OperonDBS 0.7.0__tar.gz → 0.7.2__tar.gz

{operondbs-0.7.0 → operondbs-0.7.2}/.github/workflows/publish.yml

@@ -34,6 +34,17 @@ jobs:
           path: dist/*.tar.gz
           if-no-files-found: error
 
+  documentation:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install -e '.[docs]'
+      - run: sphinx-build -W --keep-going -b html docs docs/_build/html
+
   wheels:
     strategy:
       fail-fast: false

operondbs-0.7.0/.github/workflows/deploy.yml → operondbs-0.7.2/.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: deploy
+name: test
 
 on:
   push:
@@ -25,24 +25,3 @@ jobs:
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           report_type: test_results
-
-  frozen-release-test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v6
-      - uses: actions/setup-python@v7
-        with:
-          python-version: "3.14"
-      - run: python -m pip install -e '.[build]'
-      - run: python tools/build.py
-
-  documentation:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v6
-      - uses: actions/setup-python@v7
-        with:
-          python-version: "3.12"
-      - run: python -m pip install --upgrade pip
-      - run: python -m pip install -e '.[docs]'
-      - run: sphinx-build -W --keep-going -b html docs docs/_build/html

{operondbs-0.7.0 → operondbs-0.7.2}/AGENTS.md

@@ -26,7 +26,7 @@ principle-to-implementation mapping.
 
 Current version markers (must stay consistent across code and docs):
 
-- `operon` 0.6.2 (`pyproject.toml`)
+- `operon` 0.7.0 (`pyproject.toml`)
 - database schema 2.9 (`operon/database.py`, `SCHEMA_VERSION`)
 - metadata schema 1.4 (`operon/schema.py`, `METADATA_SCHEMA_VERSION`)
 
@@ -55,7 +55,13 @@ The project is licensed AGPL-3.0-or-later (`LICENSE` at the repo root).
     checksum verification) and `sftp://` / `remote://` URL fetching.
   - `operon/tui/` — Textual-based terminal UI (`operon tui`, optional `tui`
     extra): Home dashboard, Entities browser, Files browser, workflow-run
-    monitor, a Decisions screen, and a Config screen. Read access lives in
+    monitor, a Decisions screen, a Config screen, a Publish screen (nav key
+    `7`; release builder + selective export builder with read-only previews),
+    a Coverage screen (nav key `8`; taxonomy snapshots, reference sets,
+    coverage report generation and `COV_*` report browsing), and the import
+    dataset wizard (`operon/tui/screens/import_wizard.py`; Home button or
+    global `i`, except on the Files screen where `i` stays ingest). Read
+    access lives in
     `operon/tui/data.py` and is strictly read-only (short-lived read-only
     connections only). Phase 2 write operations (evaluate, curate,
     retire/restore, ingest, verify, QC batch) live in
@@ -64,7 +70,12 @@ The project is licensed AGPL-3.0-or-later (`LICENSE` at the repo root).
     (identical `changes`/`workflow_runs` provenance), and returns plain
     dicts; writable connections are never held by the UI. Every write in the
     UI follows form/plan preview → equivalent CLI command shown → explicit
-    Confirm → background worker → notify + reload or inline error. The
+    Confirm → background worker → notify + reload or inline error. Phase 3
+    actions in the same module: `import_dataset` (commits wizard drafts
+    through the shared single-transaction `import_wizard._commit`),
+    `reserve_entity_ids`, `create_release`, `export`, and `run_coverage`
+    (a below-threshold coverage report returns `exit_code=1` in the result
+    dict — a warning, not an exception). The
     Config screen (`operon/tui/screens/config.py`, nav key `6`) edits
     `config/profiles/*.yaml` (kind `qc`) and single recipes inside
     `config/tools.yaml` through structured control-based forms (no free-text
@@ -101,9 +112,6 @@ The project is licensed AGPL-3.0-or-later (`LICENSE` at the repo root).
   (`.readthedocs.yaml`).
 - `benchmarks/` — representative entity sets for QC performance diagnostics
   (see `docs/*/operations/qc-performance.md`).
-- `tools/build.py` — the only standalone-application release entry point.
-- `build/release/v<version>/` — generated cx_Freeze application releases,
-  including third-party licenses and corresponding source.
 
