From 4fcb95318fc49c2686607b6e9752de4e72235b1b Mon Sep 17 00:00:00 2001
From: tligui_y <yasmine.tligui@psi.ch>
Date: Thu, 28 Aug 2025 12:11:04 +0200
Subject: [PATCH] Update action.yml

---
 action.yml | 44 +++++++++++++++++++++++++++++++-------------
 1 file changed, 31 insertions(+), 13 deletions(-)

diff --git a/action.yml b/action.yml
index 6c01987..c706fd4 100644
--- a/action.yml
+++ b/action.yml
@@ -198,7 +198,7 @@ runs:
             }
             ;;
           conda)
-            conda install -y pytest pytest-cov pytest-json-report coverage >> "$LOG_FILE" 2>&1 || {
+            conda run -n ci-env pip install pytest pytest-cov pytest-json-report coverage >> "$LOG_FILE" 2>&1 || {
               exit 1
             }
             ;;
@@ -311,8 +311,26 @@ runs:
 
         echo "" >> $LOG_FILE
         echo "📈 Generating coverage summary..." >> $LOG_FILE
-        pixi run coverage combine > /dev/null 2>> outputs/coverage-error.log || true
-        pixi run coverage report --format=markdown > markdown/coverage-summary.md 2>> outputs/coverage-error.log && {
+
+        # define runner commands depending on env
+        case "${{ inputs.env }}" in
+          pixi)
+            COV_RUN="pixi run coverage"
+            PY_RUN="pixi run python"
+            ;;
+          conda)
+            COV_RUN="conda run -n ci-env coverage"
+            PY_RUN="conda run -n ci-env python"
+            ;;
+          pip)
+            COV_RUN="coverage"
+            PY_RUN="python"
+            ;;
+        esac
+
+        # run coverage
+        $COV_RUN combine > /dev/null 2>> outputs/coverage-error.log || true
+        $COV_RUN report --format=markdown > markdown/coverage-summary.md 2>> outputs/coverage-error.log && {
           echo "✅ Coverage summary generated" >> $LOG_FILE
         } || {
           echo "❌ Coverage summary generation failed" >> $LOG_FILE
@@ -324,14 +342,14 @@ runs:
         echo "" >> $LOG_FILE
         echo "📊 Generating tests markdown summary..." >> $LOG_FILE
 
-        pixi run python temp-ci/json_to_md.py \
-        --input "markdown/pytest-report.json" \
-        --output "markdown/TEST-REPORT.md" \
-        --log_long "outputs/raw-test-output.log" \
-        --log_short "outputs/short-test-output.log" \
-        --params "markdown/runtime_params.json" \
-        >> "outputs/md-report.log" 2>&1 && {
-          echo "✅ Tests markdown generated" >> $LOG_FILE
+        $PY_RUN temp-ci/json_to_md.py \
+          --input "markdown/pytest-report.json" \
+          --output "markdown/TEST-REPORT.md" \
+          --log_long "outputs/raw-test-output.log" \
+          --log_short "outputs/short-test-output.log" \
+          --params "markdown/runtime_params.json" \
+          >> "outputs/md-report.log" 2>&1 && {
+            echo "✅ Tests markdown generated" >> $LOG_FILE
         } || {
             echo "❌ Tests markdown generation failed" >> $LOG_FILE
             echo "🪵 Extracting markdown generation error:" >> $LOG_FILE
@@ -341,8 +359,8 @@ runs:
 
         echo "" >> $LOG_FILE
         echo "🌳 Generating JSON tree view..." >> $LOG_FILE
-        pixi run python temp-ci/json_to_tree.py \
-          "markdown/pytest-report.json" \
+
+        $PY_RUN temp-ci/json_to_tree.py "markdown/pytest-report.json" \
           >> "outputs/json-tree-gen.log" 2>&1 && {
           echo "✅ JSON tree view generated" >> $LOG_FILE
         } || {