From b35f7f608eb9487a44342c0204db29f2c38f6cd5 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Wed, 4 Oct 2023 09:07:25 +0000
Subject: [PATCH 01/27] {2023.06}[foss/2021a] Yambo V5.1.1

---
 eessi-2023.06-eb-4.7.2-2021a.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/eessi-2023.06-eb-4.7.2-2021a.yml b/eessi-2023.06-eb-4.7.2-2021a.yml
index b7c703369b..49214fc84a 100644
--- a/eessi-2023.06-eb-4.7.2-2021a.yml
+++ b/eessi-2023.06-eb-4.7.2-2021a.yml
@@ -20,3 +20,7 @@ easyconfigs:
         options:
           from-pr: 18446
   - WRF-4.3-foss-2021a-dmpar.eb
+  - Yambo-5.1.1-foss-2021a.eb:
+        options:
+          from-pr: 18905
+      

From 05eba7313991b8c7bb49d2d00e4403c07ec289b8 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 5 Oct 2023 22:31:07 +0200
Subject: [PATCH 02/27] bio packages - set 1

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 eessi-2023.06-eb-4.8.1-2022a.yml

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
new file mode 100644
index 0000000000..86dcd7714a
--- /dev/null
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -0,0 +1,7 @@
+easyconfigs:
+  - BAMM-2.5.0-foss-2022a.eb
+  - BamTools-2.5.2-GCC-11.3.0.eb
+  - BCFtools-1.15.1-GCC-11.3.0.eb
+  - Bowtie2-2.4.5-GCC-11.3.0.eb
+  - FastTree-2.1.11-GCCcore-11.3.0.eb
+  - SAMtools-1.16.1-GCC-11.3.0.eb

From 2f85702467c4f6179e4fa94237657052860cc8f0 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 5 Oct 2023 23:17:43 +0200
Subject: [PATCH 03/27] add new easystack file to CI

---
 .github/workflows/test_eessi.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 72dc642c7d..2554ed78b3 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -25,6 +25,7 @@ jobs:
         - eessi-2023.06-eb-4.7.2-2022b.yml
         - eessi-2023.06-eb-4.7.2-system.yml
         - eessi-2023.06-eb-4.8.0-system.yml
+        - eessi-2023.06-eb-4.8.1-2022a.yml
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0

From 920fa096f0db6e94e6f1ee2bfcafd59e3637ebb8 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 07:57:08 +0200
Subject: [PATCH 04/27] reverting change on _OVERRIDE + shorter test label

---
 .github/workflows/test_eessi.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 2554ed78b3..a6bce68cf0 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -4,7 +4,7 @@ on: [push, pull_request, workflow_dispatch]
 permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
-  eessi_pilot_repo:
+  pilot:
     runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
@@ -39,13 +39,15 @@ jobs:
 
         - name: Test check_missing_installations.sh script
           run: |
-              export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
+              # export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               which eb
               eb --version
+              eb --show-config
               export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
+              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               env | grep ^EESSI | sort
               echo "just run check_missing_installations.sh (should use eessi-${{matrix.EESSI_VERSION}}.yml)"
               ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}

From 37209de14f7583a8f04e44c4b55a9dda0ba9fe95 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 09:38:42 +0200
Subject: [PATCH 05/27] show EasyBuild config when running script

---
 check_missing_installations.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/check_missing_installations.sh b/check_missing_installations.sh
index 3627d1d0b5..e927f14701 100755
--- a/check_missing_installations.sh
+++ b/check_missing_installations.sh
@@ -22,6 +22,9 @@ source $TOPDIR/scripts/utils.sh
 
 source $TOPDIR/configure_easybuild
 
+echo ">> Active EasyBuild configuration when checking for missing installations:"
+${EB:-eb} --show-config
+
 echo ">> Checking for missing installations in ${EASYBUILD_INSTALLPATH}..."
 eb_missing_out=$LOCAL_TMPDIR/eb_missing.out
 ${EB:-eb} --easystack ${easystack} --missing 2>&1 | tee ${eb_missing_out}

