orca-auto 6.0.0__tar.gz

orca_auto-6.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Daehyup Sohn
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

orca_auto-6.0.0/MANIFEST.in

@@ -0,0 +1 @@
+prune extensions

orca_auto-6.0.0/PKG-INFO

@@ -0,0 +1,124 @@
+Metadata-Version: 2.4
+Name: orca_auto
+Version: 6.0.0
+Summary: ORCA_auto core: durable ORCA queues and supervised execution
+Author: Daehyup Sohn
+License: MIT License
+        
+        Copyright (c) 2026 Daehyup Sohn
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/dhsohn/orca_auto
+Project-URL: Repository, https://github.com/dhsohn/orca_auto
+Project-URL: Issues, https://github.com/dhsohn/orca_auto/issues
+Project-URL: Documentation, https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/INSTALLATION.md
+Project-URL: Changelog, https://github.com/dhsohn/orca_auto/blob/v6.0.0/CHANGELOG.md
+Keywords: orca,dft,computational-chemistry,workflow-automation,cli
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: PyYAML>=6.0.1
+Provides-Extra: workflows
+Requires-Dist: orca_auto_workflows==6.0.0; extra == "workflows"
+Provides-Extra: dev
+Requires-Dist: build>=1.2.2; extra == "dev"
+Requires-Dist: setuptools>=68.0; extra == "dev"
+Requires-Dist: wheel>=0.45.1; extra == "dev"
+Requires-Dist: import-linter>=2.12; extra == "dev"
+Requires-Dist: mypy>=1.19.1; extra == "dev"
+Requires-Dist: pytest>=9.0; extra == "dev"
+Requires-Dist: pytest-cov>=7.0.0; extra == "dev"
+Requires-Dist: ruff>=0.15.5; extra == "dev"
+Requires-Dist: types-PyYAML>=6.0.12; extra == "dev"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://raw.githubusercontent.com/dhsohn/orca_auto/v6.0.0/docs/images/banner.svg" alt="ORCA_auto — Submit durably. Execute reliably. Recover explicitly." width="680">
+</p>
+
+<p align="center">
+  <a href="https://github.com/dhsohn/orca_auto/actions/workflows/ci.yml"><img src="https://github.com/dhsohn/orca_auto/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+  <a href="https://github.com/dhsohn/orca_auto/releases/latest"><img src="https://img.shields.io/github/v/release/dhsohn/orca_auto" alt="Release"></a>
+  <a href="https://www.python.org/"><img src="https://img.shields.io/badge/python-3.11%2B-blue.svg" alt="Python 3.11+"></a>
+  <a href="https://github.com/dhsohn/orca_auto/blob/v6.0.0/LICENSE"><img src="https://img.shields.io/badge/License-MIT-blue.svg" alt="License: MIT"></a>
+</p>
+
+<p align="center"><b>English</b> · <a href="https://github.com/dhsohn/orca_auto/blob/v6.0.0/README.ko.md">한국어</a></p>
+
+ORCA_auto is a **queue-first runner for ORCA** on Linux/WSL.
+Submit calculations to a durable queue, follow their progress, and inspect
+recorded results and recovery decisions. Input design and chemical judgment
+stay with you.
+
+## Features
+
+- **Submit and close the terminal.** A successful submission saves the job to
+  disk; a supervised worker handles execution.
+- **See what happened.** Check queue status from the CLI and inspect saved
+  calculation reports and failure reasons.
+- **Recover with evidence.** Worker or host interruptions follow verified
+  recovery paths. Failed ORCA calculations are not automatically retried.
+
+## Get started
+
+Python **3.11+**, Linux/WSL2, and a separately installed ORCA engine are
+required. Supervised workers use `systemd`.
+
+```bash
+python -m pip install orca_auto==6.0.0
+```
+
+- **[Installation details](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/INSTALLATION.md)** — install Core from PyPI in a fresh environment.
+- **[Set up workers and submit your first job](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/QUICKSTART.md)** — configure a
+  source checkout, start services, and inspect the queue.
+
+**Upgrading?** Keep running calculations on their current environment. Switch
+only in an idle window; see the [upgrade guide](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/RELEASE.md#removing-ts-workflows-in-60).
+
+## In the same chemistry ecosystem
+
+[Chemvas](https://github.com/dhsohn/Chemvas) for chemical drawings,
+**ORCA_auto** for calculation execution, and
+[LLMdocx](https://github.com/dhsohn/LLMdocx) for research documents are
+independent, local-first companion tools. Data handoffs require explicit
+conversion—not an automatic end-to-end integration.
+[How the tools connect →](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/RELATED_WORK.md#local-first-companion-tools)
+
+## Documentation
+
+[Command reference](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/REFERENCE.md) · [Runtime contracts](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/PUBLIC_CONTRACTS.md) ·
+[Architecture](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/ARCHITECTURE.md) · [Services](https://github.com/dhsohn/orca_auto/blob/v6.0.0/systemd/README.md) ·
+[Discord notifications](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/DISCORD_SETUP.md)
+
+[Development](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/DEVELOPMENT.md) · [Validation](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/VALIDATION.md) ·
+[Roadmap](https://github.com/dhsohn/orca_auto/blob/v6.0.0/ROADMAP.md) · [Changelog](https://github.com/dhsohn/orca_auto/blob/v6.0.0/CHANGELOG.md)
+
+[Citation](https://github.com/dhsohn/orca_auto/blob/v6.0.0/CITATION.cff) · [Contributing](https://github.com/dhsohn/orca_auto/blob/v6.0.0/CONTRIBUTING.md) ·
+[Support](https://github.com/dhsohn/orca_auto/blob/v6.0.0/SUPPORT.md) · [Security](https://github.com/dhsohn/orca_auto/blob/v6.0.0/SECURITY.md)

