added: roundtrip test, test for output-tsv

Author: kamome1201

.github/workflows/csubst-ci.yml

@@ -80,3 +80,6 @@ jobs:
           MPLBACKEND: Agg
         run: bash ci/csubst_commands.sh
 
+      - name: Validate outputs (schema-lite)
+        shell: bash -l {0}
+        run: python ci/check_csubst_outputs.py

ci/check_csubst_outputs.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+import glob, sys, os
+
+def check_tsv(path):
+    with open(path, "r", encoding="utf-8", errors="ignore") as f:
+        lines = [l.rstrip("\n") for l in f]
+    assert len(lines) >= 2, f"{path}: 行数が少なすぎます"
+    header = lines[0].split("\t")
+    assert len(header) >= 2, f"{path}: タブ区切りのヘッダがありません"
+    # 代表的なメトリクス名の痕跡（将来名前が変わっても緩めに）
+    if os.path.basename(path).startswith("csubst_cb_stats"):
+        assert any(("omegaC" in h) or ("OCN" in h) or ("OCS" in h) for h in header), \
+            f"{path}: 代表メトリクス列が見当たりません"
+
+def main():
+    tsvs = sorted(glob.glob("csubst_*.tsv"))
+    if not tsvs:
+        print("WARN: csubst_*.tsv がありません（前段で生成できていればOKのはず）")
+        sys.exit(0)
+    for t in tsvs:
+        check_tsv(t)
+        print(f"OK: {t}")
+    # IQ-TREE中間の存在も最終確認
+    for req in ["alignment.fa.state", "alignment.fa.rate"]:
+        assert os.path.exists(req) and os.path.getsize(req) > 0, f"{req}: 見つからない/空です"
+    print("OK: IQ-TREE intermediates present")
+
+if __name__ == "__main__":
+    main()

ci/csubst_commands.sh

@@ -120,4 +120,36 @@ cp -v site.log "$ART" || true
 
 echo "OK: site finished (verified by logs and IQ-TREE intermediates)"
 
+# --- round-trip: simulate の出力を analyze へ ---
+MARKER=$(mktemp); sleep 1; touch "$MARKER"
+
+env PYTHONOPTIMIZE=1 csubst simulate \
+  --alignment_file alignment.fa \
+  --rooted_tree_file tree.nwk \
+  --foreground foreground.txt \
+  --threads 1
+
+SIM_ALN="$(find . -maxdepth 1 -type f \( -name "*.fa" -o -name "*.fasta" -o -name "*.phy" \) -newer "$MARKER" | head -n1)"
+[ -s "${SIM_ALN:-}" ] || { echo "ERROR: simulate 出力の配列ファイルが見つかりません"; exit 1; }
+
+MARKER2=$(mktemp); sleep 1; touch "$MARKER2"
+env PYTHONOPTIMIZE=1 OMP_NUM_THREADS=1 csubst analyze \
+  --alignment_file "$SIM_ALN" \
+  --rooted_tree_file tree.nwk \
+  --foreground foreground.txt \
+  --threads 1
+
+NEW_TSV2=($(find . -maxdepth 1 -type f -name "csubst_*.tsv" -newer "$MARKER2" -print))
+[ ${#NEW_TSV2[@]} -ge 1 ] || { echo "ERROR: simulate→analyze で TSV が生成されていません"; exit 1; }
+echo "OK: round-trip simulate→analyze(created): ${NEW_TSV2[*]}"
+
 echo "Command tests OK"
+
+{
+  echo "# csubst CI Summary"
+  echo
+  echo "## Generated files"
+  ls -lh | sed 's/^/- /'
+} > summary.md
+
+cp -v summary.md "$ART" || true