 ## Setup, test, and build
 
@@ -112,9 +120,8 @@ repo root; activate it or invoke `.venv/bin/python` explicitly).
 
 ```bash
 python3 -m venv .venv && source .venv/bin/activate
-python -m pip install -e '.[dev]'   # runtime + pytest + cx_Freeze + Cython +
-                                    # Sphinx; also compiles the qc parsers
-                                    # extension
+python -m pip install -e '.[dev]'   # runtime + pytest + Cython + Sphinx;
+                                    # also compiles the qc parsers extension
 
 python -m pytest                    # full suite (coverage gate: 90% branch)
 python -m pytest tests/unit         # by category: unit / integration /
@@ -123,19 +130,12 @@ python -m pytest tests/unit         # by category: unit / integration /
 python setup.py build_ext --inplace # rebuild only the Cython extension
 
 sphinx-build -W --keep-going -b html docs docs/_build/html  # strict docs build
-
-python tools/build.py               # complete standalone release -> build/release/v<version>/
 ```
 
 Run the relevant test category after any change; run the full suite before
 considering work done. CI (`.github/workflows/deploy.yml`) runs pytest on
-Python 3.10–3.14, the frozen release build, and the strict Sphinx build.
-
-`tools/build.py` compiles the Cython parser, builds the Sphinx documentation
-strictly, collects third-party license texts, builds the
-corresponding-source sdist, freezes the application, assembles the versioned
-directory, and runs the frozen executable smoke test. Do not call cx_Freeze
-directly for a release bundle.
+Python 3.10–3.14 and the strict Sphinx build. Releases are published
+exclusively to PyPI; see `docs/*/contributor/pypi-release.md`.
 
 Do not commit or perform other git mutations unless the user explicitly
 asks.
@@ -145,7 +145,7 @@ asks.
 - Python 3.10+. Treat `pyproject.toml` as the authoritative dependency
   list: `[project.dependencies]` contains core runtime dependencies, while
   `[project.optional-dependencies]` contains separately installable extras
-  (`test`, `build`, `remote`, `tui`, `docs`, `dev`). Runtime-feature extras must
+  (`test`, `docs`, `dev`). Runtime-feature extras must
   remain lazy-imported by their feature paths (e.g. Paramiko is only
   imported inside remote/SSH code); test/build extras must stay out of
   normal runtime paths. Do not promote an extra dependency to core, or add a
@@ -186,7 +186,7 @@ change:
 - Contributor-facing processes → `docs/*/contributor/`; navigation →
   `docs/*/index.md`
 
-Version markers in docs (`operon` 0.6.2, database schema 2.9, metadata
+Version markers in docs (`operon` 0.7.0, database schema 2.9, metadata
 schema 1.4) must match `pyproject.toml` and the code. Do not write the
 current values literally in Markdown sources: use the `myst_substitutions`
 references `{{ operon_version }}`, `{{ db_schema }}`, and
@@ -203,9 +203,6 @@ Sphinx-rendered); update the list above when bumping.
 
 ## Special Note For Codex/ChatGPT
 
-To ensure security, code testing in Codex/ChatGPT runs in a sandbox by default.
-However, this causes the `test_tui.py` section to experience Textual/asyncio
-cleanup blocking during testing, resulting in a "FAIL" report due to a timeout.
+Due to specific limitations of the sandbox environment, executing certain TUI test code may cause the system to freeze; this often occurs on Codex/ChatGPT. The specific reason is that when this test code runs in the sandbox, it may results a Textual/asyncio cleanup block, and reports "FAIL" due to timeout.
 
-To run the full test suite, first exclude `test_tui.py`, then run it separately
-outside the sandbox.
+If you are Codex/ChatGPT, please execute TUI-related test code OUTSIDE the sandbox.

{operondbs-0.7.0 → operondbs-0.7.2}/MANIFEST.in

@@ -12,6 +12,6 @@ recursive-include benchmarks *.tsv
 recursive-include docs *.css *.html *.js *.md *.py *.txt
 prune docs/_build
 recursive-include operon *.py *.pyx *.tcss
+recursive-include operon/tui/assets *.png *.z *.md
 recursive-include tests *.py
-recursive-include tools *.py
 exclude operon/qc_module/_parsers.c

