From e594d24401a6c828c9b8fee3536fa1f689e5834c Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 15:37:10 -0400
Subject: [PATCH 01/16] downloadrepos: allow to be used as library as well

---
 downloadrepos | 29 ++++++++++++++++++-----------
 1 file changed, 18 insertions(+), 11 deletions(-)

diff --git a/downloadrepos b/downloadrepos
index 9702c261..497e0f6e 100755
--- a/downloadrepos
+++ b/downloadrepos
@@ -1,4 +1,6 @@
 #!/bin/sh
+# This file can be used both as executable script or library to be sourced.
+# To use as library to be sourced, set DOWNLOADREPOS_AS_LIB=1 env var.
 
 downloadrepos() {
     github_repo="$1"; shift
@@ -22,16 +24,21 @@ downloadgithubrepos() {
     set +x
 }
 
-. ./default_build_params
+if [ -z "$DOWNLOADREPOS_AS_LIB" ]; then
+    # Script mode, otherwise, library mode.
+
+    . ./default_build_params
+
+    if [ -z "$1" ]; then
+        downloadgithubrepos $PAVICS_SDI_REPO $PAVICS_SDI_BRANCH
+        downloadgithubrepos $FINCH_REPO $FINCH_BRANCH
+        downloadgithubrepos $PAVICS_LANDING_REPO $PAVICS_LANDING_BRANCH
+        downloadgithubrepos $RAVEN_REPO $RAVEN_BRANCH
+        downloadgithubrepos $RAVENPY_REPO $RAVENPY_BRANCH
+        downloadgithubrepos $ESGF_COMPUTE_API_REPO $ESGF_COMPUTE_API_BRANCH
+    else
+        set -x
+        downloadrepos "$@"
+    fi
 
-if [ -z "$1" ]; then
-    downloadgithubrepos $PAVICS_SDI_REPO $PAVICS_SDI_BRANCH
-    downloadgithubrepos $FINCH_REPO $FINCH_BRANCH
-    downloadgithubrepos $PAVICS_LANDING_REPO $PAVICS_LANDING_BRANCH
-    downloadgithubrepos $RAVEN_REPO $RAVEN_BRANCH
-    downloadgithubrepos $RAVENPY_REPO $RAVENPY_BRANCH
-    downloadgithubrepos $ESGF_COMPUTE_API_REPO $ESGF_COMPUTE_API_BRANCH
-else
-    set -x
-    downloadrepos "$@"
 fi

From 5216bca1fd9f48c1bfb3ad20d6cc2ced3afff49b Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 16:24:29 -0400
Subject: [PATCH 02/16] downloadrepos: only download repos that will be tested

However, old "download all default repos" have to be preserved for
back-compat with other external scripts.

Fixes https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/issues/30
---
 downloadrepos | 51 +++++++++++++++++++++++++++++++++++++++++++--------
 testall       | 16 ++++------------
 2 files changed, 47 insertions(+), 20 deletions(-)

diff --git a/downloadrepos b/downloadrepos
index 497e0f6e..c91616cc 100755
--- a/downloadrepos
+++ b/downloadrepos
@@ -24,21 +24,56 @@ downloadgithubrepos() {
     set +x
 }
 
-if [ -z "$DOWNLOADREPOS_AS_LIB" ]; then
-    # Script mode, otherwise, library mode.
+lowercase_boolean_build_params() {
+    TEST_MAGPIE_AUTH="`echo "$TEST_MAGPIE_AUTH" | tr '[:upper:]' '[:lower:]'`"
+    TEST_PAVICS_SDI_REPO="`echo "$TEST_PAVICS_SDI_REPO" | tr '[:upper:]' '[:lower:]'`"
+    TEST_PAVICS_SDI_WEAVER="`echo "$TEST_PAVICS_SDI_WEAVER" | tr '[:upper:]' '[:lower:]'`"
+    TEST_FINCH_REPO="`echo "$TEST_FINCH_REPO" | tr '[:upper:]' '[:lower:]'`"
+    TEST_PAVICS_LANDING_REPO="`echo "$TEST_PAVICS_LANDING_REPO" | tr '[:upper:]' '[:lower:]'`"
+    TEST_RAVEN_REPO="`echo "$TEST_RAVEN_REPO" | tr '[:upper:]' '[:lower:]'`"
+    TEST_RAVENPY_REPO="`echo "$TEST_RAVENPY_REPO" | tr '[:upper:]' '[:lower:]'`"
+    TEST_ESGF_COMPUTE_API_REPO="`echo "$TEST_ESGF_COMPUTE_API_REPO" | tr '[:upper:]' '[:lower:]'`"
+    TEST_LOCAL_NOTEBOOKS="`echo "$TEST_LOCAL_NOTEBOOKS" | tr '[:upper:]' '[:lower:]'`"
+}
 
+downloadrepos_main() {
     . ./default_build_params
 
+    lowercase_boolean_build_params
+
+    if [ -z "$DOWNLOAD_ALL_DEFAULT_REPOS" ]; then
+        # Back-compat with old default behavior, used in binder/reorg-notebook
+        # and other external scripts that autodeploy tutorial notebooks (see
+        # https://github.com/bird-house/birdhouse-deploy/blob/444a7c35a31aa8ad351e47f659383ba5c2919705/birdhouse/deployment/trigger-deploy-notebook#L64-L75)
+        DOWNLOAD_ALL_DEFAULT_REPOS=true
+    fi
+
     if [ -z "$1" ]; then
-        downloadgithubrepos $PAVICS_SDI_REPO $PAVICS_SDI_BRANCH
-        downloadgithubrepos $FINCH_REPO $FINCH_BRANCH
-        downloadgithubrepos $PAVICS_LANDING_REPO $PAVICS_LANDING_BRANCH
-        downloadgithubrepos $RAVEN_REPO $RAVEN_BRANCH
-        downloadgithubrepos $RAVENPY_REPO $RAVENPY_BRANCH
-        downloadgithubrepos $ESGF_COMPUTE_API_REPO $ESGF_COMPUTE_API_BRANCH
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_PAVICS_SDI_REPO" = xtrue ]; then
+            downloadgithubrepos $PAVICS_SDI_REPO $PAVICS_SDI_BRANCH
+        fi
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_FINCH_REPO" = xtrue ]; then
+            downloadgithubrepos $FINCH_REPO $FINCH_BRANCH
+        fi
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_PAVICS_LANDING_REPO" = xtrue ]; then
+            downloadgithubrepos $PAVICS_LANDING_REPO $PAVICS_LANDING_BRANCH
+        fi
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_RAVEN_REPO" = xtrue ]; then
+            downloadgithubrepos $RAVEN_REPO $RAVEN_BRANCH
+        fi
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_RAVENPY_REPO" = xtrue ]; then
+            downloadgithubrepos $RAVENPY_REPO $RAVENPY_BRANCH
+        fi
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_ESGF_COMPUTE_API_REPO" = xtrue ]; then
+            downloadgithubrepos $ESGF_COMPUTE_API_REPO $ESGF_COMPUTE_API_BRANCH
+        fi
     else
         set -x
         downloadrepos "$@"
     fi
+}
 
