OperonDBS 0.7.2__tar.gz → 0.8.2__tar.gz

{operondbs-0.7.2 → operondbs-0.8.2}/.github/workflows/publish.yml

@@ -71,10 +71,11 @@ 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_module._parsers;
+            python -c "import operon; import operon.qc._parsers;
+            import operon.qc._alignment;
             print(operon.__version__)" && operon --help
       - uses: actions/upload-artifact@v7
         with:

operondbs-0.8.2/.github/workflows/test.yml

@@ -0,0 +1,52 @@
+name: test
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+# A newer push supersedes an in-flight run of the same ref.
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # Documentation is cheap to build and independent of the test matrix, so it
+  # runs as its own job in parallel instead of gating the ten test jobs.
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+          cache: pip
+          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
+
+  pytest:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+        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
+          python -m pip install -e '.[test]'
+          python -m pytest
+      - uses: codacy/codacy-coverage-reporter-action@v1.3.0
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

{operondbs-0.7.2 → operondbs-0.8.2}/.gitignore

@@ -5,7 +5,8 @@ dist/
 __pycache__/
 *.py[cod]
 *.so
-operon/qc_module/_parsers.c
+operon/qc/_parsers.c
+operon/qc/_alignment.c
 *.egg-info/
 *.sqlite
 *.sqlite-wal
@@ -14,6 +15,7 @@ logs/
 raw/
 standardized/
 qc/
+!operon/qc/
 analysis/
 reports/
 releases/
@@ -26,3 +28,7 @@ junit.xml
 htmlcov/
 /site/
 /docs/_build/
+/workflows/
+/HPC/
+.matrix/
+cobertura.xml

{operondbs-0.7.2 → operondbs-0.8.2}/AGENTS.md

@@ -26,8 +26,8 @@ principle-to-implementation mapping.
 
 Current version markers (must stay consistent across code and docs):
 
-- `operon` 0.7.0 (`pyproject.toml`)
-- database schema 2.9 (`operon/database.py`, `SCHEMA_VERSION`)
+- `operon` 0.8.2 (`pyproject.toml`)
+- database schema 2.11 (`operon/database.py`, `SCHEMA_VERSION`)
 - metadata schema 1.4 (`operon/schema.py`, `METADATA_SCHEMA_VERSION`)
 
 The project is licensed AGPL-3.0-or-later (`LICENSE` at the repo root).
@@ -36,17 +36,27 @@ The project is licensed AGPL-3.0-or-later (`LICENSE` at the repo root).
 
 - `operon/` — the Python package (CLI entry points: `operon/cli.py`,
   `operon/__main__.py`; console script `operon = operon.cli:main`).
-  - `operon/adapters/` — external source adapters (currently NCBI Datasets,
-    offline-first: JSON/JSONL, ZIP, or unpacked directories, plus optional
-    online download).
-  - `operon/qc_module/` — streaming FASTA/FASTQ/GFF3/protein parsers and
-    built-in QC stages. `parsers.py` is the pure-Python reference
+  - `operon/adapters/` — external source adapters: NCBI Datasets
+    (offline-first: JSON/JSONL, ZIP, or unpacked directories, plus optional
+    online download) and TimeTree (query-cache-only REST client caching the
+    verbatim responses of exact queries under `adapters_cache/timetree/`;
+    mirroring or redistribution is forbidden by TimeTree's terms).
+  - `operon/qc/` — home for all QC functionality: streaming
+    FASTA/FASTQ/GFF3/protein parsers and built-in QC stages, plus alignment
+    QC (`alignment.py`, the pure-Python multiple-alignment QC reference
+    implementation behind `operon alignment-qc`, and `_alignment.pyx`, its
+    Cython production backend; parity enforced by
+    `tests/regression/test_cython_alignment_parity.py`). `parsers.py` is the
+    pure-Python reference
     implementation; `_parsers.pyx` is the Cython-accelerated build of the
-    same API (compiled in place as `operon.qc_module._parsers`). The Cython
+    same API (compiled in place as `operon.qc._parsers`). The Cython
     module is the required production backend; the pure-Python module is the
     behavioral reference used by regression tests. Both must produce
     identical metrics and error messages (enforced by
-    `tests/regression/test_cython_parser_parity.py`).
+    `tests/regression/test_cython_parser_parity.py`). `measure.py` backs
+    `operon qc-measure`, a project-independent measurement-only path whose
+    JSON payload can be imported back through `operon import-qc` (the remote
+    built-in QC workflow).
   - `operon/execution.py` — execution backends for external commands:
     `local` subprocess, `slurm` (sbatch submit + squeue poll), and `ssh`
     (Paramiko; HPC head nodes and cloud VMs, optionally through remote
@@ -96,9 +106,18 @@ The project is licensed AGPL-3.0-or-later (`LICENSE` at the repo root).
     NCBI Taxonomy snapshots and coverage denominators), `release.py` +
     `export.py` (immutable releases and selective exports), `lifecycle.py`
     (audited reversible entity retirement), `lineage.py` (adopting external
-    workflow outputs), `backup.py`, `reports.py`, `table_import.py`,
+    workflow outputs), `sequence_tools.py` (alignment-driven domain
+    extraction and sequence selection), `classify.py` (versioned
+    sequence_classification profiles labelling `sequence_labels`),
+    `fanout.py` (data-derived fan-out of registered sequence files into
+    per-unit FASTAs under `analysis/derived/`, selected downstream by recipe
+    `file_role_prefix`), `timetree.py` (TimeTree query/calibration CLI
+    group backed by the query-cache adapter), `backup.py`, `reports.py`,
+    `table_import.py`,
     `import_wizard.py`, `entity_view.py`, `environment.py`
-    (execution-environment capture), `shutdown.py` (graceful SIGINT/SIGTERM
+    (execution-environment capture with at-capture redaction; recipe
+    `environment_policy` governs environment-aware cache reuse),
+    `shutdown.py` (graceful SIGINT/SIGTERM
     handling), `ncbi_reconcile.py` (development-era adapter anomaly repair),
     `demo.py` (deterministic synthetic demo project), `errors.py`,
     `utils.py`.
@@ -112,6 +131,11 @@ 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`).
+- `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`);
+  `defects.sh` appends to and queries the defect registry (`defects.yml`,
+  see "Defect reports" below).
 