From 54e511159e4abc7cbbe6bf652a56ee1363547337 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 11:32:24 +0200
Subject: [PATCH 06/27] run check script with and without _OVERRIDE

---
 .github/workflows/test_eessi.yml | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index a6bce68cf0..71332bca36 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -37,9 +37,22 @@ jobs:
               cvmfs_http_proxy: DIRECT
               cvmfs_repositories: pilot.nessi.no
 
-        - name: Test check_missing_installations.sh script
+        - name: Test check_missing_installations.sh script with EESSI_SOFTWARE_SUBDIR_OVERRIDE
+          run: |
+              export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
+              source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
+              module load EasyBuild
+              which eb
+              eb --version
+              eb --show-config
+              export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_OS_TYPE=linux
+              env | grep ^EESSI | sort
+              echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})"
+              ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
+
+        - name: Test check_missing_installations.sh script without EESSI_SOFTWARE_SUBDIR_OVERRIDE
           run: |
-              # export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               which eb
@@ -49,7 +62,7 @@ jobs:
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               env | grep ^EESSI | sort
-              echo "just run check_missing_installations.sh (should use eessi-${{matrix.EESSI_VERSION}}.yml)"
+              echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})"
               ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
 
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)

From 0e58034e12bed5782b9a4b81b406ad09ec3c9c92 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 11:42:43 +0200
Subject: [PATCH 07/27] run some steps if preceeding test(s) failed

---
 .github/workflows/test_eessi.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 71332bca36..a60eba47d1 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -38,6 +38,7 @@ jobs:
               cvmfs_repositories: pilot.nessi.no
 
         - name: Test check_missing_installations.sh script with EESSI_SOFTWARE_SUBDIR_OVERRIDE
+          if: '!cancelled()'
           run: |
               export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
@@ -52,6 +53,7 @@ jobs:
               ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
 
         - name: Test check_missing_installations.sh script without EESSI_SOFTWARE_SUBDIR_OVERRIDE
+          if: '!cancelled()'
           run: |
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
@@ -66,6 +68,7 @@ jobs:
               ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
 
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
+          if: '!cancelled()'
           run: |
               export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash

From 487263801c7351157404a94cb946c72475fc4069 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 14:15:33 +0200
Subject: [PATCH 08/27] updated CI to reduce number of tests

---
 .github/workflows/test_eessi.yml | 47 ++++++++++++++++----------------
 1 file changed, 23 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index a60eba47d1..1a558f1cb0 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -11,21 +11,13 @@ jobs:
       matrix:
         EESSI_VERSION:
         - 2023.06
-        EESSI_SOFTWARE_SUBDIR_OVERRIDE:
+        EESSI_SOFTWARE_SUBDIR:
         - aarch64/generic
         - x86_64/amd/zen2
         - x86_64/intel/broadwell
         - x86_64/intel/cascadelake
         - x86_64/intel/skylake_avx512
         - x86_64/generic
-        EASYSTACK_FILE:
-        - eessi-2023.06-eb-4.7.2-2021a.yml
-        - eessi-2023.06-eb-4.7.2-2021b.yml
-        - eessi-2023.06-eb-4.7.2-2022a.yml
-        - eessi-2023.06-eb-4.7.2-2022b.yml
-        - eessi-2023.06-eb-4.7.2-system.yml
-        - eessi-2023.06-eb-4.8.0-system.yml
-        - eessi-2023.06-eb-4.8.1-2022a.yml
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
@@ -40,53 +32,60 @@ jobs:
         - name: Test check_missing_installations.sh script with EESSI_SOFTWARE_SUBDIR_OVERRIDE
           if: '!cancelled()'
           run: |
-              export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
+              export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
-              which eb
               eb --version
-              eb --show-config
               export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               env | grep ^EESSI | sort
-              echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})"
-              ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
+              for easystack_file in $(ls eessi-${{matrix.EESSI_VERSION}}-eb-*.yml); do
+                  echo "check missing installations for ${easystack_file}..."
+                  ./check_missing_installations.sh ${easystack_file}
+                  ec=$?
+                  if [[ ${ec} -ne 0 ]]; then echo "missing installations found for ${easystack_file}!" >&2; exit ${ec}; fi
+              done
 
