From 03e66d87cb07fb9d7c2f7f0daff93928f6b25f2d Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 5 Apr 2024 20:51:55 +0200
Subject: [PATCH 01/39] {2023.06}[foss/2023a] QuantumESPRESSO 7.3.1

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 44952e2765..6cb243556a 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,3 +71,9 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
+  - QuantumESPRESSO-7.3.1-foss-2023a.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
+      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3257
+      options:
+        from-pr: 20138
+        include-easyblocks-from-pr: 3257

From 61a788281119974079712a3ee9b1beeaa7fb24b9 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Sun, 14 Apr 2024 13:53:43 +0200
Subject: [PATCH 02/39] Update eessi-2023.06-eb-4.9.0-2023a.yml

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 6cb243556a..1e1e7fee14 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -76,4 +76,4 @@ easyconfigs:
       # see https://github.com/easybuilders/easybuild-easyblocks/pull/3257
       options:
         from-pr: 20138
-        include-easyblocks-from-pr: 3257
+        include-easyblocks-from-pr: 3306

From f07fd8567f1154cb8b4f0ab338979caff4dbfcce Mon Sep 17 00:00:00 2001
From: torri <torri@disroot.org>
Date: Wed, 26 Jun 2024 14:03:51 +0200
Subject: [PATCH 03/39] fix for broken curl installation

---
 init/eessi_environment_variables | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 78851a9c95..d6e5b75dce 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -15,6 +15,20 @@ function show_msg {
   fi
 }
 
+function check_rhel_ca {
+
+  os=$(grep -oP '(?<=^ID_LIKE=).+' /etc/os-release | tr -d '"')
+
+  version_id=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
+  version_major=${version_id%\.*}
+
+  if [[ $os =~ "rhel" ]] && [ $version_major -gt 7 ]
+  then
+        export CURL_CA_BUNDLE=/etc/pki/tls/certs/ca-bundle.crt
+  fi
+}
+
+
 # set up minimal environment: $EESSI_PREFIX, $EESSI_VERSION, $EESSI_OS_TYPE, $EESSI_CPU_FAMILY, $EPREFIX
 source $EESSI_INIT_DIR_PATH/minimal_eessi_env
 
@@ -106,6 +120,8 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
+        # Fix wrong path for RHEL >=8 libcurl 
+	check_rhel_ca
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From 9f841a2cbcf1c27ea6d7517bbb4edba9cb3744b8 Mon Sep 17 00:00:00 2001
From: lara <lara@localhost.localdomain>
Date: Mon, 1 Jul 2024 15:03:18 +0200
Subject: [PATCH 04/39] {2023.06}[foss/2023a] CP2K 2023.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index ade226c217..bd412f1579 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - BCFtools-1.18-GCC-12.3.0.eb
+  - CP2K-2023.1-foss-2023a.eb

From 9747ee497161f23dd999094e78bae6c863c5a9fb Mon Sep 17 00:00:00 2001
From: torri <torri@disroot.org>
Date: Mon, 1 Jul 2024 16:31:37 +0200
Subject: [PATCH 05/39] simplified the implementation

---
 init/eessi_environment_variables | 20 +++++---------------
 1 file changed, 5 insertions(+), 15 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index d6e5b75dce..c28ddb45d9 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -15,20 +15,6 @@ function show_msg {
   fi
 }
 
-function check_rhel_ca {
-
-  os=$(grep -oP '(?<=^ID_LIKE=).+' /etc/os-release | tr -d '"')
-
-  version_id=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
-  version_major=${version_id%\.*}
-
-  if [[ $os =~ "rhel" ]] && [ $version_major -gt 7 ]
-  then
-        export CURL_CA_BUNDLE=/etc/pki/tls/certs/ca-bundle.crt
-  fi
-}
-
-
 # set up minimal environment: $EESSI_PREFIX, $EESSI_VERSION, $EESSI_OS_TYPE, $EESSI_CPU_FAMILY, $EPREFIX
 source $EESSI_INIT_DIR_PATH/minimal_eessi_env
 
@@ -121,7 +107,11 @@ if [ -d $EESSI_PREFIX ]; then
           fi
 
         # Fix wrong path for RHEL >=8 libcurl 
-	check_rhel_ca
+	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
+        if [ -f $rhel_libcurl_file ]; then
+          show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
+          export CURL_CA_BUNDLE=$rhel_libcurl_file
+        fi
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From ba8de248ef1de35d2eecb359dd33ebcdb3981da0 Mon Sep 17 00:00:00 2001
From: lara <lara@localhost.localdomain>
Date: Tue, 2 Jul 2024 12:22:46 +0200
Subject: [PATCH 06/39] add from-pr 20951 for ARM support

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml                 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index bd412f1579..5d4aa9a772 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,3 +1,6 @@
 easyconfigs:
   - BCFtools-1.18-GCC-12.3.0.eb
-  - CP2K-2023.1-foss-2023a.eb
+  - CP2K-2023.1-foss-2023a.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
+      options:
+        from-pr: 20951

