From 22be21aeb0437fe19d7c639f556ac5467e31bfb0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 6 Mar 2023 09:58:28 +0000
Subject: [PATCH 01/59] adding easyblocks: cargo.py

---
 easybuild/easyblocks/generic/cargo.py | 129 ++++++++++++++++++++++++++
 1 file changed, 129 insertions(+)
 create mode 100644 easybuild/easyblocks/generic/cargo.py

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
new file mode 100644
index 0000000000..d59e0fee16
--- /dev/null
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -0,0 +1,129 @@
+##
+# Copyright 2009-2023 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for installing Cargo packages (Rust lang package system)
+
+@author: Mikael Oehman (Chalmers University of Technology)
+"""
+
+import os
+import glob
+
+import easybuild.tools.environment as env
+from easybuild.framework.easyconfig import CUSTOM
+from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.build_log import EasyBuildError
+from easybuild.tools.run import run_cmd
+from easybuild.tools.config import build_option
+from easybuild.tools.filetools import remove_file, write_file, extract_file, compute_checksum
+
+CRATESIO_SOURCE = "https://crates.io/api/v1/crates"
+
+class Cargo(EasyBlock):
+    """Support for installing Cargo packages (Rust)"""
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Define extra easyconfig parameters specific to Cargo"""
+        extra_vars = EasyBlock.extra_options(extra_vars)
+        extra_vars.update({
+            #'tests': [True, "Build tests", CUSTOM],
+            'offline': [True, "Build tests", CUSTOM],
+            'lto': [False, "Build with link time optimization", CUSTOM],
+        })
+
+        #if 'source_urls' not in extra_vars:
+        #    extra_vars['source_urls'] = [CRATESIO_SOURCE]
+
+        #extra_vars['download_filename'] = '%(name)s/%(version)s/download'
+
+        return extra_vars
+
+    def __init__(self, *args, **kwargs):
+        """Constructor for Simpack easyblock."""
+        super(Cargo, self).__init__(*args, **kwargs)
+        env.setvar('CARGO_HOME', os.path.join(self.builddir, '.cargo'))
+        env.setvar('RUSTC', 'rustc')
+        env.setvar('RUSTDOC', 'rustdoc')
+        env.setvar('RUSTFMT', 'rustfmt')
+        optarch = build_option('optarch')
+        if not optarch:
+            optarch = 'native'
+        env.setvar('RUSTFLAGS', '-C target-cpu=%s' % optarch)
+        env.setvar('RUST_LOG', 'DEBUG')
+        env.setvar('RUST_BACKTRACE', '1')
+
+    def configure_step(self):
+        pass
+
+    def extract_step(self):
+        """Populate all vendored deps with required .cargo-checksum.json"""
+        EasyBlock.extract_step(self)
+        for source in self.src:
+            dirname = source["name"].rsplit('.', maxsplit=2)[0]
+            self.log.info('creating .cargo-checksums.json file for : %s', dirname)
+            chksum = compute_checksum(source['path'], checksum_type='sha256')
+            chkfile = '%s/%s/.cargo-checksum.json' % (self.builddir, dirname)
+            write_file(chkfile, '{"files":{},"package":"%s"}' % chksum)
+
+    def build_step(self):
+        """Build with cargo"""
+        parallel = ''
+        if self.cfg['parallel']:
+            parallel = "-j %s" % self.cfg['parallel']
+
+        tests = ''
+        if self.cfg['tests']:
+            parallel = "--tests"
+
+        offline = ''
+        if self.cfg['offline']:
+            parallel = "--offline"
+
+        profile = 'debug' if self.toolchain.options.get('debug', None) else 'release'
+
+        lto = ''
+        if self.cfg['lto']:
+            parallel = '--config profile.%s.lto=true' % profile
+
+        run_cmd('rustc --print cfg', log_all=True, simple=True)  # for tracking in log file
+        #remove_file('Cargo.lock')  # attempt to circumvent the checksum-check that cargo build does, but it still looks for the checksum json file.
+        # Can't figure out how to supply this via command line
+        write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
+        cmd = '%s cargo build --profile=%s %s %s %s %s %s' % (self.cfg['prebuildopts'], profile, offline, lto, tests, parallel, self.cfg['buildopts']) 
+        run_cmd(cmd, log_all=True, simple=True)
+
+    def test_step(self):
+        """Test with cargo"""
+        if self.cfg['tests']:
+            profile = 'debug' if self.toolchain.options.get('debug', None) else 'release'
+            cmd = "%s cargo test --profile=%s %s" % (self.cfg['pretestopts'], profile, self.cfg['testopts'])
+            run_cmd(cmd, log_all=True, simple=True)
+
+    def install_step(self):
+        """Install with cargo"""
+        cmd = "%s cargo install --offline --root %s --path . %s" % (self.cfg['preinstallopts'], self.installdir, self.cfg['installopts'])
+        run_cmd(cmd, log_all=True, simple=True)
+

From 7cc78df9e16c19e52da8872301f13b192bb2d3c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 6 Mar 2023 14:54:31 +0000
Subject: [PATCH 02/59] Fix hound errors

---
 easybuild/easyblocks/generic/cargo.py | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index d59e0fee16..6e5514b713 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -29,15 +29,14 @@
 """
 
 import os
-import glob
 
 import easybuild.tools.environment as env
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.framework.easyblock import EasyBlock
-from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.run import run_cmd
 from easybuild.tools.config import build_option
-from easybuild.tools.filetools import remove_file, write_file, extract_file, compute_checksum
+from easybuild.tools.filetools import write_file, compute_checksum
+# from easybuild.tools.filetools import remove_file
 
 CRATESIO_SOURCE = "https://crates.io/api/v1/crates"
 
@@ -49,15 +48,15 @@ def extra_options(extra_vars=None):
         """Define extra easyconfig parameters specific to Cargo"""
         extra_vars = EasyBlock.extra_options(extra_vars)
         extra_vars.update({
-            #'tests': [True, "Build tests", CUSTOM],
+            # 'tests': [True, "Build tests", CUSTOM],
             'offline': [True, "Build tests", CUSTOM],
             'lto': [False, "Build with link time optimization", CUSTOM],
         })
 
-        #if 'source_urls' not in extra_vars:
+        # if 'source_urls' not in extra_vars:
         #    extra_vars['source_urls'] = [CRATESIO_SOURCE]
 
-        #extra_vars['download_filename'] = '%(name)s/%(version)s/download'
+        # extra_vars['download_filename_template'] = '%(name)s/%(version)s/download'
 
         return extra_vars
 
@@ -109,10 +108,12 @@ def build_step(self):
             parallel = '--config profile.%s.lto=true' % profile
 
         run_cmd('rustc --print cfg', log_all=True, simple=True)  # for tracking in log file
-        #remove_file('Cargo.lock')  # attempt to circumvent the checksum-check that cargo build does, but it still looks for the checksum json file.
+        # attempt to circumvent the checksum-check that cargo build does, but it still looks for the checksum json file
+        # remove_file('Cargo.lock')
         # Can't figure out how to supply this via command line
         write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
-        cmd = '%s cargo build --profile=%s %s %s %s %s %s' % (self.cfg['prebuildopts'], profile, offline, lto, tests, parallel, self.cfg['buildopts']) 
+        cmd = '%s cargo build --profile=%s %s %s %s %s %s' % (
+            self.cfg['prebuildopts'], profile, offline, lto, tests, parallel, self.cfg['buildopts']) 
         run_cmd(cmd, log_all=True, simple=True)
 
     def test_step(self):
@@ -124,6 +125,7 @@ def test_step(self):
 
     def install_step(self):
         """Install with cargo"""
-        cmd = "%s cargo install --offline --root %s --path . %s" % (self.cfg['preinstallopts'], self.installdir, self.cfg['installopts'])
+        cmd = "%s cargo install --offline --root %s --path . %s" % (
+            self.cfg['preinstallopts'], self.installdir, self.cfg['installopts'])
         run_cmd(cmd, log_all=True, simple=True)
 

From df16d823e370b15d75a2471c4dc43a2372894e77 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 6 Mar 2023 14:55:09 +0000
Subject: [PATCH 03/59] Fix hound errors

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 6e5514b713..1967a91686 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -40,6 +40,7 @@
 
 CRATESIO_SOURCE = "https://crates.io/api/v1/crates"
 
+
 class Cargo(EasyBlock):
     """Support for installing Cargo packages (Rust)"""
 
@@ -128,4 +129,3 @@ def install_step(self):
         cmd = "%s cargo install --offline --root %s --path . %s" % (
             self.cfg['preinstallopts'], self.installdir, self.cfg['installopts'])
         run_cmd(cmd, log_all=True, simple=True)
-

From 863dfb82bb27664becfad6d23983472aa492a7ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 6 Mar 2023 14:55:41 +0000
Subject: [PATCH 04/59] Fix hound errors

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 1967a91686..fd717f11c5 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -114,7 +114,7 @@ def build_step(self):
         # Can't figure out how to supply this via command line
         write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
         cmd = '%s cargo build --profile=%s %s %s %s %s %s' % (
-            self.cfg['prebuildopts'], profile, offline, lto, tests, parallel, self.cfg['buildopts']) 
+            self.cfg['prebuildopts'], profile, offline, lto, tests, parallel, self.cfg['buildopts'])
         run_cmd(cmd, log_all=True, simple=True)
 
     def test_step(self):

From f93988fe1f6e4da05f3e43b14b3b4aa868dc6825 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 6 Mar 2023 15:10:36 +0000
Subject: [PATCH 05/59] Use profile consistently

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index fd717f11c5..29a9bf03d6 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -88,6 +88,10 @@ def extract_step(self):
             chkfile = '%s/%s/.cargo-checksum.json' % (self.builddir, dirname)
             write_file(chkfile, '{"files":{},"package":"%s"}' % chksum)
 
+    @property
+    def profile(self):
+        return 'debug' if self.toolchain.options.get('debug', None) else 'release'
+
     def build_step(self):
         """Build with cargo"""
         parallel = ''
@@ -102,11 +106,9 @@ def build_step(self):
         if self.cfg['offline']:
             parallel = "--offline"
 
-        profile = 'debug' if self.toolchain.options.get('debug', None) else 'release'
-
         lto = ''
         if self.cfg['lto']:
-            parallel = '--config profile.%s.lto=true' % profile
+            parallel = '--config profile.%s.lto=true' % self.profile
 
         run_cmd('rustc --print cfg', log_all=True, simple=True)  # for tracking in log file
         # attempt to circumvent the checksum-check that cargo build does, but it still looks for the checksum json file
@@ -114,18 +116,17 @@ def build_step(self):
         # Can't figure out how to supply this via command line
         write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
         cmd = '%s cargo build --profile=%s %s %s %s %s %s' % (
-            self.cfg['prebuildopts'], profile, offline, lto, tests, parallel, self.cfg['buildopts'])
+            self.cfg['prebuildopts'], self.profile, offline, lto, tests, parallel, self.cfg['buildopts'])
         run_cmd(cmd, log_all=True, simple=True)
 
     def test_step(self):
         """Test with cargo"""
         if self.cfg['tests']:
-            profile = 'debug' if self.toolchain.options.get('debug', None) else 'release'
-            cmd = "%s cargo test --profile=%s %s" % (self.cfg['pretestopts'], profile, self.cfg['testopts'])
+            cmd = "%s cargo test --profile=%s %s" % (self.cfg['pretestopts'], self.profile, self.cfg['testopts'])
             run_cmd(cmd, log_all=True, simple=True)
 
     def install_step(self):
         """Install with cargo"""
-        cmd = "%s cargo install --offline --root %s --path . %s" % (
-            self.cfg['preinstallopts'], self.installdir, self.cfg['installopts'])
+        cmd = "%s cargo install --profile=%s --offline --root %s --path . %s" % (
+            self.cfg['preinstallopts'], self.profile, self.installdir, self.cfg['installopts'])
         run_cmd(cmd, log_all=True, simple=True)

From 3740be163d3f7be92417a1b6f2d075d6c06c0237 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 6 Mar 2023 15:14:58 +0000
Subject: [PATCH 06/59] Fix copy/paste typo

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 29a9bf03d6..86e4335d4f 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -62,7 +62,7 @@ def extra_options(extra_vars=None):
         return extra_vars
 
     def __init__(self, *args, **kwargs):
-        """Constructor for Simpack easyblock."""
+        """Constructor for Cargo easyblock."""
         super(Cargo, self).__init__(*args, **kwargs)
         env.setvar('CARGO_HOME', os.path.join(self.builddir, '.cargo'))
         env.setvar('RUSTC', 'rustc')

From c2d40b20429e155209c9e9a87a4bf9317847224f Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Thu, 16 Mar 2023 08:57:27 +0000
Subject: [PATCH 07/59] Fail out if the MATLAB install key is not set

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

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index e1b65d77a8..50405f4a8d 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -159,7 +159,10 @@ def install_step(self):
 
         keys = self.cfg['key']
         if keys is None:
-            keys = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000')
+            try:
+                keys = os.environ['EB_MATLAB_KEY']
+            except KeyError:
+                raise EasyBuildError("The MATLAB install key is not set.")
         if isinstance(keys, string_type):
             keys = keys.split(',')
 