         - name: Test check_missing_installations.sh script without EESSI_SOFTWARE_SUBDIR_OVERRIDE
           if: '!cancelled()'
           run: |
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
-              which eb
               eb --version
-              eb --show-config
               export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
-              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
+              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
-              echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})"
-              ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
+              for easystack_file in $(ls eessi-${{matrix.EESSI_VERSION}}-eb-*.yml); do
+                  echo "check missing installations for ${easystack_file}..."
+                  ./check_missing_installations.sh ${easystack_file}
+                  ec=$?
+                  if [[ ${ec} -ne 0 ]]; then echo "missing installations found for ${easystack_file}!" >&2; exit ${ec}; fi
+              done
 
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
           if: '!cancelled()'
           run: |
-              export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
               source /cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               which eb
               eb --version
               export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
+              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
-              echo "modify easystack file by adding a missing package (GCC/8.3.0)"
-              echo "  - GCC-8.3.0:" >> ${{matrix.EASYSTACK_FILE}}
-              tail -n 5 ${{matrix.EASYSTACK_FILE}}
+              # create dummy easystack file with a single entry (something that is not installed in EESSI)
+              easystack_file="test.yml"
+              echo "easyconfigs:" > ${easystack_file}
+              echo "  - GCC-8.3.0:" >> ${easystack_file}
+              echo "created easystack file '${easystack_file}' with a missing installation (GCC/8.3.0):"
+              cat ${easystack_file}
               # note, check_missing_installations.sh exits 1 if a package was
               # missing, which is intepreted as false (exit code based, not
               # boolean logic), hence when the script exits 0 if no package was
               # missing it is interpreted as true, thus the test did not capture
               # the missing package
-              if ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}; then
+              if ./check_missing_installations.sh ${easystack_file}; then
                 echo "did NOT capture missing package; test FAILED"
                 exit 1
               else

From 5300d767d4f859a674f38ca0752c382fb97db850 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 14:17:13 +0200
Subject: [PATCH 09/27] call 'eb --show-config' for each easystack file being
 processed

---
 EESSI-pilot-install-software.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-pilot-install-software.sh b/EESSI-pilot-install-software.sh
index c6c51e7abc..026919157f 100755
--- a/EESSI-pilot-install-software.sh
+++ b/EESSI-pilot-install-software.sh
@@ -172,8 +172,6 @@ if [ ! -z "${shared_fs_path}" ]; then
     export EASYBUILD_SOURCEPATH=${shared_eb_sourcepath}:${EASYBUILD_SOURCEPATH}
 fi
 
-${EB} --show-config
-
 echo ">> Setting up \$MODULEPATH..."
 # make sure no modules are loaded
 module --force purge
@@ -200,6 +198,8 @@ for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[
     # load EasyBuild module (will be installed if it's not available yet)
     source ${TOPDIR}/load_easybuild_module.sh ${eb_version}
 
+    ${EB} --show-config
+
     echo_green "All set, let's start installing some software with EasyBuild v${eb_version} in ${EASYBUILD_INSTALLPATH}..."
 
     if [ -f ${easystack_file} ]; then

From 7cd9277bbb73739a0e6aa465b1b044e25055502d Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 14:45:00 +0200
Subject: [PATCH 10/27] revert back to have yml-file times architecture tests