From 51c6b1c998a69d8dd4a75f4f83b101b5ba81f1b4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Jul 2024 10:51:41 +0200
Subject: [PATCH 07/39] improve comment that explains setting of
 `$CURL_CA_BUNDLE` on RHEL-based systems

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 init/eessi_environment_variables | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index c28ddb45d9..f5bb387955 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -107,6 +107,9 @@ if [ -d $EESSI_PREFIX ]; then
           fi
 
         # Fix wrong path for RHEL >=8 libcurl 
+	# This is required here because we ship curl in our compat layer. If we only provided
+	# curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
+	# hook (or via an Lmod hook)
 	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
         if [ -f $rhel_libcurl_file ]; then
           show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"

From d56cd31a81ae2a88adf8ca6b0d15e11df5624d7a Mon Sep 17 00:00:00 2001
From: lara <lara@localhost.localdomain>
Date: Wed, 3 Jul 2024 12:07:22 +0200
Subject: [PATCH 08/39] add hook for missing installation check on aarch64

---
 eb_hooks.py | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index e6f0cf0dd2..b4862cb572 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -294,6 +294,22 @@ def parse_hook_lammps_remove_deps_for_CI_aarch64(ec, *args, **kwargs):
         raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
 
 
+def parse_hook_CP2K_remove_deps_for_aarch64(ec, *args, **kwargs):
+    """
+    Remove x86_64 specific dependencies for the CI and missing installations to pass on aarch64
+    """
+    if ec.name == 'CP2K' and ec.version in ('2023.1',):
+        if os.getenv('EESSI_CPU_FAMILY') == 'aarch64':
+            # LIBXSMM is not supported on ARM with GCC 12.2.0 and 12.3.0
+            # See https://www.cp2k.org/dev:compiler_support
+            # See https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
+            # we need this hook because we check for missing installations for all CPU targets
+            # on an x86_64 VM in GitHub Actions (so condition based on ARCH in LAMMPS easyconfig is always true)
+            ec['dependencies'] = [dep for dep in ec['dependencies'] if dep[0] not in ('libxsmm',)]
+    else:
+        raise EasyBuildError("CP2K-specific hook triggered for non-CP2K easyconfig?!")]
+
+
 def pre_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwargs):
     """
     Solve issues with compiling or running the tests on both
@@ -693,6 +709,7 @@ def inject_gpu_property(ec):
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
     'LAMMPS': parse_hook_lammps_remove_deps_for_CI_aarch64,
+    'CP2K': parse_hook_CP2K_remove_deps_for_aarch64,
     'OpenBLAS': parse_hook_openblas_relax_lapack_tests_num_errors,
     'pybind11': parse_hook_pybind11_replace_catch2,
     'Qt5': parse_hook_qt5_check_qtwebengine_disable,

From 95dd8a02239cbff967a3a5e51e3186398693bfed Mon Sep 17 00:00:00 2001
From: lara <lara@localhost.localdomain>
Date: Wed, 3 Jul 2024 12:56:06 +0200
Subject: [PATCH 09/39] fix CP2K hook

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index b4862cb572..4dc39c2fe8 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -307,7 +307,7 @@ def parse_hook_CP2K_remove_deps_for_aarch64(ec, *args, **kwargs):
             # on an x86_64 VM in GitHub Actions (so condition based on ARCH in LAMMPS easyconfig is always true)
             ec['dependencies'] = [dep for dep in ec['dependencies'] if dep[0] not in ('libxsmm',)]
     else:
-        raise EasyBuildError("CP2K-specific hook triggered for non-CP2K easyconfig?!")]
+        raise EasyBuildError("CP2K-specific hook triggered for non-CP2K easyconfig?!")
 
 
 def pre_prepare_hook_highway_handle_test_compilation_issues(self, *args, **kwargs):

From 085e32a603842363607eeb10743f1f20107afd27 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Sat, 6 Jul 2024 12:10:46 +0200
Subject: [PATCH 10/39] {2023.06}[foss/2023a] Extrae 4.2.0

Alternative to #554
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index 38bfa81142..fd26743499 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,3 +1,7 @@
 easyconfigs:
   - IPython-8.17.2-GCCcore-13.2.0.eb
   - dlb-3.4-gompi-2023b.eb
+  - Extrae-4.2.0-gompi-2023b.eb:
+      options:
+        from-pr: 20690
+        include-easyblocks-from-pr: 3339

From 7cb667929694c8a330a5e3f4921ea97e258f933a Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sun, 7 Jul 2024 12:56:29 +0200
Subject: [PATCH 11/39] Re-add hook from #554 but keep running tests

---
 eb_hooks.py | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index e6f0cf0dd2..42b230c006 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -1,5 +1,6 @@
 # Hooks to customize how EasyBuild installs software in EESSI
 # see https://docs.easybuild.io/en/latest/Hooks.html
+import glob
 import os
 import re
 
@@ -353,6 +354,31 @@ def pre_configure_hook_BLIS_a64fx(self, *args, **kwargs):
     else:
         raise EasyBuildError("BLIS-specific hook triggered for non-BLIS easyconfig?!")
 
