OperonDBS 0.8.0__tar.gz → 0.8.3__tar.gz

{operondbs-0.8.0 → operondbs-0.8.3}/.github/workflows/publish.yml

@@ -43,7 +43,9 @@ jobs:
           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
+      - run: |
+          sphinx-build -W --keep-going -b html docs/en docs/_build/en/html
+          sphinx-build -W --keep-going -b html docs/zh docs/_build/zh/html
 
   wheels:
     strategy:
@@ -71,7 +73,7 @@ jobs:
       - run: python -m cibuildwheel --output-dir wheelhouse
         env:
           CIBW_ARCHS: ${{ matrix.architecture }}
-          CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-* cp314-*"
+          CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-* cp314-* cp315-*"
           CIBW_SKIP: "*-musllinux_*"
           CIBW_TEST_COMMAND: >-
             python -c "import operon; import operon.qc._parsers;

{operondbs-0.8.0 → operondbs-0.8.3}/.github/workflows/test.yml

@@ -25,27 +25,30 @@ jobs:
           cache-dependency-path: pyproject.toml
       - 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
+      - run: |
+          sphinx-build -W --keep-going -b html docs/en docs/_build/en/html
+          sphinx-build -W --keep-going -b html docs/zh docs/_build/zh/html
 
   pytest:
     strategy:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest ]
-        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14", "3.15"]
     runs-on: ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v7
         with:
+          allow-prereleases: true
+          check-latest: true
           python-version: ${{ matrix.python-version }}
           cache: pip
           cache-dependency-path: pyproject.toml
-      - run: python -m pip install --upgrade pip
-      - run: python -m pip install -e '.[test]'
-      - run: python -m pytest -n 2 --dist loadfile
-      - if: ${{ !cancelled() }}
-        uses: codecov/codecov-action@v7
+      - run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e '.[test]'
+          python -m pytest
+      - uses: codacy/codacy-coverage-reporter-action@v1.3.0
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          report_type: test_results
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

{operondbs-0.8.0 → operondbs-0.8.3}/.gitignore

@@ -29,5 +29,6 @@ htmlcov/
 /site/
 /docs/_build/
 /workflows/
-/HPC/
+/others/
 .matrix/
+cobertura.xml

{operondbs-0.8.0 → operondbs-0.8.3}/AGENTS.md

@@ -26,7 +26,7 @@ principle-to-implementation mapping.
 
 Current version markers (must stay consistent across code and docs):
 
-- `operon` 0.8.0 (`pyproject.toml`)
+- `operon` 0.8.3 (`pyproject.toml`)
 - database schema 2.11 (`operon/database.py`, `SCHEMA_VERSION`)
 - metadata schema 1.4 (`operon/schema.py`, `METADATA_SCHEMA_VERSION`)
 