---
 .github/workflows/test_eessi.yml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 1a558f1cb0..832d4cf74f 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -18,6 +18,14 @@ jobs:
         - x86_64/intel/cascadelake
         - x86_64/intel/skylake_avx512
         - x86_64/generic
+        EASYSTACK_FILE:
+        - eessi-2023.06-eb-4.7.2-2021a.yml
+        - eessi-2023.06-eb-4.7.2-2021b.yml
+        - eessi-2023.06-eb-4.7.2-2022a.yml
+        - eessi-2023.06-eb-4.7.2-2022b.yml
+        - eessi-2023.06-eb-4.7.2-system.yml
+        - eessi-2023.06-eb-4.8.0-system.yml
+        - eessi-2023.06-eb-4.8.1-2022a.yml
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
@@ -39,12 +47,8 @@ jobs:
               export EESSI_PREFIX=/cvmfs/pilot.nessi.no/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               env | grep ^EESSI | sort
-              for easystack_file in $(ls eessi-${{matrix.EESSI_VERSION}}-eb-*.yml); do
-                  echo "check missing installations for ${easystack_file}..."
-                  ./check_missing_installations.sh ${easystack_file}
-                  ec=$?
-                  if [[ ${ec} -ne 0 ]]; then echo "missing installations found for ${easystack_file}!" >&2; exit ${ec}; fi
-              done
+              echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})"
+              ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
 
         - name: Test check_missing_installations.sh script without EESSI_SOFTWARE_SUBDIR_OVERRIDE
           if: '!cancelled()'
@@ -56,12 +60,8 @@ jobs:
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
-              for easystack_file in $(ls eessi-${{matrix.EESSI_VERSION}}-eb-*.yml); do
-                  echo "check missing installations for ${easystack_file}..."
-                  ./check_missing_installations.sh ${easystack_file}
-                  ec=$?
-                  if [[ ${ec} -ne 0 ]]; then echo "missing installations found for ${easystack_file}!" >&2; exit ${ec}; fi
-              done
+              echo "just run check_missing_installations.sh (should use ${{matrix.EASYSTACK_FILE}})"
+              ./check_missing_installations.sh ${{matrix.EASYSTACK_FILE}}
 
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
           if: '!cancelled()'

From b9f784ca8ddd2b8d9bda9d7ede03e0623c6dc992 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 18:27:58 +0200
Subject: [PATCH 11/27] {2023.06}[foss/2022a] add common dependencies - set 1

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 86dcd7714a..b1bbe71da7 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -5,3 +5,6 @@ easyconfigs:
   - Bowtie2-2.4.5-GCC-11.3.0.eb
   - FastTree-2.1.11-GCCcore-11.3.0.eb
   - SAMtools-1.16.1-GCC-11.3.0.eb
+  - gzip-1.12-GCCcore-11.3.0.eb
+  - lz4-1.9.3-GCCcore-11.3.0.eb
+  - zstd-1.5.2-GCCcore-11.3.0.eb

From f8265a14f57b220a38c9faf1c7b049fb401e0db3 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 18:36:36 +0200
Subject: [PATCH 12/27] add Java to set

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index b1bbe71da7..f8caa95a54 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -5,6 +5,8 @@ easyconfigs:
   - Bowtie2-2.4.5-GCC-11.3.0.eb
   - FastTree-2.1.11-GCCcore-11.3.0.eb
   - SAMtools-1.16.1-GCC-11.3.0.eb
+  # wraps around Java/11.0.20
+  - Java-11.eb
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb

From f0b5fda7edcaaae28bb37d10546ae5112b6348ab Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 18:43:04 +0200
Subject: [PATCH 13/27] move Java to stack file for system toolchain

---
 .github/workflows/test_eessi.yml  | 1 +
 eessi-2023.06-eb-4.8.1-2022a.yml  | 2 --
 eessi-2023.06-eb-4.8.1-system.yml | 3 +++
 3 files changed, 4 insertions(+), 2 deletions(-)
 create mode 100644 eessi-2023.06-eb-4.8.1-system.yml

