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 01/14] 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 02/14] 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 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 03/14] 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 04/14] 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 05/14] 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 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 06/14] 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 07/14] 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 08/14] 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 09/14] 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 10/14] 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 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 11/14] 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 12/14] 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 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 13/14] 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 14/14] 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([