5 100644
--- a/easybuild/easyblocks/p/pytorch.py
+++ b/easybuild/easyblocks/p/pytorch.py
@@ -248,143 +248,145 @@ def _set_cache_dir(self):
 
     def test_step(self):
         """Run unit tests"""
+        self._set_cache_dir()
+        # Pretend to be on FB CI which disables some tests, especially those which download stuff
+        env.setvar('SANDCASTLE', '1')
+        # Skip this test(s) which is very flaky
+        env.setvar('SKIP_TEST_BOTTLENECK', '1')
+        # Parse excluded_tests and flatten into space separated string
+        excluded_tests = []
+        for arch, tests in self.cfg['excluded_tests'].items():
+            if not arch or arch == get_cpu_architecture():
+                excluded_tests.extend(tests)
+        # -x should not be used if there are no excluded tests
+        if excluded_tests:
+            excluded_tests = ['-x'] + excluded_tests
+        self.cfg.template_values.update({
+            'python': self.python_cmd,
+            'excluded_tests': ' '.join(excluded_tests)
+        })
 
-        # Must not run this unless runtest is actually set to a command,
-        # otherwise PythonPackage.test_step doesn't return the expected "out, ec" values which makes the code crash
-        if isinstance(self.cfg['runtest'], string_type):
-            cmd = self.cfg['runtest']
-        if self.cfg['runtest'] and cmd is not None:
-            self._set_cache_dir()
-            # Pretend to be on FB CI which disables some tests, especially those which download stuff
-            env.setvar('SANDCASTLE', '1')
-            # Skip this test(s) which is very flaky
-            env.setvar('SKIP_TEST_BOTTLENECK', '1')
-            # Parse excluded_tests and flatten into space separated string
-            excluded_tests = []
-            for arch, tests in self.cfg['excluded_tests'].items():
-                if not arch or arch == get_cpu_architecture():
-                    excluded_tests.extend(tests)
-            # -x should not be used if there are no excluded tests
-            if excluded_tests:
-                excluded_tests = ['-x'] + excluded_tests
-            self.cfg.template_values.update({
-                'python': self.python_cmd,
-                'excluded_tests': ' '.join(excluded_tests)
-            })
-
-            tests_out, tests_ec = super(EB_PyTorch, self).test_step(return_output_ec=True)
-
-            def get_count_for_pattern(regex, text):
-                """Match the regexp containing a single group and return the integer value of the matched group.
-                   Return zero if no or more than 1 match was found and warn for the latter case
-                """
-                match = re.findall(regex, text)
-                if len(match) == 1:
-                    return int(match[0])
-                elif len(match) > 1:
-                    # Shouldn't happen, but means something went wrong with the regular expressions.
-                    # Throw warning, as the build might be fine, no need to error on this.
-                    warn_msg = "Error in counting the number of test failures in the output of the PyTorch test suite.\n"
-                    warn_msg += "Please check the EasyBuild log to verify the number of failures (if any) was acceptable."
-                    print_warning(warn_msg)
-                return 0
-
-            # Create clear summary report
-            failure_report = ""
-            failure_cnt = 0
-            error_cnt = 0
-            failed_test_suites = []
-
-            # Grep for patterns like:
-            # Ran 219 tests in 67.325s
-            #
-            # FAILED (errors=10, skipped=190, expected failures=6)
-            # test_fx failed!
-            regex = (r"^Ran (?P<test_cnt>[0-9]+) tests.*$\n\n"
-                     r"FAILED \((?P<failure_summary>.*)\)$\n"
-                     r"(?:^(?:(?!failed!).)*$\n)*"
-                     r"(?P<failed_test_suite_name>.*) failed!(?: Received signal: \w+)?\s*$")
-
-            for m in re.finditer(regex, tests_out, re.M):
-                # E.g. 'failures=3, errors=10, skipped=190, expected failures=6'
-                failure_summary = m.group('failure_summary')
-                total, test_suite = m.group('test_cnt', 'failed_test_suite_name')
-                failure_report += "{test_suite} ({total} total tests, {failure_summary})\n".format(
-                        test_suite=test_suite, total=total, failure_summary=failure_summary
-                    )
-                failure_cnt += get_count_for_pattern(r"(?<!expected )failures=([0-9]+)", failure_summary)
-                error_cnt += get_count_for_pattern(r"errors=([0-9]+)", failure_summary)
-                failed_test_suites.append(test_suite)
-
-            # Grep for patterns like:
-            # ===================== 2 failed, 128 passed, 2 skipped, 2 warnings in 3.43s =====================
-            regex = r"^=+ (?P<failure_summary>.*) in [0-9]+\.*[0-9]*[a-zA-Z]* =+$\n(?P<failed_test_suite_name>.*) failed!$"
-
-            for m in re.finditer(regex, tests_out, re.M):
-                # E.g. '2 failed, 128 passed, 2 skipped, 2 warnings'
-                failure_summary = m.group('failure_summary')
-                test_suite = m.group('failed_test_suite_name')
-                failure_report += "{test_suite} ({failure_summary})\n".format(
-                        test_suite=test_suite, failure_summary=failure_summary
-                    )
-                failure_cnt += get_count_for_pattern(r"([0-9]+) failed", failure_summary)
-                error_cnt += get_count_for_pattern(r"([0-9]+) error", failure_summary)
-                failed_test_suites.append(test_suite)
-
-            # Make the names unique and sorted
-            failed_test_suites = sorted(set(failed_test_suites))
-            # Gather all failed tests suites in case we missed any (e.g. when it exited due to syntax errors)
-            # Also unique and sorted to be able to compare the lists below
-            all_failed_test_suites = sorted(set(
-                re.findall(r"^(?P<test_name>.*) failed!(?: Received signal: \w+)?\s*$", tests_out, re.M)
-            ))
-            # If we missed any test suites prepend a list of all failed test suites
-            if failed_test_suites != all_failed_test_suites:
-                failure_report_save = failure_report
-                failure_report = 'Failed tests (suites/files):\n'
-                failure_report += '\n'.join('* %s' % t for t in all_failed_test_suites)
-                if failure_report_save:
-                    failure_report += '\n' + failure_report_save
-
-            # Calculate total number of unsuccesful and total tests
-            failed_test_cnt = failure_cnt + error_cnt
-            test_cnt = sum(int(hit) for hit in re.findall(r"^Ran (?P<test_cnt>[0-9]+) tests in", tests_out, re.M))
-
-            if failed_test_cnt > 0:
-                max_failed_tests = self.cfg['max_failed_tests']
-
-                failure_or_failures = 'failure' if failure_cnt == 1 else 'failures'
-                error_or_errors = 'error' if error_cnt == 1 else 'errors'
-                msg = "%d test %s, %d test %s (out of %d):\n" % (
-                    failure_cnt, failure_or_failures, error_cnt, error_or_errors, test_cnt
+        test_result = super(EB_PyTorch, self).test_step(return_output_ec=True)
+        if test_result is None:
+            if self.cfg['runtest'] or self.cfg['runtest'] is None:
+                msg = "runtest must be set to a command to run."
+            else:
+                msg = "Do not set runtest to False, use --skip-test-step instead."
+            raise EasyBuildError(msg)
+
+        tests_out, tests_ec = test_result
+
+        def get_count_for_pattern(regex, text):
+            """Match the regexp containing a single group and return the integer value of the matched group.
+               Return zero if no or more than 1 match was found and warn for the latter case
+            """
+            match = re.findall(regex, text)
+            if len(match) == 1:
+                return int(match[0])
+            elif len(match) > 1:
+                # Shouldn't happen, but means something went wrong with the regular expressions.
+                # Throw warning, as the build might be fine, no need to error on this.
+                warn_msg = "Error in counting the number of test failures in the output of the PyTorch test suite.\n"
+                warn_msg += "Please check the EasyBuild log to verify the number of failures (if any) was acceptable."
+                print_warning(warn_msg)
+            return 0
+
+        # Create clear summary report
+        failure_report = ""
+        failure_cnt = 0
+        error_cnt = 0
+        failed_test_suites = []
+
+        # Grep for patterns like:
+        # Ran 219 tests in 67.325s
+        #
+        # FAILED (errors=10, skipped=190, expected failures=6)
+        # test_fx failed!
+        regex = (r"^Ran (?P<test_cnt>[0-9]+) tests.*$\n\n"
+                 r"FAILED \((?P<failure_summary>.*)\)$\n"
+                 r"(?:^(?:(?!failed!).)*$\n)*"
+                 r"(?P<failed_test_suite_name>.*) failed!(?: Received signal: \w+)?\s*$")
+
+        for m in re.finditer(regex, tests_out, re.M):
+            # E.g. 'failures=3, errors=10, skipped=190, expected failures=6'
+            failure_summary = m.group('failure_summary')
+            total, test_suite = m.group('test_cnt', 'failed_test_suite_name')
+            failure_report += "{test_suite} ({total} total tests, {failure_summary})\n".format(
+                    test_suite=test_suite, total=total, failure_summary=failure_summary
                 )
-                msg += failure_report
-
-                # If no tests are supposed to fail or some failed for which we were not able to count errors fail now
-                if max_failed_tests == 0 or failed_test_suites != all_failed_test_suites:
-                    raise EasyBuildError(msg)
-                else:
-                    msg += '\n\n' + ' '.join([
-                        "The PyTorch test suite is known to include some flaky tests,",
-                        "which may fail depending on the specifics of the system or the context in which they are run.",
-                        "For this PyTorch installation, EasyBuild allows up to %d tests to fail." % max_failed_tests,
-                        "We recommend to double check that the failing tests listed above ",
-                        "are known to be flaky, or do not affect your intended usage of PyTorch.",
-                        "In case of doubt, reach out to the EasyBuild community (via GitHub, Slack, or mailing list).",
-                    ])
-                    # Print to console, the user should really be aware that we are accepting failing tests here...
-                    print_warning(msg)
-
-                    # Also log this warning in the file log
-                    self.log.warning(msg)
-
-                    if failed_test_cnt > max_failed_tests:
-                        raise EasyBuildError("Too many failed tests (%d), maximum allowed is %d",
-                                             failed_test_cnt, max_failed_tests)
-            elif failure_report:
-                raise EasyBuildError("Test command had non-zero exit code (%s)!\n%s", tests_ec, failure_report)
-            elif tests_ec:
-                raise EasyBuildError("Test command had non-zero exit code (%s), but no failed tests found?!", tests_ec)
+            failure_cnt += get_count_for_pattern(r"(?<!expected )failures=([0-9]+)", failure_summary)
+            error_cnt += get_count_for_pattern(r"errors=([0-9]+)", failure_summary)
+            failed_test_suites.append(test_suite)
+
+        # Grep for patterns like:
+        # ===================== 2 failed, 128 passed, 2 skipped, 2 warnings in 3.43s =====================
+        regex = r"^=+ (?P<failure_summary>.*) in [0-9]+\.*[0-9]*[a-zA-Z]* =+$\n(?P<failed_test_suite_name>.*) failed!$"
+
+        for m in re.finditer(regex, tests_out, re.M):
+            # E.g. '2 failed, 128 passed, 2 skipped, 2 warnings'
+            failure_summary = m.group('failure_summary')
+            test_suite = m.group('failed_test_suite_name')
+            failure_report += "{test_suite} ({failure_summary})\n".format(
+                    test_suite=test_suite, failure_summary=failure_summary
+                )
+            failure_cnt += get_count_for_pattern(r"([0-9]+) failed", failure_summary)
+            error_cnt += get_count_for_pattern(r"([0-9]+) error", failure_summary)
+            failed_test_suites.append(test_suite)
+
+        # Make the names unique and sorted
+        failed_test_suites = sorted(set(failed_test_suites))
+        # Gather all failed tests suites in case we missed any (e.g. when it exited due to syntax errors)
+        # Also unique and sorted to be able to compare the lists below
+        all_failed_test_suites = sorted(set(
+            re.findall(r"^(?P<test_name>.*) failed!(?: Received signal: \w+)?\s*$", tests_out, re.M)
+        ))
+        # If we missed any test suites prepend a list of all failed test suites
+        if failed_test_suites != all_failed_test_suites:
+            failure_report_save = failure_report
+            failure_report = 'Failed tests (suites/files):\n'
+            failure_report += '\n'.join('* %s' % t for t in all_failed_test_suites)
+            if failure_report_save:
+                failure_report += '\n' + failure_report_save
+
+        # Calculate total number of unsuccesful and total tests
+        failed_test_cnt = failure_cnt + error_cnt
+        test_cnt = sum(int(hit) for hit in re.findall(r"^Ran (?P<test_cnt>[0-9]+) tests in", tests_out, re.M))
+
+        if failed_test_cnt > 0:
+            max_failed_tests = self.cfg['max_failed_tests']
+
+            failure_or_failures = 'failure' if failure_cnt == 1 else 'failures'
+            error_or_errors = 'error' if error_cnt == 1 else 'errors'
+            msg = "%d test %s, %d test %s (out of %d):\n" % (
+                failure_cnt, failure_or_failures, error_cnt, error_or_errors, test_cnt
+            )
+            msg += failure_report
+
+            # If no tests are supposed to fail or some failed for which we were not able to count errors fail now
+            if max_failed_tests == 0 or failed_test_suites != all_failed_test_suites:
+                raise EasyBuildError(msg)
+            else:
+                msg += '\n\n' + ' '.join([
+                    "The PyTorch test suite is known to include some flaky tests,",
+                    "which may fail depending on the specifics of the system or the context in which they are run.",
+                    "For this PyTorch installation, EasyBuild allows up to %d tests to fail." % max_failed_tests,
+                    "We recommend to double check that the failing tests listed above ",
+                    "are known to be flaky, or do not affect your intended usage of PyTorch.",
+                    "In case of doubt, reach out to the EasyBuild community (via GitHub, Slack, or mailing list).",
+                ])
+                # Print to console, the user should really be aware that we are accepting failing tests here...
+                print_warning(msg)
+
+                # Also log this warning in the file log
+                self.log.warning(msg)
+
+                if failed_test_cnt > max_failed_tests:
+                    raise EasyBuildError("Too many failed tests (%d), maximum allowed is %d",
+                                         failed_test_cnt, max_failed_tests)
+        elif failure_report:
+            raise EasyBuildError("Test command had non-zero exit code (%s)!\n%s", tests_ec, failure_report)
+        elif tests_ec:
+            raise EasyBuildError("Test command had non-zero exit code (%s), but no failed tests found?!", tests_ec)
 