orca_auto-6.0.0/README.md

@@ -0,0 +1,63 @@
+<p align="center">
+  <img src="https://raw.githubusercontent.com/dhsohn/orca_auto/v6.0.0/docs/images/banner.svg" alt="ORCA_auto — Submit durably. Execute reliably. Recover explicitly." width="680">
+</p>
+
+<p align="center">
+  <a href="https://github.com/dhsohn/orca_auto/actions/workflows/ci.yml"><img src="https://github.com/dhsohn/orca_auto/actions/workflows/ci.yml/badge.svg" alt="CI"></a>
+  <a href="https://github.com/dhsohn/orca_auto/releases/latest"><img src="https://img.shields.io/github/v/release/dhsohn/orca_auto" alt="Release"></a>
+  <a href="https://www.python.org/"><img src="https://img.shields.io/badge/python-3.11%2B-blue.svg" alt="Python 3.11+"></a>
+  <a href="https://github.com/dhsohn/orca_auto/blob/v6.0.0/LICENSE"><img src="https://img.shields.io/badge/License-MIT-blue.svg" alt="License: MIT"></a>
+</p>
+
+<p align="center"><b>English</b> · <a href="https://github.com/dhsohn/orca_auto/blob/v6.0.0/README.ko.md">한국어</a></p>
+
+ORCA_auto is a **queue-first runner for ORCA** on Linux/WSL.
+Submit calculations to a durable queue, follow their progress, and inspect
+recorded results and recovery decisions. Input design and chemical judgment
+stay with you.
+
+## Features
+
+- **Submit and close the terminal.** A successful submission saves the job to
+  disk; a supervised worker handles execution.
+- **See what happened.** Check queue status from the CLI and inspect saved
+  calculation reports and failure reasons.
+- **Recover with evidence.** Worker or host interruptions follow verified
+  recovery paths. Failed ORCA calculations are not automatically retried.
+
+## Get started
+
+Python **3.11+**, Linux/WSL2, and a separately installed ORCA engine are
+required. Supervised workers use `systemd`.
+
+```bash
+python -m pip install orca_auto==6.0.0
+```
+
+- **[Installation details](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/INSTALLATION.md)** — install Core from PyPI in a fresh environment.
+- **[Set up workers and submit your first job](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/QUICKSTART.md)** — configure a
+  source checkout, start services, and inspect the queue.
+
+**Upgrading?** Keep running calculations on their current environment. Switch
+only in an idle window; see the [upgrade guide](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/RELEASE.md#removing-ts-workflows-in-60).
+
+## In the same chemistry ecosystem
+
+[Chemvas](https://github.com/dhsohn/Chemvas) for chemical drawings,
+**ORCA_auto** for calculation execution, and
+[LLMdocx](https://github.com/dhsohn/LLMdocx) for research documents are
+independent, local-first companion tools. Data handoffs require explicit
+conversion—not an automatic end-to-end integration.
+[How the tools connect →](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/RELATED_WORK.md#local-first-companion-tools)
+
+## Documentation
+
+[Command reference](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/REFERENCE.md) · [Runtime contracts](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/PUBLIC_CONTRACTS.md) ·
+[Architecture](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/ARCHITECTURE.md) · [Services](https://github.com/dhsohn/orca_auto/blob/v6.0.0/systemd/README.md) ·
+[Discord notifications](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/DISCORD_SETUP.md)
+
+[Development](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/DEVELOPMENT.md) · [Validation](https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/VALIDATION.md) ·
+[Roadmap](https://github.com/dhsohn/orca_auto/blob/v6.0.0/ROADMAP.md) · [Changelog](https://github.com/dhsohn/orca_auto/blob/v6.0.0/CHANGELOG.md)
+
+[Citation](https://github.com/dhsohn/orca_auto/blob/v6.0.0/CITATION.cff) · [Contributing](https://github.com/dhsohn/orca_auto/blob/v6.0.0/CONTRIBUTING.md) ·
+[Support](https://github.com/dhsohn/orca_auto/blob/v6.0.0/SUPPORT.md) · [Security](https://github.com/dhsohn/orca_auto/blob/v6.0.0/SECURITY.md)