{operondbs-0.7.0 → operondbs-0.7.2}/OperonDBS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OperonDBS
-Version: 0.7.0
+Version: 0.7.2
 Summary: Operon the Database System: Archive, Quality-Control, Organize, Analyze and Release Your Bio-Data
 Author-email: hyli360 <lihuanyu2003@gmail.com>
 License-Expression: AGPL-3.0-or-later
@@ -32,20 +32,13 @@ Requires-Dist: pytest>=8.0; extra == "test"
 Requires-Dist: setuptools>=77; extra == "test"
 Requires-Dist: textual>=8.0; extra == "test"
 Requires-Dist: cython>=3.0; extra == "test"
-Provides-Extra: build
-Requires-Dist: cx-Freeze>=8.4; extra == "build"
-Requires-Dist: myst-parser<5,>=4.0; extra == "build"
-Requires-Dist: Sphinx<9,>=7.4; extra == "build"
-Requires-Dist: sphinx-rtd-theme<4,>=3.0; extra == "build"
-Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "build"
-Requires-Dist: cython>=3.0; extra == "build"
 Provides-Extra: docs
 Requires-Dist: Sphinx<9,>=7.4; extra == "docs"
 Requires-Dist: myst-parser<5,>=4.0; extra == "docs"
 Requires-Dist: sphinx-rtd-theme<4,>=3.0; extra == "docs"
+Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "docs"
 Provides-Extra: dev
 Requires-Dist: coverage>=7.0; extra == "dev"
-Requires-Dist: cx-Freeze>=8.4; extra == "dev"
 Requires-Dist: cython>=3.0; extra == "dev"
 Requires-Dist: pytest-cov>=7.0; extra == "dev"
 Requires-Dist: pytest>=8.0; extra == "dev"
@@ -57,7 +50,7 @@ Dynamic: license-file
 
 # Operon
 
-[![deploy status](https://github.com/HYLi360/Operon/actions/workflows/deploy.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/deploy.yml) [![codecov](https://codecov.io/gh/HYLi360/Operon/branch/master/graph/badge.svg?token=BC4LD8UPL2)](https://codecov.io/gh/HYLi360/Operon)
+[![test status](https://github.com/HYLi360/Operon/actions/workflows/test.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/HYLi360/Operon/branch/master/graph/badge.svg?token=BC4LD8UPL2)](https://codecov.io/gh/HYLi360/Operon)
 
 A Python-based, **file-based database** designed for large-scale genomic data, used for archiving, quality control, analysis, and deterministic automation.
 
@@ -78,7 +71,7 @@ A Python-based, **file-based database** designed for large-scale genomic data, u
 
 - Python 3.10+
 - Runtime dependencies: `PyYAML`, `requests`, `aiohttp`, `Biopython`, `Paramiko`, `Textual`, and `questionary`; the built-in QC acceleration extension is compiled when the package is built
-- Optional extras: `test` (pytest and Cython), `build` (cx_Freeze, Cython, and documentation tooling), `docs` (documentation tooling), and `dev` (all development/build dependencies)
+- Optional extras: `test` (pytest and Cython), `docs` (documentation tooling), and `dev` (all development/build dependencies)
 