From 1b42d6feb7d1a52ff848c76a84beb94ee38e5510 Mon Sep 17 00:00:00 2001
From: Xin Wu <xin.wu@uni-paderborn.de>
Date: Thu, 16 Mar 2023 13:57:47 +0100
Subject: [PATCH 08/59] inform users that gpu package (instead of kokkos) is
 used for building LAMMPS

---
 easybuild/easyblocks/l/lammps.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyblocks/l/lammps.py b/easybuild/easyblocks/l/lammps.py
index 5c3d77fdb0..4bcfc42d9d 100644
--- a/easybuild/easyblocks/l/lammps.py
+++ b/easybuild/easyblocks/l/lammps.py
@@ -372,6 +372,7 @@ def configure_step(self, **kwargs):
 
         # CUDA only
         elif self.cuda:
+            print_msg("Using gpu (not Kokkos) arch: CPU - %s, GPU - %s" % (processor_arch, gpu_arch))
             self.cfg.update('configopts', '-D%sGPU=on' % self.pkg_prefix)
             self.cfg.update('configopts', '-DGPU_API=cuda')
             self.cfg.update('configopts', '-DGPU_ARCH=%s' % get_cuda_gpu_arch(cuda_cc))

From b1a7072d0848d52b6f8c0e178e5663777aca1343 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Sun, 19 Mar 2023 22:53:56 +0000
Subject: [PATCH 09/59] Add support for crate list, minor other fixes

---
 easybuild/easyblocks/generic/cargo.py | 31 +++++++++++++++------------
 1 file changed, 17 insertions(+), 14 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 86e4335d4f..a2093b642a 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -36,7 +36,6 @@
 from easybuild.tools.run import run_cmd
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import write_file, compute_checksum
-# from easybuild.tools.filetools import remove_file
 
 CRATESIO_SOURCE = "https://crates.io/api/v1/crates"
 
@@ -49,16 +48,12 @@ def extra_options(extra_vars=None):
         """Define extra easyconfig parameters specific to Cargo"""
         extra_vars = EasyBlock.extra_options(extra_vars)
         extra_vars.update({
-            # 'tests': [True, "Build tests", CUSTOM],
-            'offline': [True, "Build tests", CUSTOM],
+            'enable_tests': [True, "Enable building of tests", CUSTOM],
+            'offline': [True, "Build offline", CUSTOM],
             'lto': [False, "Build with link time optimization", CUSTOM],
+            'crates': [[], "List of (crate, version) tuples to use", CUSTOM],
         })
 
-        # if 'source_urls' not in extra_vars:
-        #    extra_vars['source_urls'] = [CRATESIO_SOURCE]
-
-        # extra_vars['download_filename_template'] = '%(name)s/%(version)s/download'
-
         return extra_vars
 
     def __init__(self, *args, **kwargs):
@@ -75,6 +70,16 @@ def __init__(self, *args, **kwargs):
         env.setvar('RUST_LOG', 'DEBUG')
         env.setvar('RUST_BACKTRACE', '1')
 
+        # Populate sources from "crates" list of tuples
+        sources = self.cfg['sources']
+        for crate, version in self.cfg['crates']:
+            sources.append({
+                'download_filename': crate + '/' + version + '/download',
+                'filename': crate + '-' + version + '.tar.gz',
+                'source_urls': CRATESIO_SOURCE,
+            })
+        self.cfg.update('sources', sources)
+
     def configure_step(self):
         pass
 
@@ -99,29 +104,27 @@ def build_step(self):
             parallel = "-j %s" % self.cfg['parallel']
 
         tests = ''
-        if self.cfg['tests']:
+        if self.cfg['enable_tests']:
             parallel = "--tests"
 
         offline = ''
         if self.cfg['offline']:
             parallel = "--offline"
+            # Replace crates-io with vendored sources
+            write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
 
         lto = ''
         if self.cfg['lto']:
             parallel = '--config profile.%s.lto=true' % self.profile
 
         run_cmd('rustc --print cfg', log_all=True, simple=True)  # for tracking in log file
-        # attempt to circumvent the checksum-check that cargo build does, but it still looks for the checksum json file
-        # remove_file('Cargo.lock')
-        # Can't figure out how to supply this via command line
-        write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
         cmd = '%s cargo build --profile=%s %s %s %s %s %s' % (
             self.cfg['prebuildopts'], self.profile, offline, lto, tests, parallel, self.cfg['buildopts'])
         run_cmd(cmd, log_all=True, simple=True)
 
     def test_step(self):
         """Test with cargo"""
-        if self.cfg['tests']:
+        if self.cfg['enable_tests']:
             cmd = "%s cargo test --profile=%s %s" % (self.cfg['pretestopts'], self.profile, self.cfg['testopts'])
             run_cmd(cmd, log_all=True, simple=True)
 

From 5fc85e06050286960f32548ac54a5e1f5784188d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 20 Mar 2023 16:34:04 +0100
Subject: [PATCH 10/59] bump version to 4.7.2dev

---
 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 d634d41d22..fdd68d6024 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')
+VERSION = LooseVersion('4.7.2.dev0')
 UNKNOWN = 'UNKNOWN'
 
 

From 20dca5b087a7ba26b4666d32dc6935184159d7b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Mon, 20 Mar 2023 23:30:24 +0000
Subject: [PATCH 11/59] Use alt location for crates

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index a2093b642a..037cf9300c 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -76,7 +76,8 @@ def __init__(self, *args, **kwargs):
             sources.append({
                 'download_filename': crate + '/' + version + '/download',
                 'filename': crate + '-' + version + '.tar.gz',
-                'source_urls': CRATESIO_SOURCE,
+                'source_urls': [CRATESIO_SOURCE],
+                'alt_location': 'crates.io',
             })
         self.cfg.update('sources', sources)
 

From 0274027cca85e1fbb41146f7445ef7893f45160c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 22 Mar 2023 18:57:43 +0100
Subject: [PATCH 12/59] don't check for RPATH sections in binaries compiled
 with Go

---
 easybuild/easyblocks/generic/gopackage.py | 77 ++++++++++++++++++++++-
 1 file changed, 76 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/generic/gopackage.py b/easybuild/easyblocks/generic/gopackage.py
index c06f724437..aca57c99d0 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -28,14 +28,17 @@
 @author: Pavel Grochal (INUITS)
 """
 import os
+import re
 from distutils.version import LooseVersion
 
 import easybuild.tools.environment as env
-from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.easyblock import DEFAULT_BIN_LIB_SUBDIRS, 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 easybuild.tools.systemtools import get_linked_libs_raw
 
 
 class GoPackage(EasyBlock):
@@ -149,3 +152,75 @@ def sanity_check_step(self):
         custom_commands = ['%s --help' % self.name.lower()]
 
         super(GoPackage, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
+
+    def sanity_check_rpath(self, rpath_dirs=None):
+        """Sanity check binaries/libraries w.r.t. RPATH linking."""
+
+        self.log.info("Checking RPATH linkage for binaries/libraries...")
+
+        fails = []
+
+        # hard reset $LD_LIBRARY_PATH before running RPATH sanity check
+        orig_env = env.unset_env_vars(['LD_LIBRARY_PATH'])
+
+        self.log.debug("$LD_LIBRARY_PATH during RPATH sanity check: %s", os.getenv('LD_LIBRARY_PATH', '(empty)'))
+        self.log.debug("List of loaded modules: %s", self.modules_tool.list())
+
+        not_found_regex = re.compile(r'(\S+)\s*\=\>\s*not found')
+        readelf_rpath_regex = re.compile('(RPATH)', re.M)
+
+        # List of libraries that should be exempt from the RPATH sanity check;
+        # For example, libcuda.so.1 should never be RPATH-ed by design,
+        # see https://github.com/easybuilders/easybuild-framework/issues/4095
+        filter_rpath_sanity_libs = build_option('filter_rpath_sanity_libs')
+        msg = "Ignoring the following libraries if they are not found by RPATH sanity check: %s"
+        self.log.info(msg, filter_rpath_sanity_libs)
+
+        if rpath_dirs is None:
+            rpath_dirs = self.cfg['bin_lib_subdirs'] or self.bin_lib_subdirs()
+
+        if not rpath_dirs:
+            rpath_dirs = DEFAULT_BIN_LIB_SUBDIRS
+            self.log.info("Using default subdirectories for binaries/libraries to verify RPATH linking: %s",
+                          rpath_dirs)
+        else:
+            self.log.info("Using specified subdirectories for binaries/libraries to verify RPATH linking: %s",
+                          rpath_dirs)
+
+        for dirpath in [os.path.join(self.installdir, d) for d in rpath_dirs]:
+            if os.path.exists(dirpath):
+                self.log.debug("Sanity checking RPATH for files in %s", dirpath)
+
+                for path in [os.path.join(dirpath, x) for x in os.listdir(dirpath)]:
+                    self.log.debug("Sanity checking RPATH for %s", path)
+
+                    out = get_linked_libs_raw(path)
+
+                    if out is None:
+                        msg = "Failed to determine dynamically linked libraries for %s, "
+                        msg += "so skipping it in RPATH sanity check"
+                        self.log.debug(msg, path)
+                    else:
+                        # check whether all required libraries are found via 'ldd'
+                        matches = re.findall(not_found_regex, out)
+                        if len(matches) > 0:  # Some libraries are not found via 'ldd'
+                            # For each match, check if the library is in the exception list
+                            for match in matches:
+                                if match in filter_rpath_sanity_libs:
+                                    msg = "Library %s not found for %s, but ignored "
+                                    msg += "since it is on the rpath exception list: %s"
+                                    self.log.info(msg, match, path, filter_rpath_sanity_libs)
+                                else:
+                                    fail_msg = "Library %s not found for %s; " % (match, path)
+                                    fail_msg += "RPATH linking is enabled, but not implemented for Go packages."
+                                    fail_msg += "See https://github.com/easybuilders/easybuild-easyconfigs/issues/17516"
+                                    self.log.warning(fail_msg)
+                                    fails.append(fail_msg)
+                        else:
+                            self.log.debug("Output of 'ldd %s' checked, looks OK", path)
+            else:
+                self.log.debug("Not sanity checking files in non-existing directory %s", dirpath)
+
+        env.restore_env_vars(orig_env)
+
+        return fails

From bb3a98fc0a2f885d45a11c48f3f8de774981ab05 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Wed, 22 Mar 2023 22:12:33 +0100
Subject: [PATCH 13/59] remove unused variable

---
 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 aca57c99d0..16e2a2d1d7 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -167,7 +167,6 @@ def sanity_check_rpath(self, rpath_dirs=None):
         self.log.debug("List of loaded modules: %s", self.modules_tool.list())
 
         not_found_regex = re.compile(r'(\S+)\s*\=\>\s*not found')
-        readelf_rpath_regex = re.compile('(RPATH)', re.M)
 
         # List of libraries that should be exempt from the RPATH sanity check;
         # For example, libcuda.so.1 should never be RPATH-ed by design,

From e4553ff3a0117e5654f2e07d76bef79fc3f336a1 Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Mon, 27 Mar 2023 11:13:43 +0100
Subject: [PATCH 14/59] use string '0' instead of to avoid problems when
 opensll version is not determined

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

diff --git a/easybuild/easyblocks/o/openssl_wrapper.py b/easybuild/easyblocks/o/openssl_wrapper.py
index bd6c50341e..f73a5e5295 100644
--- a/easybuild/easyblocks/o/openssl_wrapper.py
+++ b/easybuild/easyblocks/o/openssl_wrapper.py
@@ -162,7 +162,7 @@ def __init__(self, *args, **kwargs):
             for solib in solibs:
                 system_solib = find_library_path(solib)
                 if system_solib:
-                    openssl_version = 0
+                    openssl_version = '0'
                     # get version of system library filename
                     try:
                         openssl_version = full_version_regex.search(os.path.realpath(system_solib)).group(0)

From 2fff8d2e5eb4d4fb69b2847da492a113e9116c6c Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Wed, 29 Mar 2023 08:53:48 +0100
Subject: [PATCH 15/59] better error message

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

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index 50405f4a8d..7c493abb4e 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -162,7 +162,8 @@ def install_step(self):
             try:
                 keys = os.environ['EB_MATLAB_KEY']
             except KeyError:
-                raise EasyBuildError("The MATLAB install key is not set.")
+                raise EasyBuildError("The MATLAB install key is not set. This can be set either with the environment "
+									 "variable EB_MATLAB_KEY or by the easyconfig variable 'key'.")
         if isinstance(keys, string_type):
             keys = keys.split(',')
 

From a98f4a5aa26d40b7d51f89bdf2de364ee924047a Mon Sep 17 00:00:00 2001
From: Simon Branford <4967+branfosj@users.noreply.github.com>
Date: Wed, 29 Mar 2023 08:54:25 +0100
Subject: [PATCH 16/59] spaces vs tabs