orca_auto-6.0.0/pyproject.toml

@@ -0,0 +1,335 @@
+[build-system]
+requires = ["setuptools>=68.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "orca_auto"
+version = "6.0.0"
+description = "ORCA_auto core: durable ORCA queues and supervised execution"
+readme = "README.md"
+requires-python = ">=3.11"
+license = { file = "LICENSE" }
+authors = [
+    { name = "Daehyup Sohn" },
+]
+keywords = [
+    "orca",
+    "dft",
+    "computational-chemistry",
+    "workflow-automation",
+    "cli",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+dependencies = [
+    "PyYAML>=6.0.1",
+]
+
+[project.urls]
+Homepage = "https://github.com/dhsohn/orca_auto"
+Repository = "https://github.com/dhsohn/orca_auto"
+Issues = "https://github.com/dhsohn/orca_auto/issues"
+Documentation = "https://github.com/dhsohn/orca_auto/blob/v6.0.0/docs/INSTALLATION.md"
+Changelog = "https://github.com/dhsohn/orca_auto/blob/v6.0.0/CHANGELOG.md"
+
+[project.optional-dependencies]
+workflows = ["orca_auto_workflows==6.0.0"]
+dev = [
+    "build>=1.2.2",
+    "setuptools>=68.0",
+    "wheel>=0.45.1",
+    "import-linter>=2.12",
+    "mypy>=1.19.1",
+    "pytest>=9.0",
+    "pytest-cov>=7.0.0",
+    "ruff>=0.15.5",
+    "types-PyYAML>=6.0.12",
+]
+
+[project.scripts]
+orca_auto = "orca_auto.cli:main"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["orca_auto*"]
+
+[tool.ruff]
+target-version = "py311"
+line-length = 100
+src = [".", "src", "extensions/workflows/src"]
+
+[tool.ruff.lint]
+# Layout (including line length) is owned by `ruff format`, which
+# `scripts/check.sh` enforces via `ruff format --check`. `E501` is intentionally
+# omitted so the formatter stays the single source of truth for line wrapping.
+select = [
+    "E4",
+    "E7",
+    "E9",
+    "F",
+    "I",
+    "B",
+    "BLE",
+    "FURB162",
+    "FURB188",
+    "PYI034",
+    "UP",
+    "RUF100",
+]
+# UP042 (str-Enum -> StrEnum) changes `str()`/format semantics of status enums
+# that are serialized and compared as plain strings; keep the str mixin.
+ignore = ["UP042"]
+
+[tool.mypy]
+python_version = "3.11"
+files = ["src/orca_auto", "extensions/workflows/src/orca_auto/flow", "tests"]
+mypy_path = ["src", "extensions/workflows/src"]
+pretty = true
+show_error_codes = true
+warn_unused_configs = true
+explicit_package_bases = true
+
+# The strict-style mypy options apply to the whole orca_auto package; every
+# module under src already passes them, so a new or moved module is strict
+# by default. Tests stay on the non-strict top-level config until the full
+# src+tests tree passes the equivalent strict flags, at which point the
+# options move to [tool.mypy].
+[[tool.mypy.overrides]]
+module = ["orca_auto", "orca_auto.*"]
+check_untyped_defs = true
+disallow_any_generics = true
+disallow_incomplete_defs = true
+disallow_untyped_calls = true
+disallow_untyped_defs = true
+no_implicit_optional = true
+strict_equality = true
+warn_return_any = true
+warn_unused_ignores = true
+
+# Layering is enforced by import-linter (`lint-imports`, run by scripts/check.sh
+# and therefore by CI). Engine wiring crosses layers only through lazy string
+# module paths (core/engine_catalog.py). The absent-workflows subprocess tests
+# additionally exercise this dynamic seam, which static import checks cannot see.
+[tool.importlinter]
+root_packages = ["orca_auto"]
+exclude_type_checking_imports = true
+
+[[tool.importlinter.contracts]]