+def pre_configure_hook_extrae(self, *args, **kwargs):
+    """
+    Pre-configure hook for Extrae
+    - avoid use of 'which' in configure script
+    - specify correct path to binutils (in compat layer)
+    """
+    if self.name == 'Extrae':
+
+        # determine path to Prefix installation in compat layer via $EPREFIX
+        eprefix = get_eessi_envvar('EPREFIX')
+
+        binutils_lib_path_glob_pattern = os.path.join(eprefix, 'usr', 'lib*', 'binutils', '*-pc-linux-gnu', '2.*')
+        binutils_lib_path = glob.glob(binutils_lib_path_glob_pattern)
+        if len(binutils_lib_path) == 1:
+            self.cfg.update('configopts', '--with-binutils=' + binutils_lib_path[0])
+        else:
+            raise EasyBuildError("Failed to isolate path for binutils libraries using %s, got %s",
+                                 binutils_lib_path_glob_pattern, binutils_lib_path)
+
+        # replace use of 'which' with 'command -v', since 'which' is broken in EESSI build container;
+        # this must be done *after* running configure script, because initial configuration re-writes configure script,
+        # and problem due to use of which only pops up when running make ?!
+        self.cfg.update('prebuildopts', "cp config/mpi-macros.m4 config/mpi-macros.m4.orig && sed -i 's/`which /`command -v /g' config/mpi-macros.m4 && ")
+    else:
+        raise EasyBuildError("Extrae-specific hook triggered for non-Extrae easyconfig?!")
 
 def pre_configure_hook_gromacs(self, *args, **kwargs):
     """
@@ -711,6 +737,7 @@ def inject_gpu_property(ec):
 PRE_CONFIGURE_HOOKS = {
     'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
     'BLIS': pre_configure_hook_BLIS_a64fx,
+    'Extrae': pre_configure_hook_extrae,
     'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,

From d6d5a2bb5c2eead7cd931ea307ea4cd3b44bf9db Mon Sep 17 00:00:00 2001
From: Helena Vela Beltran <47674829+hvelab@users.noreply.github.com>
Date: Mon, 8 Jul 2024 17:18:02 +0200
Subject: [PATCH 12/39] Update init/eessi_environment_variables

Add bigger comment

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 init/eessi_environment_variables | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index f5bb387955..9417d5b2a2 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -106,15 +106,15 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
-        # Fix wrong path for RHEL >=8 libcurl 
-	# This is required here because we ship curl in our compat layer. If we only provided
-	# curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
-	# hook (or via an Lmod hook)
-	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
-        if [ -f $rhel_libcurl_file ]; then
-          show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
-          export CURL_CA_BUNDLE=$rhel_libcurl_file
-        fi
+          # Fix wrong path for RHEL >=8 libcurl 
+	  # This is required here because we ship curl in our compat layer. If we only provided
+	  # curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
+	  # hook (or via an Lmod hook)
+	  rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
+          if [ -f $rhel_libcurl_file ]; then
+            show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
+            export CURL_CA_BUNDLE=$rhel_libcurl_file
+          fi
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From 0fef63a6ce712956e04b9cb007c21565d624f1fa Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 9 Jul 2024 00:15:40 +0200
Subject: [PATCH 13/39] Update eb_hooks.py

---
 eb_hooks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 42b230c006..f43b695266 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -365,7 +365,7 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
         # determine path to Prefix installation in compat layer via $EPREFIX
         eprefix = get_eessi_envvar('EPREFIX')
 
-        binutils_lib_path_glob_pattern = os.path.join(eprefix, 'usr', 'lib*', 'binutils', '*-pc-linux-gnu', '2.*')
+        binutils_lib_path_glob_pattern = os.path.join(eprefix, 'usr', 'lib*', 'binutils', '*-linux-gnu', '2.*')
         binutils_lib_path = glob.glob(binutils_lib_path_glob_pattern)
         if len(binutils_lib_path) == 1:
             self.cfg.update('configopts', '--with-binutils=' + binutils_lib_path[0])

From 28eabaaefcde5b112b60e8c94f46494ab7b0944e Mon Sep 17 00:00:00 2001
From: Xin An <xina@int5.local.snellius.surf.nl>
Date: Fri, 12 Jul 2024 12:11:19 +0200
Subject: [PATCH 14/39] {2023.06}[gfbf/2023b] Pystencils 1.3.4

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 15c02951d7..3963f79ecd 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,3 +58,4 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb

