D-sudoasd · Sep 26, 2026 · Sep 26, 2026 · Sep 26, 2026 · Sep 26, 2026 · Sep 26, 2026
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,11 @@
+# Keep hashed scientific fixtures, evidence, and manuscript sources identical
+# when a Windows checkout has core.autocrlf enabled.
+validation_cases/**/*.md text eol=lf
+validation_cases/**/*.json text eol=lf
+validation_cases/**/*.csv text eol=lf
+validation_cases/**/*.cif text eol=lf
+src/diffractscout/benchmark_data/*.cif text eol=lf
+src/diffractscout/benchmark_data/*.json text eol=lf
+scripts/compare_reference_engines.py text eol=lf
+paper/*.md text eol=lf
+paper/*.bib text eol=lf
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -87,6 +87,15 @@ jobs:
         run: |
           python -c "import mp_api, pymatgen; from diffractscout.providers.materials_project import _matrix; assert _matrix([[1 if i == j else 0 for j in range(6)] for i in range(6)]) is not None"
           pytest -q tests/test_provider_helpers.py
+      - name: Compare independent diffraction and elasticity implementations
+        run: python scripts/compare_reference_engines.py --output ci_reference_engines
+      - name: Upload independent numerical comparison
+        if: always()
+        uses: actions/upload-artifact@v7
+        with:
+          name: reference-engines-python-${{ matrix.python-version }}
+          path: ci_reference_engines
+          if-no-files-found: warn
 
   cross-platform-smoke:
     name: Smoke / ${{ matrix.os }}
@@ -174,11 +183,15 @@ jobs:
           wheel-test/bin/diffractscout --version
           wheel-test/bin/diffractscout demo -o wheel_demo
           wheel-test/bin/diffractscout verify wheel_demo
+          wheel-test/bin/diffractscout inspect wheel_demo --json
           wheel-test/bin/diffractscout benchmark -o wheel_benchmark
           wheel_cif=$(wheel-test/bin/python -c "import pathlib,diffractscout; print(pathlib.Path(diffractscout.__file__).with_name('benchmark_data')/'fcc_al.cif')")
           test -f "$wheel_cif"
-          wheel-test/bin/diffractscout-quick-export "$wheel_cif" -o wheel_quick.xlsx
+          wheel-test/bin/diffractscout preset save -o wheel_preset.json --no-patterns
+          wheel-test/bin/diffractscout preset show wheel_preset.json --json
+          wheel-test/bin/diffractscout-quick-export "$wheel_cif" -o wheel_quick.xlsx --preset wheel_preset.json
           wheel-test/bin/diffractscout verify wheel_quick_bundle
+          wheel-test/bin/diffractscout inspect wheel_quick_bundle --json
           test -x wheel-test/bin/diffractscout-gui
       - name: Upload distributions
         uses: actions/upload-artifact@v7

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,22 @@ All notable changes are recorded here. The project follows semantic versioning a
 
 ### Added
 
+- Reusable CLI/desktop analysis presets and read-only inspection of verified
+  result bundles, with explicit command-line override semantics. Presets exclude
+  credentials, paths, overwrite authorization, and manual tensor overrides.
+- Reproducible comparisons with pymatgen for synthetic diffraction peak
+  positions and cubic directional moduli, with numerical reports retained by CI.
+- Revised JOSS manuscript, software-comparison references, and evidence-based
+  submission documentation.
+- Separate evidence-file input for JOSS readiness checks, so final verification
+  records can reference a committed source without changing its Git identity.
+- Excel result overview and worksheet navigation, semantic header colors,
+  consistent scientific number formats, frozen phase columns, expandable
+  detail columns, and phase-relative intensity bars without changing canonical
+  data-sheet headers or stored scientific values.
+- Separate Excel preview, permanent workbook-copy, and result-folder actions,
+  with phase/reflection/diagnostic counts in completion feedback.
+
 - Windows launchers: `启动DiffractScout.bat` (GUI) and `quick_export_diffractscout.bat` (drag-and-drop quick-export with Excel next to the first input).
 - Packaging stub `scripts/package_windows_portable.py` documenting a future PyInstaller portable layout (`--help` / `--print-recipe`; no freeze yet).
 - Optional dependencies `figures` (matplotlib) and `gui-dnd` (tkinterdnd2); `paper` remains as a matplotlib alias.
@@ -22,6 +38,15 @@ All notable changes are recorded here. The project follows semantic versioning a
 