+if [ -z "$DOWNLOADREPOS_AS_LIB" ]; then
+    # Script mode, not library mode.
+    downloadrepos_main "$@"
 fi
diff --git a/testall b/testall
index 621a915d..ec943fb4 100755
--- a/testall
+++ b/testall
@@ -37,7 +37,10 @@ fi
 git clean -fdx
 
 # download all additional repos containing extra notebooks to test
-./downloadrepos
+DOWNLOADREPOS_AS_LIB=1
+. ./downloadrepos
+DOWNLOAD_ALL_DEFAULT_REPOS=false
+downloadrepos_main
 
 # 'export' useful vars so they can be used by the CONFIG_OVERRIDE_SCRIPT_URL in runtest.
 
@@ -86,17 +89,6 @@ rm -v $RAVENPY_REPO_NAME-$RAVENPY_BRANCH/pyproject.toml
 rm -v $ESGF_COMPUTE_API_REPO_NAME-$ESGF_COMPUTE_API_BRANCH/setup.cfg
 rm -v $ESGF_COMPUTE_API_REPO_NAME-$ESGF_COMPUTE_API_BRANCH/tox.ini
 
-# lowercase
-TEST_MAGPIE_AUTH="`echo "$TEST_MAGPIE_AUTH" | tr '[:upper:]' '[:lower:]'`"
-TEST_PAVICS_SDI_REPO="`echo "$TEST_PAVICS_SDI_REPO" | tr '[:upper:]' '[:lower:]'`"
-TEST_PAVICS_SDI_WEAVER="`echo "$TEST_PAVICS_SDI_WEAVER" | tr '[:upper:]' '[:lower:]'`"
-TEST_FINCH_REPO="`echo "$TEST_FINCH_REPO" | tr '[:upper:]' '[:lower:]'`"
-TEST_PAVICS_LANDING_REPO="`echo "$TEST_PAVICS_LANDING_REPO" | tr '[:upper:]' '[:lower:]'`"
-TEST_RAVEN_REPO="`echo "$TEST_RAVEN_REPO" | tr '[:upper:]' '[:lower:]'`"
-TEST_RAVENPY_REPO="`echo "$TEST_RAVENPY_REPO" | tr '[:upper:]' '[:lower:]'`"
-TEST_ESGF_COMPUTE_API_REPO="`echo "$TEST_ESGF_COMPUTE_API_REPO" | tr '[:upper:]' '[:lower:]'`"
-TEST_LOCAL_NOTEBOOKS="`echo "$TEST_LOCAL_NOTEBOOKS" | tr '[:upper:]' '[:lower:]'`"
-
 NOTEBOOKS_TO_TEST=""
 if [ x"$TEST_MAGPIE_AUTH" = xtrue ]; then
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST notebooks-auth/*.ipynb"

From 57936f573532193080c6ceb75771c500f34c5619 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 17:25:56 -0400
Subject: [PATCH 03/16] testall: make processing here available to other repos
 via downloadrepos

---
 downloadrepos | 65 +++++++++++++++++++++++++++++++++++++++------------
 testall       | 58 +++++++++++++++++++--------------------------
 2 files changed, 74 insertions(+), 49 deletions(-)

diff --git a/downloadrepos b/downloadrepos
index c91616cc..f7f1b20e 100755
--- a/downloadrepos
+++ b/downloadrepos
@@ -24,16 +24,51 @@ downloadgithubrepos() {
     set +x
 }
 
+# USAGE: VAR_TO_LOWER="$(lowercase "$VAR_TO_LOWER")"
+lowercase() {
+    echo "$1" | tr '[:upper:]' '[:lower:]'
+}
+
 lowercase_boolean_build_params() {
-    TEST_MAGPIE_AUTH="`echo "$TEST_MAGPIE_AUTH" | tr '[:upper:]' '[:lower:]'`"
-    TEST_PAVICS_SDI_REPO="`echo "$TEST_PAVICS_SDI_REPO" | tr '[:upper:]' '[:lower:]'`"
-    TEST_PAVICS_SDI_WEAVER="`echo "$TEST_PAVICS_SDI_WEAVER" | tr '[:upper:]' '[:lower:]'`"
-    TEST_FINCH_REPO="`echo "$TEST_FINCH_REPO" | tr '[:upper:]' '[:lower:]'`"
-    TEST_PAVICS_LANDING_REPO="`echo "$TEST_PAVICS_LANDING_REPO" | tr '[:upper:]' '[:lower:]'`"
-    TEST_RAVEN_REPO="`echo "$TEST_RAVEN_REPO" | tr '[:upper:]' '[:lower:]'`"
-    TEST_RAVENPY_REPO="`echo "$TEST_RAVENPY_REPO" | tr '[:upper:]' '[:lower:]'`"
-    TEST_ESGF_COMPUTE_API_REPO="`echo "$TEST_ESGF_COMPUTE_API_REPO" | tr '[:upper:]' '[:lower:]'`"
-    TEST_LOCAL_NOTEBOOKS="`echo "$TEST_LOCAL_NOTEBOOKS" | tr '[:upper:]' '[:lower:]'`"
+    TEST_MAGPIE_AUTH="$(lowercase "$TEST_MAGPIE_AUTH")"
+    TEST_PAVICS_SDI_REPO="$(lowercase "$TEST_PAVICS_SDI_REPO")"
+    TEST_PAVICS_SDI_WEAVER="$(lowercase "$TEST_PAVICS_SDI_WEAVER")"
+    TEST_FINCH_REPO="$(lowercase "$TEST_FINCH_REPO")"
+    TEST_PAVICS_LANDING_REPO="$(lowercase "$TEST_PAVICS_LANDING_REPO")"
+    TEST_RAVEN_REPO="$(lowercase "$TEST_RAVEN_REPO")"
+    TEST_RAVENPY_REPO="$(lowercase "$TEST_RAVENPY_REPO")"
+    TEST_ESGF_COMPUTE_API_REPO="$(lowercase "$TEST_ESGF_COMPUTE_API_REPO")"
+    TEST_LOCAL_NOTEBOOKS="$(lowercase "$TEST_LOCAL_NOTEBOOKS")"
+}
+
+# Replace all slash (/) by dash (-) because (/) is illegal in folder name
+# for branch name of the format "feature/my_wizbang-feature".
+# Github does the same when downloading repo archive by downloadrepos above.
+# USAGE: export BRANCH_NAME="$(sanitize_branch_name "$BRANCH_NAME")"
+sanitize_branch_name() {
+    echo "$1" | sed "s@/@-@g"
+}
+
+# Ex: extract 'pavics-sdi' from 'Ouranosinc/pavics-sdi'.
+# USAGE: REPO_NAME_ONLY="$(extract_repo_name "$REPO_NAME")"
+extract_repo_name() {
+    echo "$1" | sed "s@^.*/@@g"
+}
+
+# Branches that have allowed characters such as '+' other than alphanum, '-', '_' and '.' are converted to '-' in archives.
+# USAGE: FOLDER_NAME="$(sanitize_extracted_folder_name "$FOLDER_NAME")"
+sanitize_extracted_folder_name() {
+    echo "$1" | sed "s@[^a-zA-Z0-9_\-\.]@-@g"
+}
+
+# Presence of setup.cfg, tox.ini, pyproject.toml files confuse py.test execution rootdir discovery.
+# USAGE: delete_files_confusing_pytest "$CHECKOUT_DIR"
+delete_files_confusing_pytest() {
+    for afile in setup.cfg tox.ini pyproject.toml; do
+        if [ -f "$1/$afile" ]; then
+            rm -v "$1/$afile"
+        fi
+    done
 }
 