 ## Install
 
@@ -95,14 +88,6 @@ For an editable checkout, run from the repository root:
 python -m pip install -e '.[dev]'
 ```
 
-PyPI installation does not use cx_Freeze. To build the separately distributed
-standalone application instead:
-
-```bash
-python -m pip install -e '.[build]'
-python tools/build.py
-```
-
 ## Documentation
 
 The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). To build the Sphinx site locally:

{operondbs-0.7.0 → operondbs-0.7.2}/OperonDBS.egg-info/SOURCES.txt

@@ -7,8 +7,8 @@ README.md
 README_ZH.md
 pyproject.toml
 setup.py
-.github/workflows/deploy.yml
 .github/workflows/publish.yml
+.github/workflows/test.yml
 OperonDBS.egg-info/PKG-INFO
 OperonDBS.egg-info/SOURCES.txt
 OperonDBS.egg-info/dependency_links.txt
@@ -33,7 +33,6 @@ docs/en/architecture/overview.md
 docs/en/architecture/qc-and-rules.md
 docs/en/architecture/release-lifecycle.md
 docs/en/architecture/taxonomy-coverage.md
-docs/en/contributor/application-release.md
 docs/en/contributor/development-testing.md
 docs/en/contributor/documentation-deployment.md
 docs/en/contributor/index.md
@@ -85,7 +84,6 @@ docs/zh/architecture/overview.md
 docs/zh/architecture/qc-and-rules.md
 docs/zh/architecture/release-lifecycle.md
 docs/zh/architecture/taxonomy-coverage.md
-docs/zh/contributor/application-release.md
 docs/zh/contributor/development-testing.md
 docs/zh/contributor/documentation-deployment.md
 docs/zh/contributor/index.md
@@ -167,14 +165,21 @@ operon/tui/actions.py
 operon/tui/app.py
 operon/tui/app.tcss
 operon/tui/data.py
+operon/tui/splash.py
+operon/tui/splash_terminal.py
+operon/tui/assets/splash.png
+operon/tui/assets/splash.rgb.z
 operon/tui/screens/__init__.py
 operon/tui/screens/common.py
 operon/tui/screens/config.py
+operon/tui/screens/coverage.py
 operon/tui/screens/decisions.py
 operon/tui/screens/entities.py
 operon/tui/screens/files.py
 operon/tui/screens/files_ops.py
 operon/tui/screens/home.py
+operon/tui/screens/import_wizard.py
+operon/tui/screens/publish.py
 operon/tui/screens/runs.py
 tests/__init__.py
 tests/helpers.py
@@ -184,11 +189,11 @@ tests/integration/__init__.py
 tests/integration/test_analysis_resume.py
 tests/integration/test_analysis_shutdown.py
 tests/integration/test_analysis_tools.py
-tests/integration/test_application_build.py
 tests/integration/test_execution_backends.py
 tests/integration/test_lineage_cascade.py
 tests/integration/test_ncbi_datasets_adapter.py
 tests/integration/test_pipeline_and_release.py
+tests/integration/test_python_packaging.py
 tests/integration/test_taxonomy_coverage.py
 tests/regression/__init__.py
 tests/regression/test_correctness.py
@@ -227,7 +232,8 @@ tests/unit/test_taxonomy_edges.py
 tests/unit/test_tools_edges.py
 tests/unit/test_tui.py
 tests/unit/test_tui_config.py
+tests/unit/test_tui_publish.py
+tests/unit/test_tui_splash_terminal.py
 tests/unit/test_tui_writes.py
 tests/unit/test_views_release_reports_edges.py
-tests/unit/test_workflow_cli.py
-tools/build.py
+tests/unit/test_workflow_cli.py

{operondbs-0.7.0 → operondbs-0.7.2}/OperonDBS.egg-info/requires.txt

@@ -6,19 +6,8 @@ questionary>=2.1
 requests>=2.32
 textual>=8.0
 
-[build]
-cx-Freeze>=8.4
-myst-parser<5,>=4.0
-Sphinx<9,>=7.4
-sphinx-rtd-theme<4,>=3.0
-cython>=3.0
-
-[build:python_version < "3.11"]
-tomli>=2.0
-
 [dev]
 coverage>=7.0
-cx-Freeze>=8.4
 cython>=3.0
 pytest-cov>=7.0
 pytest>=8.0
@@ -34,6 +23,9 @@ Sphinx<9,>=7.4
 myst-parser<5,>=4.0
 sphinx-rtd-theme<4,>=3.0
 
+[docs:python_version < "3.11"]
+tomli>=2.0
+
 [test]
 coverage>=7.0
 paramiko>=3.4

{operondbs-0.7.0 → operondbs-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OperonDBS
-Version: 0.7.0
+Version: 0.7.2
 Summary: Operon the Database System: Archive, Quality-Control, Organize, Analyze and Release Your Bio-Data
 Author-email: hyli360 <lihuanyu2003@gmail.com>
 License-Expression: AGPL-3.0-or-later
@@ -32,20 +32,13 @@ Requires-Dist: pytest>=8.0; extra == "test"
 Requires-Dist: setuptools>=77; extra == "test"
 Requires-Dist: textual>=8.0; extra == "test"
 Requires-Dist: cython>=3.0; extra == "test"
-Provides-Extra: build
-Requires-Dist: cx-Freeze>=8.4; extra == "build"
-Requires-Dist: myst-parser<5,>=4.0; extra == "build"
-Requires-Dist: Sphinx<9,>=7.4; extra == "build"
-Requires-Dist: sphinx-rtd-theme<4,>=3.0; extra == "build"
-Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "build"
-Requires-Dist: cython>=3.0; extra == "build"
 Provides-Extra: docs
 Requires-Dist: Sphinx<9,>=7.4; extra == "docs"
 Requires-Dist: myst-parser<5,>=4.0; extra == "docs"
 Requires-Dist: sphinx-rtd-theme<4,>=3.0; extra == "docs"
+Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "docs"
 Provides-Extra: dev
 Requires-Dist: coverage>=7.0; extra == "dev"
-Requires-Dist: cx-Freeze>=8.4; extra == "dev"
 Requires-Dist: cython>=3.0; extra == "dev"
 Requires-Dist: pytest-cov>=7.0; extra == "dev"
 Requires-Dist: pytest>=8.0; extra == "dev"
@@ -57,7 +50,7 @@ Dynamic: license-file
 
 # Operon
 
-[![deploy status](https://github.com/HYLi360/Operon/actions/workflows/deploy.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/deploy.yml) [![codecov](https://codecov.io/gh/HYLi360/Operon/branch/master/graph/badge.svg?token=BC4LD8UPL2)](https://codecov.io/gh/HYLi360/Operon)
+[![test status](https://github.com/HYLi360/Operon/actions/workflows/test.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/HYLi360/Operon/branch/master/graph/badge.svg?token=BC4LD8UPL2)](https://codecov.io/gh/HYLi360/Operon)
 
 A Python-based, **file-based database** designed for large-scale genomic data, used for archiving, quality control, analysis, and deterministic automation.
 
@@ -78,7 +71,7 @@ A Python-based, **file-based database** designed for large-scale genomic data, u
 
 - Python 3.10+
 - Runtime dependencies: `PyYAML`, `requests`, `aiohttp`, `Biopython`, `Paramiko`, `Textual`, and `questionary`; the built-in QC acceleration extension is compiled when the package is built
-- Optional extras: `test` (pytest and Cython), `build` (cx_Freeze, Cython, and documentation tooling), `docs` (documentation tooling), and `dev` (all development/build dependencies)
+- Optional extras: `test` (pytest and Cython), `docs` (documentation tooling), and `dev` (all development/build dependencies)
 
 ## Install
 
@@ -95,14 +88,6 @@ For an editable checkout, run from the repository root:
 python -m pip install -e '.[dev]'
 ```
 