 ## Setup, test, and build
 
@@ -123,22 +147,48 @@ python3 -m venv .venv && source .venv/bin/activate
 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                    # full suite (coverage gate: >=95% combined
+                                    # line+branch, and >=95% branch coverage)
 python -m pytest tests/unit         # by category: unit / integration /
                                     # regression / compatibility
 
+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
+
 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
 ```
 
 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 and the strict Sphinx build. Releases are published
-exclusively to PyPI; see `docs/*/contributor/pypi-release.md`.
+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`.
+
+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
 
-Do not commit or perform other git mutations unless the user explicitly
-asks.
+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
 
@@ -170,6 +220,27 @@ asks.
   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**.
+
+## 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
 
@@ -186,7 +257,7 @@ change:
 - Contributor-facing processes → `docs/*/contributor/`; navigation →
   `docs/*/index.md`
 
-Version markers in docs (`operon` 0.7.0, database schema 2.9, metadata
+Version markers in docs (`operon` 0.8.2, 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
@@ -203,6 +274,9 @@ 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-0.7.2 → operondbs-0.8.2}/MANIFEST.in

@@ -14,4 +14,5 @@ prune docs/_build
 recursive-include operon *.py *.pyx *.tcss
 recursive-include operon/tui/assets *.png *.z *.md
 recursive-include tests *.py
-exclude operon/qc_module/_parsers.c
+exclude operon/qc/_parsers.c
+exclude operon/qc/_alignment.c

{operondbs-0.7.2 → operondbs-0.8.2}/OperonDBS.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OperonDBS
-Version: 0.7.2
+Version: 0.8.2
 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
@@ -8,30 +8,26 @@ Project-URL: Repository, https://github.com/HYLi360/Operon
 Project-URL: Issues, https://github.com/HYLi360/Operon/issues
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: aiohttp>=3.9
 Requires-Dist: biopython>=1.85
-Requires-Dist: PyYAML>=6.0
 Requires-Dist: paramiko>=3.4
+Requires-Dist: PyYAML>=6.0
 Requires-Dist: questionary>=2.1
 Requires-Dist: requests>=2.32
 Requires-Dist: textual>=8.0
 Provides-Extra: test
 Requires-Dist: coverage>=7.0; extra == "test"
+Requires-Dist: cython>=3.0; extra == "test"
 Requires-Dist: paramiko>=3.4; extra == "test"
-Requires-Dist: pytest-cov>=7.0; extra == "test"
 Requires-Dist: pytest>=8.0; extra == "test"
+Requires-Dist: pytest-cov>=7.0; extra == "test"
+Requires-Dist: pytest-xdist>=3.8; extra == "test"
 Requires-Dist: setuptools>=77; extra == "test"
 Requires-Dist: textual>=8.0; extra == "test"
-Requires-Dist: cython>=3.0; extra == "test"
 Provides-Extra: docs
 Requires-Dist: Sphinx<9,>=7.4; extra == "docs"
 Requires-Dist: myst-parser<5,>=4.0; extra == "docs"
@@ -40,17 +36,24 @@ Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "docs"
 Provides-Extra: dev
 Requires-Dist: coverage>=7.0; extra == "dev"
 Requires-Dist: cython>=3.0; extra == "dev"
-Requires-Dist: pytest-cov>=7.0; extra == "dev"
 Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=7.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.8; extra == "dev"
+Requires-Dist: setuptools>=77; extra == "dev"
 Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "dev"
 Requires-Dist: Sphinx<9,>=7.4; extra == "dev"