 downloadrepos_main() {
@@ -49,22 +84,22 @@ downloadrepos_main() {
     fi
 
     if [ -z "$1" ]; then
-        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_PAVICS_SDI_REPO" = xtrue ]; then
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue ] || [ x"$TEST_PAVICS_SDI_REPO" = xtrue ]; then
             downloadgithubrepos $PAVICS_SDI_REPO $PAVICS_SDI_BRANCH
         fi
-        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_FINCH_REPO" = xtrue ]; then
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue ] || [ x"$TEST_FINCH_REPO" = xtrue ]; then
             downloadgithubrepos $FINCH_REPO $FINCH_BRANCH
         fi
-        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_PAVICS_LANDING_REPO" = xtrue ]; then
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue ] || [ x"$TEST_PAVICS_LANDING_REPO" = xtrue ]; then
             downloadgithubrepos $PAVICS_LANDING_REPO $PAVICS_LANDING_BRANCH
         fi
-        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_RAVEN_REPO" = xtrue ]; then
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue ] || [ x"$TEST_RAVEN_REPO" = xtrue ]; then
             downloadgithubrepos $RAVEN_REPO $RAVEN_BRANCH
         fi
-        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_RAVENPY_REPO" = xtrue ]; then
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue ] || [ x"$TEST_RAVENPY_REPO" = xtrue ]; then
             downloadgithubrepos $RAVENPY_REPO $RAVENPY_BRANCH
         fi
-        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue -o x"$TEST_ESGF_COMPUTE_API_REPO" = xtrue ]; then
+        if [ x"$DOWNLOAD_ALL_DEFAULT_REPOS" = xtrue ] || [ x"$TEST_ESGF_COMPUTE_API_REPO" = xtrue ]; then
             downloadgithubrepos $ESGF_COMPUTE_API_REPO $ESGF_COMPUTE_API_BRANCH
         fi
     else
diff --git a/testall b/testall
index ec943fb4..89d5c18e 100755
--- a/testall
+++ b/testall
@@ -43,33 +43,28 @@ DOWNLOAD_ALL_DEFAULT_REPOS=false
 downloadrepos_main
 
 # 'export' useful vars so they can be used by the CONFIG_OVERRIDE_SCRIPT_URL in runtest.
-
-# replace all slash (/) by dash (-) because (/) is illegal in folder name
-# for branch name of the format "feature/my_wizbang-feature"
-# github does the same when downloading repo archive by downloadrepos above
-export PAVICS_SDI_BRANCH="`echo "$PAVICS_SDI_BRANCH" | sed "s@/@-@g"`"
-export PAVICS_SDI_REPO_NAME="`echo "$PAVICS_SDI_REPO" | sed "s@^.*/@@g"`"
-export FINCH_BRANCH="`echo "$FINCH_BRANCH" | sed "s@/@-@g"`"
-export FINCH_REPO_NAME="`echo "$FINCH_REPO" | sed "s@^.*/@@g"`"
-export PAVICS_LANDING_BRANCH="`echo "$PAVICS_LANDING_BRANCH" | sed "s@/@-@g"`"
-export PAVICS_LANDING_REPO_NAME="`echo "$PAVICS_LANDING_REPO" | sed "s@^.*/@@g"`"
-export RAVEN_BRANCH="`echo "$RAVEN_BRANCH" | sed "s@/@-@g"`"
-export RAVEN_REPO_NAME="`echo "$RAVEN_REPO" | sed "s@^.*/@@g"`"
-export RAVENPY_BRANCH="`echo "$RAVENPY_BRANCH" | sed "s@/@-@g"`"
-export RAVENPY_REPO_NAME="`echo "$RAVENPY_REPO" | sed "s@^.*/@@g"`"
-export ESGF_COMPUTE_API_BRANCH="`echo "$ESGF_COMPUTE_API_BRANCH" | sed "s@/@-@g"`"
-export ESGF_COMPUTE_API_REPO_NAME="`echo "$ESGF_COMPUTE_API_REPO" | sed "s@^.*/@@g"`"
-
-# branches that have allowed characters such as '+' other than alphanum, '-' and '_' are converted to '-' in archives
-export PAVICS_SDI_DIR=`echo "${PAVICS_SDI_REPO_NAME}-${PAVICS_SDI_BRANCH}" | sed "s@[^a-zA-Z0-9_\-\.]@-@g"`
-export FINCH_DIR=`echo "${FINCH_REPO_NAME}-${FINCH_BRANCH}" | sed "s@[^a-zA-Z0-9_\-\.]@-@g"`
-export PAVICS_LANDING_DIR=`echo "${PAVICS_LANDING_REPO_NAME}-${PAVICS_LANDING_BRANCH}" | sed "s@[^a-zA-Z0-9_\-\.]@-@g"`
-export RAVEN_DIR=`echo "${RAVEN_REPO_NAME}-${RAVEN_BRANCH}" | sed "s@[^a-zA-Z0-9_\-\.]@-@g"`
-export RAVENPY_DIR=`echo "${RAVENPY_REPO_NAME}-${RAVENPY_BRANCH}" | sed "s@[^a-zA-Z0-9_\-\.]@-@g"`
-export ESGF_COMPUTE_API_DIR=`echo "${ESGF_COMPUTE_API_REPO_NAME}-${ESGF_COMPUTE_API_BRANCH}" | sed "s@[^a-zA-Z0-9_\-\.]@-@g"`
+export PAVICS_SDI_BRANCH="$(sanitize_branch_name "$PAVICS_SDI_BRANCH")"
+export PAVICS_SDI_REPO_NAME="$(extract_repo_name "$PAVICS_SDI_REPO")"
+export FINCH_BRANCH="$(sanitize_branch_name "$FINCH_BRANCH")"
+export FINCH_REPO_NAME="$(extract_repo_name "$FINCH_REPO")"
+export PAVICS_LANDING_BRANCH="$(sanitize_branch_name "$PAVICS_LANDING_BRANCH")"
+export PAVICS_LANDING_REPO_NAME="$(extract_repo_name "$PAVICS_LANDING_REPO")"
+export RAVEN_BRANCH="$(sanitize_branch_name "$RAVEN_BRANCH")"
+export RAVEN_REPO_NAME="$(extract_repo_name "$RAVEN_REPO")"
+export RAVENPY_BRANCH="$(sanitize_branch_name "$RAVENPY_BRANCH")"
+export RAVENPY_REPO_NAME="$(extract_repo_name "$RAVENPY_REPO")"
+export ESGF_COMPUTE_API_BRANCH="$(sanitize_branch_name "$ESGF_COMPUTE_API_BRANCH")"
+export ESGF_COMPUTE_API_REPO_NAME="$(extract_repo_name "$ESGF_COMPUTE_API_REPO")"
+
+export PAVICS_SDI_DIR="$(sanitize_extracted_folder_name "${PAVICS_SDI_REPO_NAME}-${PAVICS_SDI_BRANCH}")"
+export FINCH_DIR="$(sanitize_extracted_folder_name "${FINCH_REPO_NAME}-${FINCH_BRANCH}")"
+export PAVICS_LANDING_DIR="$(sanitize_extracted_folder_name "${PAVICS_LANDING_REPO_NAME}-${PAVICS_LANDING_BRANCH}")"
+export RAVEN_DIR="$(sanitize_extracted_folder_name "${RAVEN_REPO_NAME}-${RAVEN_BRANCH}")"
+export RAVENPY_DIR="$(sanitize_extracted_folder_name "${RAVENPY_REPO_NAME}-${RAVENPY_BRANCH}")"
+export ESGF_COMPUTE_API_DIR="$(sanitize_extracted_folder_name "${ESGF_COMPUTE_API_REPO_NAME}-${ESGF_COMPUTE_API_BRANCH}")"
 