@@ -83,17 +83,48 @@ The project is licensed AGPL-3.0-or-later (`LICENSE` at the repo root).
     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`
+    `reserve_entity_ids`, `create_release`, `export`, `run_coverage`
     (a below-threshold coverage report returns `exit_code=1` in the result
-    dict — a warning, not an exception). The
+    dict — a warning, not an exception), `preflight_backend`, `run_analysis`
+    (backing the AnalyzeModal launched from the Config screen's Run analysis
+    button or the Tasks screen's New analysis button; the modal mirrors
+    `--backend` — project default / local / slurm / ssh — and preflights the
+    selection inline, and cancellation sets the core's cooperative
+    `cancel_event`, so a queued Slurm job or array is cancelled with one
+    `scancel`), `run_external` (backing the Tasks screen's Run external
+    dialog, which mirrors `run-external` field by field and opens the run
+    record when it finishes) and `write_analysis_report` (backing the
+    Analysis hits browser's Export button: it runs the same read-only query
+    and the same renderer as `report analysis --hits --format … --out …`, so
+    the file is byte-identical and, like that command, writes no provenance
+    rows). Phase 3 also covers the
+    derived-artifact loop: `run_classify` (the Config screen's Run classify
+    dialog, mirroring `classify-sequences` with the CLI's summary and a re-run
+    button), and — on the Files screen — `extract_domains`, `select_sequences`,
+    `adopt` and `fanout` (modals in `operon/tui/screens/derived_ops.py`:
+    extract/select chain into the adopt dialog with `derived_from` prefilled and
+    leave their output unregistered, adopt's manifest mode previews before
+    Confirm, and fanout's dry run is a mandatory preflight). Read-only TUI views added for `report analysis --hits` (alignment
+    hits with the CLI's filters and columns) and for `sequence_labels` (the
+    classify-sequences output: a per-file section in the Files detail plus
+    the project-wide label summary behind the Files screen's `l` binding), which
+    has no CLI reader at all. The
     Config screen (`operon/tui/screens/config.py`, nav key `6`) edits
-    `config/profiles/*.yaml` (kind `qc`) and single recipes inside
+    `config/profiles/*.yaml` (kind `qc` and kind `sequence_classification` —
+    each kind has its own form, dispatched by the document's own kind, with the
+    classification widgets in `operon/tui/screens/config_classification.py`
+    and `actions.save_classification_profile` sharing `save_profile`'s version,
+    snapshot and rollback machinery; a profile whose conditions nest deeper
+    than one `any:`/`not:` level opens read-only) and single recipes inside
     `config/tools.yaml` through structured control-based forms (no free-text
     YAML): every save bumps the `version`, records the same content-addressed
     snapshot the CLI records (`qc_profiles` / `recipe_snapshots`), and
     restores the previous file bytes on failure; keys the forms do not model
     are preserved verbatim; history modals restore snapshots into the editor
     as the next version; tools-check runs in a worker with per-row updates.
+    `operon/tui/parity.py` is the CLI/TUI parity registry: every CLI leaf
+    command is registered `implemented`/`cli-only`/`planned`, enforced by
+    `tests/unit/test_tui_cli_parity.py` (see Conventions).
     Textual is imported only inside this package, which the `tui` command
     handler imports lazily.
   - Other top-level modules by responsibility: `database.py` (SQLite schema
@@ -127,13 +158,23 @@ The project is licensed AGPL-3.0-or-later (`LICENSE` at the repo root).
 - `docs/` — Sphinx documentation in two mirrored language trees, `docs/en/`
   and `docs/zh/`, each split into `overview.md`, `getting-started/`,
   `guides/`, `architecture/`, `reference/`, `operations/`, and
-  `contributor/`. Built with `docs/conf.py`; published via Read the Docs
-  (`.readthedocs.yaml`).
+  `contributor/`. Each tree is a Sphinx project of its own
+  (`docs/<language>/conf.py`, sharing settings from `docs/conf_common.py`) and
+  a Read the Docs project of its own, linked there as parent and translation:
+  `operonproject` (English) and `operonproject-zh` (Chinese). Read the Docs
+  accepts no build-configuration file name other than `.readthedocs.yaml`, so
+  each tree carries one next to its `conf.py`
+  (`docs/<language>/.readthedocs.yaml`) and the dashboard points the project at
+  that path. `docs/locales/` is the catalog directory
+  for a future gettext-maintained language; `tests/unit/test_docs_projects.py`
+  guards the layout.
 - `benchmarks/` — representative entity sets for QC performance diagnostics
   (see `docs/*/operations/qc-performance.md`).
 - `scripts/` — local developer tooling; `setup-test-matrix.sh` and
   `run-test-matrix.sh` build and drive the uv-managed Python 3.10–3.14
-  matrix under .matrix/ (see `docs/*/contributor/development-testing.md`).
+  matrix under .matrix/ (see `docs/*/contributor/development-testing.md`);
+  `defects.sh` appends to and queries the defect registry (`defects.yml`,
+  see "Defect reports" below).
 