     def test_cases_step(self):
         self._set_cache_dir()

From 1714017478e60e2fa003f5ebba71ae9128fd1446 Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Thu, 9 Feb 2023 14:06:28 +0000
Subject: [PATCH 42/87] use with self.cfg.disable_templating():

---
 easybuild/easyblocks/generic/cmakemake.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/generic/cmakemake.py b/easybuild/easyblocks/generic/cmakemake.py
index 8bf841f313..c16c101bbe 100644
--- a/easybuild/easyblocks/generic/cmakemake.py
+++ b/easybuild/easyblocks/generic/cmakemake.py
@@ -143,16 +143,14 @@ def prepend_config_opts(self, config_opts):
         """Prepends configure options (-Dkey=value) to configopts ignoring those already set"""
         # need to disable template resolution or it will remain the same for all runs
         self.cfg.enable_templating = False
+        with self.cfg.disable_templating():
+            cfg_configopts = self.cfg['configopts']
 
-        cfg_configopts = self.cfg['configopts']
         # All options are of the form '-D<key>=<value>'
         new_opts = ' '.join('-D%s=%s' % (key, value) for key, value in config_opts.items()
                             if '-D%s=' % key not in cfg_configopts)
         self.cfg['configopts'] = ' '.join([new_opts, cfg_configopts])
 
-        # re-enable template resolution
-        self.cfg.enable_templating = True
-
     def configure_step(self, srcdir=None, builddir=None):
         """Configure build using cmake"""
 

From 7622313e4e7764ded6162056522c5cd07660e93e Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Thu, 9 Feb 2023 14:20:48 +0000
Subject: [PATCH 43/87] removed forgotten enable_templating = False line

---
 easybuild/easyblocks/generic/cmakemake.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/cmakemake.py b/easybuild/easyblocks/generic/cmakemake.py
index c16c101bbe..48cdae593a 100644
--- a/easybuild/easyblocks/generic/cmakemake.py
+++ b/easybuild/easyblocks/generic/cmakemake.py
@@ -142,7 +142,6 @@ def build_type(self):
     def prepend_config_opts(self, config_opts):
         """Prepends configure options (-Dkey=value) to configopts ignoring those already set"""
         # need to disable template resolution or it will remain the same for all runs
-        self.cfg.enable_templating = False
         with self.cfg.disable_templating():
             cfg_configopts = self.cfg['configopts']
 

From 8fff3f64e743be21af2131b408253854bc9fe4fb Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Thu, 9 Feb 2023 15:35:36 +0100
Subject: [PATCH 44/87] reverse test of runtest and clarify error message.

---
 easybuild/easyblocks/p/pytorch.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/p/pytorch.py b/easybuild/easyblocks/p/pytorch.py
index f4fd1e80f5..252bc09741 100644
--- a/easybuild/easyblocks/p/pytorch.py
+++ b/easybuild/easyblocks/p/pytorch.py
@@ -268,10 +268,10 @@ def test_step(self):
 
         test_result = super(EB_PyTorch, self).test_step(return_output_ec=True)
         if test_result is None:
-            if self.cfg['runtest'] or self.cfg['runtest'] is None:
-                msg = "runtest must be set to a command to run."
+            if self.cfg['runtest'] is False:
+                msg = "Do not set 'runtest' to False, use --skip-test-step instead."
             else:
-                msg = "Do not set runtest to False, use --skip-test-step instead."
+                msg = "Tests did not run. Make sure 'runtest' is set to a command."
             raise EasyBuildError(msg)
 
         tests_out, tests_ec = test_result

From 1d7fa6225b207ab19898fa61ac93405e131fad8d Mon Sep 17 00:00:00 2001
From: Alexander Grund <alexander.grund@tu-dresden.de>
Date: Thu, 9 Feb 2023 16:18:37 +0100
Subject: [PATCH 45/87] Fix to check for existance of config option in
 FlexiBLAS

Only checking for `key` might match where it should not.
Use the full `"-Dkey="` as the search string.
---
 easybuild/easyblocks/f/flexiblas.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/f/flexiblas.py b/easybuild/easyblocks/f/flexiblas.py
index 2a63c1650e..ab6fabfc50 100644
--- a/easybuild/easyblocks/f/flexiblas.py
+++ b/easybuild/easyblocks/f/flexiblas.py
@@ -138,7 +138,7 @@ def configure_step(self):
         # to allow easyconfig to override specifies settings
         for key, value in sorted(configopts.items()):
             opt = '-D%s=' % key
-            if key not in self.cfg['configopts']:
+            if opt not in self.cfg['configopts']:
                 self.cfg.update('configopts', opt + "'%s'" % value)
 
         # specify compiler commands with absolute paths, to ensure that RPATH wrapper scripts are used

From 6e30d90d2ba539f3be24eda20f906270ce82b50a Mon Sep 17 00:00:00 2001
From: Randy Pittman <randallpittman@outlook.com>
Date: Tue, 14 Feb 2023 14:38:17 -0800
Subject: [PATCH 46/87] Use older `ncgen -H` for older netCDF

Fixes #2888.
---
 easybuild/easyblocks/n/netcdf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/n/netcdf.py b/easybuild/easyblocks/n/netcdf.py
index 9ac62ff72c..45017748bb 100644
--- a/easybuild/easyblocks/n/netcdf.py
+++ b/easybuild/easyblocks/n/netcdf.py
@@ -143,7 +143,7 @@ def sanity_check_step(self):
 
         custom_commands = [
             "nc-config --help",
-            "ncgen -h",
+            "ncgen -h" if LooseVersion(self.version) > LooseVersion("4.6.1") else "ncgen -H",
         ]
 
         super(EB_netCDF, self).sanity_check_step(custom_commands=custom_commands, custom_paths=custom_paths)

From 566249a3f9ccfd9de8213efe48ecc8f17163fe5d Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 15 Feb 2023 17:05:55 +0100
Subject: [PATCH 47/87] always use -x option

---
 easybuild/easyblocks/generic/gopackage.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/generic/gopackage.py b/easybuild/easyblocks/generic/gopackage.py
index b94845b8cd..2dcc34c5d7 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -127,14 +127,12 @@ def build_step(self):
     def install_step(self):
         """Install Go package to a custom path"""
 
-        if build_option('debug'):
-            self.cfg['installopts'] = '-x ' + self.cfg['installopts']
-
         # actually install Go package
         cmd = ' '.join([
             self.cfg['preinstallopts'],
             'go',
             'install',
+            '-x',
             self.cfg['installopts'],
         ])
         run_cmd(cmd, log_all=True, log_ok=True, simple=True)

From 574190c5714a7fd7e6c1d44fa4e14df0e8c3eb26 Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 15 Feb 2023 17:06:54 +0100
Subject: [PATCH 48/87] remove stale update

---
 easybuild/easyblocks/generic/gopackage.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/gopackage.py b/easybuild/easyblocks/generic/gopackage.py
index 2dcc34c5d7..f60ef94daf 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -34,7 +34,6 @@
 from easybuild.framework.easyblock import EasyBlock
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.config import build_option
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.run import run_cmd
 

From a2323ecc5419ac1e639fe56b90154c37b78f2a7d Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 15 Feb 2023 17:42:48 +0100
Subject: [PATCH 49/87] add comment

---
 easybuild/easyblocks/generic/gopackage.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easybuild/easyblocks/generic/gopackage.py b/easybuild/easyblocks/generic/gopackage.py
index f60ef94daf..aa51ea05cb 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -131,6 +131,8 @@ def install_step(self):
             self.cfg['preinstallopts'],
             'go',
             'install',
+            # print commands as they are executed,
+            # such as downloads and installs of package deps as listed in the go.mod file
             '-x',
             self.cfg['installopts'],
         ])