 # lowercase VERIFY_SSL string
-VERIFY_SSL="`echo "$VERIFY_SSL" | tr '[:upper:]' '[:lower:]'`"
+VERIFY_SSL="$(lowercase "$VERIFY_SSL")"
 if [ x"$VERIFY_SSL" = xfalse ]; then
     # if Env var DISABLE_VERIFY_SSL is present, notebook should disable ssl
     # cert verification
@@ -79,15 +74,6 @@ if [ x"$VERIFY_SSL" = xfalse ]; then
     echo "setting env var DISABLE_VERIFY_SSL for notebooks"
 fi
 
-# presence of setup.cfg, tox.ini, pyproject.toml files confuse py.test execution rootdir discovery
-rm -v $FINCH_REPO_NAME-$FINCH_BRANCH/setup.cfg
-rm -v $RAVEN_REPO_NAME-$RAVEN_BRANCH/setup.cfg
-rm -v $RAVEN_REPO_NAME-$RAVEN_BRANCH/pyproject.toml
-rm -v $RAVENPY_REPO_NAME-$RAVENPY_BRANCH/setup.cfg
-rm -v $RAVENPY_REPO_NAME-$RAVENPY_BRANCH/tox.ini
-rm -v $RAVENPY_REPO_NAME-$RAVENPY_BRANCH/pyproject.toml
-rm -v $ESGF_COMPUTE_API_REPO_NAME-$ESGF_COMPUTE_API_BRANCH/setup.cfg
-rm -v $ESGF_COMPUTE_API_REPO_NAME-$ESGF_COMPUTE_API_BRANCH/tox.ini
 
 NOTEBOOKS_TO_TEST=""
 if [ x"$TEST_MAGPIE_AUTH" = xtrue ]; then
@@ -100,6 +86,7 @@ if [ x"$TEST_PAVICS_SDI_REPO" = xtrue ]; then
     fi
 fi
 if [ x"$TEST_FINCH_REPO" = xtrue ]; then
+    delete_files_confusing_pytest "$FINCH_DIR"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${FINCH_DIR}/docs/source/notebooks/*.ipynb"
 fi
 
@@ -118,13 +105,16 @@ if [ x"$TEST_PAVICS_LANDING_REPO" = xtrue ]; then
 fi
 
 if [ x"$TEST_RAVEN_REPO" = xtrue ]; then
+    delete_files_confusing_pytest "$RAVEN_DIR"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${RAVEN_DIR}/docs/source/notebooks/*.ipynb"
 fi
 if [ x"$TEST_RAVENPY_REPO" = xtrue ]; then
+    delete_files_confusing_pytest "$RAVENPY_DIR"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${RAVENPY_DIR}/docs/notebooks/*.ipynb"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${RAVENPY_DIR}/docs/notebooks/paper/*.ipynb"
 fi
 if [ x"$TEST_ESGF_COMPUTE_API_REPO" = xtrue ]; then
+    delete_files_confusing_pytest "$ESGF_COMPUTE_API_DIR"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${ESGF_COMPUTE_API_DIR}/examples/*.ipynb"
 fi
 

From cccae703298d8c75c18ce555a0eb1f985d763878 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 17:30:37 -0400
Subject: [PATCH 04/16] testall: make available all functions in downloadrepos
 to CONFIG_PARAMETERS_SCRIPT_URL

---
 testall | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/testall b/testall
index 89d5c18e..e928ba57 100755
--- a/testall
+++ b/testall
@@ -2,6 +2,9 @@
 
 . ./default_build_params
 
+DOWNLOADREPOS_AS_LIB=1
+. ./downloadrepos
+
 set -x
 
 # Allow full override of ALL Jenkins params before running test suite.
@@ -37,8 +40,6 @@ fi
 git clean -fdx
 
 # download all additional repos containing extra notebooks to test
-DOWNLOADREPOS_AS_LIB=1
-. ./downloadrepos
 DOWNLOAD_ALL_DEFAULT_REPOS=false
 downloadrepos_main
 

From b84da182ee205e9983229e50fa4fce8b1d5cbcd6 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 18:05:26 -0400
Subject: [PATCH 05/16] Jenkins: all artifacts are now under buildout/ so
 easier to add new nb from new repos

No need to update 'archiveArtifacts' in Jenkinsfile anymore.

Since we only download enabled repos, we could not hardcode artifact repo list anyways.