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 832d4cf74f..64269d2982 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -26,6 +26,7 @@ jobs:
         - eessi-2023.06-eb-4.7.2-system.yml
         - eessi-2023.06-eb-4.8.0-system.yml
         - eessi-2023.06-eb-4.8.1-2022a.yml
+        - eessi-2023.06-eb-4.8.1-system.yml
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index f8caa95a54..b1bbe71da7 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -5,8 +5,6 @@ easyconfigs:
   - Bowtie2-2.4.5-GCC-11.3.0.eb
   - FastTree-2.1.11-GCCcore-11.3.0.eb
   - SAMtools-1.16.1-GCC-11.3.0.eb
-  # wraps around Java/11.0.20
-  - Java-11.eb
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
diff --git a/eessi-2023.06-eb-4.8.1-system.yml b/eessi-2023.06-eb-4.8.1-system.yml
new file mode 100644
index 0000000000..fb3f7af4cb
--- /dev/null
+++ b/eessi-2023.06-eb-4.8.1-system.yml
@@ -0,0 +1,3 @@
+easyconfigs:
+  # wraps around Java/11.0.20
+  - Java-11.eb

From 3fc94ed6ac3889c3d0f5afe19a89bcb4ac867732 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 19:49:04 +0200
Subject: [PATCH 14/27] filter out .modulerc.lua (for Java) in
 create_tarball.sh, see EESSI/software-layer PR-327

---
 create_tarball.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index b6c72b341d..65f6efc2dc 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -52,7 +52,7 @@ if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules ]; then
     find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules -type l | grep -v '/\.wh\.' >> ${files_list}
     # module files and symlinks
     find ${pilot_version}/software/${os}/${cpu_arch_subdir}/modules/all -type f -o -type l \
-        | grep -v '/\.wh\.' | sed -e 's/.lua$//' | sed -e 's@.*/modules/all/@@g' | sort -u \
+        | grep -v '/\.wh\.' | grep -v '/\.modulerc\.lua' | sed -e 's/.lua$//' | sed -e 's@.*/modules/all/@@g' | sort -u \
         >> ${module_files_list}
 fi
 if [ -d ${pilot_version}/software/${os}/${cpu_arch_subdir}/software -a -r ${module_files_list} ]; then

From e7a627e67bf064b8220687721673840e38a38d08 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 21:14:32 +0200
Subject: [PATCH 15/27] {2023.06}[foss/2022a] add Boost.Python/1.79.0

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index b1bbe71da7..dcbdce0935 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -8,3 +8,4 @@ easyconfigs:
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
+  - Boost.Python-1.79.0-GCC-11.3.0.eb

From 290e3cbcb6a64e8716e9158d0e93bc1f137d676f Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 21:26:54 +0200
Subject: [PATCH 16/27] {2023.06}[foss/2022a] add bio packages - set 2

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index b1bbe71da7..993f9db4d5 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -8,3 +8,10 @@ easyconfigs:
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
+  - AdapterRemoval-2.3.3-GCC-11.3.0.eb
+  - BBMap-39.01-GCC-11.3.0.eb
+  - Beast-2.7.3-GCC-11.3.0.eb
+  - BEDTools-2.30.0-GCC-11.3.0.eb
+  - Bio-DB-HTS-3.01-GCC-11.3.0.eb
+  - Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb
+  - BWA-0.7.17-GCCcore-11.3.0.eb

From 3351f05dd462a70983588f4976501118465dd2e2 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 22:22:35 +0200
Subject: [PATCH 17/27] {2023.06}[foss/2022a] add NCO/5.1.0

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index b1bbe71da7..58b6864d81 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -8,3 +8,4 @@ easyconfigs:
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
+  - NCO-5.1.0-foss-2022a.eb

From 0a62656688dd14984fcb27f0185e86a9b1fec6e8 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 22:46:02 +0200
Subject: [PATCH 18/27] removed BBMap because it failed to build

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 993f9db4d5..679b1c8092 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -9,7 +9,6 @@ easyconfigs:
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
   - AdapterRemoval-2.3.3-GCC-11.3.0.eb
-  - BBMap-39.01-GCC-11.3.0.eb
   - Beast-2.7.3-GCC-11.3.0.eb
   - BEDTools-2.30.0-GCC-11.3.0.eb
   - Bio-DB-HTS-3.01-GCC-11.3.0.eb

From 5935726294e83c8d8e5baf65b7072d1292ff6d2f Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Fri, 6 Oct 2023 22:57:47 +0200
Subject: [PATCH 19/27] use updated CMakeMake easyblock for netCDF