+name = "Layered architecture: flow -> orca -> core"
+type = "layers"
+layers = [
+    "orca_auto.flow",
+    "orca_auto.orca",
+    "orca_auto.core",
+]
+
+[[tool.importlinter.contracts]]
+name = "Messaging never imports the notification layer"
+type = "forbidden"
+source_modules = ["orca_auto.core.messaging"]
+forbidden_modules = ["orca_auto.core.notifications"]
+
+[[tool.importlinter.contracts]]
+name = "ORCA domain and worker policy never import CLI commands"
+type = "forbidden"
+source_modules = [
+    "orca_auto.orca.execution",
+    "orca_auto.orca.run_context",
+    "orca_auto.orca.submission",
+    "orca_auto.orca.worker_execution",
+    "orca_auto.orca.queue",
+]
+forbidden_modules = ["orca_auto.orca.commands"]
+
+[[tool.importlinter.contracts]]
+name = "ORCA state reading stays below mutation and report publication"
+type = "forbidden"
+source_modules = ["orca_auto.orca.state_reading"]
+forbidden_modules = [
+    "orca_auto.orca.state",
+    "orca_auto.orca.report",
+]
+
+[[tool.importlinter.contracts]]
+name = "ORCA structure and frequency evidence never depend on human reports"
+type = "forbidden"
+source_modules = [
+    "orca_auto.orca.evidence",
+    "orca_auto.orca.frequencies",
+]
+forbidden_modules = ["orca_auto.orca.report"]
+
+[[tool.importlinter.contracts]]
+name = "Workflow structure evidence and selection never depend on SI presentation"
+type = "forbidden"
+source_modules = [
+    "orca_auto.flow.orca_stage_evidence",
+    "orca_auto.flow.conformer_selection",
+]
+forbidden_modules = ["orca_auto.orca.report.si", "orca_auto.orca.report.frequencies"]
+
+[[tool.importlinter.contracts]]
+name = "Workflow stage views stay below orchestration wiring"
+type = "forbidden"
+source_modules = [
+    "orca_auto.flow.orchestration.stage_view_mutators",
+    "orca_auto.flow.orchestration.stage_views",
+]
+forbidden_modules = [
+    "orca_auto.flow.orchestration.advance",
+    "orca_auto.flow.orchestration.advance_phases",
+    "orca_auto.flow.orchestration.services",
+]
+
+[[tool.importlinter.contracts]]
+name = "Workflow report evidence consumers stay below rendering"
+type = "forbidden"
+source_modules = [
+    "orca_auto.flow.workflow.report_collection",
+    "orca_auto.flow.workflow.report_diagnostics",
+    "orca_auto.flow.workflow.report_energy_evidence",
+    "orca_auto.flow.workflow.machine",
+    "orca_auto.flow.workflow.notifications",
+    "orca_auto.flow.workflow.si.collection",
+]
+forbidden_modules = ["orca_auto.flow.workflow.report_rendering"]
+
+[[tool.importlinter.contracts]]
+name = "Workflow report collection stays above evidence readers"
+type = "layers"
+layers = [
+    "orca_auto.flow.workflow.report_collection",
+    "orca_auto.flow.workflow.report_energy_evidence",
+    "orca_auto.flow.workflow.report_diagnostics",
+]
+
+[[tool.importlinter.contracts]]
+name = "Workflow SI layers: publication over rendering over collection"
+type = "layers"
+layers = [
+    "orca_auto.flow.workflow.si.publication",
+    "orca_auto.flow.workflow.si.rendering",
+    "orca_auto.flow.workflow.si.collection",
+]
+
+[[tool.importlinter.contracts]]
+name = "Systemd CLI layers: independent command owners over freshness over units over plan"
+type = "layers"
+layers = [
+    "orca_auto.cli_systemd_apply | orca_auto.cli_systemd_restart | orca_auto.cli_systemd_status",
+    "orca_auto.cli_systemd_restart_guard",
+    "orca_auto.cli_systemd_freshness",
+    "orca_auto.cli_systemd_units",