DEFAULT_PRODUCTION_HOST also overridable for other repos.
---
 Jenkinsfile | 11 +----------
 runtest     | 34 +++++++++++++++++++++-------------
 testall     |  1 +
 3 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index cadb2e9a..7782d360 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -144,16 +144,7 @@ Note this is another run, will double the time and no guaranty to have same erro
 
     post {
         always {
-            archiveArtifacts(artifacts: 'notebooks/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'pavics-sdi-*/docs/source/notebooks/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'pavics-sdi-*/docs/source/notebook-components/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'finch-*/docs/source/notebooks/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'raven-*/docs/source/notebooks/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'RavenPy-*/docs/notebooks/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'RavenPy-*/docs/notebooks/paper/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'esgf-compute-api-*/examples/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'PAVICS-landing-*/content/notebooks/climate_indicators/*.ipynb', fingerprint: true)
-            archiveArtifacts(artifacts: 'buildout/*.output.ipynb', fingerprint: true, allowEmptyArchive: true)
+            archiveArtifacts(artifacts: 'buildout/*.ipynb', fingerprint: true, allowEmptyArchive: true)
             archiveArtifacts(artifacts: 'buildout/env-dump/', fingerprint: true)
         }
 	unsuccessful {  // Run if the current builds status is "Aborted", "Failure" or "Unstable"
diff --git a/runtest b/runtest
index 1ab8bb50..eca5a7d8 100755
--- a/runtest
+++ b/runtest
@@ -1,6 +1,10 @@
 #!/bin/sh
 
-DEFAULT_PRODUCTION_HOST="pavics.ouranos.ca"
+# Load shared functions, make available to CONFIG_OVERRIDE_SCRIPT_URL.
+DOWNLOADREPOS_AS_LIB=1
+. ./downloadrepos
+
+DEFAULT_PRODUCTION_HOST="${DEFAULT_PRODUCTION_HOST:=pavics.ouranos.ca}"
 
 NOTEBOOKS="$1"
 if [ -z "$NOTEBOOKS" ]; then
@@ -67,7 +71,7 @@ py.test --nbval $NOTEBOOKS --nbval-sanitize-with notebooks/output-sanitize.cfg $
 EXIT_CODE="$?"
 
 # lowercase SAVE_RESULTING_NOTEBOOK string
-SAVE_RESULTING_NOTEBOOK="`echo "$SAVE_RESULTING_NOTEBOOK" | tr '[:upper:]' '[:lower:]'`"
+SAVE_RESULTING_NOTEBOOK="$(lowercase "$SAVE_RESULTING_NOTEBOOK")"
 
 
 # save notebooks resulting from the run
@@ -79,15 +83,19 @@ SAVE_RESULTING_NOTEBOOK="`echo "$SAVE_RESULTING_NOTEBOOK" | tr '[:upper:]' '[:lo
 # work-around as nbval can not save the result of the run
 # see https://github.com/computationalmodelling/nbval/issues/112
 
-if [ x"$SAVE_RESULTING_NOTEBOOK" = xtrue ]; then
-    mkdir -p buildout
-    for nb in $NOTEBOOKS; do
-        filename="`basename "$nb"`"
-        filename="`echo "$filename" | sed "s/.ipynb$//"`"  # remove .ipynb ext
-        if [ -e "buildout/${filename}.output.ipynb" ]; then
-            # prevent name clash
-            filename="${filename}_`date '+%s'`"
-        fi
+mkdir -p buildout/
+for nb in $NOTEBOOKS; do
+    filename="$(basename "$nb")"
+    filename="$(echo "$filename" | sed "s/.ipynb$//")"  # remove .ipynb ext
+    if [ -e "buildout/${filename}.ipynb" ]; then
+        # prevent name clash
+        filename="${filename}_$(date '+%s')"
+    fi
+
+    # Save original notebooks that we sed replace the PAVICS_HOST.
+    cp "$nb" "buildout/${filename}.ipynb"
+
+    if [ x"$SAVE_RESULTING_NOTEBOOK" = xtrue ]; then
         # Timeout must not be more than 240s (4 mins). Default in Jenkinsfile.
         # Tutorial notebooks should be fast so user do not lose patience waiting
         # for them to run.  If more than 4 mins, in addition to simplifying the
@@ -95,8 +103,8 @@ if [ x"$SAVE_RESULTING_NOTEBOOK" = xtrue ]; then
         jupyter nbconvert --to notebook --execute \
             --ExecutePreprocessor.timeout=${SAVE_RESULTING_NOTEBOOK_TIMEOUT:=240} --allow-errors \
             --output-dir buildout --output "${filename}.output.ipynb" "$nb"
-    done
-fi
+    fi
+done
 
 # exit with return code from py.test
 exit $EXIT_CODE
diff --git a/testall b/testall
index e928ba57..1e053052 100755
--- a/testall
+++ b/testall
@@ -2,6 +2,7 @@
 
 . ./default_build_params
 
+# Load shared functions, make available to CONFIG_PARAMETERS_SCRIPT_URL.
 DOWNLOADREPOS_AS_LIB=1
 . ./downloadrepos
 

From cfe5f95a85a4ca21dd630dd46850ac5252105632 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 18:36:13 -0400
Subject: [PATCH 06/16] testall: git clean before CONFIG_PARAMETERS_SCRIPT_URL
 to avoid wiping files created by the script

---
 testall | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/testall b/testall
index 1e053052..6b254d6e 100755
--- a/testall
+++ b/testall
@@ -8,6 +8,9 @@ DOWNLOADREPOS_AS_LIB=1
 
 set -x
 
+# emulate "clean after checkout" of single branch pipeline
+git clean -fdx
+
 # Allow full override of ALL Jenkins params before running test suite.
 # Intended to overrride all params in Jenkinsfile.
 #
@@ -37,9 +40,6 @@ if [ -n "$CONFIG_PARAMETERS_SCRIPT_URL" ]; then
     . "$TMP_PARAMS_OVERRIDE"
 fi
 
-# emulate "clean after checkout" of single branch pipeline
-git clean -fdx
-
 # download all additional repos containing extra notebooks to test
 DOWNLOAD_ALL_DEFAULT_REPOS=false
 downloadrepos_main

From 7253e6aa6d410dcedeaaf1a6a89eed3067103e6e Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 18:55:12 -0400
Subject: [PATCH 07/16] runtest: allow to override --nbval-sanitize-with from
 CONFIG_OVERRIDE_SCRIPT_URL

---
 runtest | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/runtest b/runtest
index eca5a7d8..e8048502 100755
--- a/runtest
+++ b/runtest
@@ -67,7 +67,8 @@ if [ -n "$CONFIG_OVERRIDE_SCRIPT_URL" ]; then
     fi
 fi
 
-py.test --nbval $NOTEBOOKS --nbval-sanitize-with notebooks/output-sanitize.cfg $PYTEST_EXTRA_OPTS
+# CONFIG_OVERRIDE_SCRIPT_URL can override NBVAL_SANITIZE_CFG_FILE.
+py.test --nbval $NOTEBOOKS --nbval-sanitize-with "${NBVAL_SANITIZE_CFG_FILE:=notebooks/output-sanitize.cfg}" $PYTEST_EXTRA_OPTS
 EXIT_CODE="$?"
 
