Add paper 05 syndrome workflow code

examples/paper_runs/paper_05/01_build_syndrome_circuits.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "01_build_syndrome_circuits")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/build_repetition_syndrome.py" \
+  --out-dir "${OUT_DIR}" \
+  --n-data "${LIDMAS_P5_N_DATA:-5}" \
+  --targets "${LIDMAS_P5_TARGETS:-all}"
+
+echo "paper_05 step 01 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/02_run_local_simulation.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "02_local_simulation")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/run_local_repetition_sampler.py" \
+  --out-dir "${OUT_DIR}" \
+  --n-data "${LIDMAS_P5_N_DATA:-5}" \
+  --targets "${LIDMAS_P5_TARGETS:-all}" \
+  --shots "${LIDMAS_P5_SHOTS:-256}" \
+  --measurement-error-rate "${LIDMAS_P5_LOCAL_MEAS_ERROR:-0.02}" \
+  --background-data-error-rate "${LIDMAS_P5_LOCAL_DATA_ERROR:-0.0}" \
+  --seed "${LIDMAS_P5_SEED:-20260705}"
+
+echo "paper_05 step 02 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/03_fetch_ibm_runtime_results.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "03_ibm_runtime")"
+SUBMISSION_JSON="${OUT_DIR}/ibm_runtime_submission.json"
+RESULT_JSON="${OUT_DIR}/ibm_repetition_results.json"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+if [ ! -f "${SUBMISSION_JSON}" ]; then
+  echo "Error: ${SUBMISSION_JSON} not found. Submit the IBM job first." >&2
+  exit 1
+fi
+
+fetch_args=()
+if [ "${LIDMAS_P5_IBM_STATUS_ONLY:-0}" = "1" ]; then
+  fetch_args+=(--status-only)
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/fetch_ibm_repetition_results.py" \
+  --submission-json "${SUBMISSION_JSON}" \
+  --out-json "${RESULT_JSON}" \
+  --result-timeout "${LIDMAS_P5_IBM_RESULT_TIMEOUT:-300}" \
+  ${fetch_args[@]+"${fetch_args[@]}"}
+
+if [ "${LIDMAS_P5_IBM_STATUS_ONLY:-0}" = "1" ]; then
+  echo "paper_05 IBM status check complete."
+else
+  echo "paper_05 IBM result fetch complete: ${RESULT_JSON}"
+fi