 ## Setup, test, and build
 
@@ -152,20 +193,42 @@ python -m pytest tests/unit         # by category: unit / integration /
 
 python -m pytest --lf -q --no-cov   # iterate: last failures, no coverage
 python -m pytest -n 4 --dist loadfile   # parallel full suite (xdist, in the dev/test extras)
-scripts/run-test-matrix.sh          # whole suite on 3.10-3.14 concurrently
+scripts/run-test-matrix.sh          # whole suite on 3.10-3.15 concurrently
 
 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
+sphinx-build -W --keep-going -b html docs/en docs/_build/en/html  # strict build,
+sphinx-build -W --keep-going -b html docs/zh docs/_build/zh/html  # one per language
 ```
 
 Run the relevant test category after any change; run the full suite before
-considering work done. CI (`.github/workflows/test.yml`) runs pytest on
-Python 3.10–3.14 and the strict Sphinx build. Releases are published
-exclusively to PyPI; see `docs/*/contributor/pypi-release.md`.
+considering work done.
 
-Do not commit or perform other git mutations unless the user explicitly
-asks.
+CI (`.github/workflows/test.yml`) runs pytest on Python 3.10–3.15 and the strict
+Sphinx build. Releases are published exclusively to PyPI; see `docs/*/contributor/pypi-release.md`.
+
+The project uses `pytest-xdist` to parallel testing. Avoid sharing state between tests
+to prevent unexpected or random test results.
+
+> Running `python -m pytest` directly takes approx 35 seconds
+> (auto: 24 workers). Running the local test matrix takes 3 minutes
+> (6 jobs × 4 workers), or 4~5min (6 jobs × 2 workers in default).
+> 
+> Measured on Intel Core i7-13700HX (16c24t).
+
+## Git
+
+If the user requests or grants permission, do `git commit` after modify.
+Avoid including overly large changes in a single commit. For commit messages,
+follow the pattern used in the last five commits; otherwise, the Conventional
+Commits guidelines.
+
+**DO NOT** push any commit or tag unless the user **explicitly** requests that.
+
+If times out, assume the user is not present and that a GPG signature
+is required. Add `-c commit.gpgsign=false` behind `git` may help (However,
+re-signing will reset the commit hash, and corrupt the defects.yml. Please
+proceed with caution).
 
 ## Conventions
 
@@ -193,15 +256,34 @@ asks.
   bytes must raise `ConflictError`; identical bytes must be idempotent.
 - Manual overrides (e.g. `curate`, forced `set-state`) must always be
   recorded in the `changes` audit table.
+- CLI-first: new capabilities land in the CLI/core first, and the TUI never
+  runs ahead of the CLI. Any change to CLI commands, flags, or the TUI
+  surface must update the parity registry `operon/tui/parity.py` in the same
+  commit — the parity tests in `tests/unit/test_tui_cli_parity.py` fail
+  otherwise. Commands intentionally not offered in the TUI are registered
+  `cli-only` with a reason; known gaps are registered `planned` with a
+  milestone.
 - `docs/*/operations/database-compatibility.md` lists migration code that
   exists only for pre-1.0 databases and is scheduled for removal at the 1.0
   release; check it before touching `operon/database.py` migrations or the
   NCBI adapter's schema-upgrade path.
-- The `operon.qc` module uses CFFI (specifically, Cython), so static analysis
-  tools, such as `flake8`, will report "undefined reference" errors (F821).
-  Using `# noqa: F821` behind the line **ONLY** when importing `operon.qc`
-  and an F821 error is likely to occur. Globally ignoring F821 is **STRICKLY
-  PROHIBITED**.
+- Using `ruff` to re-format the code.
+
+## Defect reports
+
+Confirmed defects are tracked in the machine-readable registry
+`defects.yml` at the repository root (plus any `defects/*.yml` shards;
+`scripts/defects.sh` appends and queries records). The full process is in
+`docs/*/contributor/defect-tracking.md`; the binding rules are:
+
+1. **Register first.** When an audit or investigation confirms a defect,
+   append its `ODR-XXXX` record to `defects.yml` before the fix lands.
