From db8e1fabdcb04da8ef6e39c4f1100346a36cd99f Mon Sep 17 00:00:00 2001
From: David Landa Marban <dmar@norceresearch.no>
Date: Fri, 14 Aug 2026 13:41:09 +0200
Subject: [PATCH] Bash scripts to check for papers outputs

---
 tests/scripts/docs_all.sh                     |  2 +-
 ...check_figures.sh => docs_check_outputs.sh} |  6 +--
 tests/scripts/paper_2025.sh                   | 46 ++++++++++++++++++
 tests/scripts/paper_ecmor2026.sh              | 47 ++++++++++++++++++-
 4 files changed, 95 insertions(+), 6 deletions(-)
 rename tests/scripts/{docs_check_figures.sh => docs_check_outputs.sh} (85%)

diff --git a/tests/scripts/docs_all.sh b/tests/scripts/docs_all.sh
index 095771f..2b40768 100644
--- a/tests/scripts/docs_all.sh
+++ b/tests/scripts/docs_all.sh
@@ -3,4 +3,4 @@
 . tests/scripts/docs_non-regular_boundaries.sh &
 wait
 
-. ./tests/scripts/docs_check_figures.sh
+. ./tests/scripts/docs_check_outputs.sh
diff --git a/tests/scripts/docs_check_figures.sh b/tests/scripts/docs_check_outputs.sh
similarity index 85%
rename from tests/scripts/docs_check_figures.sh
rename to tests/scripts/docs_check_outputs.sh
index ad8c747..f0fb3ab 100644
--- a/tests/scripts/docs_check_figures.sh
+++ b/tests/scripts/docs_check_outputs.sh
@@ -10,7 +10,7 @@ files=(
   "test_outputs/regular_boundaries/regional_rpr-3.png"
 )
 
-missing_file="test_outputs/missing_figures.txt"
+missing_file="test_outputs/missing_docs_files.txt"
 missing=0
 