From 8f1c579a3cf21843411c3b205df85379b4aa6acd Mon Sep 17 00:00:00 2001
From: Samuel Moors <samuel.moors@vub.be>
Date: Wed, 15 Feb 2023 17:45:12 +0100
Subject: [PATCH 50/87] tweak comment

---
 easybuild/easyblocks/generic/gopackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/gopackage.py b/easybuild/easyblocks/generic/gopackage.py
index aa51ea05cb..c06f724437 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -132,7 +132,7 @@ def install_step(self):
             'go',
             'install',
             # print commands as they are executed,
-            # such as downloads and installs of package deps as listed in the go.mod file
+            # including downloading and installing of package deps as listed in the go.mod file
             '-x',
             self.cfg['installopts'],
         ])

From 00efdf1823d74d84ce6c05b5d61f6ccd134f7b0a Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 8 Feb 2023 15:54:59 +0100
Subject: [PATCH 51/87] add deprecation notice to RPackage extensions with
 relative paths in start_dir

---
 easybuild/easyblocks/generic/rpackage.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/rpackage.py b/easybuild/easyblocks/generic/rpackage.py
index 190e416db0..897408503c 100644
--- a/easybuild/easyblocks/generic/rpackage.py
+++ b/easybuild/easyblocks/generic/rpackage.py
@@ -134,10 +134,19 @@ def make_cmdline_cmd(self, prefix=None):
         else:
             prefix = ''
 
+        loc = self.start_dir
+        if loc is None:
+            loc = self.ext_dir or self.ext_src
+        elif not os.path.isabs(loc):
+            # TODO: deprecated behaviour in framework 4.7.1, remove after 5.0
+            loc = os.path.join(self.ext_dir or os.path.sep, loc)
+            deprecation_msg = "Found relative path in start_dir, please upgrade to easybuild-framework>=4.7.1"
+            self.log.deprecated(deprecation_msg, '5.0')
+
         cmd = ' '.join([
             self.cfg['preinstallopts'],
             "R CMD INSTALL",
-            self.start_dir,
+            loc,
             confargs,
             confvars,
             prefix,

From 016118af4c54d9b604d91132e65a6020232443f7 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Thu, 16 Feb 2023 11:17:42 +0000
Subject: [PATCH 52/87] apply suggestions from review

---
 easybuild/easyblocks/s/scipy.py | 31 +++++++++++++++++++++----------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 1df30766b9..9473a2f145 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -54,8 +54,9 @@ def extra_options():
         """Easyconfig parameters specific to scipy."""
         extra_vars = ({
             'enable_slow_tests': [False, "Run scipy test suite, including tests marked as slow", CUSTOM],
-            # ignore tests by default to maintain behaviour in older easyconfigs
-            'ignore_test_result': [None, "Run scipy test suite, but ignore result (only log)", CUSTOM],
+            # ignore test failures by default in scipy < 1.9 to maintain behaviour in older easyconfigs
+            'ignore_test_result': [None, "Run scipy test suite, but ignore test failures (True/False/None). Default "
+                                         "(None) implies True for scipy < 1.9, and False for scipy ?= 1.9", CUSTOM],
         })
 
         return PythonPackage.extra_options(extra_vars=extra_vars)
@@ -68,17 +69,27 @@ def __init__(self, *args, **kwargs):
 
         if LooseVersion(self.version) >= LooseVersion('1.9'):
             self.use_meson = True
+
             # enforce scipy test suite results if not explicitly disabled for scipy >= 1.9
             if self.cfg['ignore_test_result'] is None:
-                self.cfg['ignore_test_result'] = True
-            # ignore installopts inherited from FortranPythonPackage
-            self.cfg['installopts'] = ""
+                self.cfg['ignore_test_result'] = False
+
+            # strip inherited PythonPackage installopts
+            installopts = self.cfg['installopts']
+            pythonpackage_installopts = ['--no-deps', '--ignore-installed', '--no-index', '--egg',
+                                         '--zip-ok', '--no-index']
+            self.log.info("Stripping inherited PythonPackage installopts %s from installopts %s",
+                          pythonpackage_installopts, installopts)
+            for i in pythonpackage_installopts:
+                installopts.replace(i, '')
+            self.cfg['installopts'] = installopts
+
         else:
             self.use_meson = False
 
         if self.cfg['ignore_test_result']:
-            # maintains compatibility with easyconfigs predating scipy 1.9. Runs tests (serially) in
-            # a way that exits with code 0 regardless of test results, see:
+            # can be used to maintain compatibility with easyconfigs predating scipy 1.9. Runs tests
+            # (serially) in a way that exits with code 0 regardless of test results, see:
             # https://github.com/easybuilders/easybuild-easyblocks/issues/2237
             self.testcmd = "cd .. && %(python)s -c 'import numpy; import scipy; scipy.test(verbose=2)'"
         else:
@@ -106,8 +117,8 @@ def configure_step(self):
             else:
                 raise EasyBuildError("Unknown BLAS/LAPACK library used: %s", lapack_lib)
 
-            configopts = '-Dblas=%(blas_lapack)s -Dlapack=%(blas_lapack)s' % {'blas_lapack': blas_lapack}
-            self.cfg.update('configopts', configopts)
+            for opt in ('blas', 'lapack'):
+                self.cfg.update('configopts', '-D%(opt)s=%(blas_lapack)s' % {'opt': opt, 'blas_lapack': blas_lapack})
 
             # need to have already installed extensions in PATH, PYTHONPATH for configure/build/install steps
             pythonpath = os.getenv('PYTHONPATH')
@@ -120,6 +131,7 @@ def configure_step(self):
             MesonNinja.configure_step(self)
 
         else:
+            # scipy < 1.9.0 uses install procedure using setup.py
             FortranPythonPackage.configure_step(self)
 
         if LooseVersion(self.version) >= LooseVersion('0.13'):
@@ -184,7 +196,6 @@ def install_step(self):
         """Custom install step for scipy: use ninja for scipy >= 1.9.0"""
         if self.use_meson:
             MesonNinja.install_step(self)
-
         else:
             FortranPythonPackage.install_step(self)
 

From a69b47f42eef6eddb57c2a403580fc7f89e12b57 Mon Sep 17 00:00:00 2001
From: Jasper <65227842+jfgrimm@users.noreply.github.com>
Date: Thu, 16 Feb 2023 13:38:32 +0000
Subject: [PATCH 53/87] Update easybuild/easyblocks/s/scipy.py

Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com>
---
 easybuild/easyblocks/s/scipy.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 9473a2f145..77504eed40 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -81,7 +81,7 @@ def __init__(self, *args, **kwargs):
             self.log.info("Stripping inherited PythonPackage installopts %s from installopts %s",
                           pythonpackage_installopts, installopts)
             for i in pythonpackage_installopts:
-                installopts.replace(i, '')
+                installopts = installopts.replace(i, '')
             self.cfg['installopts'] = installopts
 
         else:

From f2b4131c0821019b47d96568fc604ee0bcf20de0 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Tue, 21 Feb 2023 13:47:20 +0100
Subject: [PATCH 54/87] split depot path in JuliaPackage with os.pathsep

---
 easybuild/easyblocks/generic/juliapackage.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/juliapackage.py b/easybuild/easyblocks/generic/juliapackage.py
index 2490bc2823..ff8bc74298 100644
--- a/easybuild/easyblocks/generic/juliapackage.py
+++ b/easybuild/easyblocks/generic/juliapackage.py
@@ -99,8 +99,10 @@ def install_step(self):
         # extensions in a bundle can share their DEPOT_PATH
         # see https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
         depot_path = os.getenv('JULIA_DEPOT_PATH', '')
+        if depot_path:
+            depot_path = depot_path.split(os.pathsep)
         if self.installdir not in depot_path:
-            depot_path = ':'.join([depot for depot in (self.installdir, depot_path) if depot])
+            depot_path = os.pathsep.join([depot for depot in (self.installdir, depot_path) if depot])
             env.setvar('JULIA_DEPOT_PATH', depot_path)
 
         # command sequence for Julia.Pkg

From b360347928de191ec945dab106dbb8d5e98337d9 Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Tue, 21 Feb 2023 15:44:30 +0000
Subject: [PATCH 55/87] allow disabling pybind11 tests

---
 easybuild/easyblocks/p/pybind11.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/p/pybind11.py b/easybuild/easyblocks/p/pybind11.py
index 09d711b28c..1174d23a13 100644
--- a/easybuild/easyblocks/p/pybind11.py
+++ b/easybuild/easyblocks/p/pybind11.py
@@ -70,8 +70,9 @@ def configure_step(self):
 
     def test_step(self):
         """Run pybind11 tests"""
-        # always run tests
-        self.cfg['runtest'] = 'check'
+        # always run tests unless explicitly disabled
+        if self.cfg['runtest'] is not False:
+            self.cfg['runtest'] = 'check'
         super(EB_pybind11, self).test_step()
 
     def install_step(self):

From c99e441abb542ab67f74fb4075e5ce695eb0903d Mon Sep 17 00:00:00 2001
From: Maxime Boissonneault <maxime.boissonneault@calculquebec.ca>
Date: Tue, 21 Feb 2023 11:16:37 -0500
Subject: [PATCH 56/87] Update easybuild/easyblocks/p/pybind11.py

Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com>
---
 easybuild/easyblocks/p/pybind11.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/p/pybind11.py b/easybuild/easyblocks/p/pybind11.py
index 1174d23a13..d964ffb9ac 100644
--- a/easybuild/easyblocks/p/pybind11.py
+++ b/easybuild/easyblocks/p/pybind11.py
@@ -70,7 +70,7 @@ def configure_step(self):
 
     def test_step(self):
         """Run pybind11 tests"""
-        # always run tests unless explicitly disabled
+        # run tests unless explicitly disabled
         if self.cfg['runtest'] is not False:
             self.cfg['runtest'] = 'check'
         super(EB_pybind11, self).test_step()

From d6e4e25d5d5a10bceb87885fb16d421b7e4f4502 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Francisco=20Jos=C3=A9=20Gonz=C3=A1lez=20Carrillo?=
 <francisco.gonzalez@hpcnow.com>
Date: Wed, 22 Feb 2023 12:00:38 +0100
Subject: [PATCH 57/87] Adding support for postinstallcmds in easybuildmeta

---
 easybuild/easyblocks/e/easybuildmeta.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyblocks/e/easybuildmeta.py b/easybuild/easyblocks/e/easybuildmeta.py
index baac89baa0..f0ff1f340a 100644
--- a/easybuild/easyblocks/e/easybuildmeta.py
+++ b/easybuild/easyblocks/e/easybuildmeta.py
@@ -157,6 +157,7 @@ def install_step(self):
     def post_install_step(self):
         """Remove setuptools.pth file that hard includes a system-wide (site-packages) path, if it is there."""
 