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

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index 7c493abb4e..643fa73878 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -163,7 +163,7 @@ def install_step(self):
                 keys = os.environ['EB_MATLAB_KEY']
             except KeyError:
                 raise EasyBuildError("The MATLAB install key is not set. This can be set either with the environment "
-									 "variable EB_MATLAB_KEY or by the easyconfig variable 'key'.")
+                                     "variable EB_MATLAB_KEY or by the easyconfig variable 'key'.")
         if isinstance(keys, string_type):
             keys = keys.split(',')
 

From f10d6a1f3daa4f904e2be455ca6cc22462d8fd71 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 29 Mar 2023 18:52:38 +0200
Subject: [PATCH 17/59] Join argument list, fix typos

---
 easybuild/easyblocks/generic/cargo.py | 62 ++++++++++++++++++++-------
 1 file changed, 46 insertions(+), 16 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 037cf9300c..e99457857a 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -85,14 +85,25 @@ def configure_step(self):
         pass
 
     def extract_step(self):
-        """Populate all vendored deps with required .cargo-checksum.json"""
-        EasyBlock.extract_step(self)
-        for source in self.src:
-            dirname = source["name"].rsplit('.', maxsplit=2)[0]
-            self.log.info('creating .cargo-checksums.json file for : %s', dirname)
-            chksum = compute_checksum(source['path'], checksum_type='sha256')
-            chkfile = '%s/%s/.cargo-checksum.json' % (self.builddir, dirname)
-            write_file(chkfile, '{"files":{},"package":"%s"}' % chksum)
+        """
+        Unpack the source files and populate them with required .cargo-checksum.json if offline
+        """
+        for src in self.src:
+            self.log.info("Unpacking source %s" % src['name'])
+            srcdir = extract_file(src['path'], self.builddir, cmd=src['cmd'],
+                                  extra_options=self.cfg['unpack_options'], change_into_dir=False)
+            change_dir(srcdir)
+            if srcdir:
+                self.src[self.src.index(src)]['finalpath'] = srcdir
+            else:
+                raise EasyBuildError("Unpacking source %s failed", src['name'])
+
+            # Create checksum file for all sources required for 
+            if self.cfg['offline']:
+                self.log.info('creating .cargo-checksums.json file for : %s', srcdir)
+                chksum = compute_checksum(src['path'], checksum_type='sha256')
+                chkfile = '%s/%s/.cargo-checksum.json' % (self.builddir, srcdir)
+                write_file(chkfile, '{"files":{},"package":"%s"}' % chksum)
 
     @property
     def profile(self):
@@ -106,31 +117,50 @@ def build_step(self):
 
         tests = ''
         if self.cfg['enable_tests']:
-            parallel = "--tests"
+            tests = "--tests"
 
         offline = ''
         if self.cfg['offline']:
-            parallel = "--offline"
+            offline = "--offline"
             # Replace crates-io with vendored sources
             write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
 
         lto = ''
         if self.cfg['lto']:
-            parallel = '--config profile.%s.lto=true' % self.profile
+            lto = '--config profile.%s.lto=true' % self.profile
 
         run_cmd('rustc --print cfg', log_all=True, simple=True)  # for tracking in log file
-        cmd = '%s cargo build --profile=%s %s %s %s %s %s' % (
-            self.cfg['prebuildopts'], self.profile, offline, lto, tests, parallel, self.cfg['buildopts'])
+        cmd = ' '.join([
+            self.cfg['prebuildopts'],
+            'cargo build',
+            '--profile=' + self.profile,
+            offline,
+            lto,
+            tests,
+            parallel,
+            self.cfg['buildopts'],
+        ])
         run_cmd(cmd, log_all=True, simple=True)
 
     def test_step(self):
         """Test with cargo"""
         if self.cfg['enable_tests']:
-            cmd = "%s cargo test --profile=%s %s" % (self.cfg['pretestopts'], self.profile, self.cfg['testopts'])
+            cmd = ' '.join([
+                self.cfg['pretestopts'],
+                'cargo test',
+                '--profile=' + self.profile,
+                self.cfg['testopts'],
+            ])
             run_cmd(cmd, log_all=True, simple=True)
 
     def install_step(self):
         """Install with cargo"""
-        cmd = "%s cargo install --profile=%s --offline --root %s --path . %s" % (
-            self.cfg['preinstallopts'], self.profile, self.installdir, self.cfg['installopts'])
+        cmd = ' '.join([
+            self.cfg['preinstallopts'],
+            'cargo install'
+            '--profile=' + self.profile,
+            '--root=' + self.installdir,
+            '--path=.',
+            self.cfg['installopts'],
+        ])
         run_cmd(cmd, log_all=True, simple=True)

From 7904bf08fdad4dc4a400a2682706f8b9893f48bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 29 Mar 2023 19:15:17 +0200
Subject: [PATCH 18/59] Add missing import for change_dir

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index e99457857a..f184b70b8b 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -31,8 +31,10 @@
 import os
 
 import easybuild.tools.environment as env
+from easybuild.tools.build_log import EasyBuildError
 from easybuild.framework.easyconfig import CUSTOM
 from easybuild.framework.easyblock import EasyBlock
+from easybuild.tools.filetools import extract_file, change_dir
 from easybuild.tools.run import run_cmd
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import write_file, compute_checksum

From ecf69fd3caabd71330af83fc8796a97b91ac24b5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 29 Mar 2023 19:19:15 +0200
Subject: [PATCH 19/59] Fix trailing space

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index f184b70b8b..e658ec15c8 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -100,7 +100,7 @@ def extract_step(self):
             else:
                 raise EasyBuildError("Unpacking source %s failed", src['name'])
 
-            # Create checksum file for all sources required for 
+            # Create checksum file for all sources required by vendored crates.io sources
             if self.cfg['offline']:
                 self.log.info('creating .cargo-checksums.json file for : %s', srcdir)
                 chksum = compute_checksum(src['path'], checksum_type='sha256')

From 9d4225bcdf220ea5d928b57c502d9da805a00797 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 29 Mar 2023 20:26:06 +0200
Subject: [PATCH 20/59] Fix cargo checksum into each extracted dir

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index e658ec15c8..c33d3b3551 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -90,7 +90,9 @@ def extract_step(self):
         """
         Unpack the source files and populate them with required .cargo-checksum.json if offline
         """
+        dirs = set()
         for src in self.src:
+            existing_dirs = set(os.listdir(self.builddir))
             self.log.info("Unpacking source %s" % src['name'])
             srcdir = extract_file(src['path'], self.builddir, cmd=src['cmd'],
                                   extra_options=self.cfg['unpack_options'], change_into_dir=False)
@@ -101,10 +103,12 @@ def extract_step(self):
                 raise EasyBuildError("Unpacking source %s failed", src['name'])
 
             # Create checksum file for all sources required by vendored crates.io sources
-            if self.cfg['offline']:
-                self.log.info('creating .cargo-checksums.json file for : %s', srcdir)
+            new_dirs = set(os.listdir(self.builddir)) - existing_dirs
+            if self.cfg['offline'] and len(new_dirs) == 1:
+                cratedir = new_dirs.pop()
+                self.log.info('creating .cargo-checksums.json file for : %s', cratedir)
                 chksum = compute_checksum(src['path'], checksum_type='sha256')
-                chkfile = '%s/%s/.cargo-checksum.json' % (self.builddir, srcdir)
+                chkfile = os.path.join(self.builddir, cratedir, '.cargo-checksum.json')
                 write_file(chkfile, '{"files":{},"package":"%s"}' % chksum)
 
     @property
@@ -159,7 +163,7 @@ def install_step(self):
         """Install with cargo"""
         cmd = ' '.join([
             self.cfg['preinstallopts'],
-            'cargo install'
+            'cargo install',
             '--profile=' + self.profile,
             '--root=' + self.installdir,
             '--path=.',

From 10b604dc3d2b614198ca6daa82ca492b8222b27f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 29 Mar 2023 20:27:39 +0200
Subject: [PATCH 21/59] Remove unused var

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index c33d3b3551..b87898ad9a 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -90,7 +90,6 @@ def extract_step(self):
         """
         Unpack the source files and populate them with required .cargo-checksum.json if offline
         """
-        dirs = set()
         for src in self.src:
             existing_dirs = set(os.listdir(self.builddir))
             self.log.info("Unpacking source %s" % src['name'])

From 827e30092811aa8b537c0b94b46ebf3363cacf94 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 30 Mar 2023 09:18:45 +0200
Subject: [PATCH 22/59] Update both messages for Kokkos and GPU package

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

diff --git a/easybuild/easyblocks/l/lammps.py b/easybuild/easyblocks/l/lammps.py
index 4bcfc42d9d..d026696a4d 100644
--- a/easybuild/easyblocks/l/lammps.py
+++ b/easybuild/easyblocks/l/lammps.py
@@ -346,7 +346,7 @@ def configure_step(self, **kwargs):
         # https://lammps.sandia.gov/doc/Build_extras.html
         # KOKKOS
         if self.cfg['kokkos']:
-            print_msg("Using Kokkos arch: CPU - %s, GPU - %s" % (processor_arch, gpu_arch))
+            print_msg("Using Kokkos package with arch: CPU - %s, GPU - %s" % (processor_arch, gpu_arch))
             self.cfg.update('configopts', '-D%sKOKKOS=on' % self.pkg_prefix)
 
             if self.toolchain.options.get('openmp', None):
@@ -372,7 +372,7 @@ def configure_step(self, **kwargs):
 
         # CUDA only
         elif self.cuda:
-            print_msg("Using gpu (not Kokkos) arch: CPU - %s, GPU - %s" % (processor_arch, gpu_arch))
+            print_msg("Using GPU package (not Kokkos) with arch: CPU - %s, GPU - %s" % (processor_arch, gpu_arch))
             self.cfg.update('configopts', '-D%sGPU=on' % self.pkg_prefix)
             self.cfg.update('configopts', '-DGPU_API=cuda')
             self.cfg.update('configopts', '-DGPU_ARCH=%s' % get_cuda_gpu_arch(cuda_cc))

From 1ee031d9de457a0003b47320f31e0c7ecc79aa0b Mon Sep 17 00:00:00 2001
From: Simon Branford <s.j.branford@bham.ac.uk>
Date: Sat, 1 Apr 2023 14:22:02 +0100
Subject: [PATCH 23/59] use FlexiBLAS for newer PyTorch versions

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

diff --git a/easybuild/easyblocks/p/pytorch.py b/easybuild/easyblocks/p/pytorch.py
index 252bc09741..2783db4707 100644
--- a/easybuild/easyblocks/p/pytorch.py
+++ b/easybuild/easyblocks/p/pytorch.py
@@ -155,6 +155,9 @@ def configure_step(self):
         if get_software_root('imkl'):
             options.append('BLAS=MKL')
             options.append('INTEL_MKL_DIR=$MKLROOT')
+        elif pytorch_version >= '1.11.0' and get_software_root('FlexiBLAS'):
+            options.append('BLAS=FlexiBLAS')
+            options.append('WITH_BLAS=flexi')
         elif pytorch_version >= '1.9.0' and get_software_root('BLIS'):
             options.append('BLAS=BLIS')
             options.append('BLIS_HOME=' + get_software_root('BLIS'))

From d04f012061fa8a559834b1b22afdf8bd32019bda Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 13 Apr 2023 04:13:17 +0200
Subject: [PATCH 24/59] Include script for generating crate list

---
 easybuild/easyblocks/generic/cargo.py | 55 +++++++++++++++++++++++++--
 1 file changed, 52 insertions(+), 3 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index b87898ad9a..588c0be6a1 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -52,7 +52,7 @@ def extra_options(extra_vars=None):
         extra_vars.update({
             'enable_tests': [True, "Enable building of tests", CUSTOM],
             'offline': [True, "Build offline", CUSTOM],
-            'lto': [False, "Build with link time optimization", CUSTOM],
+            'lto': [None, "Override default LTO flag ('fat', 'thin', 'off')", CUSTOM],
             'crates': [[], "List of (crate, version) tuples to use", CUSTOM],
         })
 