-PyPI installation does not use cx_Freeze. To build the separately distributed
-standalone application instead:
-
-```bash
-python -m pip install -e '.[build]'
-python tools/build.py
-```
-
 ## Documentation
 
 The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). To build the Sphinx site locally:

{operondbs-0.7.0 → operondbs-0.7.2}/README.md

@@ -1,6 +1,6 @@
 # Operon
 
-[![deploy status](https://github.com/HYLi360/Operon/actions/workflows/deploy.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/deploy.yml) [![codecov](https://codecov.io/gh/HYLi360/Operon/branch/master/graph/badge.svg?token=BC4LD8UPL2)](https://codecov.io/gh/HYLi360/Operon)
+[![test status](https://github.com/HYLi360/Operon/actions/workflows/test.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/HYLi360/Operon/branch/master/graph/badge.svg?token=BC4LD8UPL2)](https://codecov.io/gh/HYLi360/Operon)
 
 A Python-based, **file-based database** designed for large-scale genomic data, used for archiving, quality control, analysis, and deterministic automation.
 
@@ -21,7 +21,7 @@ A Python-based, **file-based database** designed for large-scale genomic data, u
 
 - Python 3.10+
 - Runtime dependencies: `PyYAML`, `requests`, `aiohttp`, `Biopython`, `Paramiko`, `Textual`, and `questionary`; the built-in QC acceleration extension is compiled when the package is built
-- Optional extras: `test` (pytest and Cython), `build` (cx_Freeze, Cython, and documentation tooling), `docs` (documentation tooling), and `dev` (all development/build dependencies)
+- Optional extras: `test` (pytest and Cython), `docs` (documentation tooling), and `dev` (all development/build dependencies)
 