+        super(EB_EasyBuildMeta, self).post_install_step()
         setuptools_pth = os.path.join(self.installdir, self.pylibdir, 'setuptools.pth')
         if os.path.exists(setuptools_pth):
             setuptools_pth_txt = read_file(setuptools_pth)

From 4c11ffaf6bfe91309596bf22cf0f2198d3bde4c7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 23 Feb 2023 09:40:16 +0100
Subject: [PATCH 58/87] add blank line in post_install_step method of
 EasyBuildMeta easyblock to improve readability

---
 easybuild/easyblocks/e/easybuildmeta.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyblocks/e/easybuildmeta.py b/easybuild/easyblocks/e/easybuildmeta.py
index f0ff1f340a..f4b52ff921 100644
--- a/easybuild/easyblocks/e/easybuildmeta.py
+++ b/easybuild/easyblocks/e/easybuildmeta.py
@@ -158,6 +158,7 @@ def post_install_step(self):
         """Remove setuptools.pth file that hard includes a system-wide (site-packages) path, if it is there."""
 
         super(EB_EasyBuildMeta, self).post_install_step()
+
         setuptools_pth = os.path.join(self.installdir, self.pylibdir, 'setuptools.pth')
         if os.path.exists(setuptools_pth):
             setuptools_pth_txt = read_file(setuptools_pth)

From 91cee1036d35f229f132c94e361456b65598f581 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Fri, 24 Feb 2023 13:30:33 +0100
Subject: [PATCH 59/87] Added GPU support to ELPA EasyBlock. If CUDA is
 specified in the EasyConfig, automatically enable nvidia GPU support

---
 easybuild/easyblocks/e/elpa.py | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index 8ac4856207..116bd2abea 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -39,7 +39,7 @@
 from easybuild.tools.systemtools import get_cpu_features, get_shared_lib_ext
 from easybuild.tools.toolchain.compiler import OPTARCH_GENERIC
 from easybuild.tools.utilities import nub
-
+from easybuild.tools.modules import get_software_root
 
 ELPA_CPU_FEATURE_FLAGS = ['avx', 'avx2', 'avx512f', 'vsx', 'sse4_2']
 
@@ -176,6 +176,28 @@ def run_all_steps(self, *args, **kwargs):
 
         return super(EB_ELPA, self).run_all_steps(*args, **kwargs)
 
+    def configure_step(self):
+        """Configure step for ELPA"""
+
+        # Add nvidia GPU support if requested
+        cuda_root = get_software_root('CUDA')
+        self.log.info("Got cuda root: %s", cuda_root)
+        if cuda_root:
+            self.cfg.update('configopts', '--enable-nvidia-gpu')
+            self.cfg.update('configopts', '--with-cuda-path=%s' % cuda_root)
+            self.cfg.update('configopts', '--with-cuda-sdk-path=%s' % cuda_root)
+
+            cuda_cc = build_option('cuda_compute_capabilities') or self.cfg['cuda_compute_capabilities']
+            if not cuda_cc:
+                raise EasyBuildError('List of CUDA compute capabilities must be specified, either via '
+                                     'cuda_compute_capabilities easyconfig parameter or via '
+                                     '--cuda-compute-capabilities')
+            cuda_cc_string = ','.join(['sm_%s' % x.replace('.', '') for x in cuda_cc])
+            self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=%s' % cuda_cc_string)
+            self.log.info("Enabling nvidia GPU support for compute capabilitie: %s", cuda_cc_string)
+
+        super(EB_ELPA, self).configure_step()
+
     def patch_step(self, *args, **kwargs):
         """Patch manual_cpp script to avoid using hardcoded /usr/bin/python."""
         super(EB_ELPA, self).patch_step(*args, **kwargs)

From ca7775227ef921e480599428ef29ad8002c6480b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Fri, 24 Feb 2023 13:46:58 +0100
Subject: [PATCH 60/87] Currently, ELPA only supports passing one architecture
 to --with-NVIDIA-GPU-compute-capability=VALUE

---
 easybuild/easyblocks/e/elpa.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index 116bd2abea..189c99068c 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -192,6 +192,12 @@ def configure_step(self):
                 raise EasyBuildError('List of CUDA compute capabilities must be specified, either via '
                                      'cuda_compute_capabilities easyconfig parameter or via '
                                      '--cuda-compute-capabilities')
+
+            # ELPA's --with-NVIDIA-GPU-compute-capability only accepts a single architecture
+            if len(cuda_cc) > 1:
+                raise EasyBuildError('ELPA currently only supports specifying one architecture when '
+                                     'building. You specified cuda-compute-capabilities: %s', cuda_cc)
+
             cuda_cc_string = ','.join(['sm_%s' % x.replace('.', '') for x in cuda_cc])
             self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=%s' % cuda_cc_string)
             self.log.info("Enabling nvidia GPU support for compute capabilitie: %s", cuda_cc_string)

From 4865037803d4b98837845f07c94a94f678995f1b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Fri, 24 Feb 2023 17:35:27 +0100
Subject: [PATCH 61/87] Make sure to set CPP, as newer ELPA configures require
 it

---
 easybuild/easyblocks/e/elpa.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index 189c99068c..cdbce5f23c 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -31,6 +31,7 @@
 """
 import os
 
+import easybuild.tools.environment as env
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.tools.build_log import EasyBuildError
@@ -202,6 +203,17 @@ def configure_step(self):
             self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=%s' % cuda_cc_string)
             self.log.info("Enabling nvidia GPU support for compute capabilitie: %s", cuda_cc_string)
 
+        # From v2022.05.001 onwards, the config complains if CPP is not set
+        env_dict = env.read_environment({'cxx': 'CXX', 'cpp': 'CPP'})
+        if 'cxx' in env_dict:
+            if 'cpp' in env_dict and env_dict['cxx'] != env_dict['cpp']:
+                self.log.warning("Overwriting value of CPP (%s) with the value for CXX (%s)",
+                                 env_dict['cpp'], env_dict['cxx'])
+            env.setvar('CPP', env_dict['cxx'])
+        else:
+            raise EasyBuildError('ELPA requires CPP to be set. EasyBuild tried setting it based on the value of CXX, '
+                                 'but could not retreive a value for CXX')
+
         super(EB_ELPA, self).configure_step()
 
     def patch_step(self, *args, **kwargs):

From 6642b40e99c847f3e30c3ba02e38e31fca2ca457 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Fri, 24 Feb 2023 18:55:57 +0100
Subject: [PATCH 62/87] Set CPP env var to cpp. This is valid for GCC, but we
 might make to make this neater and read it from the compiler definition from
 easybuild-framework. Still discussing that on EB slack

---
 easybuild/easyblocks/e/elpa.py | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index cdbce5f23c..51742b1d0d 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -204,15 +204,9 @@ def configure_step(self):
             self.log.info("Enabling nvidia GPU support for compute capabilitie: %s", cuda_cc_string)
 
         # From v2022.05.001 onwards, the config complains if CPP is not set
-        env_dict = env.read_environment({'cxx': 'CXX', 'cpp': 'CPP'})
-        if 'cxx' in env_dict:
-            if 'cpp' in env_dict and env_dict['cxx'] != env_dict['cpp']:
-                self.log.warning("Overwriting value of CPP (%s) with the value for CXX (%s)",
-                                 env_dict['cpp'], env_dict['cxx'])
-            env.setvar('CPP', env_dict['cxx'])
-        else:
-            raise EasyBuildError('ELPA requires CPP to be set. EasyBuild tried setting it based on the value of CXX, '
-                                 'but could not retreive a value for CXX')
+        # Need to make this neater so that it is either set by easybuild-framework, OR query the toolchain for something like COMPILER_CPP
+        # Discussing that right now on EB Slack...
+        env.setvar('CPP', 'cpp')
 
         super(EB_ELPA, self).configure_step()
 

From a11a1a4ddc2e5730df59bb008e7dff9684a804d0 Mon Sep 17 00:00:00 2001
From: Sven Hansen <sven.hansen2@rwth-aachen.de>
Date: Fri, 24 Feb 2023 23:19:38 +0100
Subject: [PATCH 63/87] update Maple easyblock for v2022

---
 easybuild/easyblocks/m/maple.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/m/maple.py b/easybuild/easyblocks/m/maple.py
index 14621e8515..bf3b75f2aa 100644
--- a/easybuild/easyblocks/m/maple.py
+++ b/easybuild/easyblocks/m/maple.py
@@ -30,6 +30,7 @@
 @author: Kenneth Hoste (Ghent University)
 @author: Pieter De Baets (Ghent University)
 @author: Jens Timmerman (Ghent University)
+@author: Sven Hansen (RWTH Aachen University)
 """
 import glob
 import os
@@ -61,6 +62,8 @@ def install_step(self):
             "Do you accept this license? [y/n]:": 'y',
             'ENTER AN ABSOLUTE PATH, OR PRESS <ENTER> TO ACCEPT THE DEFAULT :': self.installdir,
             'IS THIS CORRECT? (Y/N):': 'Y',
+            'Language Selection\n\nPlease select the installation language\n[1] English - English\n[2] Japanese - \n'
+            'Please choose an option [1] : ': '1',
             'Do you wish to have a shortcut installed on your desktop? ->1- Yes 2- No ENTER THE NUMBER ' +
             'FOR YOUR CHOICE, OR PRESS <ENTER> TO ACCEPT THE DEFAULT::': '2',
             "Do you wish to have a shortcut installed on your desktop? [Y/n]:": 'n',
@@ -83,6 +86,7 @@ def install_step(self):
             r"\[1\] Single Server.*\n.*\nPlease choose an option \[.\] :": '1',
             r"Port number \[[0-9]+\]:": '',
             r"Enable periodic checking for Maple .* updates after installation \[Y/n\]:": 'n',
+            r'Pre-Installation Summary[\s\S]*': '',
         }
 
         no_qa = [
@@ -91,10 +95,10 @@ def install_step(self):
             'Launching installer...',
             "Configuring the installer for this system's environment...",
             'Unpacking the JRE...',
-            r'\[[-|]*',
+            r'\[[-|#|]*',
         ]
 
-        run_cmd_qa(cmd, qa, std_qa=std_qa, no_qa=no_qa, log_all=True, simple=True)
+        run_cmd_qa(cmd, qa, std_qa=std_qa, no_qa=no_qa, log_all=True, simple=True, maxhits=150)
 
         upgrade_installers = glob.glob(os.path.join(self.builddir, 'Maple*Upgrade*'))
         if upgrade_installers:

From 1b639923f34f011f5d087b914a293855425e3913 Mon Sep 17 00:00:00 2001
From: Sven Hansen <sven.hansen2@rwth-aachen.de>
Date: Fri, 24 Feb 2023 23:20:40 +0100
Subject: [PATCH 64/87] allow custom license server ports in Maple easyblock