From 2ca3684b845165425af638daaea27897fd1cbe7e Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 14:29:19 +0200
Subject: [PATCH 15/39] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 3963f79ecd..8d9779c59c 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,4 +58,7 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
-  - pystencils-1.3.4-gfbf-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
+        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From 641288af0c2bc1d1e35d411815465abdeb8a1ddc Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:08:14 +0200
Subject: [PATCH 16/39] Update eessi-2023.06-eb-4.9.0-2023b.yml

Remove pystencils
---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 8d9779c59c..15c02951d7 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,7 +58,3 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
-  - pystencils-1.3.4-gfbf-2023b.eb:
-      options:
-        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
-        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From bb8b4aa1442c032b88d6cacc94b2d8f42cce3721 Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:10:02 +0200
Subject: [PATCH 17/39] add pystencils

update eessi-2023.06-eb-4.9.2-2023b
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index 38bfa81142..e0057f18ab 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,3 +1,7 @@
 easyconfigs:
   - IPython-8.17.2-GCCcore-13.2.0.eb
   - dlb-3.4-gompi-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
+        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From f204afa5d804dee715476ac3d2a96e8e69fa6842 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 15 Jul 2024 10:47:34 +0200
Subject: [PATCH 18/39] Add MetalWalls to easystack file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 4b58cb6106..0cdbd4b5b3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -74,3 +74,4 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
+  - MetalWalls-21.06.1-foss-2023a.eb

From 58fb56f2a8f2fb11d5df2b8332388ace82eda993 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Tue, 16 Jul 2024 14:41:39 +0200
Subject: [PATCH 19/39] Switch target to EB 4.9.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 -
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 0cdbd4b5b3..4b58cb6106 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -74,4 +74,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - MetalWalls-21.06.1-foss-2023a.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index 34ec3257e8..e7730d1eb6 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -15,3 +15,4 @@ easyconfigs:
   - LSD2-2.4.1-GCCcore-12.3.0.eb
   - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
   - ncbi-vdb-3.0.10-gompi-2023a.eb
+  - MetalWalls-21.06.1-foss-2023a.eb

From a7a895408c9b194cd8aeff27dd5f17f54a5fc514 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 17 Jul 2024 13:45:39 +0200
Subject: [PATCH 20/39] Move changes to latest eb release

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                | 6 ------
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml                | 6 ++++++
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 428c1ac77f..4b58cb6106 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -74,9 +74,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - QuantumESPRESSO-7.3.1-foss-2023a.eb:
-      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
-      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3257
-      options:
-        from-pr: 20138
-        include-easyblocks-from-pr: 3257
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index e7730d1eb6..af69b288e8 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -16,3 +16,9 @@ easyconfigs:
   - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
   - ncbi-vdb-3.0.10-gompi-2023a.eb
   - MetalWalls-21.06.1-foss-2023a.eb
+  - QuantumESPRESSO-7.3.1-foss-2023a.eb:
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
+      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3338
+      options:
+        from-pr: 20138
+        include-easyblocks-from-pr: 3338

From 0ab0440e4ee990bbe76d7e8b7d0912701b21e8fa Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 17 Jul 2024 14:00:00 +0200
Subject: [PATCH 21/39] Allow initialisation scripts to be used with bash < 4.2

---
 init/bash                        | 2 +-
 init/eessi_defaults              | 2 +-
 init/eessi_environment_variables | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/init/bash b/init/bash
index 93471e075e..4ad09f6a1b 100644
--- a/init/bash
+++ b/init/bash
@@ -1,7 +1,7 @@
 function show_msg {
   # only echo msg if EESSI_SILENT is unset
   msg=$1
-  if [[ ! -v EESSI_SILENT ]]; then
+  if [[ -z ${EESSI_SILENT+x} ]]; then
     echo "$msg"
   fi
 }
diff --git a/init/eessi_defaults b/init/eessi_defaults
index c1ce82d1ce..654a829425 100644
--- a/init/eessi_defaults
+++ b/init/eessi_defaults
@@ -12,7 +12,7 @@
 if [[ $(uname -m) == "riscv64" ]]; then
     export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/riscv.eessi.io}"
     export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=20240402}"
-    if [[ ! -v EESSI_SILENT ]]; then
+    if [[ -z ${EESSI_SILENT+x} ]]; then
         echo "RISC-V architecture detected, but there is no RISC-V support yet in the production repository."
         echo "Automatically switching to version ${EESSI_VERSION} of the RISC-V development repository ${EESSI_CVMFS_REPO}."
         echo "For more details about this repository, see https://www.eessi.io/docs/repositories/riscv.eessi.io/."
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 9417d5b2a2..3e35f845a1 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -10,7 +10,7 @@ function error() {
 function show_msg {
   # only echo msg if EESSI_SILENT is unset
   msg=$1
-  if [[ ! -v EESSI_SILENT ]]; then
+  if [[ -z ${EESSI_SILENT+x} ]]; then
     echo "$msg"
   fi
 }