 # lowercase SAVE_RESULTING_NOTEBOOK string

From d93b229d5b679a8033506433b779b717639ad583 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 19:11:23 -0400
Subject: [PATCH 08/16] downloadrepos: avoid set +x because it hides all
 subsequent commands from being logged

---
 downloadrepos | 2 --
 1 file changed, 2 deletions(-)

diff --git a/downloadrepos b/downloadrepos
index f7f1b20e..a9d87658 100755
--- a/downloadrepos
+++ b/downloadrepos
@@ -15,13 +15,11 @@ downloadgithubrepos() {
     repo_owner="`echo "$owner_and_repo_name" | sed "s@/.*\\$@@g"`"
     repo_name="`echo "$owner_and_repo_name" | sed "s@^.*/@@g"`"
     repo_branch="$1"; shift
-    set -x
     # clean up other previously downloaded branches of the same repo as well
     rm -rf ${repo_name}-*
     ls | grep $repo_name
     downloadrepos https://github.com/$repo_owner/$repo_name "$repo_branch"
     ls | grep $repo_name
-    set +x
 }
 
 # USAGE: VAR_TO_LOWER="$(lowercase "$VAR_TO_LOWER")"

From 9160053016260a1b8fbeea8a77af76dc49855ba4 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 19:40:09 -0400
Subject: [PATCH 09/16] jenkins sample override: demo runnings notebooks from
 an external repo

---
 .../jenkins-params-external-repos.include.sh  | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 test-override/jenkins-params-external-repos.include.sh

diff --git a/test-override/jenkins-params-external-repos.include.sh b/test-override/jenkins-params-external-repos.include.sh
new file mode 100644
index 00000000..b62858a6
--- /dev/null
+++ b/test-override/jenkins-params-external-repos.include.sh
@@ -0,0 +1,47 @@
+#!/bin/sh
+#
+# Sample Jenkins params override script to demonstrate running new notebooks
+# from an external repo and on-the-fly CONFIG_OVERRIDE_SCRIPT_URL file creation.
+#
+# This script is intended for param CONFIG_PARAMETERS_SCRIPT_URL.
+
+# Scenario: we want to run notebooks from an external repo, unknown to current Jenkins config.
+# https://github.com/roocs/rook/tree/master/notebooks/*.ipynb
+
+# Disable all existing default repos to avoid downloading them and running them.
+TEST_PAVICS_SDI_REPO="false"
+TEST_FINCH_REPO="false"
+TEST_PAVICS_LANDING_REPO="false"
+TEST_LOCAL_NOTEBOOKS="false"
+
+# Set new external repo vars.  Need 'export' so CONFIG_OVERRIDE_SCRIPT_URL can see them.
+export ROOK_REPO="roocs/rook"
+export ROOK_BRANCH="master"
+
+# Not checking for expected output, just checking whether the code can run without errors.
+PYTEST_EXTRA_OPTS="$PYTEST_EXTRA_OPTS --nbval-lax"
+
+# Create CONFIG_OVERRIDE_SCRIPT_URL file on-the-fly to run the notebooks from
+# our external repo.
+
+CONFIG_OVERRIDE_SCRIPT_URL="/tmp/custom-repos.include.sh"
+
+# Populate the content of our CONFIG_OVERRIDE_SCRIPT_URL.
+echo '
+#!/bin/sh
+# Sample config override script to run new notebooks from new external repo.
+
+# Replicate processing steps in 'testall' script.
+
+# Download the external repo.
+downloadgithubrepos $ROOK_REPO $ROOK_BRANCH
+
+# Prep vars for including new nbs in nb list to test.
+ROOK_REPO_NAME="$(extract_repo_name "$ROOK_REPO")"
+ROOK_DIR="$(sanitize_extracted_folder_name "${ROOK_REPO_NAME}-${ROOK_BRANCH}")"
+
+delete_files_confusing_pytest "$ROOK_DIR"
+
+# Set new nbs as nb list to test.
+NOTEBOOKS="$ROOK_DIR/notebooks/*.ipynb"
+' > "$CONFIG_OVERRIDE_SCRIPT_URL"

From 25c0abb438c43b6d8de313e98684dca5846b0231 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Tue, 14 May 2024 19:47:29 -0400
Subject: [PATCH 10/16] runtest: CONFIG_PARAMETERS_SCRIPT_URL can override
 DEFAULT_PRODUCTION_HOST

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

diff --git a/runtest b/runtest
index e8048502..a4ae259c 100755
--- a/runtest
+++ b/runtest
@@ -4,6 +4,7 @@
 DOWNLOADREPOS_AS_LIB=1
 . ./downloadrepos
 
+# CONFIG_PARAMETERS_SCRIPT_URL can override DEFAULT_PRODUCTION_HOST.
 DEFAULT_PRODUCTION_HOST="${DEFAULT_PRODUCTION_HOST:=pavics.ouranos.ca}"
 
 NOTEBOOKS="$1"

From 01824907bcef64218b071d9a6504334c05780d60 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Thu, 16 May 2024 16:22:05 -0400
Subject: [PATCH 11/16] runtest: add repo and branch name to archived nbs name
 to id which repo they came from and further avoid name clash

---
 runtest | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/runtest b/runtest
index a4ae259c..e7ab37a3 100755
--- a/runtest
+++ b/runtest
@@ -87,7 +87,8 @@ SAVE_RESULTING_NOTEBOOK="$(lowercase "$SAVE_RESULTING_NOTEBOOK")"
 
 mkdir -p buildout/
 for nb in $NOTEBOOKS; do
-    filename="$(basename "$nb")"
+    repo_branch_name="$(extract_repo_name "$nb")"
+    filename="${repo_branch_name}--$(basename "$nb")"
     filename="$(echo "$filename" | sed "s/.ipynb$//")"  # remove .ipynb ext
     if [ -e "buildout/${filename}.ipynb" ]; then
         # prevent name clash

From 36fba3d24d7755f84b2cc232928517f3e2a9f5c2 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Thu, 31 Oct 2024 11:33:05 -0400
Subject: [PATCH 12/16] testall: try to avoid delete_files_confusing_pytest by
 using py.test with --rootdir

---
 downloadrepos                                          | 10 ----------
 runtest                                                |  2 +-
 test-override/jenkins-params-external-repos.include.sh |  2 --
 testall                                                |  4 ----
 4 files changed, 1 insertion(+), 17 deletions(-)

diff --git a/downloadrepos b/downloadrepos
index a9d87658..f0d0249b 100755
--- a/downloadrepos
+++ b/downloadrepos
@@ -59,16 +59,6 @@ sanitize_extracted_folder_name() {
     echo "$1" | sed "s@[^a-zA-Z0-9_\-\.]@-@g"
 }
 
-# Presence of setup.cfg, tox.ini, pyproject.toml files confuse py.test execution rootdir discovery.
-# USAGE: delete_files_confusing_pytest "$CHECKOUT_DIR"
-delete_files_confusing_pytest() {
-    for afile in setup.cfg tox.ini pyproject.toml; do
-        if [ -f "$1/$afile" ]; then
-            rm -v "$1/$afile"
-        fi
-    done
-}
-
 downloadrepos_main() {
     . ./default_build_params
 
diff --git a/runtest b/runtest
index e7ab37a3..956c467e 100755
--- a/runtest
+++ b/runtest
@@ -69,7 +69,7 @@ if [ -n "$CONFIG_OVERRIDE_SCRIPT_URL" ]; then
 fi
 
 # CONFIG_OVERRIDE_SCRIPT_URL can override NBVAL_SANITIZE_CFG_FILE.
-py.test --nbval $NOTEBOOKS --nbval-sanitize-with "${NBVAL_SANITIZE_CFG_FILE:=notebooks/output-sanitize.cfg}" $PYTEST_EXTRA_OPTS
+py.test --rootdir=. --nbval $NOTEBOOKS --nbval-sanitize-with "${NBVAL_SANITIZE_CFG_FILE:=notebooks/output-sanitize.cfg}" $PYTEST_EXTRA_OPTS
 EXIT_CODE="$?"
 