 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.
 

{operondbs-0.7.2 → operondbs-0.8.2}/OperonDBS.egg-info/SOURCES.txt

@@ -33,6 +33,7 @@ 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
@@ -50,8 +51,10 @@ docs/en/guides/file-archiving.md
 docs/en/guides/index.md
 docs/en/guides/metadata-import.md
 docs/en/guides/ncbi-datasets.md
+docs/en/guides/phylogenetics-workflow.md
 docs/en/guides/qc-profiles.md
 docs/en/guides/remote-execution.md
+docs/en/guides/remote-first.md
 docs/en/guides/remote-storage.md
 docs/en/guides/taxonomy-coverage.md
 docs/en/guides/troubleshooting.md
@@ -73,6 +76,7 @@ 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/zh/index.md
 docs/zh/overview.md
 docs/zh/architecture/extensibility.md
@@ -84,6 +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
@@ -101,8 +106,10 @@ docs/zh/guides/file-archiving.md
 docs/zh/guides/index.md
 docs/zh/guides/metadata-import.md
 docs/zh/guides/ncbi-datasets.md
+docs/zh/guides/phylogenetics-workflow.md
 docs/zh/guides/qc-profiles.md
 docs/zh/guides/remote-execution.md
+docs/zh/guides/remote-first.md
 docs/zh/guides/remote-storage.md
 docs/zh/guides/taxonomy-coverage.md
 docs/zh/guides/troubleshooting.md
@@ -124,9 +131,11 @@ 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
+operon/classify.py
 operon/cli.py
 operon/config.py
 operon/coverage.py
@@ -134,9 +143,11 @@ operon/database.py
 operon/demo.py
 operon/entity_view.py
 operon/environment.py
+operon/environment_capture.py
 operon/errors.py
 operon/execution.py
 operon/export.py
+operon/fanout.py
 operon/files.py
 operon/import_wizard.py
 operon/lifecycle.py
@@ -149,17 +160,24 @@ operon/remotes.py
 operon/reports.py
 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
 operon/tools.py
 operon/utils.py
 operon/workflow.py
 operon/adapters/__init__.py
 operon/adapters/ncbi_datasets.py
-operon/qc_module/__init__.py
-operon/qc_module/_parsers.pyx
-operon/qc_module/parsers.py
+operon/adapters/timetree.py
+operon/qc/__init__.py
+operon/qc/_alignment.pyx
+operon/qc/_parsers.pyx
+operon/qc/alignment.py
+operon/qc/measure.py
+operon/qc/parsers.py
 operon/tui/__init__.py
 operon/tui/actions.py
 operon/tui/app.py
@@ -186,53 +204,82 @@ 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
+tests/integration/test_classify_sequences.py
 tests/integration/test_execution_backends.py
+tests/integration/test_fanout_analyze.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_qc_remote_measure.py
 tests/integration/test_taxonomy_coverage.py
 tests/regression/__init__.py
 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
 tests/unit/test_cli_edges.py
 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_versions.py
 tests/unit/test_environment.py
+tests/unit/test_environment_capture.py
 tests/unit/test_execution.py
 tests/unit/test_execution_edges.py
 tests/unit/test_export.py
+tests/unit/test_fanout.py
 tests/unit/test_files_edges.py
+tests/unit/test_follow.py
 tests/unit/test_import_backup_show.py
 tests/unit/test_import_wizard_edges.py
 tests/unit/test_lifecycle.py
 tests/unit/test_lineage.py
+tests/unit/test_misc_coverage_more.py
+tests/unit/test_ncbi_coverage_gaps.py
 tests/unit/test_ncbi_edge_cases.py
 tests/unit/test_ncbi_reconcile_edges.py
 tests/unit/test_parser_edge_paths.py
 tests/unit/test_qc_and_rules.py
 tests/unit/test_qc_edges_more.py
+tests/unit/test_qc_measure.py
+tests/unit/test_qc_remote_only.py
 tests/unit/test_recipe_history.py
+tests/unit/test_remote_taxonomy_more.py
+tests/unit/test_remote_transport_edges.py
 tests/unit/test_remotes.py