@@ -131,8 +131,8 @@ def build_step(self):
             write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
 
         lto = ''
-        if self.cfg['lto']:
-            lto = '--config profile.%s.lto=true' % self.profile
+        if self.cfg['lto'] is not None:
+            lto = '--config profile.%s.lto=\\"%s\\"' % (self.profile, self.cfg['lto'])
 
         run_cmd('rustc --print cfg', log_all=True, simple=True)  # for tracking in log file
         cmd = ' '.join([
@@ -150,22 +150,71 @@ def build_step(self):
     def test_step(self):
         """Test with cargo"""
         if self.cfg['enable_tests']:
+            offline = ''
+            if self.cfg['offline']:
+                offline = "--offline"
+
             cmd = ' '.join([
                 self.cfg['pretestopts'],
                 'cargo test',
                 '--profile=' + self.profile,
+                offline,
                 self.cfg['testopts'],
             ])
             run_cmd(cmd, log_all=True, simple=True)
 
     def install_step(self):
         """Install with cargo"""
+        offline = ''
+        if self.cfg['offline']:
+            offline = "--offline"
+
         cmd = ' '.join([
             self.cfg['preinstallopts'],
             'cargo install',
             '--profile=' + self.profile,
+            offline,
             '--root=' + self.installdir,
             '--path=.',
             self.cfg['installopts'],
         ])
         run_cmd(cmd, log_all=True, simple=True)
+
+
+def generate_crate_list(sourcedir):
+    """Helper for generating crate list"""
+    import toml
+
+    cargo_toml = toml.load(os.path.join(sourcedir, 'Cargo.toml'))
+    cargo_lock = toml.load(os.path.join(sourcedir, 'Cargo.lock'))
+
+    app_name = cargo_toml['package']['name']
+    deps = cargo_lock['package']
+
+    app_in_cratesio = False
+    crates = []
+    other_crates = []
+    for dep in deps:
+        name = dep['name']
+        version = dep['version']
+        if 'source' in dep and dep['source'] == 'registry+https://github.com/rust-lang/crates.io-index':
+            if name == app_name:
+                app_in_cratesio = True  # exclude app itself, needs to be first in crates list
+            else:
+                crates.append((name, version))
+        else:
+            other_crates.append((name, version))
+    return app_in_cratesio, crates, other_crates
+
+
+if __name__ == '__main__':
+    import sys
+    app_in_cratesio, crates, _ = generate_crate_list(sys.argv[1])
+    if app_in_cratesio or crates:
+        print('crates = [')
+        if app_in_cratesio:
+            print('    (name, version),')
+        for name, version in crates:
+            print("    ('" + name + "', '" + version + "'),")
+        print(']')
+    

From e83b8c6efc5e05499cc803a79ea84b71e0d3322d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 13 Apr 2023 10:19:47 +0200
Subject: [PATCH 25/59] Trailing whitespace

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 588c0be6a1..4187edaeae 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -217,4 +217,4 @@ def generate_crate_list(sourcedir):
         for name, version in crates:
             print("    ('" + name + "', '" + version + "'),")
         print(']')
-    
+

From 00c0f101c78e3d29c091544ee5540b3e3a453582 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 13 Apr 2023 11:06:35 +0200
Subject: [PATCH 26/59] blank line

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 4187edaeae..1890d373aa 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -217,4 +217,3 @@ def generate_crate_list(sourcedir):
         for name, version in crates:
             print("    ('" + name + "', '" + version + "'),")
         print(']')
-

From 94b8c73743b1e2086c5433b74254d74a3068fd6a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 21 Apr 2023 17:29:24 +0200
Subject: [PATCH 27/59] prevent copy-pasting of code by using the parameter
 added in https://github.com/easybuilders/easybuild-framework/pull/4249

---
 easybuild/easyblocks/generic/gopackage.py | 78 +----------------------
 1 file changed, 2 insertions(+), 76 deletions(-)

diff --git a/easybuild/easyblocks/generic/gopackage.py b/easybuild/easyblocks/generic/gopackage.py
index 16e2a2d1d7..55695fc51e 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -28,17 +28,14 @@
 @author: Pavel Grochal (INUITS)
 """
 import os
-import re
 from distutils.version import LooseVersion
 
 import easybuild.tools.environment as env
-from easybuild.framework.easyblock import DEFAULT_BIN_LIB_SUBDIRS, EasyBlock
+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 easybuild.tools.systemtools import get_linked_libs_raw
 
 
 class GoPackage(EasyBlock):
@@ -134,9 +131,6 @@ def install_step(self):
             self.cfg['preinstallopts'],
             'go',
             'install',
-            # print commands as they are executed,
-            # including downloading and installing of package deps as listed in the go.mod file
-            '-x',
             self.cfg['installopts'],
         ])
         run_cmd(cmd, log_all=True, log_ok=True, simple=True)
@@ -154,72 +148,4 @@ def sanity_check_step(self):
         super(GoPackage, self).sanity_check_step(custom_paths=custom_paths, custom_commands=custom_commands)
 
     def sanity_check_rpath(self, rpath_dirs=None):
-        """Sanity check binaries/libraries w.r.t. RPATH linking."""
-
-        self.log.info("Checking RPATH linkage for binaries/libraries...")
-
-        fails = []
-
-        # hard reset $LD_LIBRARY_PATH before running RPATH sanity check
-        orig_env = env.unset_env_vars(['LD_LIBRARY_PATH'])
-
-        self.log.debug("$LD_LIBRARY_PATH during RPATH sanity check: %s", os.getenv('LD_LIBRARY_PATH', '(empty)'))
-        self.log.debug("List of loaded modules: %s", self.modules_tool.list())
-
-        not_found_regex = re.compile(r'(\S+)\s*\=\>\s*not found')
-
-        # List of libraries that should be exempt from the RPATH sanity check;
-        # For example, libcuda.so.1 should never be RPATH-ed by design,
-        # see https://github.com/easybuilders/easybuild-framework/issues/4095
-        filter_rpath_sanity_libs = build_option('filter_rpath_sanity_libs')
-        msg = "Ignoring the following libraries if they are not found by RPATH sanity check: %s"
-        self.log.info(msg, filter_rpath_sanity_libs)
-
-        if rpath_dirs is None:
-            rpath_dirs = self.cfg['bin_lib_subdirs'] or self.bin_lib_subdirs()
-
-        if not rpath_dirs:
-            rpath_dirs = DEFAULT_BIN_LIB_SUBDIRS
-            self.log.info("Using default subdirectories for binaries/libraries to verify RPATH linking: %s",
-                          rpath_dirs)
-        else:
-            self.log.info("Using specified subdirectories for binaries/libraries to verify RPATH linking: %s",
-                          rpath_dirs)
-
-        for dirpath in [os.path.join(self.installdir, d) for d in rpath_dirs]:
-            if os.path.exists(dirpath):
-                self.log.debug("Sanity checking RPATH for files in %s", dirpath)
-
-                for path in [os.path.join(dirpath, x) for x in os.listdir(dirpath)]:
-                    self.log.debug("Sanity checking RPATH for %s", path)
-
-                    out = get_linked_libs_raw(path)
-
-                    if out is None:
-                        msg = "Failed to determine dynamically linked libraries for %s, "
-                        msg += "so skipping it in RPATH sanity check"
-                        self.log.debug(msg, path)
-                    else:
-                        # check whether all required libraries are found via 'ldd'
-                        matches = re.findall(not_found_regex, out)
-                        if len(matches) > 0:  # Some libraries are not found via 'ldd'
-                            # For each match, check if the library is in the exception list
-                            for match in matches:
-                                if match in filter_rpath_sanity_libs:
-                                    msg = "Library %s not found for %s, but ignored "
-                                    msg += "since it is on the rpath exception list: %s"
-                                    self.log.info(msg, match, path, filter_rpath_sanity_libs)
-                                else:
-                                    fail_msg = "Library %s not found for %s; " % (match, path)
-                                    fail_msg += "RPATH linking is enabled, but not implemented for Go packages."
-                                    fail_msg += "See https://github.com/easybuilders/easybuild-easyconfigs/issues/17516"
-                                    self.log.warning(fail_msg)
-                                    fails.append(fail_msg)
-                        else:
-                            self.log.debug("Output of 'ldd %s' checked, looks OK", path)
-            else:
-                self.log.debug("Not sanity checking files in non-existing directory %s", dirpath)
-
-        env.restore_env_vars(orig_env)
-
-        return fails
+        super(GoPackage, self).sanity_check_rpath(rpath_dirs=rpath_dirs, check_readelf_rpath=False)

From d4e6a94c5b4124a67aa700d72ec8c4c445c170fb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 21 Apr 2023 17:36:04 +0200
Subject: [PATCH 28/59] Merge latest changes from develop

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

diff --git a/easybuild/easyblocks/generic/gopackage.py b/easybuild/easyblocks/generic/gopackage.py
index 55695fc51e..5c2d96bdc9 100644
--- a/easybuild/easyblocks/generic/gopackage.py
+++ b/easybuild/easyblocks/generic/gopackage.py
@@ -131,6 +131,9 @@ def install_step(self):
             self.cfg['preinstallopts'],
             'go',
             'install',
+            # print commands as they are executed,
+            # including downloading and installing of package deps as listed in the go.mod file
+            '-x',
             self.cfg['installopts'],
         ])
         run_cmd(cmd, log_all=True, log_ok=True, simple=True)

From 55ec455c6adbc05a6e5beb6f0b69167311370ed0 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 21 Apr 2023 21:57:03 +0200
Subject: [PATCH 29/59] ensure that --sysroot is passed to linker

---
 easybuild/easyblocks/g/gcc.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/easybuild/easyblocks/g/gcc.py b/easybuild/easyblocks/g/gcc.py
index 9069e3ea37..9bf640253c 100644
--- a/easybuild/easyblocks/g/gcc.py
+++ b/easybuild/easyblocks/g/gcc.py
@@ -357,9 +357,6 @@ def configure_step(self):
             # (see https://gcc.gnu.org/install/configure.html)
             self.cfg.update('configopts', '--with-sysroot=%s' % sysroot)
 
-            # avoid that --sysroot is passed to linker by patching value for SYSROOT_SPEC in gcc/gcc.c
-            apply_regex_substitutions(os.path.join('gcc', 'gcc.c'), [('--sysroot=%R', '')])
-
             # prefix dynamic linkers with sysroot
             # this patches lines like:
             # #define GLIBC_DYNAMIC_LINKER64 "/lib64/ld-linux-x86-64.so.2"

From f15f3006b5ee7d99ce3934bf3d4a6655564b49ba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 2 May 2023 01:13:28 +0200
Subject: [PATCH 30/59] Add cargopythonpackage

---
 easybuild/easyblocks/generic/cargo.py         | 30 ++++------
 .../easyblocks/generic/cargopythonpackage.py  | 60 +++++++++++++++++++
 2 files changed, 72 insertions(+), 18 deletions(-)
 create mode 100644 easybuild/easyblocks/generic/cargopythonpackage.py

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 1890d373aa..29e990e31a 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -83,6 +83,14 @@ def __init__(self, *args, **kwargs):
             })
         self.cfg.update('sources', sources)
 
+        if self.cfg['offline']:
+            # Replace crates-io with vendored sources using build dir wide toml file in CARGO_HOME
+            # because the rust source subdirectories might differ with python packages
+            config_toml = os.path.join(self.builddir, '.cargo', 'config.toml')
+            write_file(config_toml, '[source.crates-io]\ndirectory="%s"' % self.builddir)
+            # Use environment variable since it would also be passed along to builds triggered via python packages
+            env.setvar('CARGO_NET_OFFLINE', 'true')
+
     def configure_step(self):
         pass
 
@@ -124,12 +132,6 @@ def build_step(self):
         if self.cfg['enable_tests']:
             tests = "--tests"
 
-        offline = ''
-        if self.cfg['offline']:
-            offline = "--offline"
-            # Replace crates-io with vendored sources
-            write_file('.cargo/config.toml', '[source.crates-io]\ndirectory=".."', append=True)
-
         lto = ''
         if self.cfg['lto'] is not None:
             lto = '--config profile.%s.lto=\\"%s\\"' % (self.profile, self.cfg['lto'])
@@ -139,7 +141,6 @@ def build_step(self):
             self.cfg['prebuildopts'],
             'cargo build',
             '--profile=' + self.profile,
-            offline,
             lto,
             tests,
             parallel,
@@ -150,30 +151,20 @@ def build_step(self):
     def test_step(self):
         """Test with cargo"""
         if self.cfg['enable_tests']:
-            offline = ''
-            if self.cfg['offline']:
-                offline = "--offline"
-
             cmd = ' '.join([
                 self.cfg['pretestopts'],
                 'cargo test',
                 '--profile=' + self.profile,
-                offline,
                 self.cfg['testopts'],
             ])
             run_cmd(cmd, log_all=True, simple=True)
 
     def install_step(self):
         """Install with cargo"""
-        offline = ''
-        if self.cfg['offline']:
-            offline = "--offline"
-
         cmd = ' '.join([
             self.cfg['preinstallopts'],
             'cargo install',
             '--profile=' + self.profile,
-            offline,
             '--root=' + self.installdir,
             '--path=.',
             self.cfg['installopts'],
@@ -189,6 +180,7 @@ def generate_crate_list(sourcedir):
     cargo_lock = toml.load(os.path.join(sourcedir, 'Cargo.lock'))
 
     app_name = cargo_toml['package']['name']
+    print(app_name)
     deps = cargo_lock['package']
 
     app_in_cratesio = False
@@ -199,6 +191,7 @@ def generate_crate_list(sourcedir):
         version = dep['version']
         if 'source' in dep and dep['source'] == 'registry+https://github.com/rust-lang/crates.io-index':
             if name == app_name:
+                print('check')
                 app_in_cratesio = True  # exclude app itself, needs to be first in crates list
             else:
                 crates.append((name, version))
@@ -209,7 +202,8 @@ def generate_crate_list(sourcedir):
 