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 58b6864d81..13f0383a88 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -8,4 +8,9 @@ easyconfigs:
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
+  - netCDF-4.9.0-gompi-2022b.eb:
+      # use updated CMakeMake easyblock to avoid that -DCMAKE_SKIP_RPATH=ON is used, which breaks the netCDF test step
+      # see https://github.com/easybuilders/easybuild-easyblocks/pull/3012
+      options:
+        include-easyblocks-from-pr: 3012
   - NCO-5.1.0-foss-2022a.eb

From 5fcf6f2df41e48a7f4dabb7cbbe52a3fe5b4bbc2 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 7 Oct 2023 08:03:13 +0200
Subject: [PATCH 20/27] build netCDF for 2022a (was 2022b)

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 13f0383a88..4a7243338f 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -8,7 +8,7 @@ easyconfigs:
   - gzip-1.12-GCCcore-11.3.0.eb
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
-  - netCDF-4.9.0-gompi-2022b.eb:
+  - netCDF-4.9.0-gompi-2022a.eb:
       # use updated CMakeMake easyblock to avoid that -DCMAKE_SKIP_RPATH=ON is used, which breaks the netCDF test step
       # see https://github.com/easybuilders/easybuild-easyblocks/pull/3012
       options:

From 5fcd337e2ce23c73c2b0a412b0ea179c08797c98 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 7 Oct 2023 09:29:05 +0200
Subject: [PATCH 21/27] remove Beast (dependency Clang failed on aarch64)

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 679b1c8092..8e31b0ce23 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -9,7 +9,6 @@ easyconfigs:
   - lz4-1.9.3-GCCcore-11.3.0.eb
   - zstd-1.5.2-GCCcore-11.3.0.eb
   - AdapterRemoval-2.3.3-GCC-11.3.0.eb
-  - Beast-2.7.3-GCC-11.3.0.eb
   - BEDTools-2.30.0-GCC-11.3.0.eb
   - Bio-DB-HTS-3.01-GCC-11.3.0.eb
   - Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb

From b48487dea43de4a79e9e7c9d001ff537318c895c Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 7 Oct 2023 20:49:32 +0200
Subject: [PATCH 22/27] removed BWA, also fails on aarch64/generic

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 82a10ccba5..a76d41020d 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -17,4 +17,3 @@ easyconfigs:
   - NCO-5.1.0-foss-2022a.eb
   - AdapterRemoval-2.3.3-GCC-11.3.0.eb
   - BEDTools-2.30.0-GCC-11.3.0.eb
-  - BWA-0.7.17-GCCcore-11.3.0.eb

From f3482bde4fc7aa07a765271372e7a44f9b02a379 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 7 Oct 2023 21:05:28 +0200
Subject: [PATCH 23/27] {2023.06}[foss/2022a] add bio paackages - set 3

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index a09af3fe4b..677ff41958 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -15,3 +15,12 @@ easyconfigs:
       options:
         include-easyblocks-from-pr: 3012
   - NCO-5.1.0-foss-2022a.eb
+  - Pysam-0.20.0-GCC-11.3.0.eb
+  - TransDecoder-5.5.0-GCC-11.3.0.eb
+  - VCFtools-0.1.16-GCC-11.3.0.eb
+  - VSEARCH-2.22.1-GCC-11.3.0.eb
+  - XML-LibXML-2.0207-GCCcore-11.3.0.eb
+  - CMake-3.24.3-GCCcore-11.3.0.eb
+  - elfutils-0.187-GCCcore-11.3.0.eb
+  - Ninja-1.10.2-GCCcore-11.3.0.eb
+  - Z3-4.10.2-GCCcore-11.3.0.eb

From 28d26a6d96031d6cfd988464c97919e7649f3d8f Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 7 Oct 2023 21:31:14 +0200
Subject: [PATCH 24/27] {2023.06}[foss/2022a] add oneTBB

