OperonDBS 0.8.2__tar.gz → 0.8.4__tar.gz

{operondbs-0.8.2 → operondbs-0.8.4}/.github/workflows/publish.yml

@@ -8,7 +8,46 @@ permissions:
   contents: read
 
 jobs:
+  verify-release:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      actions: read
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ github.event.release.tag_name }}
+          fetch-depth: 0
+          persist-credentials: false
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - run: python -m pip install --upgrade pip pyyaml
+      - name: The tagged commit passed its own CI run
+        env:
+          GH_TOKEN: ${{ github.token }}
+          RELEASE_TAG: ${{ github.event.release.tag_name }}
+        run: |
+          sha=$(git rev-parse HEAD)
+          conclusion=$(gh api \
+            "repos/${{ github.repository }}/actions/workflows/test.yml/runs?head_sha=$sha&per_page=1" \
+            --jq '.workflow_runs[0].conclusion // "no run"')
+          echo "$RELEASE_TAG -> $sha: test.yml concluded '$conclusion'"
+          if [ "$conclusion" != "success" ]; then
+            echo "::error::test.yml on $sha concluded '$conclusion'; rerun it (gh run rerun) before releasing"
+            exit 1
+          fi
+      - name: Import the maintainer's published GPG key
+        run: |
+          curl -sSL "https://github.com/${{ github.repository_owner }}.gpg" | gpg --import
+          gpg --list-keys --with-colons | grep '^pub' | wc -l
+      - name: Release preflight
+        env:
+          RELEASE_TAG: ${{ github.event.release.tag_name }}
+        run: scripts/release-preflight.sh --ci --tag "$RELEASE_TAG"
+
   source-distribution:
+    needs: verify-release
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
@@ -35,6 +74,7 @@ jobs:
           if-no-files-found: error
 
   documentation:
+    needs: verify-release
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
@@ -43,9 +83,12 @@ 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:
+    needs: verify-release
     strategy:
       fail-fast: false
       matrix:
@@ -84,7 +127,7 @@ jobs:
           if-no-files-found: error
 
   pypi-publish:
-    needs: [source-distribution, wheels]
+    needs: [verify-release, source-distribution, wheels]
     runs-on: ubuntu-latest
     environment:
       name: pypi

{operondbs-0.8.2 → operondbs-0.8.4}/.github/workflows/test.yml

@@ -25,7 +25,9 @@ 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:

{operondbs-0.8.2 → operondbs-0.8.4}/.gitignore

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

{operondbs-0.8.2 → operondbs-0.8.4}/AGENTS.md

@@ -26,7 +26,7 @@ principle-to-implementation mapping.
 
 Current version markers (must stay consistent across code and docs):
 
-- `operon` 0.8.2 (`pyproject.toml`)
+- `operon` 0.8.4 (`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
@@ -127,15 +158,24 @@ 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
+  `run-test-matrix.sh` build and drive the uv-managed Python 3.10–3.15
   matrix under .matrix/ (see `docs/*/contributor/development-testing.md`);
-  `defects.sh` appends to and queries the defect registry (`defects.yml`,
-  see "Defect reports" below).
+  `release-preflight.sh` is the release gate and the script the publish
+  workflow runs on the tag; `defects.sh` appends to and queries the defect
+  registry (`defects.yml`, see "Defect reports" below).
 
 ## Setup, test, and build
 
@@ -154,25 +194,37 @@ 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 3.10-3.15 concurrently
+scripts/setup-test-matrix.sh        # once per machine: uv-managed 3.10-3.15 venvs
+scripts/run-test-matrix.sh          # whole suite on 3.10-3.15, in waves
+                                    # (MATRIX_CONCURRENCY / MATRIX_JOBS override the split)
+scripts/release-preflight.sh        # the release gate: version, full suite, both doc
+                                    # trees, defect registry, matrix evidence for HEAD;
+                                    # --run-matrix runs the matrix inside the gate, and
+                                    # --tag vX.Y.Z asserts the tag's name/signature/target
 
 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 3.10–3.15 and the strict
-Sphinx build. Releases are published exclusively to PyPI; see `docs/*/contributor/pypi-release.md`.
+Sphinx build. Releases are published exclusively to PyPI, and
+`.github/workflows/publish.yml` builds nothing and uploads nothing until its
+`verify-release` job has seen a `success` conclusion for the tagged commit's `test`
+run *and* a passing `scripts/release-preflight.sh --ci --tag <tag>`; 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).
+> (auto: 24 workers). Running the local test matrix takes about 5 minutes
+> (6 versions, 3 at a time × 7 workers by default; `MATRIX_CONCURRENCY` /
+> `MATRIX_JOBS` override the split).
 > 
 > Measured on Intel Core i7-13700HX (16c24t).
 
@@ -216,15 +268,18 @@ proceed with caution).
   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
 
@@ -256,12 +311,15 @@ 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` 0.8.2, database schema 2.11, metadata
+Version markers in docs (`operon` 0.8.4, 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

{operondbs-0.8.2 → operondbs-0.8.4}/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-0.8.2 → operondbs-0.8.4}/OperonDBS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OperonDBS
-Version: 0.8.2
+Version: 0.8.4
 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
@@ -93,11 +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-0.8.2 → operondbs-0.8.4}/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
@@ -77,6 +74,9 @@ 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
@@ -183,21 +183,30 @@ 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
@@ -233,6 +242,7 @@ 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
@@ -276,8 +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-0.8.2 → operondbs-0.8.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OperonDBS
-Version: 0.8.2
+Version: 0.8.4
 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
@@ -93,11 +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-0.8.2 → operondbs-0.8.4}/README.md

@@ -45,11 +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-0.8.2 → operondbs-0.8.4}/README_ZH.md

@@ -43,11 +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。