 if __name__ == '__main__':
     import sys
-    app_in_cratesio, crates, _ = generate_crate_list(sys.argv[1])
+    app_in_cratesio, crates, other = generate_crate_list(sys.argv[1])
+    print(other)
     if app_in_cratesio or crates:
         print('crates = [')
         if app_in_cratesio:
diff --git a/easybuild/easyblocks/generic/cargopythonpackage.py b/easybuild/easyblocks/generic/cargopythonpackage.py
new file mode 100644
index 0000000000..ae1292512b
--- /dev/null
+++ b/easybuild/easyblocks/generic/cargopythonpackage.py
@@ -0,0 +1,60 @@
+##
+# Copyright 2009-2023 Ghent University
+#
+# This file is part of EasyBuild,
+# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
+# with support of Ghent University (http://ugent.be/hpc),
+# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
+# Flemish Research Foundation (FWO) (http://www.fwo.be/en)
+# and the Department of Economy, Science and Innovation (EWI) (http://www.ewi-vlaanderen.be/en).
+#
+# https://github.com/easybuilders/easybuild
+#
+# EasyBuild is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation v2.
+#
+# EasyBuild is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with EasyBuild.  If not, see <http://www.gnu.org/licenses/>.
+##
+"""
+EasyBuild support for installing Cargo packages (Rust lang package system)
+
+@author: Mikael Oehman (Chalmers University of Technology)
+"""
+
+import os
+
+from easybuild.easyblocks.generic.cargo import Cargo
+from easybuild.easyblocks.generic.pythonpackage import PythonPackage
+
+
+class CargoPythonPackage(PythonPackage, Cargo):  # PythonPackage must come first to take precedence
+    """Build a Python package with setup from Cargo but build/install step from PythonPackage
+
+    The cargo init step will set up the environment variables for rustc and vendor sources
+    but all the build steps are triggered via normal PythonPackage steps like normal.
+    """
+
+    @staticmethod
+    def extra_options(extra_vars=None):
+        """Define extra easyconfig parameters specific to Cargo"""
+        extra_vars = PythonPackage.extra_options(extra_vars)
+        extra_vars = Cargo.extra_options(extra_vars)  # not all extra options here will used here
+
+        return extra_vars
+
+    def __init__(self, *args, **kwargs):
+        """Constructor for CargoPythonPackage easyblock."""
+        Cargo.__init__(self, *args, **kwargs)
+        return PythonPackage.__init__(self, *args, **kwargs)
+
+    def extract_step(self):
+        """Specifically use the overloaded variant from Cargo as is populates vendored sources with checksums."""
+        return Cargo.extract_step(self)
+

From 13807fb9ab1a869c135d87c2eb4b13d5b411f3b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 2 May 2023 01:28:58 +0200
Subject: [PATCH 31/59] Fix code style

---
 easybuild/easyblocks/generic/cargopythonpackage.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargopythonpackage.py b/easybuild/easyblocks/generic/cargopythonpackage.py
index ae1292512b..71a8778fa4 100644
--- a/easybuild/easyblocks/generic/cargopythonpackage.py
+++ b/easybuild/easyblocks/generic/cargopythonpackage.py
@@ -28,8 +28,6 @@
 @author: Mikael Oehman (Chalmers University of Technology)
 """
 
-import os
-
 from easybuild.easyblocks.generic.cargo import Cargo
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage
 
@@ -57,4 +55,3 @@ def __init__(self, *args, **kwargs):
     def extract_step(self):
         """Specifically use the overloaded variant from Cargo as is populates vendored sources with checksums."""
         return Cargo.extract_step(self)
-

From 85113256cd16e38edcce8c0ae10f813652f6bc04 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 2 May 2023 02:28:33 +0200
Subject: [PATCH 32/59] Move config.toml modifications to extract step

---
 easybuild/easyblocks/generic/cargo.py         | 20 ++++++++++---------
 .../easyblocks/generic/cargopythonpackage.py  |  2 ++
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 29e990e31a..562a1f69fe 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -61,7 +61,8 @@ def extra_options(extra_vars=None):
     def __init__(self, *args, **kwargs):
         """Constructor for Cargo easyblock."""
         super(Cargo, self).__init__(*args, **kwargs)
-        env.setvar('CARGO_HOME', os.path.join(self.builddir, '.cargo'))
+        self.cargo_home = os.path.join(self.builddir, '.cargo')
+        env.setvar('CARGO_HOME', self.cargo_home)
         env.setvar('RUSTC', 'rustc')
         env.setvar('RUSTDOC', 'rustdoc')
         env.setvar('RUSTFMT', 'rustfmt')
@@ -83,14 +84,6 @@ def __init__(self, *args, **kwargs):
             })
         self.cfg.update('sources', sources)
 
-        if self.cfg['offline']:
-            # Replace crates-io with vendored sources using build dir wide toml file in CARGO_HOME
-            # because the rust source subdirectories might differ with python packages
-            config_toml = os.path.join(self.builddir, '.cargo', 'config.toml')
-            write_file(config_toml, '[source.crates-io]\ndirectory="%s"' % self.builddir)
-            # Use environment variable since it would also be passed along to builds triggered via python packages
-            env.setvar('CARGO_NET_OFFLINE', 'true')
-
     def configure_step(self):
         pass
 
@@ -98,6 +91,15 @@ def extract_step(self):
         """
         Unpack the source files and populate them with required .cargo-checksum.json if offline
         """
+        if self.cfg['offline']:
+            self.log.info("Setting vendored crates-io dir")
+            # Replace crates-io with vendored sources using build dir wide toml file in CARGO_HOME
+            # because the rust source subdirectories might differ with python packages
+            config_toml = os.path.join(self.cargo_home, 'config.toml')
+            write_file(config_toml, '[source.crates-io]\ndirectory="%s"' % self.builddir)
+            # Use environment variable since it would also be passed along to builds triggered via python packages
+            env.setvar('CARGO_NET_OFFLINE', 'true')
+
         for src in self.src:
             existing_dirs = set(os.listdir(self.builddir))
             self.log.info("Unpacking source %s" % src['name'])
diff --git a/easybuild/easyblocks/generic/cargopythonpackage.py b/easybuild/easyblocks/generic/cargopythonpackage.py
index 71a8778fa4..21011d9e97 100644
--- a/easybuild/easyblocks/generic/cargopythonpackage.py
+++ b/easybuild/easyblocks/generic/cargopythonpackage.py
@@ -49,7 +49,9 @@ def extra_options(extra_vars=None):
 
     def __init__(self, *args, **kwargs):
         """Constructor for CargoPythonPackage easyblock."""
+        print("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2")
         Cargo.__init__(self, *args, **kwargs)
+        self.log.info("CHECK B")
         return PythonPackage.__init__(self, *args, **kwargs)
 
     def extract_step(self):

From 9067045460fa50f78577b34cb3a73c57b7be5c2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Tue, 2 May 2023 02:34:27 +0200
Subject: [PATCH 33/59] Remove debug prints

---
 easybuild/easyblocks/generic/cargopythonpackage.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargopythonpackage.py b/easybuild/easyblocks/generic/cargopythonpackage.py
index 21011d9e97..71a8778fa4 100644
--- a/easybuild/easyblocks/generic/cargopythonpackage.py
+++ b/easybuild/easyblocks/generic/cargopythonpackage.py
@@ -49,9 +49,7 @@ def extra_options(extra_vars=None):
 
     def __init__(self, *args, **kwargs):
         """Constructor for CargoPythonPackage easyblock."""
-        print("XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2")
         Cargo.__init__(self, *args, **kwargs)
-        self.log.info("CHECK B")
         return PythonPackage.__init__(self, *args, **kwargs)
 
     def extract_step(self):

From 86aca20d15def4261c22a8af57b1aee467daa893 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 3 May 2023 03:33:17 +0200
Subject: [PATCH 34/59] Add output log to matlab installs, parse for common
 errors

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

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index 643fa73878..1bd4ef1b6b 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -55,6 +55,7 @@ def __init__(self, *args, **kwargs):
         super(EB_MATLAB, self).__init__(*args, **kwargs)
         self.comp_fam = None
         self.configfile = os.path.join(self.builddir, 'my_installer_input.txt')
+        self.outputfile = os.path.join(self.builddir, 'my_installer_output.txt')
 
     @staticmethod
     def extra_options():
@@ -98,12 +99,14 @@ def configure_step(self):
             regagree = re.compile(br"^# agreeToLicense=.*", re.M)
             regmode = re.compile(br"^# mode=.*", re.M)
             reglicpath = re.compile(br"^# licensePath=.*", re.M)
+            regoutfile = re.compile(br"^# outputFile=.*", re.M)
 
             # must use byte-strings here when using Python 3, see above
             config = regdest.sub(b"destinationFolder=%s" % self.installdir.encode('utf-8'), config)
             config = regagree.sub(b"agreeToLicense=Yes", config)
             config = regmode.sub(b"mode=silent", config)
             config = reglicpath.sub(b"licensePath=%s" % licfile.encode('utf-8'), config)
+            config = regoutfile.sub(b"outputFile=\"%s\"" % self.outputfile, config)
 
             write_file(self.configfile, config)
 
@@ -188,6 +191,9 @@ def install_step(self):
             # check installer output for known signs of trouble
             patterns = [
                 "Error: You have entered an invalid File Installation Key",
+                "Not a valid key",
+                "Exiting with status -2",
+                "End - Unsuccessful",
             ]
 
             for pattern in patterns:
@@ -195,6 +201,12 @@ def install_step(self):
                 if regex.search(out):
                     raise EasyBuildError("Found error pattern '%s' in output of installation command '%s': %s",
                                          regex.pattern, cmd, out)
+                
+                with open(self.outputfile) as f:
+                    if regex.search(f.read()):
+                        raise EasyBuildError("Found error pattern '%s' in output file of installer",
+                                             regex.pattern)
+
 
     def sanity_check_step(self):
         """Custom sanity check for MATLAB."""

From 0264c37d531156e1fe89361afb3d3f0da3a6922a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 3 May 2023 03:36:54 +0200
Subject: [PATCH 35/59] Fix style

---
 easybuild/easyblocks/m/matlab.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index 1bd4ef1b6b..575cf94b4f 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -201,13 +201,11 @@ def install_step(self):
                 if regex.search(out):
                     raise EasyBuildError("Found error pattern '%s' in output of installation command '%s': %s",
                                          regex.pattern, cmd, out)
-                
                 with open(self.outputfile) as f:
                     if regex.search(f.read()):
                         raise EasyBuildError("Found error pattern '%s' in output file of installer",
                                              regex.pattern)
 
-
     def sanity_check_step(self):
         """Custom sanity check for MATLAB."""
         custom_paths = {

From 5f3d769ab3c38308e4fbd06e22fc2619e51fa197 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 3 May 2023 03:47:42 +0200
Subject: [PATCH 36/59] Add missing utf-8 encoding

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

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index 575cf94b4f..8c1a4df514 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -106,7 +106,7 @@ def configure_step(self):
             config = regagree.sub(b"agreeToLicense=Yes", config)
             config = regmode.sub(b"mode=silent", config)
             config = reglicpath.sub(b"licensePath=%s" % licfile.encode('utf-8'), config)
-            config = regoutfile.sub(b"outputFile=\"%s\"" % self.outputfile, config)
+            config = regoutfile.sub(b"outputFile=\"%s\"" % self.outputfile.encode('utf-8'), config)
 
             write_file(self.configfile, config)
 

From c1fbbae8beb821bc348f26a099baf8fe572822e2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 3 May 2023 03:58:47 +0200
Subject: [PATCH 37/59] Remove quotes around file path as matlab doesn't like
 that

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

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index 8c1a4df514..f147bc993c 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -106,7 +106,7 @@ def configure_step(self):
             config = regagree.sub(b"agreeToLicense=Yes", config)
             config = regmode.sub(b"mode=silent", config)
             config = reglicpath.sub(b"licensePath=%s" % licfile.encode('utf-8'), config)
-            config = regoutfile.sub(b"outputFile=\"%s\"" % self.outputfile.encode('utf-8'), config)
+            config = regoutfile.sub(b"outputFile=%s" % self.outputfile.encode('utf-8'), config)
 
             write_file(self.configfile, config)
 

From f0ededc1afc7e6261d330797eab67e877465ea31 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 3 May 2023 16:18:29 +0200
Subject: [PATCH 38/59] Broaden patterns to find in matlab errors

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

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index f147bc993c..a0f04b1748 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -192,7 +192,9 @@ def install_step(self):
             patterns = [
                 "Error: You have entered an invalid File Installation Key",
                 "Not a valid key",
-                "Exiting with status -2",
+                "All selected products are already installed",
+                "The application encountered an unexpected error and needs to close",
+                "Exiting with status -\\d",
                 "End - Unsuccessful",
             ]
 

From f04ea9604ff3c13070a2388978d87962d22c52ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 May 2023 00:16:00 +0200
Subject: [PATCH 39/59] Allow gurobi to use EB_GUROBI_LICENSE_FILE environment
 variable

---
 easybuild/easyblocks/g/gurobi.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/easybuild/easyblocks/g/gurobi.py b/easybuild/easyblocks/g/gurobi.py
index a02938ac12..923cc28f2f 100644
--- a/easybuild/easyblocks/g/gurobi.py
+++ b/easybuild/easyblocks/g/gurobi.py
@@ -55,22 +55,25 @@ def __init__(self, *args, **kwargs):
         """Easyblock constructor, define custom class variables specific to Gurobi."""
         super(EB_Gurobi, self).__init__(*args, **kwargs)
 