From 5ff9d1660c736ddf88052035fa7a10a6ac7a33c1 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 18 Jul 2024 16:02:55 +0200
Subject: [PATCH 22/39] Fixes for ARM

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                 | 4 ++--
 eb_hooks.py                                                  | 5 ++++-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index bc7bee302a..3f18d02db5 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -7,5 +7,5 @@ easyconfigs:
         from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7
   - Extrae-4.2.0-gompi-2023b.eb:
       options:
-        from-pr: 20690
-        include-easyblocks-from-pr: 3339
+        from-pr: 21017
+        include-easyblocks-from-pr: 3393
diff --git a/eb_hooks.py b/eb_hooks.py
index ec08e96847..73adce90f1 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -362,7 +362,7 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
     """
     Pre-configure hook for Extrae
     - avoid use of 'which' in configure script
-    - specify correct path to binutils (in compat layer)
+    - specify correct path to binutils/zlib (in compat layer)
     """
     if self.name == 'Extrae':
 
@@ -377,6 +377,9 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
             raise EasyBuildError("Failed to isolate path for binutils libraries using %s, got %s",
                                  binutils_lib_path_glob_pattern, binutils_lib_path)
 
+        # zlib is a filtered dependency, so we need to manually specify it's location to avoid the host version
+        self.cfg.update('configopts', '--with-libz=' + eprefix)
+
         # replace use of 'which' with 'command -v', since 'which' is broken in EESSI build container;
         # this must be done *after* running configure script, because initial configuration re-writes configure script,
         # and problem due to use of which only pops up when running make ?!

From 192e494b56603dcead6b30c19e00064efe7b2769 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 18 Jul 2024 16:59:47 +0200
Subject: [PATCH 23/39] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index 3f18d02db5..f118e94adb 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -7,5 +7,7 @@ easyconfigs:
         from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7
   - Extrae-4.2.0-gompi-2023b.eb:
       options:
-        from-pr: 21017
-        include-easyblocks-from-pr: 3393
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21017
+        from-commit: 120f4d56efebd2bc61382db4c84a664a339c66cf
+        # see https://github.com/easybuilders/easybuild-easyblocks/pull/3393
+        include-easyblocks-from-commit: c4951c78d62fa5cf8e9f6fe0ead212d2a4d7cb9c

From 8b350fd435924a18705d1869c0bc87be15d76465 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 18 Jul 2024 18:02:08 +0200
Subject: [PATCH 24/39] Update eessi-2023.06-eb-4.9.2-2023a.yml

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index ed9896191b..f40d7d85e1 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -19,4 +19,4 @@ easyconfigs:
   - CP2K-2023.1-foss-2023a.eb:
       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
       options:
-        from-pr: 20951
\ No newline at end of file
+        from-pr: 20951

From c0bec39b3c0528f9bde6f91c853f08b75cee1796 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 09:28:03 +0200
Subject: [PATCH 25/39] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml                  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index f40d7d85e1..bd6c767260 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -17,6 +17,6 @@ easyconfigs:
   - ncbi-vdb-3.0.10-gompi-2023a.eb
   - MetalWalls-21.06.1-foss-2023a.eb
   - CP2K-2023.1-foss-2023a.eb:
-      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
       options:
-        from-pr: 20951
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
+        from-commit: a92667fe32396bbd4106243658625f7ff2adcd68

From a61925fb430a0e1b1adaf22f8e7e7c81a782dadf Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 09:34:19 +0200
Subject: [PATCH 26/39] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml              | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index af69b288e8..67cc4bc155 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -17,8 +17,8 @@ easyconfigs:
   - ncbi-vdb-3.0.10-gompi-2023a.eb
   - MetalWalls-21.06.1-foss-2023a.eb
   - QuantumESPRESSO-7.3.1-foss-2023a.eb:
-      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
-      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3338
       options:
-        from-pr: 20138
-        include-easyblocks-from-pr: 3338
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20138
+        from-commit: dbdaacc0739fdee91baa9123864ea4428cf21273
+        # see https://github.com/easybuilders/easybuild-easyblocks/pull/3338
+        include-easyblocks-from-commit: 32e45bd1f2d916732ca5852d55d17fa4d99e388b

From 1660e048811192f8d072815963e960fdd9620828 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 09:49:39 +0200
Subject: [PATCH 27/39] Remove duplicate testing of PRs

---
 .github/workflows/test-software.eessi.io.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-software.eessi.io.yml b/.github/workflows/test-software.eessi.io.yml
index 06c02c8834..d4d980901f 100644
--- a/.github/workflows/test-software.eessi.io.yml
+++ b/.github/workflows/test-software.eessi.io.yml
@@ -1,6 +1,10 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Check for missing software installations in software.eessi.io
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
+  workflow_dispatch:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:

