kamome1201
diff --git a/‎.github/workflows/csubst-ci.yml‎
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diff --git a/‎ci/check_csubst_outputs.py‎
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diff --git a/‎ci/csubst_cli.sh‎
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+name: csubst ci
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+  workflow_dispatch:
+
+concurrency:
+  group: csubst-ci-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  smoke:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python: ['3.9', '3.10', '3.11', '3.12']
+        install: [source]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: csubst-smoke
+          create-args: >-
+            python=${{ matrix.python }}
+            iqtree numpy scipy cython biopython requests pip
+          condarc: |
+            channels:
+              - conda-forge
+              - bioconda
+              - defaults
+            channel_priority: strict
+          cache-environment: true
+          cache-downloads: true
+
+      # post の ENOENT 回避
+      - name: Workaround micromamba post-step quirks
+        if: always()
+        run: |
+          mkdir -p "$RUNNER_TEMP/setup-micromamba"
+          : > "$RUNNER_TEMP/setup-micromamba/micromamba-shell"
+          touch "$HOME/.bash_profile"
+          grep -q 'micromamba activate csubst-smoke' "$HOME/.bash_profile" \
+            || echo 'micromamba activate csubst-smoke' >> "$HOME/.bash_profile"
+
+      # pyvolve を pip から
+      - name: Install pyvolve (pip)
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          pip install --no-input pyvolve==1.1.0
+
+      - name: Install runtime deps
+        shell: bash -l {0}
+        run: |
+          micromamba install -y \
+            numpy=1.26.* cython=0.29.* iqtree \
+            conda-forge::biopython conda-forge::requests
+
+      - name: Install csubst (from source)
+        if: matrix.install == 'source'
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          pip install --no-build-isolation .
+
+      # --- Smoke ---
+      - name: Run smoke test
+        shell: bash -l {0}
+        run: bash ci/csubst_smoke.sh
+
+      # --- CLI tests ---
+      - name: Run CLI tests
+        shell: bash -l {0}
+        run: bash ci/csubst_cli.sh
+
+      - name: Upload artifacts (always)
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: smoke-and-cli-${{ matrix.os }}-${{ matrix.install }}
+          path: |
+            $RUNNER_TEMP/csubst_smoke/_artifacts*
+          if-no-files-found: ignore
+          retention-days: 7
+
+      # PyMOL の有無を検出（heredoc の閉じは行頭に PY）
+      - name: Check PyMOL
+        id: pymol
+        shell: bash -l {0}
+        run: |
+          HAVE=$(python - <<'PY'
+try:
+    import pymol  # noqa: F401
+    print("true")
+except Exception:
+    print("false")
+PY
+          )
+          echo "have=$HAVE" >> "$GITHUB_OUTPUT"
+
+      - name: Run command tests
+        shell: bash -l {0}
+        env:
+          MPLBACKEND: Agg
+          HAVE_PYMOL: ${{ steps.pymol.outputs.have }}
+        run: bash ci/csubst_commands.sh
+
+      - name: Validate outputs (schema-lite)
+        shell: bash -l {0}
+        run: python ci/check_csubst_outputs.py