---
 easybuild/easyblocks/m/maple.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/m/maple.py b/easybuild/easyblocks/m/maple.py
index bf3b75f2aa..65868877ff 100644
--- a/easybuild/easyblocks/m/maple.py
+++ b/easybuild/easyblocks/m/maple.py
@@ -72,7 +72,7 @@ def install_step(self):
             'PRESS <ENTER> TO EXIT THE INSTALLER:': '',
             'License server (DEFAULT: ):': self.cfg['license_server'],
             "License server []:": self.cfg['license_server'],
-            'Port number (optional) (DEFAULT: ):': '',
+            'Port number (optional) (DEFAULT: ):': self.cfg['license_server_port'] or '',
             '->1- Configure toolbox for Matlab 2- Do not configure at this time ENTER THE NUMBER FOR YOUR CHOICE, ' +
             'OR PRESS <ENTER> TO ACCEPT THE DEFAULT::': '2',
             "MATLAB Configuration [y/N]:": 'n',
@@ -84,7 +84,7 @@ def install_step(self):
             r"Choose Install Folder \[.*\]:": self.installdir,
             r"\[2\] Network License.*\nPlease choose an option \[.\] :": '2',
             r"\[1\] Single Server.*\n.*\nPlease choose an option \[.\] :": '1',
-            r"Port number \[[0-9]+\]:": '',
+            r"Port number \[[0-9]+\]:": self.cfg['license_server_port'] or '',
             r"Enable periodic checking for Maple .* updates after installation \[Y/n\]:": 'n',
             r'Pre-Installation Summary[\s\S]*': '',
         }

From 41b424c47091f1a6686ace61700a73d87ced8f66 Mon Sep 17 00:00:00 2001
From: Jasper Grimm <jasper.grimm@york.ac.uk>
Date: Sat, 25 Feb 2023 09:00:24 +0000
Subject: [PATCH 65/87] fix default ignore_test_result logic

---
 easybuild/easyblocks/s/scipy.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 77504eed40..2ba91030dc 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -56,7 +56,7 @@ def extra_options():
             'enable_slow_tests': [False, "Run scipy test suite, including tests marked as slow", CUSTOM],
             # ignore test failures by default in scipy < 1.9 to maintain behaviour in older easyconfigs
             'ignore_test_result': [None, "Run scipy test suite, but ignore test failures (True/False/None). Default "
-                                         "(None) implies True for scipy < 1.9, and False for scipy ?= 1.9", CUSTOM],
+                                         "(None) implies True for scipy < 1.9, and False for scipy >= 1.9", CUSTOM],
         })
 
         return PythonPackage.extra_options(extra_vars=extra_vars)
@@ -71,9 +71,6 @@ def __init__(self, *args, **kwargs):
             self.use_meson = True
 
             # enforce scipy test suite results if not explicitly disabled for scipy >= 1.9
-            if self.cfg['ignore_test_result'] is None:
-                self.cfg['ignore_test_result'] = False
-
             # strip inherited PythonPackage installopts
             installopts = self.cfg['installopts']
             pythonpackage_installopts = ['--no-deps', '--ignore-installed', '--no-index', '--egg',
@@ -87,6 +84,13 @@ def __init__(self, *args, **kwargs):
         else:
             self.use_meson = False
 
+        if self.cfg['ignore_test_result'] is None:
+            # enforce scipy test suite results if not explicitly disabled for scipy >= 1.9
+            if self.use_meson:
+                self.cfg['ignore_test_result'] = False
+            else:
+                self.cfg['ignore_test_result'] = True
+
         if self.cfg['ignore_test_result']:
             # can be used to maintain compatibility with easyconfigs predating scipy 1.9. Runs tests
             # (serially) in a way that exits with code 0 regardless of test results, see:

From f53a4c67e8f56155d7dc4ac5ca2a995e0ee8a028 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Feb 2023 10:10:39 +0100
Subject: [PATCH 66/87] simplify logic to set default value for
 ignore_test_result in scipy easyblock

---
 easybuild/easyblocks/s/scipy.py | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 2ba91030dc..1c21a01fc2 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -54,7 +54,6 @@ def extra_options():
         """Easyconfig parameters specific to scipy."""
         extra_vars = ({
             'enable_slow_tests': [False, "Run scipy test suite, including tests marked as slow", CUSTOM],
-            # ignore test failures by default in scipy < 1.9 to maintain behaviour in older easyconfigs
             'ignore_test_result': [None, "Run scipy test suite, but ignore test failures (True/False/None). Default "
                                          "(None) implies True for scipy < 1.9, and False for scipy >= 1.9", CUSTOM],
         })
@@ -85,16 +84,15 @@ def __init__(self, *args, **kwargs):
             self.use_meson = False
 
         if self.cfg['ignore_test_result'] is None:
-            # enforce scipy test suite results if not explicitly disabled for scipy >= 1.9
-            if self.use_meson:
-                self.cfg['ignore_test_result'] = False
-            else:
-                self.cfg['ignore_test_result'] = True
+            # automatically ignore scipy test suite results for scipy < 1.9, as we did in older easyconfigs
+            self.cfg['ignore_test_result'] = LooseVersion(self.version) < '1.9'
+            self.log.info("ignore_test_result not specified, so automatically set to %s for scipy %s",
+                          self.cfg['ignore_test_result'], self.version)
 
         if self.cfg['ignore_test_result']:
-            # can be used to maintain compatibility with easyconfigs predating scipy 1.9. Runs tests
-            # (serially) in a way that exits with code 0 regardless of test results, see:
-            # https://github.com/easybuilders/easybuild-easyblocks/issues/2237
+            # used to maintain compatibility with easyconfigs predating scipy 1.9;
+            # runs tests (serially) in a way that exits with code 0 regardless of test results,
+            # see https://github.com/easybuilders/easybuild-easyblocks/issues/2237
             self.testcmd = "cd .. && %(python)s -c 'import numpy; import scipy; scipy.test(verbose=2)'"
         else:
             self.testcmd = " && ".join([

From 82472980646e5117c0783618e6319d4f3f4f0d52 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Feb 2023 19:15:13 +0100
Subject: [PATCH 67/87] relax glob pattern to find Mathematica install script

---
 easybuild/easyblocks/m/mathematica.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/m/mathematica.py b/easybuild/easyblocks/m/mathematica.py
index 13a3080ff4..9f1fb78827 100644
--- a/easybuild/easyblocks/m/mathematica.py
+++ b/easybuild/easyblocks/m/mathematica.py
@@ -68,7 +68,7 @@ def install_step(self):
         install_script_glob = '%s_%s_LINUX*.sh' % (self.name, self.version)
         # Starting at V13, Mathematica have renamed their install file...
         if LooseVersion(self.version) >= LooseVersion("13"):
-            install_script_glob = '%s_%s_BNDL_LINUX*.sh' % (self.name, self.version)
+            install_script_glob = '%s_%s_*LINUX*.sh' % (self.name, self.version)
 
         matches = glob.glob(install_script_glob)
         if len(matches) == 1:

From b587ae82fd739f7831fbeb7c1e90b413bc56ee50 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Feb 2023 19:22:25 +0100
Subject: [PATCH 68/87] fix linking numexpr with Intel MKL's VML library for
 imkl >= 2021.x

---
 easybuild/easyblocks/n/numexpr.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/n/numexpr.py b/easybuild/easyblocks/n/numexpr.py
index b5d23e73d0..81ba8d8f0a 100644
--- a/easybuild/easyblocks/n/numexpr.py
+++ b/easybuild/easyblocks/n/numexpr.py
@@ -55,12 +55,16 @@ def __init__(self, *args, **kwargs):
 
         self.imkl_root = None
 
+    def prepare_step(self, *args, **kwargs):
+        """Custom prepare step for numexpr: check whether we're building on top of Intel MKL."""
+        super(EB_numexpr, self).prepare_step(*args, **kwargs)
+
+        self.imkl_root = get_software_root('imkl')
+
     def configure_step(self):
         """Custom configuration procedure for numexpr."""
         super(EB_numexpr, self).configure_step()
 
-        self.imkl_root = get_software_root('imkl')
-
         # if Intel MKL is available, set up site.cfg such that the right VML library is used;
         # this makes a *big* difference in terms of performance;
         # see also https://github.com/pydata/numexpr/blob/master/site.cfg.example
@@ -122,8 +126,15 @@ def sanity_check_step(self):
 
         custom_commands = []
 
+        # imkl_root may still be None, for example when running with --sanity-check-only
+        if self.imkl_root is None:
+            self.imkl_root = get_software_root('imkl')
+
         # if Intel MKL is available, make sure VML is used
         if self.imkl_root:
-            custom_commands.append("python -c 'import numexpr; assert(numexpr.use_vml)'")
+            custom_commands.extend([
+                "python -c 'import numexpr; assert(numexpr.use_vml)'",
+                """python -c "import numexpr; numexpr.set_vml_accuracy_mode('low')" """,
+            ])
 
         return super(EB_numexpr, self).sanity_check_step(custom_commands=custom_commands)

From b372286d0b1074cdd269e251e4694a0bc1f20970 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Feb 2023 23:00:22 +0100
Subject: [PATCH 69/87] use libmkl_rt to link numexpr with imkl >= 2021.x

---
 easybuild/easyblocks/n/numexpr.py | 19 +++----------------
 1 file changed, 3 insertions(+), 16 deletions(-)

diff --git a/easybuild/easyblocks/n/numexpr.py b/easybuild/easyblocks/n/numexpr.py
index 81ba8d8f0a..deafddb122 100644
--- a/easybuild/easyblocks/n/numexpr.py
+++ b/easybuild/easyblocks/n/numexpr.py
@@ -28,7 +28,6 @@
 import os
 from distutils.version import LooseVersion
 
-import easybuild.tools.toolchain as toolchain
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import write_file
@@ -55,16 +54,12 @@ def __init__(self, *args, **kwargs):
 
         self.imkl_root = None
 
-    def prepare_step(self, *args, **kwargs):
-        """Custom prepare step for numexpr: check whether we're building on top of Intel MKL."""
-        super(EB_numexpr, self).prepare_step(*args, **kwargs)
-
-        self.imkl_root = get_software_root('imkl')
-
     def configure_step(self):
         """Custom configuration procedure for numexpr."""
         super(EB_numexpr, self).configure_step()
 
+        self.imkl_root = get_software_root('imkl')
+
         # if Intel MKL is available, set up site.cfg such that the right VML library is used;
         # this makes a *big* difference in terms of performance;
         # see also https://github.com/pydata/numexpr/blob/master/site.cfg.example
@@ -84,20 +79,12 @@ def configure_step(self):
 
             mkl_ver = get_software_version('imkl')
 
-            comp_fam = self.toolchain.comp_family()
-            self.log.info("Using toolchain with compiler family %s", comp_fam)
-
             if LooseVersion(mkl_ver) >= LooseVersion('2021'):
                 mkl_lib_dirs = [
                     os.path.join(self.imkl_root, 'mkl', 'latest', 'lib', 'intel64'),
                 ]
                 mkl_include_dirs = os.path.join(self.imkl_root, 'mkl', 'latest', 'include')
-                if comp_fam == toolchain.INTELCOMP:
-                    mkl_libs = ['mkl_intel_lp64', 'mkl_intel_thread', 'mkl_core', 'iomp5']
-                elif comp_fam == toolchain.GCC:
-                    mkl_libs = ['mkl_intel_lp64', 'mkl_gnu_thread', 'mkl_core', 'gomp']
-                else:
-                    raise EasyBuildError("Unknown compiler family, don't know how to link MKL libraries: %s", comp_fam)
+                mkl_libs = ['mkl_rt']
             else:
                 mkl_lib_dirs = [
                     os.path.join(self.imkl_root, 'mkl', 'lib', 'intel64'),