+2. **One commit per defect.** The fix and its regression tests ride in the
+   same commit; fill in `fix_commit` when committing.
+3. **Close the test loop.** Regression tests for a defect carry
+   `@pytest.mark.bug("ODR-XXXX")`, and every `fixed`/`verified` record
+   lists at least one such test; `tests/unit/test_defect_registry.py`
+   validates the registry schema and both directions of this closure.
 
 ## Documentation sync
 
@@ -217,12 +299,15 @@ change:
   `docs/*/operations/`
 - Contributor-facing processes → `docs/*/contributor/`; navigation →
   `docs/*/index.md`
+- The set of language projects → `docs/<language>/conf.py`, its
+  `docs/<language>/.readthedocs.yaml`, and the registry in
+  `tests/unit/test_docs_projects.py`
 
-Version markers in docs (`operon` 0.8.0, database schema 2.11, metadata
+Version markers in docs (`operon` 0.8.3, database schema 2.11, 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
-`{{ metadata_schema }}`, which `docs/conf.py` resolves from the single
+`{{ metadata_schema }}`, which `docs/conf_common.py` resolves from the single
 sources above at build time. Substitutions expand in paragraph text only,
 never inside code spans or fenced code blocks — examples there use
 `<version>` placeholders instead. Intentional historical pins stay literal — either on the
@@ -235,6 +320,9 @@ Sphinx-rendered); update the list above when bumping.
 
 ## Special Note For Codex/ChatGPT
 
-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.
+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
+result a Textual/asyncio cleanup block, and reports "FAIL" due to timeout.
 
 If you are Codex/ChatGPT, please execute TUI-related test code OUTSIDE the sandbox.

{operondbs-0.8.0 → operondbs-0.8.3}/MANIFEST.in

@@ -4,12 +4,13 @@ include LICENSE
 include MANIFEST.in
 include README.md
 include README_ZH.md
-include .readthedocs.yaml
+include docs/en/.readthedocs.yaml
+include docs/zh/.readthedocs.yaml
 include pyproject.toml
 include setup.py
 recursive-include .github *.yml
 recursive-include benchmarks *.tsv
-recursive-include docs *.css *.html *.js *.md *.py *.txt
+recursive-include docs *.css *.html *.js *.md *.po *.py *.txt
 prune docs/_build
 recursive-include operon *.py *.pyx *.tcss
 recursive-include operon/tui/assets *.png *.z *.md

{operondbs-0.8.0 → operondbs-0.8.3}/OperonDBS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OperonDBS
-Version: 0.8.0
+Version: 0.8.3
 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
@@ -46,9 +46,14 @@ Requires-Dist: myst-parser<5,>=4.0; extra == "dev"
 Requires-Dist: sphinx-rtd-theme<4,>=3.0; extra == "dev"
 Dynamic: license-file
 
-# Operon
+# Operon the Database System
 
-[![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)
+[![test status](https://github.com/HYLi360/Operon/actions/workflows/test.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/test.yml)
+[![RtD badge](https://img.shields.io/badge/Read-the_Document-blue?style=flat)](https://operonproject.readthedocs.io/)
+![PyPI Version](https://img.shields.io/pypi/v/OperonDBS?link=https%3A%2F%2Fpypi.org%2Fproject%2FOperonDBS%2F)
+![GitHub commit activity](https://img.shields.io/github/commit-activity/t/HYLi360/Operon?logo=github)
+[![Codacy Code quality Badge](https://app.codacy.com/project/badge/Grade/47d652651ff645ff86fa0646768a08b3)](https://app.codacy.com/gh/HYLi360/Operon/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![Codacy Coverage Badge](https://app.codacy.com/project/badge/Coverage/47d652651ff645ff86fa0646768a08b3)](https://app.codacy.com/gh/HYLi360/Operon/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
 
 A Python-based, **file-based database** designed for large-scale genomic data, used for archiving, quality control, analysis, and deterministic automation.
 
@@ -88,11 +93,12 @@ python -m pip install -e '.[dev]'
 
 ## Documentation
 
-The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). To build the Sphinx site locally:
+The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). Each language is its own Sphinx project; build both without warnings:
 