 ## Install
 
@@ -38,14 +38,6 @@ For an editable checkout, run from the repository root:
 python -m pip install -e '.[dev]'
 ```
 
-PyPI installation does not use cx_Freeze. To build the separately distributed
-standalone application instead:
-
-```bash
-python -m pip install -e '.[build]'
-python tools/build.py
-```
-
 ## Documentation
 
 The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). To build the Sphinx site locally:

{operondbs-0.7.0 → operondbs-0.7.2}/README_ZH.md

@@ -1,6 +1,6 @@
 # Operon
 
-[![deploy status](https://github.com/HYLi360/Operon/actions/workflows/deploy.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/deploy.yml) [![codecov](https://codecov.io/gh/HYLi360/Operon/branch/master/graph/badge.svg?token=BC4LD8UPL2)](https://codecov.io/gh/HYLi360/Operon)
+[![test status](https://github.com/HYLi360/Operon/actions/workflows/test.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/HYLi360/Operon/branch/master/graph/badge.svg?token=BC4LD8UPL2)](https://codecov.io/gh/HYLi360/Operon)
 
 一个基于 Python 的、面向大规模基因组数据的**基于文件的数据库**，用于归档、质控、分析与确定性自动化处理。
 
@@ -19,7 +19,7 @@
 
 - Python 3.10 及以上版本
 - 运行时依赖：`PyYAML`、`requests`、`aiohttp`、`Biopython`、`Paramiko`、`Textual` 与 `questionary`；内置 QC 加速扩展在构建软件包时编译
-- 可选 extras：`test`（pytest 与 Cython）、`build`（cx_Freeze、Cython 与文档工具）、`docs`（文档工具）和 `dev`（全部开发/构建依赖）
+- 可选 extras：`test`（pytest 与 Cython）、`docs`（文档工具）和 `dev`（全部开发/构建依赖）
 
 ## 安装
 
@@ -36,13 +36,6 @@ python -m pip install OperonDBS
 python -m pip install -e '.[dev]'
 ```
 
-PyPI 安装不使用 cx_Freeze。若要另行构建独立可执行应用：
-
-```bash
-python -m pip install -e '.[build]'
-python tools/build.py
-```
-
 ## 文档
 
 完整文档同时维护[中文](docs/zh/index.md)和[英文](docs/en/index.md)版本。本地构建 Sphinx 站点：

{operondbs-0.7.0 → operondbs-0.7.2}/docs/conf.py

@@ -16,8 +16,8 @@ DOCS_DIR = Path(__file__).resolve().parent
 REPO_ROOT = DOCS_DIR.parent
 
 project = "Operon"
-author = "Operon contributors"
-copyright = "2026, Operon contributors"
+author = "Project Operon Development Group"
+copyright = f"2026, {author}. All Rights Reserved."
 
 
 def _package_version() -> str:

{operondbs-0.7.0 → operondbs-0.7.2}/docs/en/architecture/files-and-storage.md

@@ -25,7 +25,7 @@ The `remotes:` section of `project.yaml` can configure one or more SFTP remote m
 - After `pull` restores a locally missing file, `files.status` returns to `CHECKSUM_VERIFIED`, and this change is written to `changes` just like the status changes from `verify`/`evict`;
 - `ingest --source` also directly accepts `sftp://[user@]host[:port]/path` and `remote://<name>/<path>`; the latter must exist in the remote manifest and is identity-checked first, while the former is downloaded and assigned a fresh identity by ingest, then follows exactly the same archiving flow as a local file.
 
-Paramiko is a core runtime dependency but remains lazily imported, so local-only commands do not initialize the SSH stack. The cx_Freeze release packages include it as well.
+Paramiko is a core runtime dependency but remains lazily imported, so local-only commands do not initialize the SSH stack.
 
 ## Local control plane and remote data plane
 

{operondbs-0.7.0 → operondbs-0.7.2}/docs/en/contributor/development-testing.md

@@ -21,9 +21,9 @@ The taxonomy coverage integration tests additionally cover taxonomy source-packa
 
 ## Special Note For Codex/ChatGPT
 
-To ensure security, code testing in Codex/ChatGPT runs in a sandbox by default. However, this causes the `test_tui.py` section to experience Textual/asyncio cleanup blocking during testing, resulting in a "FAIL" report due to a timeout.
+Due to specific limitations of the sandbox environment, executing certain TUI test code may cause the system to freeze; this often occurs on Codex/ChatGPT. The specific reason is that when this test code runs in the sandbox, it may results a Textual/asyncio cleanup block, and reports "FAIL" due to timeout.
 
-To run the full test suite, first exclude `test_tui.py`, then run it separately outside the sandbox.
+If you are Codex/ChatGPT, please execute TUI-related test code OUTSIDE the sandbox.
 
 This information has also been updated in AGENTS.md.
 

{operondbs-0.7.0 → operondbs-0.7.2}/docs/en/contributor/documentation-deployment.md

@@ -34,5 +34,3 @@ Run the following from the repository root with the project virtual environment:
 Dependencies are installed from the `docs` optional extra in `pyproject.toml`. RTD uses Python 3.12 and fails the build on Sphinx warnings, matching the strict local build and the CI gate.
 