 ### Fixed
 
+- Preserved saved changes in temporary Excel previews when closing the GUI.
+- Rejected `.xlsx` quick-export targets combined with disabled Excel output
+  before writing, and reported the retained bundle workbook if publishing its
+  separate Excel copy fails.
+- Prevented concurrent preset saves from replacing a newly created target
+  without explicit overwrite authorization.
+- Reported CLI error diagnostics with their actual severity and exposed the
+  generated result files in completion summaries.
+
 - Windows `quick_export_diffractscout.bat` now uses `scripts/diffractscout_entry.py`
   and the same checkout interpreter order as the GUI launcher (repository
   `.venv`, then `python`, then `py -3`), so drag-and-drop works after the README

diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@
 
 **DiffractScout turns a chemical-system question or a folder of CIF files into a verifiable theoretical powder-diffraction reference bundle.** It preserves database identity, exact CIF hashes, structural diagnostics, radiation settings, optional elastic-tensor provenance, indexed reflections, warnings, and file checksums in one workflow.
 
-[中文说明](README.zh-CN.md) · [API](docs/API.md) · [GUI guide](docs/GUI.md) · [Scientific contracts](docs/SCIENTIFIC_CONTRACTS.md) · [Validation](docs/VALIDATION.md) · [Release procedure](docs/RELEASE.md) · [JOSS readiness](docs/JOSS_READINESS.md)
+[中文说明](README.zh-CN.md) · [CLI guide](docs/CLI.md) · [API](docs/API.md) · [GUI guide](docs/GUI.md) · [Scientific contracts](docs/SCIENTIFIC_CONTRACTS.md) · [Validation](docs/VALIDATION.md) · [Release procedure](docs/RELEASE.md) · [JOSS readiness](docs/JOSS_READINESS.md)
 
 ## Why this software exists
 
@@ -61,6 +61,24 @@ DiffractScout reimplements the CIF2Peaks desktop workflow inside a provenance-fi
 
 Column-name mapping and intensity-channel aliases: [docs/SCHEMA_ALIASES.md](docs/SCHEMA_ALIASES.md). Engine semantics vs CIF2Peaks/pymatgen: [docs/ENGINE_PARITY.md](docs/ENGINE_PARITY.md).
 
+Excel results include an overview with worksheet navigation, grouped table
+headers, consistent scientific number formats, frozen phase columns, and
+phase-relative intensity bars. The GUI can save/load analysis presets and
+offers separate Excel preview, permanent-copy, and result-folder actions.
+See [Working with Excel results](docs/EXCEL.md).
+
+The CLI can save and reuse the same parameter presets and inspect a completed
+bundle after verifying its integrity:
+
+```bash
+diffractscout preset save -o presets/energy-30.json --energy-keV 30
+diffractscout analyze path/to/cifs -o outputs/run --preset presets/energy-30.json
+diffractscout inspect outputs/run --json
+```
+
+Explicit command-line options override preset values. See the [CLI guide](docs/CLI.md)
+for batch exit statuses, radiation overrides, and parameter-file handling.
+
 When a *d*-spacing filter is used, the inclusive Bragg intersection is stored
 separately from the requested angular window. `provenance.json` and phase
 metadata distinguish `requested_two_theta_range_deg`,
@@ -197,6 +215,10 @@ PASS
 
 Set `SOURCE_DATE_EPOCH` when an archive requires reproducible generated timestamps. See [docs/ANALYTIC_BENCHMARKS.md](docs/ANALYTIC_BENCHMARKS.md).
 