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index a09af3fe4b..b483523198 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -15,3 +15,4 @@ easyconfigs:
       options:
         include-easyblocks-from-pr: 3012
   - NCO-5.1.0-foss-2022a.eb
+  - tbb-2021.5.0-GCCcore-11.3.0.eb

From 335b63d396b5eaf40ebb56ab33d3a8b8e96cad82 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 7 Oct 2023 21:43:23 +0200
Subject: [PATCH 25/27] removed VSEARCH, failed to build for all architectures

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index 677ff41958..dc2377459d 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -18,7 +18,6 @@ easyconfigs:
   - Pysam-0.20.0-GCC-11.3.0.eb
   - TransDecoder-5.5.0-GCC-11.3.0.eb
   - VCFtools-0.1.16-GCC-11.3.0.eb
-  - VSEARCH-2.22.1-GCC-11.3.0.eb
   - XML-LibXML-2.0207-GCCcore-11.3.0.eb
   - CMake-3.24.3-GCCcore-11.3.0.eb
   - elfutils-0.187-GCCcore-11.3.0.eb

From f69f0be5354c068180eaebcf8e53c2182b5edd7d Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 7 Oct 2023 22:18:06 +0200
Subject: [PATCH 26/27] {2023.06}[foss/2022a] add SciPy-bundle

---
 eb_hooks.py                      | 24 ++++++++++++++++++++++++
 eessi-2023.06-eb-4.8.1-2022a.yml |  1 +
 2 files changed, 25 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index e66b21278d..084b78e5e0 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -18,6 +18,9 @@
     from distutils.version import LooseVersion
 
 
+CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1'
+
+
 EESSI_RPATH_OVERRIDE_ATTR = 'orig_rpath_override_dirs'
 
 
@@ -248,6 +251,23 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs):
     else:
         raise EasyBuildError("WRF-specific hook triggered for non-WRF 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:
+        PRE_TEST_HOOKS[self.name](self, *args, **kwargs)
+
+
+def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
+    """
+    Pre-test hook for SciPy-bundle: skip failing tests for SciPy-bundle 2021.10 (currently the only version that is failing).
+    In previous versions we were not as strict yet on the numpy/SciPy tests
+    """
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    if self.name == 'SciPy-bundle' and self.version == '2021.10' and cpu_target == CPU_TARGET_NEOVERSE_V1:
+        self.cfg['testopts'] = "|| echo ignoring failing tests" 
+
+
 PARSE_HOOKS = {
     'CGAL': parse_hook_cgal_toolchainopts_precise,
     'fontconfig': parse_hook_fontconfig_add_fonts,
@@ -265,3 +285,7 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs):
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,
     'WRF': pre_configure_hook_wrf_aarch64,
 }
+
+PRE_TEST_HOOKS = {
+    'SciPy-bundle': pre_test_hook_ignore_failing_tests_SciPybundle,
+}
diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index a09af3fe4b..7bce2c416b 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -15,3 +15,4 @@ easyconfigs:
       options:
         include-easyblocks-from-pr: 3012
   - NCO-5.1.0-foss-2022a.eb
+  - SciPy-bundle-2022.05-foss-2022a.eb

From fb0727ca9282f008214e89bf98f7d06464d3be05 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 7 Oct 2023 22:42:49 +0200
Subject: [PATCH 27/27] {2023.06}[foss/2022a] add Xvfb

---
 eessi-2023.06-eb-4.8.1-2022a.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/eessi-2023.06-eb-4.8.1-2022a.yml b/eessi-2023.06-eb-4.8.1-2022a.yml
index a09af3fe4b..b714fcdcae 100644
--- a/eessi-2023.06-eb-4.8.1-2022a.yml
+++ b/eessi-2023.06-eb-4.8.1-2022a.yml
@@ -15,3 +15,8 @@ easyconfigs:
       options:
         include-easyblocks-from-pr: 3012
   - NCO-5.1.0-foss-2022a.eb
+  - Xvfb-21.1.3-GCCcore-11.3.0.eb:
+      # enable exec permissions for xvfb-run after copying;
+      # need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works
+      options:
+        from-pr: 18834