From 138b6629be6916e2ab6e3c4f13c3a140e29f268a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 25 Feb 2023 23:03:33 +0100
Subject: [PATCH 70/87] remove unused import for EasyBuildError in numexpr
 easyblock

---
 easybuild/easyblocks/n/numexpr.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyblocks/n/numexpr.py b/easybuild/easyblocks/n/numexpr.py
index deafddb122..40e01f0cb8 100644
--- a/easybuild/easyblocks/n/numexpr.py
+++ b/easybuild/easyblocks/n/numexpr.py
@@ -29,7 +29,6 @@
 from distutils.version import LooseVersion
 
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage
-from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.filetools import write_file
 from easybuild.tools.modules import get_software_root, get_software_version
 from easybuild.tools.systemtools import get_cpu_features

From 88e4b3aab8c60afe8757641c8fb1e015ff290d3e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 26 Feb 2023 19:43:44 +0100
Subject: [PATCH 71/87] only do a more extensive check for VML support for
 numexpr >= 2.7.3

---
 easybuild/easyblocks/n/numexpr.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/n/numexpr.py b/easybuild/easyblocks/n/numexpr.py
index 40e01f0cb8..1c62b4502c 100644
--- a/easybuild/easyblocks/n/numexpr.py
+++ b/easybuild/easyblocks/n/numexpr.py
@@ -118,9 +118,10 @@ def sanity_check_step(self):
 
         # if Intel MKL is available, make sure VML is used
         if self.imkl_root:
-            custom_commands.extend([
-                "python -c 'import numexpr; assert(numexpr.use_vml)'",
-                """python -c "import numexpr; numexpr.set_vml_accuracy_mode('low')" """,
-            ])
+            custom_commands.append("python -c 'import numexpr; assert(numexpr.use_vml)'")
+
+            # for sufficiently recent versions of numexpr, also do a more extensive check for VML support
+            if LooseVersion(self.version) >= LooseVersion('2.7.3'):
+                custom_commands.append("""python -c "import numexpr; numexpr.set_vml_accuracy_mode('low')" """)
 
         return super(EB_numexpr, self).sanity_check_step(custom_commands=custom_commands)

From c687f9095d5c0616cd33a963fd7244fb5db4b907 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Mon, 27 Feb 2023 12:02:44 +0100
Subject: [PATCH 72/87] Fixed typo, added option to enable dedicated sm80
 kernel, set CPP (C preprocessor environment variable) in a way that can
 easily be extended or modified per toolchain family

---
 easybuild/easyblocks/e/elpa.py | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index 51742b1d0d..255abe4ee2 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -30,10 +30,13 @@
 @author: Kenneth Hoste (Ghent University)
 """
 import os
+from distutils.version import LooseVersion
 
 import easybuild.tools.environment as env
 from easybuild.easyblocks.generic.configuremake import ConfigureMake
 from easybuild.framework.easyconfig import CUSTOM
+from easybuild.toolchains.compiler.gcc import TC_CONSTANT_GCC
+from easybuild.toolchains.compiler.inteliccifort import TC_CONSTANT_INTELCOMP
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import apply_regex_substitutions
@@ -201,12 +204,24 @@ def configure_step(self):
 
             cuda_cc_string = ','.join(['sm_%s' % x.replace('.', '') for x in cuda_cc])
             self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=%s' % cuda_cc_string)
-            self.log.info("Enabling nvidia GPU support for compute capabilitie: %s", cuda_cc_string)
+            self.log.info("Enabling nvidia GPU support for compute capability: %s", cuda_cc_string)
+            # There is a dedicated kernel for sm80, but only from version 2021.11.001 onwards
+            if '8.0' in cuda_cc and LooseVersion(self.version) >= LooseVersion('2021.11.001'):
+                self.cfg.update('configopts', '--enable-nvidia-sm80-gpu')
 
         # From v2022.05.001 onwards, the config complains if CPP is not set
-        # Need to make this neater so that it is either set by easybuild-framework, OR query the toolchain for something like COMPILER_CPP
-        # Discussing that right now on EB Slack...
-        env.setvar('CPP', 'cpp')
+        # C preprocessor to use for given comp_fam
+        cpp_dict = {
+            TC_CONSTANT_GCC: 'cpp',
+            TC_CONSTANT_INTELCOMP: 'cpp',
+        }
+        comp_fam = self.toolchain.comp_family()
+        if comp_fam in cpp_dict:
+            env.setvar('CPP', cpp_dict[comp_fam])
+        else:
+            raise EasyBuildError('ELPA EasyBlock does not know which C preprocessor to use for the '
+                                 'current compiler family (%s). Please add the correct preprocessor '
+                                 'for this compiler family to cpp_dict in the ELPA EasyBlock', comp_fam)
 
         super(EB_ELPA, self).configure_step()
 

From 515e57df7b1184597e3545f58d13f9755bb488fb Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Mon, 27 Feb 2023 15:39:43 +0100
Subject: [PATCH 73/87] Clarify comment

---
 easybuild/easyblocks/e/elpa.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index 255abe4ee2..a69d657345 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -209,7 +209,7 @@ def configure_step(self):
             if '8.0' in cuda_cc and LooseVersion(self.version) >= LooseVersion('2021.11.001'):
                 self.cfg.update('configopts', '--enable-nvidia-sm80-gpu')
 
-        # From v2022.05.001 onwards, the config complains if CPP is not set
+        # From v2022.05.001 onwards, the config complains if CPP is not set, resulting in non-zero exit of configure
         # C preprocessor to use for given comp_fam
         cpp_dict = {
             TC_CONSTANT_GCC: 'cpp',

From 1f86084c67c75c6caacfaa772ba7a8ef06417c21 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Mon, 27 Feb 2023 15:56:37 +0100
Subject: [PATCH 74/87] Pull logic inside the if statement that checks if only
 a single cuda compute capability has been specified. Also, now check if the
 cuda_cc is larger or equal to 8.0, since you probably also want to build the
 8.0 optimized kernel if you have 8.5 capability in your system

---
 easybuild/easyblocks/e/elpa.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index a69d657345..5bff3c695b 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -198,17 +198,18 @@ def configure_step(self):
                                      '--cuda-compute-capabilities')
 
             # ELPA's --with-NVIDIA-GPU-compute-capability only accepts a single architecture
-            if len(cuda_cc) > 1:
+            if len(cuda_cc) == 1:
+                cuda_cc = cuda_cc[0]
+                cuda_cc_string = cuda_cc.replace('.', '')
+                self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=%s' % cuda_cc_string)
+                self.log.info("Enabling nvidia GPU support for compute capability: %s", cuda_cc_string)
+                # There is a dedicated kernel for sm80, but only from version 2021.11.001 onwards
+                if float(cuda_cc) >= 8.0 and LooseVersion(self.version) >= LooseVersion('2021.11.001'):
+                    self.cfg.update('configopts', '--enable-nvidia-sm80-gpu')
+            else:
                 raise EasyBuildError('ELPA currently only supports specifying one architecture when '
                                      'building. You specified cuda-compute-capabilities: %s', cuda_cc)
 
-            cuda_cc_string = ','.join(['sm_%s' % x.replace('.', '') for x in cuda_cc])
-            self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=%s' % cuda_cc_string)
-            self.log.info("Enabling nvidia GPU support for compute capability: %s", cuda_cc_string)
-            # There is a dedicated kernel for sm80, but only from version 2021.11.001 onwards
-            if '8.0' in cuda_cc and LooseVersion(self.version) >= LooseVersion('2021.11.001'):
-                self.cfg.update('configopts', '--enable-nvidia-sm80-gpu')
-
         # From v2022.05.001 onwards, the config complains if CPP is not set, resulting in non-zero exit of configure
         # C preprocessor to use for given comp_fam
         cpp_dict = {

From c3e7701f583c285d905b6879ef4f4c824d46849a Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Mon, 27 Feb 2023 15:57:59 +0100
Subject: [PATCH 75/87] Make sure sm_ gets prepended in the argument for
 --with-NVIDIA-GPU-compute-capability

---
 easybuild/easyblocks/e/elpa.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index 5bff3c695b..39ea64b41e 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -201,7 +201,7 @@ def configure_step(self):
             if len(cuda_cc) == 1:
                 cuda_cc = cuda_cc[0]
                 cuda_cc_string = cuda_cc.replace('.', '')
-                self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=%s' % cuda_cc_string)
+                self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=sm_%s' % cuda_cc_string)
                 self.log.info("Enabling nvidia GPU support for compute capability: %s", cuda_cc_string)
                 # There is a dedicated kernel for sm80, but only from version 2021.11.001 onwards
                 if float(cuda_cc) >= 8.0 and LooseVersion(self.version) >= LooseVersion('2021.11.001'):

From 8b154aba5c1e61db84f432000386907dcd18d811 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Tue, 28 Feb 2023 11:55:00 +0100
Subject: [PATCH 76/87] Reordered if-else statement to reduce indentation.
 Clarified error message that is raised

---
 easybuild/easyblocks/e/elpa.py | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index 39ea64b41e..143952cbf7 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -198,17 +198,16 @@ def configure_step(self):
                                      '--cuda-compute-capabilities')
 
             # ELPA's --with-NVIDIA-GPU-compute-capability only accepts a single architecture
-            if len(cuda_cc) == 1:
-                cuda_cc = cuda_cc[0]
-                cuda_cc_string = cuda_cc.replace('.', '')
-                self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=sm_%s' % cuda_cc_string)
-                self.log.info("Enabling nvidia GPU support for compute capability: %s", cuda_cc_string)
-                # There is a dedicated kernel for sm80, but only from version 2021.11.001 onwards
-                if float(cuda_cc) >= 8.0 and LooseVersion(self.version) >= LooseVersion('2021.11.001'):
-                    self.cfg.update('configopts', '--enable-nvidia-sm80-gpu')
-            else:
-                raise EasyBuildError('ELPA currently only supports specifying one architecture when '
+            if len(cuda_cc) != 1:
+                raise EasyBuildError('ELPA currently only supports specifying one CUDA architecture when '
                                      'building. You specified cuda-compute-capabilities: %s', cuda_cc)
+            cuda_cc = cuda_cc[0]
+            cuda_cc_string = cuda_cc.replace('.', '')
+            self.cfg.update('configopts', '--with-NVIDIA-GPU-compute-capability=sm_%s' % cuda_cc_string)
+            self.log.info("Enabling nvidia GPU support for compute capability: %s", cuda_cc_string)
+            # There is a dedicated kernel for sm80, but only from version 2021.11.001 onwards
+            if float(cuda_cc) >= 8.0 and LooseVersion(self.version) >= LooseVersion('2021.11.001'):
+                self.cfg.update('configopts', '--enable-nvidia-sm80-gpu')
 