 ```bash
 python -m pip install -e '.[docs]'
-sphinx-build -W --keep-going -b html docs docs/_build/html
+sphinx-build -W --keep-going -b html docs/en docs/_build/en/html
+sphinx-build -W --keep-going -b html docs/zh docs/_build/zh/html
 ```
 
-Read the Docs uses the repository's `.readthedocs.yaml` configuration and publishes a language-selection page with mirrored `/en/` and `/zh/` documentation trees.
+Read the Docs publishes two projects linked as parent and translation: `operonproject` (English, `https://operonproject.readthedocs.io/en/latest/`) and `operonproject-zh` (Chinese, `https://operonproject.readthedocs.io/zh-cn/latest/`), each built from its own `docs/<language>/.readthedocs.yaml`.

{operondbs-0.8.0 → operondbs-0.8.3}/OperonDBS.egg-info/SOURCES.txt

@@ -1,5 +1,4 @@
 .gitignore
-.readthedocs.yaml
 AGENTS.md
 LICENSE
 MANIFEST.in
@@ -16,12 +15,10 @@ OperonDBS.egg-info/entry_points.txt
 OperonDBS.egg-info/requires.txt
 OperonDBS.egg-info/top_level.txt
 benchmarks/qc_representative_entities.tsv
-docs/conf.py
-docs/index.md
+docs/conf_common.py
 docs/requirements.txt
-docs/_static/language-switcher.js
-docs/_static/operon.css
-docs/_templates/layout.html
+docs/en/.readthedocs.yaml
+docs/en/conf.py
 docs/en/index.md
 docs/en/overview.md
 docs/en/architecture/extensibility.md
@@ -33,6 +30,7 @@ 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/defect-tracking.md
 docs/en/contributor/development-testing.md
 docs/en/contributor/documentation-deployment.md
 docs/en/contributor/index.md
@@ -75,6 +73,10 @@ docs/en/reference/index.md
 docs/en/reference/recipe-fields.md
 docs/en/reference/recipe-overview.md
 docs/en/reference/recipe-parsers-examples.md
+docs/en/reference/resolved-issues.md
+docs/locales/README.md
+docs/zh/.readthedocs.yaml
+docs/zh/conf.py
 docs/zh/index.md
 docs/zh/overview.md
 docs/zh/architecture/extensibility.md
@@ -86,6 +88,7 @@ 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/defect-tracking.md
 docs/zh/contributor/development-testing.md
 docs/zh/contributor/documentation-deployment.md
 docs/zh/contributor/index.md
@@ -128,6 +131,7 @@ docs/zh/reference/index.md
 docs/zh/reference/recipe-fields.md
 docs/zh/reference/recipe-overview.md
 docs/zh/reference/recipe-parsers-examples.md
+docs/zh/reference/resolved-issues.md
 operon/__init__.py
 operon/__main__.py
 operon/backup.py
@@ -158,6 +162,7 @@ operon/rules.py
 operon/schema.py
 operon/sequence_tools.py
 operon/shutdown.py
+operon/sql.py
 operon/table_import.py
 operon/taxonomy.py
 operon/timetree.py
@@ -178,27 +183,37 @@ operon/tui/actions.py
 operon/tui/app.py
 operon/tui/app.tcss
 operon/tui/data.py
+operon/tui/parity.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/analyze.py
+operon/tui/screens/classify.py
 operon/tui/screens/common.py
 operon/tui/screens/config.py
+operon/tui/screens/config_classification.py
 operon/tui/screens/coverage.py
 operon/tui/screens/decisions.py
+operon/tui/screens/derived_ops.py
 operon/tui/screens/entities.py
+operon/tui/screens/environments.py
 operon/tui/screens/files.py
 operon/tui/screens/files_ops.py
+operon/tui/screens/hits.py
 operon/tui/screens/home.py
 operon/tui/screens/import_wizard.py
+operon/tui/screens/labels.py
 operon/tui/screens/publish.py
+operon/tui/screens/run_external.py
 operon/tui/screens/runs.py
 tests/__init__.py
 tests/helpers.py
 tests/compatibility/__init__.py
 tests/compatibility/test_python_support.py
 tests/integration/__init__.py
+tests/integration/test_analysis_array.py
 tests/integration/test_analysis_resume.py
 tests/integration/test_analysis_shutdown.py
 tests/integration/test_analysis_tools.py
@@ -216,6 +231,7 @@ tests/regression/test_correctness.py
 tests/regression/test_cython_alignment_parity.py
 tests/regression/test_cython_parser_parity.py
 tests/regression/test_parser_semantics.py
+tests/regression/test_sql_identifier_security.py
 tests/unit/__init__.py
 tests/unit/test_alignment_qc.py
 tests/unit/test_classify.py
@@ -224,6 +240,9 @@ tests/unit/test_config_workflow_edges.py
 tests/unit/test_core_coverage_more.py
 tests/unit/test_coverage_edges.py
 tests/unit/test_database_edges_more.py
+tests/unit/test_defect_registry.py
+tests/unit/test_defects_cli.py
+tests/unit/test_docs_projects.py
 tests/unit/test_docs_versions.py
 tests/unit/test_environment.py
 tests/unit/test_environment_capture.py
@@ -267,8 +286,12 @@ tests/unit/test_timetree_snapshots.py
 tests/unit/test_tools_edges.py
 tests/unit/test_tools_execution_more.py
 tests/unit/test_tui.py
+tests/unit/test_tui_analyze.py
+tests/unit/test_tui_cli_parity.py
 tests/unit/test_tui_config.py
+tests/unit/test_tui_derived_ops.py
 tests/unit/test_tui_flows_more.py
+tests/unit/test_tui_m3_loop.py
 tests/unit/test_tui_publish.py
 tests/unit/test_tui_screens_more.py
 tests/unit/test_tui_splash_terminal.py

{operondbs-0.8.0 → operondbs-0.8.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OperonDBS
-Version: 0.8.0
+Version: 0.8.3
 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
@@ -46,9 +46,14 @@ Requires-Dist: myst-parser<5,>=4.0; extra == "dev"
 Requires-Dist: sphinx-rtd-theme<4,>=3.0; extra == "dev"
 Dynamic: license-file
 
-# Operon
+# Operon the Database System
 
-[![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)
+[![test status](https://github.com/HYLi360/Operon/actions/workflows/test.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/test.yml)
+[![RtD badge](https://img.shields.io/badge/Read-the_Document-blue?style=flat)](https://operonproject.readthedocs.io/)
+![PyPI Version](https://img.shields.io/pypi/v/OperonDBS?link=https%3A%2F%2Fpypi.org%2Fproject%2FOperonDBS%2F)
+![GitHub commit activity](https://img.shields.io/github/commit-activity/t/HYLi360/Operon?logo=github)
+[![Codacy Code quality Badge](https://app.codacy.com/project/badge/Grade/47d652651ff645ff86fa0646768a08b3)](https://app.codacy.com/gh/HYLi360/Operon/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![Codacy Coverage Badge](https://app.codacy.com/project/badge/Coverage/47d652651ff645ff86fa0646768a08b3)](https://app.codacy.com/gh/HYLi360/Operon/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
 
 A Python-based, **file-based database** designed for large-scale genomic data, used for archiving, quality control, analysis, and deterministic automation.
 
@@ -88,11 +93,12 @@ python -m pip install -e '.[dev]'
 
 ## Documentation
 
-The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). To build the Sphinx site locally:
+The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). Each language is its own Sphinx project; build both without warnings:
 