+An optional [independent-engine comparison](validation_cases/independent_engines/README.md)
+checks the same synthetic CIFs and cubic directional moduli against pymatgen.
+CI preserves the numerical reports and dependency versions.
+
 ## Analyze local CIF files
 
 ```bash
@@ -343,7 +365,19 @@ Those repositories remain independent and unchanged by this project. Source snap
 
 ## JOSS preparation status
 
-The repository contains an OSI-approved license, installable package metadata, tests, analytic benchmarks, CI, user and API documentation, governance, examples, contribution and support routes, tag-driven deterministic release packaging, a monthly reproducibility audit, dependency-update automation, a JOSS-format manuscript, and a specific AI usage disclosure. The public-development clock began on 12 August 2026. Formal submission remains blocked by the six-month/distributed-history gate, a completed real multiphase research case, independent diffraction and elasticity validation, external engagement, and human-confirmed metadata. The immutable software archive DOI is required after successful JOSS review for the publication stage, not for the initial submission. First run `python scripts/check_release.py` to create the current-source release receipt, then use `python scripts/joss_readiness.py --stage release|submission|publication`; see [docs/JOSS_READINESS.md](docs/JOSS_READINESS.md) and [docs/JOSS_REVIEW_CHECKLIST.md](docs/JOSS_REVIEW_CHECKLIST.md).
+The repository includes an MIT license, installable package, tests, analytic and
+independent numerical comparisons, CI, documentation, contribution and support
+routes, reproducible release packaging, and a JOSS-format manuscript with AI
+disclosure. The author reports use in published research; representative
+citations and the associated software uses will be added to the submission
+record. Public development began on 12 August 2026, so the JOSS requirement for
+more than six months of active public history remains outstanding. The project
+also tracks its own scientific-validation and engagement criteria separately
+from official JOSS requirements. Run `python scripts/check_release.py` for the
+current-source software acceptance checks; see [JOSS readiness](docs/JOSS_READINESS.md)
+and the [review checklist](docs/JOSS_REVIEW_CHECKLIST.md) for the remaining
+submission evidence and author confirmations. The final archive DOI is a
+post-review publication step.
 
 ## Contributing, support, and citation
 

diff --git a/README.zh-CN.md b/README.zh-CN.md
@@ -8,7 +8,7 @@
 
 **DiffractScout 将合金/化学体系候选相检索、本地 CIF 检查、理论粉末衍射计算、可选晶面法向弹性分析和可验证结果导出连接为一个流程。** 每项结果均可追溯到数据库记录或本地文件、CIF 哈希、辐射条件、计算定义、软件版本和结构化诊断。
 
-[英文主页](README.md) · [API](docs/API.md) · [GUI 使用说明](docs/GUI.md) · [科研计算约定](docs/SCIENTIFIC_CONTRACTS.md) · [验证策略](docs/VALIDATION.md) · [发布流程](docs/RELEASE.md) · [JOSS 准备状态](docs/JOSS_READINESS.md)
+[英文主页](README.md) · [CLI 使用说明](docs/CLI.md) · [API](docs/API.md) · [GUI 使用说明](docs/GUI.md) · [科研计算约定](docs/SCIENTIFIC_CONTRACTS.md) · [验证策略](docs/VALIDATION.md) · [发布流程](docs/RELEASE.md) · [JOSS 准备状态](docs/JOSS_READINESS.md)
 
 ## 两类工作流
 
@@ -52,6 +52,18 @@ DiffractScout 在可追溯结果包中重实现了 CIF2Peaks 的主要桌面工
 
 列名与强度通道别名见 [docs/SCHEMA_ALIASES.md](docs/SCHEMA_ALIASES.md)；与 CIF2Peaks/pymatgen 引擎差异见 [docs/ENGINE_PARITY.md](docs/ENGINE_PARITY.md)。
 
+Excel 提供结果概览和工作表导航，按列的含义区分表头颜色，统一科学数值显示格式，冻结物相标识列，并用数据条辅助查看相内相对强度。界面支持保存、加载常用分析参数，以及独立的 Excel 预览、永久副本另存和结果文件夹入口。完整用法见 [Excel 结果使用说明](docs/EXCEL.md)。
+
+CLI 同样可以保存、复用参数，并校验和查看已有结果包：
+
+```powershell
+diffractscout preset save -o presets/energy-30.json --energy-keV 30
+diffractscout analyze path/to/cifs -o outputs/run --preset presets/energy-30.json
+diffractscout inspect outputs/run --json
+```
+
+命令行显式参数优先于预设。批处理退出码、辐射条件覆盖和参数文件用法见 [CLI 使用说明](docs/CLI.md)。
+
 启用 *d* 间距过滤时，程序会单独记录包含端点的 Bragg 求交结果。
 `provenance.json` 和物相元数据区分用户请求的
 `requested_two_theta_range_deg`、过滤后的
@@ -170,6 +182,8 @@ diffractscout benchmark -o outputs/analytic_benchmark
 
 该命令对简单立方、BCC、FCC、NaCl 和立方晶体方向弹性执行 45 项闭式解检查，并输出固定输入、预期值、容差、软件版本、运行环境、报告和 SHA-256 清单。成功结果为 `45/45 passed`。详见 [docs/ANALYTIC_BENCHMARKS.md](docs/ANALYTIC_BENCHMARKS.md)。
 
+另有可复现的 [pymatgen 独立数值对照](validation_cases/independent_engines/README.md)，比较相同合成 CIF 的峰位和立方晶体方向模量，并在 CI 中保留数值报告和依赖版本。
+
 ## 本地 CIF 分析
 