         # From v2022.05.001 onwards, the config complains if CPP is not set, resulting in non-zero exit of configure
         # C preprocessor to use for given comp_fam

From 40bc11790fef31a4f8d0499c5c2e35dc3308e8c1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@gcn1.local.snellius.surf.nl>
Date: Tue, 28 Feb 2023 13:38:07 +0100
Subject: [PATCH 77/87]  Moved up from .. import to maintain alphabetical order

---
 easybuild/easyblocks/e/elpa.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/e/elpa.py b/easybuild/easyblocks/e/elpa.py
index 143952cbf7..41b81e15e8 100644
--- a/easybuild/easyblocks/e/elpa.py
+++ b/easybuild/easyblocks/e/elpa.py
@@ -40,10 +40,10 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import apply_regex_substitutions
+from easybuild.tools.modules import get_software_root
 from easybuild.tools.systemtools import get_cpu_features, get_shared_lib_ext
 from easybuild.tools.toolchain.compiler import OPTARCH_GENERIC
 from easybuild.tools.utilities import nub
-from easybuild.tools.modules import get_software_root
 
 ELPA_CPU_FEATURE_FLAGS = ['avx', 'avx2', 'avx512f', 'vsx', 'sse4_2']
 

From 2207b51b4be816425ccf7aa9243988a03eba5b79 Mon Sep 17 00:00:00 2001
From: Alex Domingo <alex.domingo.toro@vub.be>
Date: Wed, 1 Mar 2023 11:43:50 +0100
Subject: [PATCH 78/87] always handle depot paths in a list in JuliaPackage

Co-authored-by: Sam Moors <smoors@users.noreply.github.com>
---
 easybuild/easyblocks/generic/juliapackage.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/generic/juliapackage.py b/easybuild/easyblocks/generic/juliapackage.py
index ff8bc74298..2e32047665 100644
--- a/easybuild/easyblocks/generic/juliapackage.py
+++ b/easybuild/easyblocks/generic/juliapackage.py
@@ -98,11 +98,11 @@ def install_step(self):
         # prepend installation directory to Julia DEPOT_PATH
         # extensions in a bundle can share their DEPOT_PATH
         # see https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
-        depot_path = os.getenv('JULIA_DEPOT_PATH', '')
+        depot_path = os.getenv('JULIA_DEPOT_PATH', [])
         if depot_path:
             depot_path = depot_path.split(os.pathsep)
         if self.installdir not in depot_path:
-            depot_path = os.pathsep.join([depot for depot in (self.installdir, depot_path) if depot])
+            depot_path = os.pathsep.join([depot for depot in [self.installdir] + depot_path if depot])
             env.setvar('JULIA_DEPOT_PATH', depot_path)
 
         # command sequence for Julia.Pkg

From 54eff72c48218d1589ea956e81a9fb6b173a4fcd Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Wed, 1 Mar 2023 13:51:16 +0000
Subject: [PATCH 79/87] Allow disabling of building tests and forward deps, and
 support version 13 for Trilinos

---
 easybuild/easyblocks/t/trilinos.py | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/t/trilinos.py b/easybuild/easyblocks/t/trilinos.py
index 4fa0ab9148..3af9614b0d 100644
--- a/easybuild/easyblocks/t/trilinos.py
+++ b/easybuild/easyblocks/t/trilinos.py
@@ -54,6 +54,8 @@ def extra_options():
         extra_vars = {
             'shared_libs': [None, "Deprecated. Use build_shared_libs", CUSTOM],
             'openmp': [True, "Enable OpenMP support", CUSTOM],
+            'forward_deps': [True, "Enable all forward dependencies", CUSTOM],
+            'build_tests': [True, "Enable building tests/examples", CUSTOM],
             'all_exts': [True, "Enable all Trilinos packages", CUSTOM],
             'skip_exts': [[], "List of Trilinos packages to skip", CUSTOM],
             'verbose': [False, "Configure for verbose output", CUSTOM],
@@ -106,9 +108,11 @@ def configure_step(self):
         if self.toolchain.options.get('usempi', None):
             self.cfg.update('configopts', "-DTPL_ENABLE_MPI:BOOL=ON")
 
-        # enable full testing
-        self.cfg.update('configopts', "-DTrilinos_ENABLE_TESTS:BOOL=ON")
-        self.cfg.update('configopts', "-DTrilinos_ENABLE_ALL_FORWARD_DEP_PACKAGES:BOOL=ON")
+        if self.cfg['build_tests']:
+            # enable full testing
+            self.cfg.update('configopts', "-DTrilinos_ENABLE_TESTS:BOOL=ON")
+        if self.cfg['forward_deps']:
+            self.cfg.update('configopts', "-DTrilinos_ENABLE_ALL_FORWARD_DEP_PACKAGES:BOOL=ON")
 
         lib_re = re.compile("^lib(.*).a$")
 
@@ -285,6 +289,11 @@ def sanity_check_step(self):
             libs.remove('Galeri')
             libs.extend(['galeri-epetra', 'galeri-xpetra'])
 
+        if LooseVersion(self.version) >= LooseVersion('13'):
+            libs.remove('GlobiPack')
+            libs.remove('Mesquite')
+            libs.remove('MOOCHO')
+
         # Get the library extension
         if self.cfg['build_shared_libs']:
             lib_ext = get_shared_lib_ext()

From f9bfd0d0140d250d0c5ae5f98157b26c93ea5865 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Wed, 1 Mar 2023 14:03:24 +0000
Subject: [PATCH 80/87] library changes from ComputeCanada

---
 easybuild/easyblocks/t/trilinos.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/t/trilinos.py b/easybuild/easyblocks/t/trilinos.py
index 3af9614b0d..aa4b911473 100644
--- a/easybuild/easyblocks/t/trilinos.py
+++ b/easybuild/easyblocks/t/trilinos.py
@@ -289,11 +289,15 @@ def sanity_check_step(self):
             libs.remove('Galeri')
             libs.extend(['galeri-epetra', 'galeri-xpetra'])
 
-        if LooseVersion(self.version) >= LooseVersion('13'):
-            libs.remove('GlobiPack')
+        # Mesquite and MOOCHO packages gone in 12.18:
+        if LooseVersion(self.version) >= LooseVersion('12.18'):
             libs.remove('Mesquite')
             libs.remove('MOOCHO')
 
+        # GlobiPack package gone in 13.0:
+        if LooseVersion(self.version) >= LooseVersion('13.0'):
+            libs.remove('GlobiPack')
+
         # Get the library extension
         if self.cfg['build_shared_libs']:
             lib_ext = get_shared_lib_ext()

From de55fd4f28aaf79b3eec21c6c433e592c79c8219 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 9 Mar 2023 09:52:56 +0100
Subject: [PATCH 81/87] update scipy easyblock to copy PKG-INFO to
 scipy-<version>.egg-info when installing with Meson/Ninja + enhance add
 sanity check command using 'pip list'

---
 easybuild/easyblocks/s/scipy.py | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 1c21a01fc2..4c8d7e0398 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -42,8 +42,8 @@
 from easybuild.easyblocks.generic.mesonninja import MesonNinja
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage, det_pylibdir
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.tools.build_log import EasyBuildError
-from easybuild.tools.filetools import change_dir, copy_dir
+from easybuild.tools.build_log import EasyBuildError, print_warning
+from easybuild.tools.filetools import change_dir, copy_dir, copy_file
 
 
 class EB_scipy(FortranPythonPackage, PythonPackage, MesonNinja):
@@ -198,6 +198,18 @@ def install_step(self):
         """Custom install step for scipy: use ninja for scipy >= 1.9.0"""
         if self.use_meson:
             MesonNinja.install_step(self)
+
+            # copy PKG-INFO file included in scipy source tarball to scipy-<version>.egg-info in installation,
+            # so pip is aware of the scipy installation (required for 'pip list', 'pip check', etc.);
+            # see also https://github.com/easybuilders/easybuild-easyblocks/issues/2901
+            pkg_info = 'PKG-INFO'
+            target_egg_info = os.path.join(self.installdir, self.pylibdir, 'scipy-%s.egg-info' % self.version)
+            if os.path.isfile(pkg_info):
+                copy_file(pkg_info, target_egg_info)
+            else:
+                cwd = os.getcwd()
+                print_warning("%s not found in %s, so can't use it to create %s!", pkg_info, cwd, target_egg_info,
+                              log=self.log)
         else:
             FortranPythonPackage.install_step(self)
 
@@ -211,4 +223,9 @@ def sanity_check_step(self, *args, **kwargs):
             'dirs': [det_pylibdir()],
         }
 
-        return PythonPackage.sanity_check_step(self, custom_paths=custom_paths)
+        # make sure that scipy is included in output of 'pip list',
+        # so that 'pip check' passes if scipy is a required dependency for another Python package;
+        # use case-insensitive match, since name is sometimes reported as 'SciPy'
+        custom_commands = [r"pip list | grep -i '^scipy[ \t]*%s[ \t]*$'" % self.version]
+
+        return PythonPackage.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands)

From bd9e6938e17a56baf61873bea2553c4175e87988 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Fri, 10 Mar 2023 11:30:27 +0000
Subject: [PATCH 82/87] correct directory to find PKG-INFO and improve sanity
 check test

Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com>
---
 easybuild/easyblocks/s/scipy.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easybuild/easyblocks/s/scipy.py b/easybuild/easyblocks/s/scipy.py
index 4c8d7e0398..823116e1e8 100644
--- a/easybuild/easyblocks/s/scipy.py
+++ b/easybuild/easyblocks/s/scipy.py
@@ -202,7 +202,7 @@ def install_step(self):
             # copy PKG-INFO file included in scipy source tarball to scipy-<version>.egg-info in installation,
             # so pip is aware of the scipy installation (required for 'pip list', 'pip check', etc.);
             # see also https://github.com/easybuilders/easybuild-easyblocks/issues/2901
-            pkg_info = 'PKG-INFO'
+            pkg_info = os.path.join(self.cfg['start_dir'], 'PKG-INFO')
             target_egg_info = os.path.join(self.installdir, self.pylibdir, 'scipy-%s.egg-info' % self.version)
             if os.path.isfile(pkg_info):
                 copy_file(pkg_info, target_egg_info)
@@ -226,6 +226,6 @@ def sanity_check_step(self, *args, **kwargs):
         # make sure that scipy is included in output of 'pip list',
         # so that 'pip check' passes if scipy is a required dependency for another Python package;
         # use case-insensitive match, since name is sometimes reported as 'SciPy'
-        custom_commands = [r"pip list | grep -i '^scipy[ \t]*%s[ \t]*$'" % self.version]
+        custom_commands = [r"pip list | grep -iE '^scipy\s+%s\s*$'" % self.version.replace('.', r'\.')]
 
         return PythonPackage.sanity_check_step(self, custom_paths=custom_paths, custom_commands=custom_commands)

From 42d5b98cb433d718af73e326eab70c7ca3843dc5 Mon Sep 17 00:00:00 2001
From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com>
Date: Tue, 14 Mar 2023 08:33:06 +0100
Subject: [PATCH 83/87] Create non-versioned symlink for python-config