 ```bash
 python -m pip install -e '.[docs]'
-sphinx-build -W --keep-going -b html docs docs/_build/html
+sphinx-build -W --keep-going -b html docs/en docs/_build/en/html
+sphinx-build -W --keep-going -b html docs/zh docs/_build/zh/html
 ```
 
-Read the Docs uses the repository's `.readthedocs.yaml` configuration and publishes a language-selection page with mirrored `/en/` and `/zh/` documentation trees.
+Read the Docs publishes two projects linked as parent and translation: `operonproject` (English, `https://operonproject.readthedocs.io/en/latest/`) and `operonproject-zh` (Chinese, `https://operonproject.readthedocs.io/zh-cn/latest/`), each built from its own `docs/<language>/.readthedocs.yaml`.

{operondbs-0.8.0 → operondbs-0.8.3}/README.md

@@ -1,6 +1,11 @@
-# Operon
+# Operon the Database System
 
-[![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)
+[![test status](https://github.com/HYLi360/Operon/actions/workflows/test.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/test.yml)
+[![RtD badge](https://img.shields.io/badge/Read-the_Document-blue?style=flat)](https://operonproject.readthedocs.io/)
+![PyPI Version](https://img.shields.io/pypi/v/OperonDBS?link=https%3A%2F%2Fpypi.org%2Fproject%2FOperonDBS%2F)
+![GitHub commit activity](https://img.shields.io/github/commit-activity/t/HYLi360/Operon?logo=github)
+[![Codacy Code quality Badge](https://app.codacy.com/project/badge/Grade/47d652651ff645ff86fa0646768a08b3)](https://app.codacy.com/gh/HYLi360/Operon/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![Codacy Coverage Badge](https://app.codacy.com/project/badge/Coverage/47d652651ff645ff86fa0646768a08b3)](https://app.codacy.com/gh/HYLi360/Operon/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
 
 A Python-based, **file-based database** designed for large-scale genomic data, used for archiving, quality control, analysis, and deterministic automation.
 
@@ -40,11 +45,12 @@ python -m pip install -e '.[dev]'
 
 ## Documentation
 
-The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). To build the Sphinx site locally:
+The complete documentation is maintained in [English](docs/en/index.md) and [Chinese](docs/zh/index.md). Each language is its own Sphinx project; build both without warnings:
 