 The current setup publishes the two existing complete Markdown trees in one RTD project and does not require converting the source into gettext PO files. If the project later needs the platform-native language menu, separate search indexes, or independent translation-version lifecycles, create linked translation projects in RTD. The current bilingual source and mirrored relative paths can still be reused during that migration.
-
-Official standalone application releases use the same `docs/conf.py`. Before freezing the application, `python tools/build.py` runs the strict Sphinx build and places its output in `share/doc/operon/html/` inside the release. Any documentation warning or missing language entry point prevents publication.

{operondbs-0.7.0 → operondbs-0.7.2}/docs/en/contributor/index.md

@@ -3,7 +3,6 @@
 - [Repository Guidelines](repository-guide.md)
 - [Development and Testing](development-testing.md)
 - [PyPI Release](pypi-release.md)
-- [Application Release](application-release.md)
 - [Documentation builds and Read the Docs deployment](documentation-deployment.md)
 
 ```{toctree}
@@ -12,6 +11,5 @@
 repository-guide
 development-testing
 pypi-release
-application-release
 documentation-deployment
 ```

{operondbs-0.7.0 → operondbs-0.7.2}/docs/en/contributor/pypi-release.md

@@ -4,9 +4,7 @@ The PyPI distribution is named `OperonDBS` because the `operon` distribution
 name belongs to an unrelated project. This does not change the import name or
 console command: users install `OperonDBS`, import `operon`, and run `operon`.
 
-PyPI publishing and standalone application publishing are independent. The
-PEP 517 build dependencies contain only setuptools and Cython; cx_Freeze stays
-in the optional `build` extra and is used only by `python tools/build.py`.
+The PEP 517 build dependencies contain only setuptools and Cython.
 
 ## GitHub Actions release
 

{operondbs-0.7.0 → operondbs-0.7.2}/docs/en/contributor/repository-guide.md

@@ -17,7 +17,6 @@
 - `operon/remotes.py`: SFTP mirrors, push/pull, and remote URL downloads.
 - `tests/`: `unit/`, `integration/`, `regression/`, `compatibility/` tests.
 - `docs/`: user, architecture, and operations documentation.
-- `build/release/v<version>/`: generated standalone application release directories.
 
 ## Collaboration conventions
 

{operondbs-0.7.0 → operondbs-0.7.2}/docs/en/getting-started/installation.md

@@ -9,7 +9,7 @@
 
 ## Platform support
 
-Linux is the primary platform for standalone application releases, local
+Linux is the primary platform for local
 Slurm, and the broad external bioinformatics tool ecosystem. macOS is
 supported for source-installed local execution and as an SSH/SFTP client,
 including remote Slurm submission to a Linux host. Local resource sampling
@@ -18,8 +18,7 @@ uses procfs when available and the system `ps` command on macOS.
 External commands configured in `tools.yaml` must themselves be installed for
 the controller platform. SSH direct execution still requires util-linux
 `setsid` on the remote host, so that compute-side mode targets Linux; this does
-not prevent a Mac from acting as the controller. Signed or notarized macOS
-standalone bundles are not currently published.
+not prevent a Mac from acting as the controller.
 
 ## Install from PyPI
 
@@ -33,9 +32,7 @@ python -m pip install OperonDBS
 ```
 
 Published wheels include the compiled QC parser. SSH/SFTP support and the TUI
-are included in the standard installation. PyPI installation does not use
-cx_Freeze; that tool is only needed for the separate standalone application
-directory.
+are included in the standard installation.
 
 ## Install from the repository
 
@@ -57,12 +54,3 @@ operon --help
 
 The first command prints `operon` followed by the installed version —
 {{ operon_version }} for the release this documentation matches.
-
-To build a standalone cx_Freeze application, install the build extra and use the unified release entry point:
-
-```bash
-python -m pip install -e '.[build]'
-python tools/build.py
-```
-
-See [Application Release](../contributor/application-release.md) for the release directory layout and validation rules.

{operondbs-0.7.0 → operondbs-0.7.2}/docs/en/operations/ncbi-recovery-migration.md

@@ -33,7 +33,7 @@ Do not point these variables at the project's parent directory, a disk root, or
 .venv/bin/python -m operon --version
 ```
 
-The full test suite must pass. If production runs a cx_Freeze build, rebuild it and complete the rehearsal below in staging with the same binary first.
+The full test suite must pass.
 
 ## 3. Record the pre-migration read-only baseline