 ```powershell
@@ -250,7 +264,7 @@ J_no_LP   = I_no_LP / V_cell²
 
 当前离线 pytest 套件覆盖成分解析、子体系枚举及组合数量上限、大小写 CIF 扫描、同名文件防覆盖、CIF 数据块和空间群解析、特殊位置占位转换、系统消光、解析结构因子、Bragg 几何、边界反射、刚度单位换算、弹性张量检查、侧车配对、资源限制、数据库失败语义、事务式输出、电子表格安全、确定性证据归档、严格清单校验和投稿准备检查。测试收集数由 pytest/CI 报告，不再复制到静态文档；另有稳定的 45 项解析科学基准。GitHub Actions 还配置了多 Python 版本、Windows/macOS、Linux 无头 GUI、wheel 安装、解析基准、发布制品、月度复现审计、依赖更新和 JOSS 论文构建。月度定时运行只记录某一公开提交的可复现状态；只有由真实缺陷、依赖更新、验证、文档改进或用户反馈形成的公开提交、Issue、Pull Request 或 Release 才构成开发活动证据。
 
-JOSS 正式投稿仍需要真实且分布式的六个月公开开发记录、真实材料用例、独立衍射与弹性验证、外部互动、人工确认的元数据，以及通过官方 Open Journals 构建并逐页检查的稿件。先执行 `python scripts/check_release.py` 生成与当前源码绑定的发布验收收据，再用 `python scripts/joss_readiness.py --stage submission --output build/joss-readiness` 生成投稿阻塞项报告。不可变软件归档 DOI 属于 JOSS 审稿完成后的 `publication` 阶段，不是初次投稿的前置条件；工作计划见 [docs/JOSS_6_MONTH_PLAN.md](docs/JOSS_6_MONTH_PLAN.md)。
+作者已确认软件用于其已发表研究，代表论文及具体使用情况将在投稿记录中补充。项目自 2026 年 8 月 12 日开始公开开发，目前尚未满足 JOSS 超过六个月的持续公开开发要求。项目自定的科学验证、社区参与要求与 JOSS 官方门槛分别列于 [投稿准备状态](docs/JOSS_READINESS.md)。先执行 `python scripts/check_release.py` 验收当前软件，再用 `python scripts/joss_readiness.py --stage submission --output build/joss-readiness` 检查待补的投稿证据和作者确认事项。最终软件归档 DOI 在审稿完成后的 `publication` 阶段补入；工作计划见 [docs/JOSS_6_MONTH_PLAN.md](docs/JOSS_6_MONTH_PLAN.md)。
 
 ## 来源与许可