examples/paper_runs/paper_05/03_submit_ibm_runtime.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "03_ibm_runtime")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+backend_args=()
+if [ -n "${LIDMAS_P5_IBM_BACKEND:-}" ]; then
+  backend_args+=(--backend "${LIDMAS_P5_IBM_BACKEND}")
+fi
+if [ -n "${IBM_QUANTUM_INSTANCE:-}" ]; then
+  backend_args+=(--instance "${IBM_QUANTUM_INSTANCE}")
+fi
+if [ "${LIDMAS_P5_IBM_WAIT:-1}" = "0" ]; then
+  backend_args+=(--no-wait)
+fi
+if [ -n "${LIDMAS_P5_IBM_RESULT_TIMEOUT:-}" ]; then
+  backend_args+=(--result-timeout "${LIDMAS_P5_IBM_RESULT_TIMEOUT}")
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/submit_ibm_repetition_sampler.py" \
+  --out-dir "${OUT_DIR}" \
+  --n-data "${LIDMAS_P5_N_DATA:-5}" \
+  --targets "${LIDMAS_P5_TARGETS:-all}" \
+  --shots "${LIDMAS_P5_IBM_SHOTS:-${LIDMAS_P5_SHOTS:-256}}" \
+  --optimization-level "${LIDMAS_P5_OPTIMIZATION_LEVEL:-1}" \
+  ${backend_args[@]+"${backend_args[@]}"}
+
+echo "paper_05 step 03 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/04_ingest_results.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "04_ingest_results")"
+LOCAL_JSON="$(paper_results_dir "02_local_simulation")/local_repetition_results.json"
+IBM_JSON="$(paper_results_dir "03_ibm_runtime")/ibm_repetition_results.json"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+raw_args=()
+if [ -f "${LOCAL_JSON}" ]; then
+  raw_args+=(--raw-json "${LOCAL_JSON}")
+fi
+if [ -f "${IBM_JSON}" ]; then
+  raw_args+=(--raw-json "${IBM_JSON}")
+fi
+
+if [ "${#raw_args[@]}" -eq 0 ]; then
+  echo "Error: no raw paper_05 result JSON files found." >&2
+  exit 1
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/ingest_repetition_results.py" \
+  --out-dir "${OUT_DIR}" \
+  "${raw_args[@]}"
+
+echo "paper_05 step 04 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/05_decode_live_syndromes.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+IN_DIR="$(paper_results_dir "04_ingest_results")"
+OUT_DIR="$(paper_results_dir "05_decode_live_syndromes")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+if ! ls "${IN_DIR}"/decoder_requests_*.ndjson >/dev/null 2>&1; then
+  "${SCRIPT_DIR}/04_ingest_results.sh"
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/decode_repetition_syndromes.py" \
+  --in-dir "${IN_DIR}" \
+  --out-dir "${OUT_DIR}"
+
+echo "paper_05 step 05 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/06_analyze_and_plot.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+IN_DIR="$(paper_results_dir "05_decode_live_syndromes")"
+OUT_DIR="$(paper_results_dir "06_analysis")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+if [ ! -f "${IN_DIR}/decoded_shots.csv" ]; then
+  "${SCRIPT_DIR}/05_decode_live_syndromes.sh"
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/analyze_live_repetition.py" \
+  --decoded-csv "${IN_DIR}/decoded_shots.csv" \
+  --out-dir "${OUT_DIR}" \
+  --manuscript-dir "${OUT_DIR}/manuscript_figures"
+
+echo "paper_05 step 06 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/11_build_qldpc_syndrome_circuits.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "11_build_qldpc_syndrome_circuits")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/build_css_ldpc_syndrome.py" \
+  --out-dir "${OUT_DIR}" \
+  --targets "${LIDMAS_P5_QLDPC_TARGETS:-all}"
+
+echo "paper_05 qLDPC step 11 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/12_run_qldpc_local_simulation.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "12_qldpc_local_simulation")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/run_local_css_ldpc_sampler.py" \
+  --out-dir "${OUT_DIR}" \
+  --targets "${LIDMAS_P5_QLDPC_TARGETS:-all}" \
+  --shots "${LIDMAS_P5_QLDPC_SHOTS:-${LIDMAS_P5_SHOTS:-256}}" \
+  --measurement-error-rate "${LIDMAS_P5_QLDPC_LOCAL_MEAS_ERROR:-0.02}" \
+  --background-data-error-rate "${LIDMAS_P5_QLDPC_LOCAL_DATA_ERROR:-0.0}" \
+  --seed "${LIDMAS_P5_QLDPC_SEED:-20260705}"
+
+echo "paper_05 qLDPC step 12 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/13_fetch_qldpc_ibm_runtime_results.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "13_qldpc_ibm_runtime")"
+SUBMISSION_JSON="${OUT_DIR}/ibm_css_ldpc_submission.json"
+RESULT_JSON="${OUT_DIR}/ibm_css_ldpc_results.json"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+if [ ! -f "${SUBMISSION_JSON}" ]; then
+  echo "Error: ${SUBMISSION_JSON} not found. Submit the IBM qLDPC job first." >&2
+  exit 1
+fi
+
+fetch_args=()
+if [ "${LIDMAS_P5_QLDPC_IBM_STATUS_ONLY:-${LIDMAS_P5_IBM_STATUS_ONLY:-0}}" = "1" ]; then
+  fetch_args+=(--status-only)
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/fetch_ibm_css_ldpc_results.py" \
+  --submission-json "${SUBMISSION_JSON}" \
+  --out-json "${RESULT_JSON}" \
+  --result-timeout "${LIDMAS_P5_QLDPC_IBM_RESULT_TIMEOUT:-${LIDMAS_P5_IBM_RESULT_TIMEOUT:-300}}" \
+  ${fetch_args[@]+"${fetch_args[@]}"}
+
+if [ "${LIDMAS_P5_QLDPC_IBM_STATUS_ONLY:-${LIDMAS_P5_IBM_STATUS_ONLY:-0}}" = "1" ]; then
+  echo "paper_05 qLDPC IBM status check complete."
+else
+  echo "paper_05 qLDPC IBM result fetch complete: ${RESULT_JSON}"
+fi