-        self.license_file = self.cfg['license_file']
-
+        # make sure license file is available
+        self.orig_license_file = self.cfg['license_file']
+        if self.orig_license_file is None:
+            self.orig_license_file = os.getenv('EB_GUROBI_LICENSE_FILE', None)
+            
+        if self.orig_license_file is None or not os.path.exists(self.cfg['license_file']):
+            raise EasyBuildError("No existing license file specified: %s", self.orig_license_file)
+ 
         if self.cfg['copy_license_file']:
             self.license_file = os.path.join(self.installdir, 'gurobi.lic')
+        else:
+            self.license_file = self.orig_license_file
 
     def install_step(self):
         """Install Gurobi and license file."""
-
-        # make sure license file is available
-        if self.cfg['license_file'] is None or not os.path.exists(self.cfg['license_file']):
-            raise EasyBuildError("No existing license file specified: %s", self.cfg['license_file'])
-
         super(EB_Gurobi, self).install_step()
 
         if self.cfg['copy_license_file']:
-            copy_file(self.cfg['license_file'], self.license_file)
+            copy_file(self.orig_license_file, self.license_file)
 
         if get_software_root('Python'):
             run_cmd("python setup.py install --prefix=%s" % self.installdir)

From 5b357e482825ef0ff52d4584537169ab26e5df3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 May 2023 00:17:40 +0200
Subject: [PATCH 40/59] Fix code style in gurobi.py

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

diff --git a/easybuild/easyblocks/g/gurobi.py b/easybuild/easyblocks/g/gurobi.py
index 923cc28f2f..45b6506916 100644
--- a/easybuild/easyblocks/g/gurobi.py
+++ b/easybuild/easyblocks/g/gurobi.py
@@ -59,10 +59,10 @@ def __init__(self, *args, **kwargs):
         self.orig_license_file = self.cfg['license_file']
         if self.orig_license_file is None:
             self.orig_license_file = os.getenv('EB_GUROBI_LICENSE_FILE', None)
-            
+
         if self.orig_license_file is None or not os.path.exists(self.cfg['license_file']):
             raise EasyBuildError("No existing license file specified: %s", self.orig_license_file)
- 
+
         if self.cfg['copy_license_file']:
             self.license_file = os.path.join(self.installdir, 'gurobi.lic')
         else:

From d1fa20a71c1e2d9fc5920f5a2d51311cb8815843 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 May 2023 00:32:59 +0200
Subject: [PATCH 41/59] Move check for non-noneness of gurobi license file into
 install step

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

diff --git a/easybuild/easyblocks/g/gurobi.py b/easybuild/easyblocks/g/gurobi.py
index 45b6506916..309511bb29 100644
--- a/easybuild/easyblocks/g/gurobi.py
+++ b/easybuild/easyblocks/g/gurobi.py
@@ -60,9 +60,6 @@ def __init__(self, *args, **kwargs):
         if self.orig_license_file is None:
             self.orig_license_file = os.getenv('EB_GUROBI_LICENSE_FILE', None)
 
-        if self.orig_license_file is None or not os.path.exists(self.cfg['license_file']):
-            raise EasyBuildError("No existing license file specified: %s", self.orig_license_file)
-
         if self.cfg['copy_license_file']:
             self.license_file = os.path.join(self.installdir, 'gurobi.lic')
         else:
@@ -73,6 +70,9 @@ def install_step(self):
         super(EB_Gurobi, self).install_step()
 
         if self.cfg['copy_license_file']:
+            if self.orig_license_file is None or not os.path.exists(self.cfg['license_file']):
+                raise EasyBuildError("No existing license file specified: %s", self.orig_license_file)
+
             copy_file(self.orig_license_file, self.license_file)
 
         if get_software_root('Python'):

From 2bc61b48c70fa5161c180a96f8d8da5cbe229115 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 May 2023 13:52:33 +0200
Subject: [PATCH 42/59] Fix use of incorrect license file variable

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

diff --git a/easybuild/easyblocks/g/gurobi.py b/easybuild/easyblocks/g/gurobi.py
index 309511bb29..49147d9a2f 100644
--- a/easybuild/easyblocks/g/gurobi.py
+++ b/easybuild/easyblocks/g/gurobi.py
@@ -70,7 +70,7 @@ def install_step(self):
         super(EB_Gurobi, self).install_step()
 
         if self.cfg['copy_license_file']:
-            if self.orig_license_file is None or not os.path.exists(self.cfg['license_file']):
+            if self.orig_license_file is None or not os.path.exists(self.orig_license_file):
                 raise EasyBuildError("No existing license file specified: %s", self.orig_license_file)
 
             copy_file(self.orig_license_file, self.license_file)

From 53410d2989a45214a951a831782b9901792f4c28 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 May 2023 15:55:28 +0200
Subject: [PATCH 43/59] Update easybuild/easyblocks/m/matlab.py

Co-authored-by: Sam Moors <smoors@users.noreply.github.com>
---
 easybuild/easyblocks/m/matlab.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easybuild/easyblocks/m/matlab.py b/easybuild/easyblocks/m/matlab.py
index a0f04b1748..b260e703de 100644
--- a/easybuild/easyblocks/m/matlab.py
+++ b/easybuild/easyblocks/m/matlab.py
@@ -194,6 +194,7 @@ def install_step(self):
                 "Not a valid key",
                 "All selected products are already installed",
                 "The application encountered an unexpected error and needs to close",
+                "Error: Unable to write to",
                 "Exiting with status -\\d",
                 "End - Unsuccessful",
             ]

From 84af134d2d983ff795680e38ebd8566906cc4335 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Thu, 4 May 2023 15:56:03 +0200
Subject: [PATCH 44/59] Add partial support for vendoring of non-crates.io
 crates

---
 easybuild/easyblocks/generic/cargo.py         | 61 +++++++++++++------
 .../easyblocks/generic/cargopythonpackage.py  |  2 +-
 2 files changed, 45 insertions(+), 18 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 562a1f69fe..43d9c29bcb 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -53,7 +53,7 @@ def extra_options(extra_vars=None):
             'enable_tests': [True, "Enable building of tests", CUSTOM],
             'offline': [True, "Build offline", CUSTOM],
             'lto': [None, "Override default LTO flag ('fat', 'thin', 'off')", CUSTOM],
-            'crates': [[], "List of (crate, version) tuples to use", CUSTOM],
+            'crates': [[], "List of (crate, version, [repo, rev]) tuples to use", CUSTOM],
         })
 
         return extra_vars
@@ -74,14 +74,25 @@ def __init__(self, *args, **kwargs):
         env.setvar('RUST_BACKTRACE', '1')
 
         # Populate sources from "crates" list of tuples
-        sources = self.cfg['sources']
-        for crate, version in self.cfg['crates']:
-            sources.append({
-                'download_filename': crate + '/' + version + '/download',
-                'filename': crate + '-' + version + '.tar.gz',
-                'source_urls': [CRATESIO_SOURCE],
-                'alt_location': 'crates.io',
-            })
+        sources = []
+        for crate_info in self.cfg['crates']:
+            if len(crate_info) == 2:
+                crate, version = crate_info
+                sources.append({
+                    'download_filename': crate + '/' + version + '/download',
+                    'filename': crate + '-' + version + '.tar.gz',
+                    'source_urls': [CRATESIO_SOURCE],
+                    'alt_location': 'crates.io',
+                })
+            else:
+                crate, version, repo, rev = crate_info
+                url, repo_name_git = repo.rsplit('/', maxsplit=1)
+                sources.append({
+                    'git_config': {'url': url, 'repo_name': repo_name_git[:-4], 'commit': rev},
+                    'filename': crate + '-' + version + '.tar.gz',
+                    'source_urls': [CRATESIO_SOURCE],
+                })
+
         self.cfg.update('sources', sources)
 
     def configure_step(self):
@@ -96,10 +107,24 @@ def extract_step(self):
             # Replace crates-io with vendored sources using build dir wide toml file in CARGO_HOME
             # because the rust source subdirectories might differ with python packages
             config_toml = os.path.join(self.cargo_home, 'config.toml')
-            write_file(config_toml, '[source.crates-io]\ndirectory="%s"' % self.builddir)
+            write_file(config_toml, '[source.vendored-sources]\ndirectory = "%s"\n\n' % self.builddir, append=True)
+            write_file(config_toml, '[source.crates-io]\ndirectory = "vendored-sources"\n\n', append=True)
+
+            # also vendor sources from other git sources:
+            # note that one repo can contain multiple packages but we should specify the source once
+            git_sources = set()
+            for crate_info in self.cfg['crates']:
+                if len(crate_info) == 4:
+                    _, _, repo, rev = crate_info
+                    git_sources.add((repo, rev))
+            for repo, rev in git_sources:
+                write_file(config_toml, '[source."%s"]\ngit = "%s"\nrev = "%s"\ndirectory = "vendored-sources"\n\n' % (
+                    repo, repo, rev), append=True)
+
             # Use environment variable since it would also be passed along to builds triggered via python packages
             env.setvar('CARGO_NET_OFFLINE', 'true')
 
+        # More work is needed here for git sources to work, especially those repos with multiple packages.
         for src in self.src:
             existing_dirs = set(os.listdir(self.builddir))
             self.log.info("Unpacking source %s" % src['name'])
@@ -182,7 +207,6 @@ def generate_crate_list(sourcedir):
     cargo_lock = toml.load(os.path.join(sourcedir, 'Cargo.lock'))
 
     app_name = cargo_toml['package']['name']
-    print(app_name)
     deps = cargo_lock['package']
 
     app_in_cratesio = False
@@ -191,12 +215,15 @@ def generate_crate_list(sourcedir):
     for dep in deps:
         name = dep['name']
         version = dep['version']
-        if 'source' in dep and dep['source'] == 'registry+https://github.com/rust-lang/crates.io-index':
+        if 'source' in dep:
             if name == app_name:
-                print('check')
-                app_in_cratesio = True  # exclude app itself, needs to be first in crates list
+                app_in_cratesio = True  # exclude app itself, needs to be first in crates list or taken from pypi
             else:
-                crates.append((name, version))
+                if dep['source'] == 'registry+https://github.com/rust-lang/crates.io-index':
+                    crates.append((name, version))
+                else:
+                    # Lock file has revision#revision in the url for some reason.
+                    crates.append((name, version, dep['source'].rsplit('#', maxsplit=1)[0]))
         else:
             other_crates.append((name, version))
     return app_in_cratesio, crates, other_crates
@@ -210,6 +237,6 @@ def generate_crate_list(sourcedir):
         print('crates = [')
         if app_in_cratesio:
             print('    (name, version),')
-        for name, version in crates:
-            print("    ('" + name + "', '" + version + "'),")
+        for crate_info in crates:
+            print("    ('" + "', '".join(crate_info) + "'),")
         print(']')
diff --git a/easybuild/easyblocks/generic/cargopythonpackage.py b/easybuild/easyblocks/generic/cargopythonpackage.py
index 71a8778fa4..a935e190a0 100644
--- a/easybuild/easyblocks/generic/cargopythonpackage.py
+++ b/easybuild/easyblocks/generic/cargopythonpackage.py
@@ -50,7 +50,7 @@ def extra_options(extra_vars=None):
     def __init__(self, *args, **kwargs):
         """Constructor for CargoPythonPackage easyblock."""
         Cargo.__init__(self, *args, **kwargs)
-        return PythonPackage.__init__(self, *args, **kwargs)
+        PythonPackage.__init__(self, *args, **kwargs)
 
     def extract_step(self):
         """Specifically use the overloaded variant from Cargo as is populates vendored sources with checksums."""