From 4d93a2d87b7289b12ab65daac9ddcc16e69a47ee Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 09:57:54 +0200
Subject: [PATCH 28/39] Restrict tests for all CI

---
 .github/workflows/scorecards.yml                  | 2 +-
 .github/workflows/test_eessi_container_script.yml | 6 +++++-
 .github/workflows/test_licenses.yml               | 5 ++++-
 .github/workflows/tests.yml                       | 5 ++++-
 .github/workflows/tests_archdetect.yml            | 5 ++++-
 .github/workflows/tests_init.yml                  | 5 ++++-
 6 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
index 5b482763f2..91c2576b7d 100644
--- a/.github/workflows/scorecards.yml
+++ b/.github/workflows/scorecards.yml
@@ -10,7 +10,7 @@ on:
     - cron: '25 15 * * 3'
   push:
     branches:
-      - '2023.06-software.eessi.io'
+      - '*-software.eessi.io'
 
 # Declare default permissions as read only.
 permissions: read-all
diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index d44788927f..fb587ec489 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -1,6 +1,10 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests for eessi_container.sh script
-on: [push, pull_request, workflow_dispatch]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
+  workflow_dispatch:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
diff --git a/.github/workflows/test_licenses.yml b/.github/workflows/test_licenses.yml
index 6b6387d47d..bf6965c620 100644
--- a/.github/workflows/test_licenses.yml
+++ b/.github/workflows/test_licenses.yml
@@ -1,6 +1,9 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Test software licenses
-on: [push, pull_request]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8249e50d9b..940614b6bb 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,6 +1,9 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests
-on: [push, pull_request]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 4f5d3d174d..f5b42b3d55 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -1,6 +1,9 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests for eessi_archdetect.sh
-on: [push, pull_request]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
diff --git a/.github/workflows/tests_init.yml b/.github/workflows/tests_init.yml
index 6c356a9184..8581681d63 100644
--- a/.github/workflows/tests_init.yml
+++ b/.github/workflows/tests_init.yml
@@ -1,6 +1,9 @@
 # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
 name: Tests for init scripts
-on: [push, pull_request]
+on:
+  push:
+    branches: [ "*-software.eessi.io" ]
+  pull_request:
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:

From 8a2eca3cf3c949cff5fb1f61e1a3ef4e6d2cdfd2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 12:06:20 +0200
Subject: [PATCH 29/39] add a hook for GObject-Introspection that prevents
 environment vars from being set if EB filters them

---
 eb_hooks.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index 73adce90f1..deea409cf4 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -387,6 +387,24 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
     else:
         raise EasyBuildError("Extrae-specific hook triggered for non-Extrae easyconfig?!")
 
+
+def pre_configure_hook_gobject_introspection(self, *args, **kwargs):
+    """
+    pre-configure hook for GObject-Introspection:
+    - prevent GObject-Introspection from setting $LD_LIBRARY_PATH if Easybuild is configured to filter it
+      that are configured to be filtered by EasyBuild, see:
+      https://github.com/EESSI/software-layer/issues/196
+    """
+    if self.name == 'GObject-Introspection':
+        # inject a line that removes all items from runtime_path_envvar that are in $EASYBUILD_FILTER_ENVVARS
+        sed_cmd = r'sed -i "s@\(^\s*runtime_path_envvar = \)\(.*\)@'
+        sed_cmd += r'\1\2\n\1 [x for x in runtime_path_envvar if not x in os.environ.get(\'EASYBUILD_FILTER_ENV_VARS\', \'\').split(\',\')]@g"'
+        sed_cmd += ' %(start_dir)s/giscanner/ccompiler.py && '
+        self.cfg.update('preconfigopts', sed_cmd)
+    else:
+        raise EasyBuildError("GObject-Introspection-specific hook triggered for non-GObject-Introspection easyconfig?!")
+
+
 def pre_configure_hook_gromacs(self, *args, **kwargs):
     """
     Pre-configure hook for GROMACS:
@@ -744,6 +762,7 @@ def inject_gpu_property(ec):
 PRE_CONFIGURE_HOOKS = {
     'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
     'BLIS': pre_configure_hook_BLIS_a64fx,
+    'GObject-Introspection': pre_configure_hook_gobject_introspection,
     'Extrae': pre_configure_hook_extrae,
     'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,

From 62c1f7d000473bd53a60fa7d814dcccf11978524 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 13:45:42 +0200
Subject: [PATCH 30/39] rebuild all GObject-Introspection versions to apply new
 hook