examples/paper_runs/paper_05/13_submit_qldpc_ibm_runtime.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "13_qldpc_ibm_runtime")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+backend_args=()
+if [ -n "${LIDMAS_P5_QLDPC_IBM_BACKEND:-${LIDMAS_P5_IBM_BACKEND:-}}" ]; then
+  backend_args+=(--backend "${LIDMAS_P5_QLDPC_IBM_BACKEND:-${LIDMAS_P5_IBM_BACKEND:-}}")
+fi
+if [ -n "${IBM_QUANTUM_INSTANCE:-}" ]; then
+  backend_args+=(--instance "${IBM_QUANTUM_INSTANCE}")
+fi
+if [ "${LIDMAS_P5_QLDPC_IBM_WAIT:-${LIDMAS_P5_IBM_WAIT:-1}}" = "0" ]; then
+  backend_args+=(--no-wait)
+fi
+if [ -n "${LIDMAS_P5_QLDPC_IBM_RESULT_TIMEOUT:-${LIDMAS_P5_IBM_RESULT_TIMEOUT:-}}" ]; then
+  backend_args+=(--result-timeout "${LIDMAS_P5_QLDPC_IBM_RESULT_TIMEOUT:-${LIDMAS_P5_IBM_RESULT_TIMEOUT:-}}")
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/submit_ibm_css_ldpc_sampler.py" \
+  --out-dir "${OUT_DIR}" \
+  --targets "${LIDMAS_P5_QLDPC_TARGETS:-all}" \
+  --shots "${LIDMAS_P5_QLDPC_IBM_SHOTS:-${LIDMAS_P5_QLDPC_SHOTS:-${LIDMAS_P5_SHOTS:-256}}}" \
+  --optimization-level "${LIDMAS_P5_QLDPC_OPTIMIZATION_LEVEL:-${LIDMAS_P5_OPTIMIZATION_LEVEL:-1}}" \
+  ${backend_args[@]+"${backend_args[@]}"}
+
+echo "paper_05 qLDPC step 13 submit complete: ${OUT_DIR}"

examples/paper_runs/paper_05/14_ingest_qldpc_results.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+OUT_DIR="$(paper_results_dir "14_ingest_qldpc_results")"
+LOCAL_JSON="$(paper_results_dir "12_qldpc_local_simulation")/local_css_ldpc_results.json"
+IBM_JSON="$(paper_results_dir "13_qldpc_ibm_runtime")/ibm_css_ldpc_results.json"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+raw_args=()
+if [ -f "${LOCAL_JSON}" ]; then
+  raw_args+=(--raw-json "${LOCAL_JSON}")
+fi
+if [ -f "${IBM_JSON}" ]; then
+  raw_args+=(--raw-json "${IBM_JSON}")
+fi
+
+if [ "${#raw_args[@]}" -eq 0 ]; then
+  echo "Error: no raw paper_05 qLDPC result JSON files found." >&2
+  exit 1
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/ingest_css_ldpc_results.py" \
+  --out-dir "${OUT_DIR}" \
+  "${raw_args[@]}"
+
+echo "paper_05 qLDPC step 14 complete: ${OUT_DIR}"

examples/paper_runs/paper_05/15_decode_qldpc_syndromes.sh

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+#!/bin/bash
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+source "${SCRIPT_DIR}/common.sh"
+
+IN_DIR="$(paper_results_dir "14_ingest_qldpc_results")"
+OUT_DIR="$(paper_results_dir "15_decode_qldpc_syndromes")"
+PY_BIN="$(paper_python_bin)"
+paper_prepare_plot_env
+
+if [ -z "${PY_BIN}" ]; then
+  echo "Error: python3 not found." >&2
+  exit 1
+fi
+
+"${PY_BIN}" "${SCRIPT_DIR}/scripts/decode_css_ldpc_syndromes.py" \
+  --in-dir "${IN_DIR}" \
+  --out-dir "${OUT_DIR}"
+
+echo "paper_05 qLDPC step 15 complete: ${OUT_DIR}"