From 348332b4fd004f9ab457677b9b7c9fd70f6babce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 5 May 2023 16:56:58 +0200
Subject: [PATCH 45/59] Fix mistake in vendoring of sources

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 43d9c29bcb..69fbfb62ae 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -103,22 +103,21 @@ def extract_step(self):
         Unpack the source files and populate them with required .cargo-checksum.json if offline
         """
         if self.cfg['offline']:
-            self.log.info("Setting vendored crates-io dir")
+            self.log.info("Setting vendored crates dir")
             # Replace crates-io with vendored sources using build dir wide toml file in CARGO_HOME
             # because the rust source subdirectories might differ with python packages
             config_toml = os.path.join(self.cargo_home, 'config.toml')
             write_file(config_toml, '[source.vendored-sources]\ndirectory = "%s"\n\n' % self.builddir, append=True)
-            write_file(config_toml, '[source.crates-io]\ndirectory = "vendored-sources"\n\n', append=True)
+            write_file(config_toml, '[source.crates-io]\nreplace-with = "vendored-sources"\n\n', append=True)
 
-            # also vendor sources from other git sources:
-            # note that one repo can contain multiple packages but we should specify the source once
+            # also vendor sources from other git sources (could be many crates for one git source)
             git_sources = set()
             for crate_info in self.cfg['crates']:
                 if len(crate_info) == 4:
                     _, _, repo, rev = crate_info
                     git_sources.add((repo, rev))
             for repo, rev in git_sources:
-                write_file(config_toml, '[source."%s"]\ngit = "%s"\nrev = "%s"\ndirectory = "vendored-sources"\n\n' % (
+                write_file(config_toml, '[source."%s"]\ngit = "%s"\nrev = "%s"\nreplace-with = "vendored-sources"\n\n' % (
                     repo, repo, rev), append=True)
 
             # Use environment variable since it would also be passed along to builds triggered via python packages

From 0803ce991acf3c2494669f7a1701293c827e9bd4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 5 May 2023 16:59:13 +0200
Subject: [PATCH 46/59] Break up long line

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 69fbfb62ae..323573eb5b 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -117,8 +117,8 @@ def extract_step(self):
                     _, _, repo, rev = crate_info
                     git_sources.add((repo, rev))
             for repo, rev in git_sources:
-                write_file(config_toml, '[source."%s"]\ngit = "%s"\nrev = "%s"\nreplace-with = "vendored-sources"\n\n' % (
-                    repo, repo, rev), append=True)
+                write_file(config_toml, '[source."%s"]\ngit = "%s"\nrev = "%s"\n' \
+                                        'replace-with = "vendored-sources"\n\n' % (repo, repo, rev), append=True)
 
             # Use environment variable since it would also be passed along to builds triggered via python packages
             env.setvar('CARGO_NET_OFFLINE', 'true')

From 480ffdc0076f5069a0e8be3b68decbdd2cbe2133 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Fri, 5 May 2023 17:09:42 +0200
Subject: [PATCH 47/59] Fix style

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 323573eb5b..c538f5c244 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -117,7 +117,7 @@ def extract_step(self):
                     _, _, repo, rev = crate_info
                     git_sources.add((repo, rev))
             for repo, rev in git_sources:
-                write_file(config_toml, '[source."%s"]\ngit = "%s"\nrev = "%s"\n' \
+                write_file(config_toml, '[source."%s"]\ngit = "%s"\nrev = "%s"\n'
                                         'replace-with = "vendored-sources"\n\n' % (repo, repo, rev), append=True)
 
             # Use environment variable since it would also be passed along to builds triggered via python packages

From b34fd4613ff19950b1ea911d7184578e618a7097 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Mikael=20=C3=96hman?= <micketeer@gmail.com>
Date: Wed, 10 May 2023 18:29:14 +0200
Subject: [PATCH 48/59] Switch cargo to extensioneasyblock to allow use as an
 extension

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index c538f5c244..50ef5542b5 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -33,7 +33,7 @@
 import easybuild.tools.environment as env
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.framework.easyconfig import CUSTOM
-from easybuild.framework.easyblock import EasyBlock
+from easybuild.framework.extensioneasyblock import ExtensionEasyBlock
 from easybuild.tools.filetools import extract_file, change_dir
 from easybuild.tools.run import run_cmd
 from easybuild.tools.config import build_option
@@ -42,13 +42,13 @@
 CRATESIO_SOURCE = "https://crates.io/api/v1/crates"
 
 
-class Cargo(EasyBlock):
+class Cargo(ExtensionEasyBlock):
     """Support for installing Cargo packages (Rust)"""
 
     @staticmethod
     def extra_options(extra_vars=None):
         """Define extra easyconfig parameters specific to Cargo"""
-        extra_vars = EasyBlock.extra_options(extra_vars)
+        extra_vars = ExtensionEasyBlock.extra_options(extra_vars)
         extra_vars.update({
             'enable_tests': [True, "Enable building of tests", CUSTOM],
             'offline': [True, "Build offline", CUSTOM],

From 6a9cba4ee8eac503ab68378ff4287cfb60d05f67 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 May 2023 15:32:28 +0200
Subject: [PATCH 49/59] force building torchvision with CUDA support if CUDA is
 included as dependency by setting $FORCE_CUDA

---
 easybuild/easyblocks/t/torchvision.py | 48 +++++++++++++++++++++++----
 1 file changed, 42 insertions(+), 6 deletions(-)

diff --git a/easybuild/easyblocks/t/torchvision.py b/easybuild/easyblocks/t/torchvision.py
index 197ff15c67..7ef971a8b9 100644
--- a/easybuild/easyblocks/t/torchvision.py
+++ b/easybuild/easyblocks/t/torchvision.py
@@ -26,12 +26,12 @@
 EasyBuild support for building and installing torchvision, implemented as an easyblock
 
 @author: Alexander Grund (TU Dresden)
+@author: Kenneth Hoste (HPC-UGent)
 """
-
 from easybuild.easyblocks.generic.pythonpackage import PythonPackage
 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.modules import get_software_version
 import easybuild.tools.environment as env
 
 
@@ -40,24 +40,60 @@ class EB_torchvision(PythonPackage):
 
     @staticmethod
     def extra_options():
-        """Change some defaults."""
+        """Change some defaults for easyconfig parameters."""
         extra_vars = PythonPackage.extra_options()
         extra_vars['use_pip'][0] = True
         extra_vars['download_dep_fail'][0] = True
         extra_vars['sanity_pip_check'][0] = True
         return extra_vars
 
+    def __init__(self, *args, **kwargs):
+        """Initialize torchvision easyblock."""
+        super(EB_torchvision, self).__init__(*args, **kwargs)
+
+        dep_names = set(dep['name'] for dep in self.cfg.dependencies())
+
+        # require that PyTorch is listed as dependency
+        if 'PyTorch' not in dep_names:
+            raise EasyBuildError('PyTorch not found as a dependency')
+
+        # enable building with GPU support if CUDA is included as dependency
+        if 'CUDA' in dep_names:
+            self.with_cuda = True
+        else:
+            self.with_cuda = False
+
     def configure_step(self):
         """Set up torchvision config"""
-        if not get_software_root('PyTorch'):
-            raise EasyBuildError('PyTorch not found as a dependency')
 
         # Note: Those can be overwritten by e.g. preinstallopts
         env.setvar('BUILD_VERSION', self.version)
         env.setvar('PYTORCH_VERSION', get_software_version('PyTorch'))
-        if get_software_root('CUDA'):
+
+        if self.with_cuda:
+            # make sure that torchvision is installed with CUDA support by setting $FORCE_CUDA
+            env.setvar('FORCE_CUDA', '1')
+            # specify CUDA compute capabilities via $TORCH_CUDA_ARCH_LIST
             cuda_cc = self.cfg['cuda_compute_capabilities'] or build_option('cuda_compute_capabilities')
             if cuda_cc:
                 env.setvar('TORCH_CUDA_ARCH_LIST', ';'.join(cuda_cc))
 
         super(EB_torchvision, self).configure_step()
+
+    def sanity_check_step(self):
+        """Custom sanity check for torchvision."""
+        custom_commands = []
+
+        # check whether torchvision was indeed built with CUDA support,
+        # cfr. https://discuss.pytorch.org/t/notimplementederror-could-not-run-torchvision-nms-with-arguments-from-\
+        #      the-cuda-backend-this-could-be-because-the-operator-doesnt-exist-for-this-backend/132352/4
+        if self.with_cuda:
+            python_code = '; '.join([
+                "import torch, torchvision",
+                "boxes = torch.tensor([[0., 1., 2., 3.]]).to('cuda')",
+                "scores = torch.randn(1).to('cuda')",
+                "print(torchvision.ops.nms(boxes, scores, 0.5))",
+            ])
+            custom_commands.append('python -c "%s"' % python_code)
+
+        super(EB_torchvision, self).sanity_check_step(custom_commands=custom_commands)

From f912a8416e00095d46681af5519a829a0cb43ceb Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 May 2023 16:20:35 +0200
Subject: [PATCH 50/59] add required PyTorch dependency to test easyconfig used
 to initialize torchvision easyblock

---
 test/easyblocks/init_easyblocks.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/test/easyblocks/init_easyblocks.py b/test/easyblocks/init_easyblocks.py
index 9f7a2a1a09..9a53f4b898 100644
--- a/test/easyblocks/init_easyblocks.py
+++ b/test/easyblocks/init_easyblocks.py
@@ -96,7 +96,7 @@ def tearDown(self):
             self.log.error("Failed to remove %s: %s" % (self.eb_file, err))
 
 
-def template_init_test(self, easyblock, name='foo', version='1.3.2', toolchain=None):
+def template_init_test(self, easyblock, name='foo', version='1.3.2', toolchain=None, deps=None):
     """Test whether all easyblocks can be initialized."""
 
     def check_extra_options_format(extra_options):
@@ -164,6 +164,9 @@ def check_extra_options_format(extra_options):
                     test_param = 'foo'
                 extra_txt += '%s = "%s"\n' % (key, test_param)
 
+        if deps:
+            extra_txt += 'dependencies = %s' % str(deps)
+
         # write easyconfig file
         self.write_ec(ebname, name=name, version=version, toolchain=toolchain, extratxt=extra_txt)
 
@@ -224,6 +227,9 @@ def innertest(self):
         elif easyblock_fn == 'openssl_wrapper.py':
             # easyblock to create OpenSSL wrapper expects an OpenSSL version
             innertest = make_inner_test(easyblock, version='1.1')
+        elif easyblock_fn == 'torchvision.py':
+            # torchvision easyblock requires that PyTorch is listed as dependency
+            innertest = make_inner_test(easyblock, name='torchvision', deps=[('PyTorch', '1.12.1')])
         else:
             innertest = make_inner_test(easyblock)
 

From d48fdc9ed1e2dacbad71ded5d6c5d5c4b930373c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 May 2023 16:27:13 +0200
Subject: [PATCH 51/59] also add required PyTorch dependency when test
 torchvision easyblock with --module-only

---
 test/easyblocks/module.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/test/easyblocks/module.py b/test/easyblocks/module.py
index 65b91f942c..e75a707532 100644
--- a/test/easyblocks/module.py
+++ b/test/easyblocks/module.py
@@ -333,7 +333,7 @@ def template_module_only_test(self, easyblock, name, version='1.3.2', extra_txt=
         self.writeEC(ebname, name=name, version=version, extratxt=extra_txt, toolchain=toolchain)
 
         # take into account that for some easyblock, particular dependencies are hard required early on
-        # (in prepare_step for exampel);
+        # (in prepare_step for example);
         # we just set the corresponding $EBROOT* environment variables here to fool it...
         req_deps = {
             # QScintilla easyblock requires that either PyQt or PyQt5 are available as dependency
@@ -460,6 +460,10 @@ def innertest(self):
         elif eb_fn == 'openssl_wrapper.py':
             # easyblock to create OpenSSL wrapper expects an OpenSSL version
             innertest = make_inner_test(easyblock, name='OpenSSL-wrapper', version='1.1')
+        elif eb_fn == 'torchvision.py':
+            # torchvision easyblock requires that PyTorch is listed as dependency
+            extra_txt = "dependencies = [('PyTorch', '1.12.1')]"
+            innertest = make_inner_test(easyblock, name='torchvision', extra_txt=extra_txt)
         elif eb_fn == 'ucx_plugins.py':
             # install fake ucx_info command (used in make_module_extra)
             tmpdir = tempfile.mkdtemp()

From eaab6fafd5ea9148687a2aeef1e0025cc8b22744 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 23 May 2023 16:41:36 +0200
Subject: [PATCH 52/59] create empty module file for requied PyTorch dependency
 when testing torchvision easyblock

---
 test/easyblocks/module.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/test/easyblocks/module.py b/test/easyblocks/module.py
index e75a707532..db44834031 100644
--- a/test/easyblocks/module.py
+++ b/test/easyblocks/module.py
@@ -118,7 +118,7 @@ class ModuleOnlyTest(TestCase):
     def writeEC(self, easyblock, name='foo', version='1.3.2', extratxt='', toolchain=None):
         """ create temporary easyconfig file """
         if toolchain is None:
-            toolchain = {'name': 'dummy', 'version': 'dummy'}
+            toolchain = {'name': 'system', 'version': 'system'}
 
         txt = '\n'.join([
             'easyblock = "%s"',
@@ -434,8 +434,9 @@ def innertest(self):
     for prgenv in ['PrgEnv-cray', 'PrgEnv-gnu', 'PrgEnv-intel', 'PrgEnv-pgi']:
         write_file(os.path.join(TMPDIR, 'modules', 'all', prgenv, '1.2.3'), "#%Module")
 
-    # add foo/1.3.2.1.1 module, required for testing ModuleAlias easyblock
-    write_file(os.path.join(TMPDIR, 'modules', 'all', 'foo', '1.2.3.4.5'), "#%Module")
+    # add empty module files for dependencies that are required for testing easyblocks
+    for dep_mod_name in ('foo/1.2.3.4.5', 'PyTorch/1.12.1'):
+        write_file(os.path.join(TMPDIR, 'modules', 'all', dep_mod_name), "#%Module")
 
     for easyblock in easyblocks:
         eb_fn = os.path.basename(easyblock)

From 45202911698f35a307f7bbc350ef6de4bb7e8929 Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Tue, 23 May 2023 16:50:50 +0200
Subject: [PATCH 53/59] comsol: Fix exec permission on files in arch bindir