 # lowercase SAVE_RESULTING_NOTEBOOK string
diff --git a/test-override/jenkins-params-external-repos.include.sh b/test-override/jenkins-params-external-repos.include.sh
index b62858a6..4b5da6bb 100644
--- a/test-override/jenkins-params-external-repos.include.sh
+++ b/test-override/jenkins-params-external-repos.include.sh
@@ -40,8 +40,6 @@ downloadgithubrepos $ROOK_REPO $ROOK_BRANCH
 ROOK_REPO_NAME="$(extract_repo_name "$ROOK_REPO")"
 ROOK_DIR="$(sanitize_extracted_folder_name "${ROOK_REPO_NAME}-${ROOK_BRANCH}")"
 
-delete_files_confusing_pytest "$ROOK_DIR"
-
 # Set new nbs as nb list to test.
 NOTEBOOKS="$ROOK_DIR/notebooks/*.ipynb"
 ' > "$CONFIG_OVERRIDE_SCRIPT_URL"
diff --git a/testall b/testall
index d6343135..9be7f395 100755
--- a/testall
+++ b/testall
@@ -88,7 +88,6 @@ if [ x"$TEST_PAVICS_SDI_REPO" = xtrue ]; then
     fi
 fi
 if [ x"$TEST_FINCH_REPO" = xtrue ]; then
-    delete_files_confusing_pytest "$FINCH_DIR"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${FINCH_DIR}/docs/source/notebooks/*.ipynb"
 fi
 
@@ -108,16 +107,13 @@ if [ x"$TEST_PAVICS_LANDING_REPO" = xtrue ]; then
 fi
 
 if [ x"$TEST_RAVEN_REPO" = xtrue ]; then
-    delete_files_confusing_pytest "$RAVEN_DIR"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${RAVEN_DIR}/docs/source/notebooks/*.ipynb"
 fi
 if [ x"$TEST_RAVENPY_REPO" = xtrue ]; then
-    delete_files_confusing_pytest "$RAVENPY_DIR"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${RAVENPY_DIR}/docs/notebooks/*.ipynb"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${RAVENPY_DIR}/docs/notebooks/paper/*.ipynb"
 fi
 if [ x"$TEST_ESGF_COMPUTE_API_REPO" = xtrue ]; then
-    delete_files_confusing_pytest "$ESGF_COMPUTE_API_DIR"
     NOTEBOOKS_TO_TEST="$NOTEBOOKS_TO_TEST ${ESGF_COMPUTE_API_DIR}/examples/*.ipynb"
 fi
 

From 5f13ec9fbabb63853eede75b4a54b4e97108e834 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Thu, 31 Oct 2024 12:14:28 -0400
Subject: [PATCH 13/16] runtest: allow saved files under buildout/ to have
 hierarchy

---
 runtest | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/runtest b/runtest
index 956c467e..32ce597e 100755
--- a/runtest
+++ b/runtest
@@ -85,18 +85,24 @@ SAVE_RESULTING_NOTEBOOK="$(lowercase "$SAVE_RESULTING_NOTEBOOK")"
 # work-around as nbval can not save the result of the run
 # see https://github.com/computationalmodelling/nbval/issues/112
 
-mkdir -p buildout/
+BUILDOUT_DIR="buildout"  # hardcode in Jenkinsfile, can not be override.
+
+mkdir -p "$BUILDOUT_DIR/"
 for nb in $NOTEBOOKS; do
     repo_branch_name="$(extract_repo_name "$nb")"
     filename="${repo_branch_name}--$(basename "$nb")"
     filename="$(echo "$filename" | sed "s/.ipynb$//")"  # remove .ipynb ext
-    if [ -e "buildout/${filename}.ipynb" ]; then
+    if [ -e "${BUILDOUT_DIR}/${filename}.ipynb" ]; then
         # prevent name clash
         filename="${filename}_$(date '+%s')"
     fi
 
     # Save original notebooks that we sed replace the PAVICS_HOST.
-    cp "$nb" "buildout/${filename}.ipynb"
+    dir_filename="$(dirname "${filename}")"
+    if [ -n "${dir_filename}" ]; then
+        mkdir -p "${BUILDOUT_DIR}/${dir_filename}"
+    fi
+    cp "$nb" "$BUILDOUT_DIR/${filename}.ipynb"
 
     if [ x"$SAVE_RESULTING_NOTEBOOK" = xtrue ]; then
         # Timeout must not be more than 240s (4 mins). Default in Jenkinsfile.
@@ -105,7 +111,7 @@ for nb in $NOTEBOOKS; do
         # notebook, should also check machine performance.
         jupyter nbconvert --to notebook --execute \
             --ExecutePreprocessor.timeout=${SAVE_RESULTING_NOTEBOOK_TIMEOUT:=240} --allow-errors \
-            --output-dir buildout --output "${filename}.output.ipynb" "$nb"
+            --output-dir "${BUILDOUT_DIR}" --output "${filename}.output.ipynb" "$nb"
     fi
 done
 

From c9c8d503c2a0c2cbac0f7dbcd056ffabb2200ee6 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Thu, 31 Oct 2024 12:49:18 -0400
Subject: [PATCH 14/16] tests: allow to override artifact nb filename format
 archived by Jenkins

---
 Jenkinsfile                                   |  2 +-
 downloadrepos                                 | 21 +++++++++++++++++++
 runtest                                       |  3 +--
 .../jenkins-params-external-repos.include.sh  |  5 +++++
 4 files changed, 28 insertions(+), 3 deletions(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index 7782d360..d608b5b9 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -144,7 +144,7 @@ Note this is another run, will double the time and no guaranty to have same erro
 
     post {
         always {
-            archiveArtifacts(artifacts: 'buildout/*.ipynb', fingerprint: true, allowEmptyArchive: true)
+            archiveArtifacts(artifacts: 'buildout/**/*.ipynb', fingerprint: true, allowEmptyArchive: true)
             archiveArtifacts(artifacts: 'buildout/env-dump/', fingerprint: true)
         }
 	unsuccessful {  // Run if the current builds status is "Aborted", "Failure" or "Unstable"
diff --git a/downloadrepos b/downloadrepos
index f0d0249b..738df87c 100755
--- a/downloadrepos
+++ b/downloadrepos
@@ -96,6 +96,27 @@ downloadrepos_main() {
     fi
 }
 