As discussed here https://easybuild.slack.com/archives/C34UA1HT7/p1678728109206609?thread_ts=1678722749.081689&cid=C34UA1HT7
---
 easybuild/easyblocks/p/python.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/p/python.py b/easybuild/easyblocks/p/python.py
index 465d069a67..f839da581b 100644
--- a/easybuild/easyblocks/p/python.py
+++ b/easybuild/easyblocks/p/python.py
@@ -444,10 +444,13 @@ def install_step(self):
 
         super(EB_Python, self).install_step()
 
-        # Create non-versioned, relative symlinks for python and pip
+        # Create non-versioned, relative symlinks for python, python-config and pip
         python_binary_path = os.path.join(self.installdir, 'bin', 'python')
         if not os.path.isfile(python_binary_path):
             symlink('python' + self.pyshortver, python_binary_path, use_abspath_source=False)
+        python_config_binary_path = os.path.join(self.installdir, 'bin', 'python-config')
+        if not os.path.isfile(python_config_binary_path):
+            symlink('python' + self.pyshortver + '-config', python_config_binary_path, use_abspath_source=False)
         if self.install_pip:
             pip_binary_path = os.path.join(self.installdir, 'bin', 'pip')
             if not os.path.isfile(pip_binary_path):

From f5649005218c00a2382f7350dec25a5faa7b170d Mon Sep 17 00:00:00 2001
From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com>
Date: Tue, 14 Mar 2023 11:12:37 +0100
Subject: [PATCH 84/87] Add extra sanity checks

---
 easybuild/easyblocks/p/python.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/p/python.py b/easybuild/easyblocks/p/python.py
index f839da581b..09a954d9f0 100644
--- a/easybuild/easyblocks/p/python.py
+++ b/easybuild/easyblocks/p/python.py
@@ -537,7 +537,13 @@ def sanity_check_step(self):
 
         pyver = 'python' + self.pyshortver
         custom_paths = {
-            'files': [os.path.join('bin', pyver), os.path.join('lib', 'lib' + pyver + abiflags + '.' + shlib_ext)],
+            'files': [
+                os.path.join('bin', pyver),
+                os.path.join('bin', 'python'),
+                os.path.join('bin', pyver + '-config'),
+                os.path.join('bin', 'python-config'),
+                os.path.join('lib', 'lib' + pyver + abiflags + '.' + shlib_ext),
+            ],
             'dirs': [os.path.join('include', pyver + abiflags), os.path.join('lib', pyver, 'lib-dynload')],
         }
 
@@ -549,6 +555,7 @@ def sanity_check_step(self):
             "python -c 'import _ctypes'",  # make sure that foreign function interface (libffi) works
             "python -c 'import _ssl'",  # make sure SSL support is enabled one way or another
             "python -c 'import readline'",  # make sure readline support was built correctly
+            "python-config --help",  # make sure that symlink was created correctly
         ]
 
         if self.install_pip:

From 7b7ad98305fee35ae1a65892e06055219a1cd6b1 Mon Sep 17 00:00:00 2001
From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com>
Date: Wed, 15 Mar 2023 08:30:34 +0100
Subject: [PATCH 85/87] Move python-config --help sanity check

---
 easybuild/easyblocks/p/python.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/p/python.py b/easybuild/easyblocks/p/python.py
index 09a954d9f0..975935cdfb 100644
--- a/easybuild/easyblocks/p/python.py
+++ b/easybuild/easyblocks/p/python.py
@@ -552,10 +552,10 @@ def sanity_check_step(self):
 
         custom_commands = [
             "python --version",
+            "python-config --help",  # make sure that symlink was created correctly
             "python -c 'import _ctypes'",  # make sure that foreign function interface (libffi) works
             "python -c 'import _ssl'",  # make sure SSL support is enabled one way or another
             "python -c 'import readline'",  # make sure readline support was built correctly
-            "python-config --help",  # make sure that symlink was created correctly
         ]
 
         if self.install_pip:

From 474f4566c10d93e522e8c5b412480ff093d43fd1 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Thu, 16 Mar 2023 22:08:37 +0100
Subject: [PATCH 86/87] prepare release notes for EasyBuild v4.7.1 + bump
 version to 4.7.1

---
 RELEASE_NOTES                    | 40 ++++++++++++++++++++++++++++++++
 easybuild/easyblocks/__init__.py |  2 +-
 2 files changed, 41 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index e71ea4acad..c3829c8e86 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -5,6 +5,46 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en
 
 The latest version of easybuild-easyblocks provides 248 software-specific easyblocks and 39 generic easyblocks.
 
+v4.7.1 (March 20th 2023)
+------------------------
+
+update/bugfix release
+
+- minor enhancements and updates, including:
+  - make NAMD easyblock aware of (pre)testopts (#2856)
+  - update MesonNinja easyblock for Meson >=0.64.0 (#2861)
+  - update scipy easyblock for scipy >= 1.9.0 to use meson/ninja  (#2862)
+  - modify logic in QScintilla easyblock to find the PyQt5 sipdir in more places (#2868)
+  - add `testinstall` custom easyconfig parameter to PythonPackage easyblock (#2872)
+  - use -x option for "go install" in GoPackage generic easyblock (#2878)
+  - allow disabling pybind11 tests with '`runtest = False`' (#2892)
+  - call parent post_install_step in EasyBuildMeta easyblock (so postinstallcmds are taken into account) (#2893)
+  - update and enhance Maple easyblock for recent versions (#2895)
+  - relax glob pattern to find Mathematica install script (#2896)
+  - implement CUDA support in the ELPA EasyBlock & fix CPP configure issue on newer ELPA versions (#2898)
+  - update Trilinos easyblock to allow disabling of building tests and forward deps + support Trilinos v13.x (#2900)
+  - enhance Python easyblock to create non-versioned symlink for python-config + check for bin/python and bin/python-config in sanity check (#2904)
+- various bug fixes, including:
+  - do not use -g77 option when installing NVHPC 22.9+ (#2819)
+  - check that sanity_check_module_loaded attribute exists before querying it in PythonPackage easyblock (#2865)
+  - fix $JULIA_DEPOT_PATH in installation of multiple JuliaPackage extensions (#2869)
+  - fix website/docs links in README (#2870)
+  - fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets (#2873)
+  - show template values of exts_default_options in PythonBundle (#2874)
+  - Fix missing initialization of CMakeMake in CMakePythonPackage (#2876)
+  - fix error when failing pip version check during PythonPackage sanity check (#2877)
+  - handle templating correctly in CMakeMake when playing with configopts (#2882)
+  - avoid crash in test step of PyTorch easyblock if runtest is not a command (#2883)
+  - fix check configure option in FlexiBLAS easyblock (#2886)
+  - Use older `ncgen -H` for older netCDF (#2889)
+  - relax glob pattern to find Mathematica install script (#2896)
+  - fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x (#2897)
+  - update scipy easyblock to copy PKG-INFO to scipy-<version>.egg-info when installing with Meson/Ninja + add sanity check command using 'pip list' (#2903)
+- other changes:
+  - only give read permissions in GitHub Actions workflows (#2863)
+  - use start dir of extension to install R packages (#2867)
+  - add deprecation notice to RPackage extensions with relative paths in start_dir (#2879)
+
 
 v4.7.0 (January 9th 2023)
 -------------------------
diff --git a/easybuild/easyblocks/__init__.py b/easybuild/easyblocks/__init__.py
index 9619ef8946..d634d41d22 100644
--- a/easybuild/easyblocks/__init__.py
+++ b/easybuild/easyblocks/__init__.py
@@ -43,7 +43,7 @@
 # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like
 #   UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0'
 # This causes problems further up the dependency chain...
-VERSION = LooseVersion('4.7.1.dev0')
+VERSION = LooseVersion('4.7.1')
 UNKNOWN = 'UNKNOWN'
 
 

From 9080685cce03807216781dac575a537275feaecc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 17 Mar 2023 08:44:52 +0100
Subject: [PATCH 87/87] minor tweaks to release notes for EasyBuild v4.7.1

---
 RELEASE_NOTES | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index c3829c8e86..96346e430c 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -11,13 +11,14 @@ v4.7.1 (March 20th 2023)
 update/bugfix release
 
 - minor enhancements and updates, including:
+  - fix TensorFlow easyblock for new versions of Bazel & TensorFlow (#2854)
   - make NAMD easyblock aware of (pre)testopts (#2856)
   - update MesonNinja easyblock for Meson >=0.64.0 (#2861)
-  - update scipy easyblock for scipy >= 1.9.0 to use meson/ninja  (#2862)
+  - update scipy easyblock for scipy >= 1.9.0 to use meson/ninja  (#2862, #2903)
   - modify logic in QScintilla easyblock to find the PyQt5 sipdir in more places (#2868)
   - add `testinstall` custom easyconfig parameter to PythonPackage easyblock (#2872)
-  - use -x option for "go install" in GoPackage generic easyblock (#2878)
-  - allow disabling pybind11 tests with '`runtest = False`' (#2892)
+  - use -x option for "go install" in GoPackage generic easyblock, to print commands as they are executed (#2878)
+  - allow disabling pybind11 tests with `runtest = False` (#2892)
   - call parent post_install_step in EasyBuildMeta easyblock (so postinstallcmds are taken into account) (#2893)
   - update and enhance Maple easyblock for recent versions (#2895)
   - relax glob pattern to find Mathematica install script (#2896)
@@ -28,21 +29,19 @@ update/bugfix release
   - do not use -g77 option when installing NVHPC 22.9+ (#2819)
   - check that sanity_check_module_loaded attribute exists before querying it in PythonPackage easyblock (#2865)
   - fix $JULIA_DEPOT_PATH in installation of multiple JuliaPackage extensions (#2869)
-  - fix website/docs links in README (#2870)
   - fix checking of CUDA/ROCR-Runtime dependencies for Clang to determine default build targets (#2873)
   - show template values of exts_default_options in PythonBundle (#2874)
-  - Fix missing initialization of CMakeMake in CMakePythonPackage (#2876)
+  - fix missing initialization of CMakeMake in CMakePythonPackage (#2876)
   - fix error when failing pip version check during PythonPackage sanity check (#2877)
   - handle templating correctly in CMakeMake when playing with configopts (#2882)
   - avoid crash in test step of PyTorch easyblock if runtest is not a command (#2883)
   - fix check configure option in FlexiBLAS easyblock (#2886)
-  - Use older `ncgen -H` for older netCDF (#2889)
-  - relax glob pattern to find Mathematica install script (#2896)
+  - use older `ncgen -H` for older netCDF (#2889)
   - fix linking numexpr with Intel MKL's VML library for imkl >= 2021.x (#2897)
-  - update scipy easyblock to copy PKG-INFO to scipy-<version>.egg-info when installing with Meson/Ninja + add sanity check command using 'pip list' (#2903)
 - other changes:
   - only give read permissions in GitHub Actions workflows (#2863)
   - use start dir of extension to install R packages (#2867)
+  - fix website/docs links in README (#2870)
   - add deprecation notice to RPackage extensions with relative paths in start_dir (#2879)