 tests/unit/test_remotes_edges.py
 tests/unit/test_rules_schema_edges.py
+tests/unit/test_schema_2_10.py
+tests/unit/test_schema_2_11.py
 tests/unit/test_schema_2_9.py
 tests/unit/test_schema_and_metadata.py
+tests/unit/test_sequence_tools.py
+tests/unit/test_sequences.py
 tests/unit/test_shutdown.py
 tests/unit/test_support_edges.py
 tests/unit/test_table_import_edges.py
 tests/unit/test_taxonomy_edges.py
+tests/unit/test_timetree.py
+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_config.py
+tests/unit/test_tui_flows_more.py
 tests/unit/test_tui_publish.py
+tests/unit/test_tui_screens_more.py
 tests/unit/test_tui_splash_terminal.py
 tests/unit/test_tui_writes.py
 tests/unit/test_views_release_reports_edges.py

{operondbs-0.7.2 → operondbs-0.8.2}/OperonDBS.egg-info/requires.txt

@@ -1,7 +1,7 @@
 aiohttp>=3.9
 biopython>=1.85
-PyYAML>=6.0
 paramiko>=3.4
+PyYAML>=6.0
 questionary>=2.1
 requests>=2.32
 textual>=8.0
@@ -9,8 +9,10 @@ textual>=8.0
 [dev]
 coverage>=7.0
 cython>=3.0
-pytest-cov>=7.0
 pytest>=8.0
+pytest-cov>=7.0
+pytest-xdist>=3.8
+setuptools>=77
 Sphinx<9,>=7.4
 myst-parser<5,>=4.0
 sphinx-rtd-theme<4,>=3.0
@@ -28,9 +30,10 @@ tomli>=2.0
 
 [test]
 coverage>=7.0
+cython>=3.0
 paramiko>=3.4
-pytest-cov>=7.0
 pytest>=8.0
+pytest-cov>=7.0
+pytest-xdist>=3.8
 setuptools>=77
 textual>=8.0
-cython>=3.0

{operondbs-0.7.2 → operondbs-0.8.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: OperonDBS
-Version: 0.7.2
+Version: 0.8.2
 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
@@ -8,30 +8,26 @@ Project-URL: Repository, https://github.com/HYLi360/Operon
 Project-URL: Issues, https://github.com/HYLi360/Operon/issues
 Classifier: Operating System :: MacOS
 Classifier: Operating System :: POSIX :: Linux
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3 :: Only
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: aiohttp>=3.9
 Requires-Dist: biopython>=1.85
-Requires-Dist: PyYAML>=6.0
 Requires-Dist: paramiko>=3.4
+Requires-Dist: PyYAML>=6.0
 Requires-Dist: questionary>=2.1
 Requires-Dist: requests>=2.32
 Requires-Dist: textual>=8.0
 Provides-Extra: test
 Requires-Dist: coverage>=7.0; extra == "test"
+Requires-Dist: cython>=3.0; extra == "test"
 Requires-Dist: paramiko>=3.4; extra == "test"
-Requires-Dist: pytest-cov>=7.0; extra == "test"
 Requires-Dist: pytest>=8.0; extra == "test"
+Requires-Dist: pytest-cov>=7.0; extra == "test"
+Requires-Dist: pytest-xdist>=3.8; extra == "test"
 Requires-Dist: setuptools>=77; extra == "test"
 Requires-Dist: textual>=8.0; extra == "test"
-Requires-Dist: cython>=3.0; extra == "test"
 Provides-Extra: docs
 Requires-Dist: Sphinx<9,>=7.4; extra == "docs"
 Requires-Dist: myst-parser<5,>=4.0; extra == "docs"
@@ -40,17 +36,24 @@ Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "docs"
 Provides-Extra: dev
 Requires-Dist: coverage>=7.0; extra == "dev"
 Requires-Dist: cython>=3.0; extra == "dev"
-Requires-Dist: pytest-cov>=7.0; extra == "dev"
 Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pytest-cov>=7.0; extra == "dev"
+Requires-Dist: pytest-xdist>=3.8; extra == "dev"
+Requires-Dist: setuptools>=77; extra == "dev"
 Requires-Dist: tomli>=2.0; python_version < "3.11" and extra == "dev"
 Requires-Dist: Sphinx<9,>=7.4; extra == "dev"
 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.
 

{operondbs-0.7.2 → operondbs-0.8.2}/README.md

@@ -1,6 +1,11 @@
-# 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)
+# 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)
+[![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.