 rm -f "$missing_file"
@@ -23,8 +23,8 @@ for f in "${files[@]}"; do
 done
 
 if (( missing == 0 )); then
-    echo "All figures exist."
+    echo "All figures and files exist."
 else
-    echo "$missing figure(s) missing."
+    echo "$missing figure(s) or file(s) missing."
     echo "See $missing_file"
 fi
diff --git a/tests/scripts/paper_2025.sh b/tests/scripts/paper_2025.sh
index b7b7ba1..163f2aa 100644
--- a/tests/scripts/paper_2025.sh
+++ b/tests/scripts/paper_2025.sh
@@ -6,3 +6,49 @@ python3 $OUT/Case2/run_case2.py &
 python3 $OUT/Case3/run_case3.py &
 python3 $OUT/Case4/run_case4.py &
 wait
+
+files=(
+    "$OUT/Case4/Case_4_site_pres_pressure.png"
+    "$OUT/Case4/Case_4_reference_saturation.png"
+    "$OUT/Case4/Case_4_difference_site_pres_pressure.png"
+    "$OUT/Case4/Case_4_reference_pressure.png"
+    "$OUT/Case4/Case_4_difference_site_pres_saturation.png"
+    "$OUT/Case4/Case_4_regional_pressure.png"
+    "$OUT/Case4/Case_4_site_pres_saturation.png"
+    "$OUT/Case4/Case_4_regional_saturation.png"
+    "$OUT/Case2/comparegrid_0_40m_sensor_pressure_over_time.png"
+    "$OUT/Case2/comparegrid_0_40m_sensor_gasfluxi+_over_time.png"
+    "$OUT/Case3/compareeveryday_sensor_pressure_over_time.png"
+    "$OUT/Case1/Case_1_maximum_pressure_difference_over_time.png"
+    "$OUT/Case1/Case_1_difference_site_flux_pressure.png"
+    "$OUT/Case1/Case_1_difference_site_flux_gasfluxi+.png"
+    "$OUT/Case1/Case_1_maximum_gasfluxi+_difference_over_time.png"
+    "$OUT/Case1/Case_1_reference_saturation.png"
+    "$OUT/Case1/Case_1_reference_pressure.png"
+    "$OUT/Case1/Case_1_reference_watfluxi+.png"
+    "$OUT/Case1/Case_1_distance_from_border.png"
+    "$OUT/Case1/Case_1_difference_site_flux_saturation.png"
+    "$OUT/Case1/Case_1_difference_site_pres_saturation.png"
+    "$OUT/Case1/Case_1_summary_PR_site_reference.png"
+    "$OUT/Case1/Case_1_difference_site_pres_gasfluxi+.png"
+    "$OUT/Case1/Case_1_difference_site_pres_pressure.png"
+)
+
+missing_file="test_outputs/missing_paper_2025_files.txt"
+missing=0
+
+rm -f "$missing_file"
+
+for f in "${files[@]}"; do
+    if [[ ! -f "$f" ]]; then
+        echo "$f" >> "$missing_file"
+        ((missing++))
+    fi
+done
+
+if (( missing == 0 )); then
+    echo "All figures and files exist."
+else
+    echo "$missing figure(s) or file(s) missing."
+    echo "See $missing_file"
+fi
diff --git a/tests/scripts/paper_ecmor2026.sh b/tests/scripts/paper_ecmor2026.sh
index 3d1cf76..0597fff 100644
--- a/tests/scripts/paper_ecmor2026.sh
+++ b/tests/scripts/paper_ecmor2026.sh
@@ -6,9 +6,52 @@ OUT="test_outputs/paper_ecmor2026"
 cp -r publications/ecmor2026/. $OUT
 cd $OUT/method
 . figure1.sh
-cd $OUT/results_2d_synthetic_model
+cd ../results_2d_synthetic_model
 . figure2.sh
 python3 figure3_table1.py
-cd $OUT/results_3d_synthetic_model
+cd ../results_3d_synthetic_model
 python3 figure4_table2.py
 cd $HOME
+
+files=(
+    "$OUT/method/figure1d_bottom.png"
+    "$OUT/method/figure1b.png"
+    "$OUT/method/figure1d_top.png"
+    "$OUT/method/figure1c_bottom.png"
+    "$OUT/method/figure1a.png"
+    "$OUT/method/figure1c_top.png"
+    "$OUT/results_2d_synthetic_model/figure2.png"
+    "$OUT/results_2d_synthetic_model/figureb_dual_vertical_tf_absolute_error_extremes_8.png"
+    "$OUT/results_2d_synthetic_model/figurea_dual_no_vertical_tf_absolute_error_extremes_8.png"
+    "$OUT/results_2d_synthetic_model/table1_error_summary.csv"
+    "$OUT/results_2d_synthetic_model/figurea_standard_absolute_error_extremes_8.png"
+    "$OUT/results_2d_synthetic_model/standard_absolute_errors.csv"
+    "$OUT/results_2d_synthetic_model/dual_no_vertical_tf_absolute_errors.csv"
+    "$OUT/results_2d_synthetic_model/dual_vertical_tf_absolute_errors.csv"
+    "$OUT/results_3d_synthetic_model/figure4a_shortest.pvd"
+    "$OUT/results_3d_synthetic_model/figure4b_intermediate-0011.vtu"
+    "$OUT/results_3d_synthetic_model/table2.csv"
+    "$OUT/results_3d_synthetic_model/figure4b_intermediate.pvd"
+    "$OUT/results_3d_synthetic_model/figure4c_longest.pvd"
+    "$OUT/results_3d_synthetic_model/figure4a_shortest-0011.vtu"
+    "$OUT/results_3d_synthetic_model/figure4c_longest-0011.vtu"
+)
+
+missing_file="test_outputs/missing_paper_ecmor2026_files.txt"
+missing=0
+
+rm -f "$missing_file"
+
+for f in "${files[@]}"; do
+    if [[ ! -f "$f" ]]; then
+        echo "$f" >> "$missing_file"
+        ((missing++))
+    fi
+done
+
+if (( missing == 0 )); then
+    echo "All figures and files exist."
+else
+    echo "$missing figure(s) or file(s) missing."
+    echo "See $missing_file"
+fi