---
 easybuild/easyblocks/c/comsol.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easybuild/easyblocks/c/comsol.py b/easybuild/easyblocks/c/comsol.py
index 09b6e44fcd..38d778a623 100644
--- a/easybuild/easyblocks/c/comsol.py
+++ b/easybuild/easyblocks/c/comsol.py
@@ -114,6 +114,11 @@ def install_step(self):
         # make sure setup script is executable
         adjust_permissions(setup_script, stat.S_IXUSR)
 
+        # make sure binaries in arch bindir is executable
+        archpath = os.path.join(self.start_dir, 'bin', 'glnxa64')
+        adjust_permissions(os.path.join(archpath, 'inflate'), stat.S_IXUSR)
+        adjust_permissions(os.path.join(archpath, 'setuplauncher'), stat.S_IXUSR)
+
         # make sure $DISPLAY is not defined, which may lead to (hard to trace) problems
         # this is a workaround for not being able to specify --nodisplay to the install scripts
         env.unset_env_vars(['DISPLAY'])

From 8c1662302a02b74e2fbfcd5640d3fd96a97f6245 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 24 May 2023 16:54:22 +0200
Subject: [PATCH 54/59] enhance Cargo constructor to avoid processing list of
 crates multiple times into sources

---
 easybuild/easyblocks/generic/cargo.py | 56 ++++++++++++++++-----------
 1 file changed, 33 insertions(+), 23 deletions(-)

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 50ef5542b5..0918f9b881 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -73,30 +73,36 @@ def __init__(self, *args, **kwargs):
         env.setvar('RUST_LOG', 'DEBUG')
         env.setvar('RUST_BACKTRACE', '1')
 
-        # Populate sources from "crates" list of tuples
-        sources = []
-        for crate_info in self.cfg['crates']:
-            if len(crate_info) == 2:
-                crate, version = crate_info
-                sources.append({
-                    'download_filename': crate + '/' + version + '/download',
-                    'filename': crate + '-' + version + '.tar.gz',
-                    'source_urls': [CRATESIO_SOURCE],
-                    'alt_location': 'crates.io',
-                })
-            else:
-                crate, version, repo, rev = crate_info
-                url, repo_name_git = repo.rsplit('/', maxsplit=1)
-                sources.append({
-                    'git_config': {'url': url, 'repo_name': repo_name_git[:-4], 'commit': rev},
-                    'filename': crate + '-' + version + '.tar.gz',
-                    'source_urls': [CRATESIO_SOURCE],
-                })
+        # Populate sources from "crates" list of tuples (only once)
+        if self.cfg['crates']:
+            # copy list of crates, so we can wipe 'crates' easyconfig paramter,
+            # to avoid that creates are processed into 'sources' easyconfig parameter again
+            # when easyblock is initialized again using same parsed easyconfig
+            # (for example when check_sha256_checksums function is called, like in easyconfigs test suite)
+            self.crates = self.cfg['crates'][:]
+            sources = []
+            for crate_info in self.cfg['crates']:
+                if len(crate_info) == 2:
+                    crate, version = crate_info
+                    sources.append({
+                        'download_filename': crate + '/' + version + '/download',
+                        'filename': crate + '-' + version + '.tar.gz',
+                        'source_urls': [CRATESIO_SOURCE],
+                        'alt_location': 'crates.io',
+                    })
+                else:
+                    crate, version, repo, rev = crate_info
+                    url, repo_name_git = repo.rsplit('/', maxsplit=1)
+                    sources.append({
+                        'git_config': {'url': url, 'repo_name': repo_name_git[:-4], 'commit': rev},
+                        'filename': crate + '-' + version + '.tar.gz',
+                        'source_urls': [CRATESIO_SOURCE],
+                    })
 
-        self.cfg.update('sources', sources)
+            self.cfg.update('sources', sources)
 
-    def configure_step(self):
-        pass
+            # set 'crates' easyconfig parameter to empty list to prevent re-processing into sources
+            self.cfg['crates'] = []
 
     def extract_step(self):
         """
@@ -112,7 +118,7 @@ def extract_step(self):
 
             # also vendor sources from other git sources (could be many crates for one git source)
             git_sources = set()
-            for crate_info in self.cfg['crates']:
+            for crate_info in self.crates:
                 if len(crate_info) == 4:
                     _, _, repo, rev = crate_info
                     git_sources.add((repo, rev))
@@ -144,6 +150,10 @@ def extract_step(self):
                 chkfile = os.path.join(self.builddir, cratedir, '.cargo-checksum.json')
                 write_file(chkfile, '{"files":{},"package":"%s"}' % chksum)
 
+    def configure_step(self):
+        """Empty configuration step."""
+        pass
+
     @property
     def profile(self):
         return 'debug' if self.toolchain.options.get('debug', None) else 'release'

From f6c717a5383ef6f5b02b0b7814884c5ac458de6f Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 24 May 2023 17:08:02 +0200
Subject: [PATCH 55/59] Update easybuild/easyblocks/generic/cargo.py

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

diff --git a/easybuild/easyblocks/generic/cargo.py b/easybuild/easyblocks/generic/cargo.py
index 0918f9b881..b511b851bc 100644
--- a/easybuild/easyblocks/generic/cargo.py
+++ b/easybuild/easyblocks/generic/cargo.py
@@ -75,7 +75,7 @@ def __init__(self, *args, **kwargs):
 
         # Populate sources from "crates" list of tuples (only once)
         if self.cfg['crates']:
-            # copy list of crates, so we can wipe 'crates' easyconfig paramter,
+            # copy list of crates, so we can wipe 'crates' easyconfig parameter,
             # to avoid that creates are processed into 'sources' easyconfig parameter again
             # when easyblock is initialized again using same parsed easyconfig
             # (for example when check_sha256_checksums function is called, like in easyconfigs test suite)

From 37ffbf6d001b82e1c3b117ddfc4f53a7b406bcdd Mon Sep 17 00:00:00 2001
From: Bart Oldeman <bart.oldeman@calculquebec.ca>
Date: Thu, 25 May 2023 11:59:41 +0000
Subject: [PATCH 56/59] Patch gcc.c* only for older sysroot-ed installations.

Check the contents of libc.so: only if the entries are prefixed, patch
gcc.c (or gcc.cc for GCC 12+), to account for the changes in
https://github.com/gentoo/gentoo/pull/28851
---
 easybuild/easyblocks/g/gcc.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/easybuild/easyblocks/g/gcc.py b/easybuild/easyblocks/g/gcc.py
index 9bf640253c..7ee469763e 100644
--- a/easybuild/easyblocks/g/gcc.py
+++ b/easybuild/easyblocks/g/gcc.py
@@ -48,7 +48,7 @@
 from easybuild.tools.build_log import EasyBuildError
 from easybuild.tools.config import build_option
 from easybuild.tools.filetools import apply_regex_substitutions, change_dir, copy_file, move_file, symlink
-from easybuild.tools.filetools import which, write_file
+from easybuild.tools.filetools import which, read_file, write_file
 from easybuild.tools.modules import get_software_root
 from easybuild.tools.run import run_cmd
 from easybuild.tools.systemtools import RISCV, check_os_dependency, get_cpu_architecture, get_cpu_family
@@ -357,6 +357,20 @@ def configure_step(self):
             # (see https://gcc.gnu.org/install/configure.html)
             self.cfg.update('configopts', '--with-sysroot=%s' % sysroot)
 
+            libc_so_candidates = [os.path.join(sysroot, x, 'libc.so') for x in
+                                  ['lib', 'lib64', os.path.join('usr', 'lib'), os.path.join('usr', 'lib64')]]
+            for libc_so in libc_so_candidates:
+                if os.path.exists(libc_so):
+                    # only patch gcc.c or gcc.cc if entries in libc.so are prefixed with sysroot
+                    if '\nGROUP ( ' + sysroot in read_file(libc_so):
+                        gccfile = os.path.join('gcc', 'gcc.c')
+                        # renamed to gcc.cc in GCC 12
+                        if not os.path.exists(gccfile):
+                            gccfile = os.path.join('gcc', 'gcc.cc')
+                        # avoid that --sysroot is passed to linker by patching value for SYSROOT_SPEC in gcc/gcc.c*
+                        apply_regex_substitutions(gccfile, [('--sysroot=%R', '')])
+                    break
+
             # prefix dynamic linkers with sysroot
             # this patches lines like:
             # #define GLIBC_DYNAMIC_LINKER64 "/lib64/ld-linux-x86-64.so.2"

From cb078d85a9bb12c447a73577137fcd8d5568b819 Mon Sep 17 00:00:00 2001
From: Sebastian Achilles <s.achilles@fz-juelich.de>
Date: Fri, 26 May 2023 11:40:45 +0200
Subject: [PATCH 57/59] prepare release notes for EasyBuild v4.7.2 + bump
 version to 4.7.2

---
 RELEASE_NOTES                    | 17 +++++++++++++++++
 easybuild/easyblocks/__init__.py |  2 +-
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 96346e430c..4210cd2941 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -5,6 +5,23 @@ 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.
 
+v4.7.2 (May 30th 2023)
+----------------------
+
+- new generic easyblock for installing Rust crates with cargo (#2902)
+- minor enhancements and updates, including:
+  - let MATLAB easyblock raise an error if the MATLAB installation key is not provided (#2905)
+  - print message to inform that GPU package (instead of Kokkos) is used for LAMMPS (#2906)
+  - enhance PyTorch easyblock to use FlexiBLAS for PyTorch >= 1.11.0 (#2915)
+- various bug fixes, including:
+  - use custom RPATH sanity check for Go packages that doesn't actually check for an RPATH section in the binary (#2913)
+  - use string '0' to avoid problems when openssl version is not determined (#2914)
+  - add output log to MATLAB installs, actually parse for common errors (#2924)
+  - enhance Gurobi easyblock to allow using $EB_GUROBI_LICENSE_FILE environment variable (#2926)
+  - force building torchvision with CUDA support if CUDA is included as dependency by setting `$FORCE_CUDA` (#2931)
+  - fix exec permission on files in arch bindir for COMSOL (#2932)
+  - enhance Cargo constructor to avoid processing list of crates multiple times into sources (#2934)
+
 v4.7.1 (March 20th 2023)
 ------------------------
 
diff --git a/easybuild/easyblocks/__init__.py b/easybuild/easyblocks/__init__.py
index fdd68d6024..f740a2523e 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('4.7.2.dev0')
+VERSION = LooseVersion('4.7.2')
 UNKNOWN = 'UNKNOWN'
 
 

From 7c7e756a17f5111ae83d1980d274f75f0e0b89d0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 27 May 2023 11:24:43 +0200
Subject: [PATCH 58/59] minor tweaks for EasyBuild v4.7.2 in release notes +
 fix release date

---
 RELEASE_NOTES | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 4210cd2941..350cf6b031 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -3,12 +3,13 @@ For more detailed information, please see the git log.
 
 These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html.
 
-The latest version of easybuild-easyblocks provides 248 software-specific easyblocks and 39 generic easyblocks.
+The latest version of easybuild-easyblocks provides 248 software-specific easyblocks and 41 generic easyblocks.
 
-v4.7.2 (May 30th 2023)
-----------------------
 
-- new generic easyblock for installing Rust crates with cargo (#2902)
+v4.7.2 (27 May 2023)
+--------------------
+
+- new generic easyblock for installing Rust crates with cargo: Cargo and CargoPythonPackage (#2902, #2934)
 - minor enhancements and updates, including:
   - let MATLAB easyblock raise an error if the MATLAB installation key is not provided (#2905)
   - print message to inform that GPU package (instead of Kokkos) is used for LAMMPS (#2906)
@@ -20,7 +21,6 @@ v4.7.2 (May 30th 2023)
   - enhance Gurobi easyblock to allow using $EB_GUROBI_LICENSE_FILE environment variable (#2926)
   - force building torchvision with CUDA support if CUDA is included as dependency by setting `$FORCE_CUDA` (#2931)
   - fix exec permission on files in arch bindir for COMSOL (#2932)
-  - enhance Cargo constructor to avoid processing list of crates multiple times into sources (#2934)
 
 v4.7.1 (March 20th 2023)
 ------------------------

From 42c96e4d81ee56ad8a2f308b3bd1c99745f6617f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 27 May 2023 21:01:56 +0200
Subject: [PATCH 59/59] include #2921 in release notes for EasyBuild v4.7.2

---
 RELEASE_NOTES | 1 +
 1 file changed, 1 insertion(+)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index 350cf6b031..f117aa07a1 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -17,6 +17,7 @@ v4.7.2 (27 May 2023)
 - various bug fixes, including:
   - use custom RPATH sanity check for Go packages that doesn't actually check for an RPATH section in the binary (#2913)
   - use string '0' to avoid problems when openssl version is not determined (#2914)
+  - update GCC easyblock to ensure that --sysroot is passed to linker (but only when it needs to be) (#2921)
   - add output log to MATLAB installs, actually parse for common errors (#2924)
   - enhance Gurobi easyblock to allow using $EB_GUROBI_LICENSE_FILE environment variable (#2926)
   - force building torchvision with CUDA support if CUDA is included as dependency by setting `$FORCE_CUDA` (#2931)