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 1/9] 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 2/9] 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 3/9] 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 4/9] 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 5/9] 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 6/9] 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 7/9] 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 8/9] 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 9/9] 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()'