---
 ...eb-4.9.2-GObject-Introspection-filter-envvars.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
new file mode 100644
index 0000000000..676a2fe548
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
@@ -0,0 +1,12 @@
+# 2024.07.19
+# GObject-Introspection sets $LD_LIBRARY_PATH (to many different paths, including $EPREFIX/lib)
+# when calling gcc, and this causes a lot of issues for, especially, scripts using /bin/bash.
+#
+# This rebuild ensures (by using a new EasyBuild hook) that GObject-Introspection will not set
+# environment variables that are configured to be filtered by EasyBuild.
+# 
+# See https://github.com/EESSI/software-layer/issues/196
+easyconfigs:
+  - GObject-Introspection-1.74.0-GCCcore-12.2.0.eb
+  - GObject-Introspection-1.76.1-GCCcore-12.3.0.eb
+  - GObject-Introspection-1.78.1-GCCcore-13.2.0.eb

From 6277bc382003651012a8196bc7667ae1a3371704 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 13:58:53 +0200
Subject: [PATCH 31/39] fix comment

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 eb_hooks.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index deea409cf4..aa9bde383a 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -391,8 +391,7 @@ def pre_configure_hook_extrae(self, *args, **kwargs):
 def pre_configure_hook_gobject_introspection(self, *args, **kwargs):
     """
     pre-configure hook for GObject-Introspection:
-    - prevent GObject-Introspection from setting $LD_LIBRARY_PATH if Easybuild is configured to filter it
-      that are configured to be filtered by EasyBuild, see:
+    - prevent GObject-Introspection from setting $LD_LIBRARY_PATH if EasyBuild is configured to filter it, see:
       https://github.com/EESSI/software-layer/issues/196
     """
     if self.name == 'GObject-Introspection':

From 5593999aa6acfaef2d235abc987a908643109cff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 14:39:10 +0200
Subject: [PATCH 32/39] remove the at-spi2-core hook

---
 eb_hooks.py | 16 ----------------
 1 file changed, 16 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index deea409cf4..00d26df37b 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -486,21 +486,6 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs):
         raise EasyBuildError("WRF-specific hook triggered for non-WRF easyconfig?!")
 
 
-def pre_configure_hook_atspi2core_filter_ld_library_path(self, *args, **kwargs):
-    """
-    pre-configure hook for at-spi2-core:
-    - instruct GObject-Introspection's g-ir-scanner tool to not set $LD_LIBRARY_PATH
-      when EasyBuild is configured to filter it, see:
-      https://github.com/EESSI/software-layer/issues/196
-    """
-    if self.name == 'at-spi2-core':
-        if build_option('filter_env_vars') and 'LD_LIBRARY_PATH' in build_option('filter_env_vars'):
-            sed_cmd = 'sed -i "s/gir_extra_args = \[/gir_extra_args = \[\\n  \'--lib-dirs-envvar=FILTER_LD_LIBRARY_PATH\',/g" %(start_dir)s/atspi/meson.build && '
-            self.cfg.update('preconfigopts', sed_cmd)
-    else:
-        raise EasyBuildError("at-spi2-core-specific hook triggered for non-at-spi2-core easyconfig?!")
-
-
 def pre_test_hook(self,*args, **kwargs):
     """Main pre-test hook: trigger custom functions based on software name."""
     if self.name in PRE_TEST_HOOKS:
@@ -760,7 +745,6 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
-    'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
     'BLIS': pre_configure_hook_BLIS_a64fx,
     'GObject-Introspection': pre_configure_hook_gobject_introspection,
     'Extrae': pre_configure_hook_extrae,

From 46a9c85149e1a9ff29bc8da9c322eda639c7f923 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 14:39:34 +0200
Subject: [PATCH 33/39] rebuild at-spi2-core with the rebuilt
 GObject-Introspection

---
 .../20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
index 676a2fe548..a61cd9705b 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars.yml
@@ -10,3 +10,5 @@ easyconfigs:
   - GObject-Introspection-1.74.0-GCCcore-12.2.0.eb
   - GObject-Introspection-1.76.1-GCCcore-12.3.0.eb
   - GObject-Introspection-1.78.1-GCCcore-13.2.0.eb
+  - at-spi2-core-2.46.0-GCCcore-12.2.0.eb
+  - at-spi2-core-2.49.91-GCCcore-12.3.0.eb

From bd328a2c357a4f1fe998d4b922363abe4461b904 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Jul 2024 15:03:34 +0200
Subject: [PATCH 34/39] Use  instead of  (CentOS6)

---
 init/eessi_archdetect.sh         | 2 +-
 init/eessi_environment_variables | 2 +-
 init/minimal_eessi_env           | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/init/eessi_archdetect.sh b/init/eessi_archdetect.sh
index e89bc75e13..ddfed1bfae 100755
--- a/init/eessi_archdetect.sh
+++ b/init/eessi_archdetect.sh
@@ -89,7 +89,7 @@ cpupath(){
         *) log "ERROR" "cpupath: Unsupported CPU architecture $machine_type"
     esac
     # spec files are located in a subfolder with this script
-    local base_dir=$(dirname $(realpath $0))
+    local base_dir=$(dirname $(readlink -f $0))
     update_arch_specs "$base_dir/arch_specs/${spec_file}"
   