 ```bash
 python -m pip install -e '.[docs]'
-sphinx-build -W --keep-going -b html docs docs/_build/html
+sphinx-build -W --keep-going -b html docs/en docs/_build/en/html
+sphinx-build -W --keep-going -b html docs/zh docs/_build/zh/html
 ```
 
-Read the Docs uses the repository's `.readthedocs.yaml` configuration and publishes a language-selection page with mirrored `/en/` and `/zh/` documentation trees.
+Read the Docs publishes two projects linked as parent and translation: `operonproject` (English, `https://operonproject.readthedocs.io/en/latest/`) and `operonproject-zh` (Chinese, `https://operonproject.readthedocs.io/zh-cn/latest/`), each built from its own `docs/<language>/.readthedocs.yaml`.

{operondbs-0.8.0 → operondbs-0.8.3}/README_ZH.md

@@ -1,6 +1,11 @@
-# Operon
+# Operon the Database System
 
-[![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)
+[![test status](https://github.com/HYLi360/Operon/actions/workflows/test.yml/badge.svg)](https://github.com/HYLi360/Operon/actions/workflows/test.yml)
+[![RtD badge](https://img.shields.io/badge/Read-the_Document-blue?style=flat)](https://operonproject.readthedocs.io/)
+![PyPI Version](https://img.shields.io/pypi/v/OperonDBS?link=https%3A%2F%2Fpypi.org%2Fproject%2FOperonDBS%2F)
+![GitHub commit activity](https://img.shields.io/github/commit-activity/t/HYLi360/Operon?logo=github)
+[![Codacy Code quality Badge](https://app.codacy.com/project/badge/Grade/47d652651ff645ff86fa0646768a08b3)](https://app.codacy.com/gh/HYLi360/Operon/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
+[![Codacy Coverage Badge](https://app.codacy.com/project/badge/Coverage/47d652651ff645ff86fa0646768a08b3)](https://app.codacy.com/gh/HYLi360/Operon/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
 
 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。
 
@@ -38,11 +43,12 @@ python -m pip install -e '.[dev]'
 
 ## 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：
+完整文档同时维护[中文](docs/zh/index.md)和[英文](docs/en/index.md)版本。每种语言是独立的 Sphinx 工程，两条构建都必须无警告通过：
 
 ```bash
 python -m pip install -e '.[docs]'
-sphinx-build -W --keep-going -b html docs docs/_build/html
+sphinx-build -W --keep-going -b html docs/en docs/_build/en/html
+sphinx-build -W --keep-going -b html docs/zh docs/_build/zh/html
 ```
 
-Read the Docs 使用仓库根目录的 `.readthedocs.yaml`，发布带语言选择入口及 `/zh/`、`/en/` 镜像目录的文档站点。
+Read the Docs 发布两个互为父项目与翻译的项目：`operonproject`（英文，`https://operonproject.readthedocs.io/en/latest/`）与 `operonproject-zh`（中文，`https://operonproject.readthedocs.io/zh-cn/latest/`），各自从 `docs/<语言>/.readthedocs.yaml` 构建。