avoid markdown in CTT feature proxy job

scripts/slurm/train_ctt_feature_proxy.sbatch

@@ -0,0 +1,74 @@
+#!/bin/bash
+#SBATCH --job-name=ctt_feature_proxy
+#SBATCH --account=def-yalda
+#SBATCH --nodes=1
+#SBATCH --ntasks=1
+#SBATCH --cpus-per-task=4
+#SBATCH --mem=16G
+#SBATCH --time=04:00:00
+#SBATCH --array=0-2
+#SBATCH --output=outputs/hpc/logs/%x_%A_%a.out
+#SBATCH --error=outputs/hpc/logs/%x_%A_%a.err
+
+set -euo pipefail
+
+PROJECT_DIR="${PROJECT_DIR:-$SLURM_SUBMIT_DIR}"
+cd "$PROJECT_DIR"
+mkdir -p outputs/hpc/logs
+
+export OMP_NUM_THREADS=1
+export OPENBLAS_NUM_THREADS=1
+export MKL_NUM_THREADS=1
+export DOVLA_TORCH_THREADS=1
+export PYTHONDONTWRITEBYTECODE=1
+
+PYTHON="${PYTHON:-$PROJECT_DIR/.venv/bin/python}"
+SEED="${SEED:-${SLURM_ARRAY_TASK_ID:-0}}"
+VARIANT="${VARIANT:-residual}"
+FEATURE_MODE="${FEATURE_MODE:-base}"
+DATASET_INDEX="${DATASET_INDEX:-data/cil_charts/train/index.json}"
+TARGET_INDEX="${TARGET_INDEX:-data/cil_charts/val/index.json}"
+NAME_PREFIX="${NAME_PREFIX:-ctt_${VARIANT}_${FEATURE_MODE}}"
+TRAIN_OUT="runs/${NAME_PREFIX}_seed${SEED}"
+VAL_OUT="runs/${NAME_PREFIX}_seed${SEED}_val_proxy"
+
+"$PYTHON" scripts/train_ctt.py \
+  --dataset "$DATASET_INDEX" \
+  --out-dir "$TRAIN_OUT" \
+  --variant "$VARIANT" \
+  --epochs "${CTT_EPOCHS:-5}" \
+  --max-charts "${CTT_MAX_CHARTS:-100000}" \
+  --neighbors "${CTT_NEIGHBORS:-8}" \
+  --lr "${CTT_LR:-0.001}" \
+  --seed "$SEED" \
+  --chart-feature-mode "$FEATURE_MODE" \
+  --pos-alignment "${CTT_POS_ALIGNMENT:-1.0}" \
+  --negative-boundary "${CTT_NEGATIVE_BOUNDARY:-0.25}" \
+  --pairwise-rank "${CTT_PAIRWISE_RANK:-1.0}" \
+  --listwise-rank "${CTT_LISTWISE_RANK:-0.5}" \
+  --cycle "${CTT_CYCLE:-0.1}" \
+  --diversity "${CTT_DIVERSITY:-0.05}" \
+  --negative-margin "${CTT_NEGATIVE_MARGIN:-0.2}" \
+  --transport-samples-per-pair "${CTT_TRANSPORT_SAMPLES_PER_PAIR:-4}" \
+  --diversity-temperature "${CTT_DIVERSITY_TEMPERATURE:-1.0}"
+
+"$PYTHON" scripts/eval_ctt_proxy.py \
+  --checkpoint "$TRAIN_OUT/model.pt" \
+  --source-index "$DATASET_INDEX" \
+  --target-index "$TARGET_INDEX" \
+  --out-dir "$VAL_OUT" \
+  --k "${CTT_PROXY_K:-16}" \
+  --max-target-charts "${CTT_MAX_TARGET_CHARTS:-69}" \
+  --neighbors "${CTT_PROXY_NEIGHBORS:-8}" \
+  --thresholds "${CTT_PROXY_THRESHOLDS:-0.20,0.40}" \
+  --no-markdown-report
+
+"$PYTHON" scripts/build_ctt_proxy_comparison.py \
+  --out-dir runs/ctt_val_proxy_comparison \
+  --no-markdown-report
+
+"$PYTHON" scripts/summarize_ctt_runs.py \
+  --run-root runs \
+  --out-csv runs/summary_ctt.csv \
+  --out-md runs/summary_ctt.md \
+  --no-markdown-report