     # Identify the host CPU vendor
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 3e35f845a1..8c10b1fca8 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -1,6 +1,6 @@
 # this script is *sourced*, not executed, so can't rely on $0 to determine path to self
 # $BASH_SOURCE points to correct path, see also http://mywiki.wooledge.org/BashFAQ/028
-EESSI_INIT_DIR_PATH=$(dirname $(realpath $BASH_SOURCE))
+EESSI_INIT_DIR_PATH=$(dirname $(readlink -f $BASH_SOURCE))
 
 function error() {
     echo -e "\e[31mERROR: $1\e[0m" >&2
diff --git a/init/minimal_eessi_env b/init/minimal_eessi_env
index 03b337ccf7..5273f27862 100644
--- a/init/minimal_eessi_env
+++ b/init/minimal_eessi_env
@@ -2,7 +2,7 @@
 #
 # this script is *sourced*, not executed, so can't rely on $0 to determine path to self
 # $BASH_SOURCE points to correct path, see also http://mywiki.wooledge.org/BashFAQ/028
-EESSI_INIT_DIR_PATH=$(dirname $(realpath $BASH_SOURCE))
+EESSI_INIT_DIR_PATH=$(dirname $(readlink -f $BASH_SOURCE))
 
 # set up defaults: EESSI_CVMFS_REPO, EESSI_VERSION
 #   script takes *_OVERRIDEs into account

From 20eafc70aec97f46f311b27fe9b44b845964f723 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Jul 2024 15:30:35 +0200
Subject: [PATCH 35/39] rebuild GObject-Introspection for zen4

---
 ....9.2-GObject-Introspection-filter-envvars-zen4.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars-zen4.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars-zen4.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars-zen4.yml
new file mode 100644
index 0000000000..2c9b411736
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240719-eb-4.9.2-GObject-Introspection-filter-envvars-zen4.yml
@@ -0,0 +1,11 @@
+# 2024.07.19
+# GObject-Introspection sets $LD_LIBRARY_PATH (to many different paths, including $EPREFIX/lib)
+# when calling gcc, and this causes a lot of issues for, especially, scripts using /bin/bash.
+#
+# This rebuild ensures (by using a new EasyBuild hook) that GObject-Introspection will not set
+# environment variables that are configured to be filtered by EasyBuild.
+# 
+# See https://github.com/EESSI/software-layer/issues/196
+easyconfigs:
+  - GObject-Introspection-1.76.1-GCCcore-12.3.0.eb
+  - GObject-Introspection-1.78.1-GCCcore-13.2.0.eb

From 55a32613d3f6c4a295186cd93e33234e88146e48 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 22 Jul 2024 13:54:55 +0000
Subject: [PATCH 36/39] {2023.06}[gompi/2022b] BLAST+ V2.14.0

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2022b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
new file mode 100644
index 0000000000..ce28312e8c
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - BLAST+-2.14.0-gompi-2022b.eb:
+      options:
+        from-commit: 1775912a1d36101d560e1355967732b07e82cd24

From 808a9032f942d1a88108a0b7d7067498b7e6e2d5 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 23 Jul 2024 10:09:09 +0200
Subject: [PATCH 37/39] {2023.06}[gompi/2023a] amdahl 0.3.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index 7e9f4ff05a..d405d17193 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -26,3 +26,4 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20951
         from-commit: a92667fe32396bbd4106243658625f7ff2adcd68
+  - amdahl-0.3.1-gompi-2023a.eb

From 7d06f13fa83c7774d74ca9a09499ee34f7f1b17b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 23 Jul 2024 15:56:21 +0200
Subject: [PATCH 38/39] add pyMBE 0.8.0

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index f118e94adb..883483f5d2 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -11,3 +11,7 @@ easyconfigs:
         from-commit: 120f4d56efebd2bc61382db4c84a664a339c66cf
         # see https://github.com/easybuilders/easybuild-easyblocks/pull/3393
         include-easyblocks-from-commit: c4951c78d62fa5cf8e9f6fe0ead212d2a4d7cb9c
+  - pyMBE-0.8.0-foss-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/21034
+        from-commit: 76e7fc6657bab64bfbec826540a3a8f0040258f2

From c0c784efbcb98389d6c61c43b2442dd07a981703 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Fri, 26 Jul 2024 18:25:45 +0200
Subject: [PATCH 39/39] Update eessi-2023.06-eb-4.9.2-2022b.yml

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2022b.yml                  | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
index ce28312e8c..7a04eaa9d3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2022b.yml
@@ -1,4 +1,2 @@
 easyconfigs:
-  - BLAST+-2.14.0-gompi-2022b.eb:
-      options:
-        from-commit: 1775912a1d36101d560e1355967732b07e82cd24
+  - BLAST+-2.14.0-gompi-2022b.eb