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+#!/usr/bin/env python3
+import glob, sys, os
+
+def check_tsv(path):
+    with open(path, "r", encoding="utf-8", errors="ignore") as f:
+        lines = [l.rstrip("\n") for l in f]
+    assert len(lines) >= 2, f"{path}: 行数が少なすぎます"
+    header = lines[0].split("\t")
+    assert len(header) >= 2, f"{path}: タブ区切りのヘッダがありません"
+    # 代表的なメトリクス名の痕跡（将来名前が変わっても緩めに）
+    if os.path.basename(path).startswith("csubst_cb_stats"):
+        assert any(("omegaC" in h) or ("OCN" in h) or ("OCS" in h) for h in header), \
+            f"{path}: 代表メトリクス列が見当たりません"
+
+def main():
+    tsvs = sorted(glob.glob("csubst_*.tsv"))
+    if not tsvs:
+        print("WARN: csubst_*.tsv がありません（前段で生成できていればOKのはず）")
+        sys.exit(0)
+    for t in tsvs:
+        check_tsv(t)
+        print(f"OK: {t}")
+    # IQ-TREE中間の存在も最終確認
+    for req in ["alignment.fa.state", "alignment.fa.rate"]:
+        assert os.path.exists(req) and os.path.getsize(req) > 0, f"{req}: 見つからない/空です"
+    print("OK: IQ-TREE intermediates present")
+
+if __name__ == "__main__":
+    main()
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+#!/usr/bin/env bash
+set -euo pipefail
+
+echo "== csubst CLI tests =="
+
+which csubst
+csubst --version || true
+
+# --- ヘルプ（主要サブコマンド/引数の存在） ---
+csubst -h | head -n 20
+csubst -h | grep -E '\banalyze\b' >/dev/null
+csubst -h | grep -E '\bdataset\b' >/dev/null
+csubst analyze -h | grep -- '--alignment_file' >/dev/null
+csubst analyze -h | grep -- '--rooted_tree_file' >/dev/null
+csubst analyze -h | grep -- '--foreground' >/dev/null
+
+# 作業ディレクトリ（smoke と共用）
+WORKDIR="${RUNNER_TEMP:-$(mktemp -d)}/csubst_smoke"
+mkdir -p "$WORKDIR"
+cd "$WORKDIR"
+
+# 最小データが無ければ生成
+if [ ! -s alignment.fa ]; then
+  csubst dataset --name PGK
+fi
+test -s alignment.fa && test -s tree.nwk && test -s foreground.txt
+
+# --- 異常系：欠損入力で失敗すること ---
+set +e
+csubst analyze --alignment_file __NO_FILE__.fa \
+  --rooted_tree_file tree.nwk --foreground foreground.txt --threads 1 >/dev/null 2>&1
+rc=$?
+set -e
+[ $rc -ne 0 ] || { echo "ERROR: 欠損入力で成功してしまった"; exit 1; }
+echo "OK: 異常系で非0終了を確認"
+
+# --- 正常系(ECM系：デフォルト) ---
+rm -f alignment.fa.{iqtree,log,rate,state,treefile} || true
+env PYTHONOPTIMIZE=1 OMP_NUM_THREADS=1 csubst analyze \
+  --alignment_file alignment.fa \
+  --rooted_tree_file tree.nwk \
+  --foreground foreground.txt \
+  --threads 1
+
+shopt -s nullglob
+CB1=(csubst_cb_*.tsv)
+[ ${#CB1[@]} -ge 1 ] || { echo "ERROR: ECM 実行後に cb TSV が無い"; exit 1; }
+[ $(wc -l < "${CB1[0]}") -ge 2 ] || { echo "ERROR: cb TSV が空"; exit 1; }
+grep $'\t' "${CB1[0]}" >/dev/null || { echo "ERROR: TSV がタブ区切りでない可能性"; exit 1; }
+
+# --- 正常系(GY系：別分岐) ---
+rm -f alignment.fa.{iqtree,log,rate,state,treefile} || true
+env PYTHONOPTIMIZE=1 OMP_NUM_THREADS=1 csubst analyze \
+  --alignment_file alignment.fa \
+  --rooted_tree_file tree.nwk \
+  --foreground foreground.txt \
+  --iqtree_model GY+F3x4+R2 \
+  --threads 1
+CB2=(csubst_cb_*.tsv)
+[ ${#CB2[@]} -ge 1 ] || { echo "ERROR: GY 実行後に cb TSV が無い"; exit 1; }
+
+# アーティファクト収集（任意）
+ART="$WORKDIR/_artifacts_cli"
+mkdir -p "$ART"
+cp -v csubst_cb_*.tsv "$ART" 2>/dev/null || true
+cp -v alignment.fa.{iqtree,log,rate,state,treefile} "$ART" 2>/dev/null || true
+
+echo "CLI tests OK"