+
+# Choose artifact filename format under buildout/ dir that is archived by Jenkins.
+#
+# The corresponding .output.ipynb will also have the same filename format.
+#
+# Override this function in CONFIG_OVERRIDE_SCRIPT_URL to choose another
+# format, see demo in test-override/jenkins-params-external-repos.include.sh.
+#
+# Ex: when given 'pavics-sdi-master/docs/source/notebooks/regridding.ipynb',
+# the current implementation will return
+# 'pavics-sdi-master__docs__source__notebooks__regridding.ipynb', which means
+# there will be
+# "buildout/pavics-sdi-master__docs__source__notebooks__regridding.ipynb" and
+# "buildout/pavics-sdi-master__docs__source__notebooks__regridding.output.ipynb"
+#
+# USAGE: artifact_filename="$(choose_artifact_filename "$original_nb_filename")"
+choose_artifact_filename() {
+    echo "$1" | sed "s@/@__@g"
+}
+
+
 if [ -z "$DOWNLOADREPOS_AS_LIB" ]; then
     # Script mode, not library mode.
     downloadrepos_main "$@"
diff --git a/runtest b/runtest
index 32ce597e..8ce841fa 100755
--- a/runtest
+++ b/runtest
@@ -89,8 +89,7 @@ BUILDOUT_DIR="buildout"  # hardcode in Jenkinsfile, can not be override.
 
 mkdir -p "$BUILDOUT_DIR/"
 for nb in $NOTEBOOKS; do
-    repo_branch_name="$(extract_repo_name "$nb")"
-    filename="${repo_branch_name}--$(basename "$nb")"
+    filename="$(choose_artifact_filename "$nb")"
     filename="$(echo "$filename" | sed "s/.ipynb$//")"  # remove .ipynb ext
     if [ -e "${BUILDOUT_DIR}/${filename}.ipynb" ]; then
         # prevent name clash
diff --git a/test-override/jenkins-params-external-repos.include.sh b/test-override/jenkins-params-external-repos.include.sh
index 4b5da6bb..fd3f374f 100644
--- a/test-override/jenkins-params-external-repos.include.sh
+++ b/test-override/jenkins-params-external-repos.include.sh
@@ -42,4 +42,9 @@ ROOK_DIR="$(sanitize_extracted_folder_name "${ROOK_REPO_NAME}-${ROOK_BRANCH}")"
 
 # Set new nbs as nb list to test.
 NOTEBOOKS="$ROOK_DIR/notebooks/*.ipynb"
+
+# Sample demo override choose_artifact_filename: keep the original file path hierarchy.
+choose_artifact_filename() {
+    echo "$1"
+}
 ' > "$CONFIG_OVERRIDE_SCRIPT_URL"

From 7fce7382e950b8fa4a05137d8b990e5331383956 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Thu, 31 Oct 2024 13:14:17 -0400
Subject: [PATCH 15/16] runtest: allow overrideable post-processing steps

---
 downloadrepos                                         | 11 +++++++++++
 runtest                                               |  5 +++++
 .../jenkins-params-external-repos.include.sh          |  8 ++++++++
 3 files changed, 24 insertions(+)

diff --git a/downloadrepos b/downloadrepos
index 738df87c..2475e8b6 100755
--- a/downloadrepos
+++ b/downloadrepos
@@ -117,6 +117,17 @@ choose_artifact_filename() {
 }
 
 
+# Any post-processing steps at the end of runtest.
+#
+# Override this function in CONFIG_OVERRIDE_SCRIPT_URL to add extra steps,
+# see demo in test-override/jenkins-params-external-repos.include.sh.
+#
+post_runtest() {
+    # Can not have empty function, have to put something here.
+    echo "Default: no post_runtest() override."
+}
+
+
 if [ -z "$DOWNLOADREPOS_AS_LIB" ]; then
     # Script mode, not library mode.
     downloadrepos_main "$@"
diff --git a/runtest b/runtest
index 8ce841fa..dd34ce14 100755
--- a/runtest
+++ b/runtest
@@ -114,5 +114,10 @@ for nb in $NOTEBOOKS; do
     fi
 done
 
+
+# Post-processing steps override in CONFIG_OVERRIDE_SCRIPT_URL.
+post_runtest
+
+
 # exit with return code from py.test
 exit $EXIT_CODE
diff --git a/test-override/jenkins-params-external-repos.include.sh b/test-override/jenkins-params-external-repos.include.sh
index fd3f374f..0b60b54a 100644
--- a/test-override/jenkins-params-external-repos.include.sh
+++ b/test-override/jenkins-params-external-repos.include.sh
@@ -47,4 +47,12 @@ NOTEBOOKS="$ROOK_DIR/notebooks/*.ipynb"
 choose_artifact_filename() {
     echo "$1"
 }
+
+# Sample demo override post_runtest: create lots of artifacts for Jenkins to
+# archive to test how Jenkins will display its archive page.
+post_runtest() {
+    for i in $(seq --equal-width 500); do
+        echo "file${i}" > "${BUILDOUT_DIR}/file${i}.ipynb"
+    done
+}
 ' > "$CONFIG_OVERRIDE_SCRIPT_URL"

From d0265f36ee5d29e4cb19b1aea8c434531e74a344 Mon Sep 17 00:00:00 2001
From: Long Vu <vu.long@ouranos.ca>
Date: Thu, 31 Oct 2024 14:18:01 -0400
Subject: [PATCH 16/16] test artifacts: shorter filename format, name clash
 already handled

---
 downloadrepos | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/downloadrepos b/downloadrepos
index 2475e8b6..e42f5d0c 100755
--- a/downloadrepos
+++ b/downloadrepos
@@ -106,14 +106,15 @@ downloadrepos_main() {
 #
 # Ex: when given 'pavics-sdi-master/docs/source/notebooks/regridding.ipynb',
 # the current implementation will return
-# 'pavics-sdi-master__docs__source__notebooks__regridding.ipynb', which means
+# 'pavics-sdi-master--regridding.ipynb', which means
 # there will be
-# "buildout/pavics-sdi-master__docs__source__notebooks__regridding.ipynb" and
-# "buildout/pavics-sdi-master__docs__source__notebooks__regridding.output.ipynb"
+# "buildout/pavics-sdi-master--regridding.ipynb" and
+# "buildout/pavics-sdi-master--regridding.output.ipynb"
 #
 # USAGE: artifact_filename="$(choose_artifact_filename "$original_nb_filename")"
 choose_artifact_filename() {
-    echo "$1" | sed "s@/@__@g"
+    repo_branch="$(echo "$1" | sed "s@/.*@@")"
+    echo "${repo_branch}--$(basename "$1")"
 }