+    "orca_auto.systemd_plan",
+]
+
+[[tool.importlinter.contracts]]
+name = "ORCA stage validation never imports materialization"
+type = "forbidden"
+source_modules = ["orca_auto.flow.orca_stage_validation"]
+forbidden_modules = ["orca_auto.flow._orca_stage_materialization"]
+
+[[tool.importlinter.contracts]]
+name = "Bounded YAML substrate never imports config policy"
+type = "forbidden"
+source_modules = ["orca_auto.core.config.bounded_yaml"]
+forbidden_modules = ["orca_auto.core.config.files"]
+
+[[tool.importlinter.contracts]]
+name = "Worker process supervision stays below CLI assembly"
+type = "forbidden"
+source_modules = ["orca_auto.cli_worker_supervision"]
+forbidden_modules = ["orca_auto.cli_workers"]
+
+[[tool.importlinter.contracts]]
+name = "Restart settings stay mutation-free"
+type = "forbidden"
+source_modules = ["orca_auto.flow.restart.settings"]
+forbidden_modules = [
+    "orca_auto.flow.restart.mutation",
+    "orca_auto.flow.restart.orca_input",
+    "orca_auto.flow.restart.stage_ops",
+]
+
+[[tool.importlinter.contracts]]
+name = "Restart mutation layers: mutation over stage ops over ORCA input"
+type = "layers"
+layers = [
+    "orca_auto.flow.restart.mutation",
+    "orca_auto.flow.restart.stage_ops",
+    "orca_auto.flow.restart.orca_input",
+]
+
+[[tool.importlinter.contracts]]
+name = "Restart settings resolve independently of the mutation owners"
+type = "forbidden"
+source_modules = [
+    "orca_auto.flow.restart.mutation",
+    "orca_auto.flow.restart.orca_input",
+    "orca_auto.flow.restart.stage_ops",
+]
+forbidden_modules = ["orca_auto.flow.restart.settings"]
+
+[[tool.importlinter.contracts]]
+name = "ORCA input syntax never imports reference scanning"
+type = "forbidden"
+source_modules = ["orca_auto.orca.input_blocks"]
+forbidden_modules = ["orca_auto.orca.input_references"]
+
+[[tool.importlinter.contracts]]
+name = "ORCA input reference scanning stays below runtime consumers"
+type = "forbidden"
+source_modules = ["orca_auto.orca.input_references"]
+forbidden_modules = [
+    "orca_auto.flow.conformer_selection",
+    "orca_auto.flow.restart.orca_input",
+    "orca_auto.orca.execution_binding",
+    "orca_auto.orca.scratch",
+]
+
+# The top-level CLI modules are the outermost layer: they compose the domain
+# packages, and no domain package may reach back up into them. Shared terminal
+# presentation and config discovery live in core so command adapters inside
+# flow can use them without crossing this boundary.
+[[tool.importlinter.contracts]]
+name = "Domain packages never import the top-level CLI layer"
+type = "forbidden"
+source_modules = ["orca_auto.core", "orca_auto.orca", "orca_auto.flow"]
+forbidden_modules = [
+    "orca_auto._process_evidence",
+    "orca_auto.activity",
+    "orca_auto.activity_labels",
+    "orca_auto.activity_rendering",
+    "orca_auto.activity_view",
+    "orca_auto.cli",
+    "orca_auto.cli_handlers",
+    "orca_auto.cli_parsers",
+    "orca_auto.cli_queue",
+    "orca_auto.cli_systemd_apply",
+    "orca_auto.cli_systemd_freshness",
+    "orca_auto.cli_systemd_restart",
+    "orca_auto.cli_systemd_restart_guard",
+    "orca_auto.cli_systemd_status",
+    "orca_auto.cli_systemd_units",
+    "orca_auto.cli_worker_supervision",
+    "orca_auto.cli_workers",
+    "orca_auto.systemd_plan",
+    "orca_auto.terminal_table",
+]
+
+[tool.coverage.run]
+source = ["src/orca_auto", "extensions/workflows/src/orca_auto/flow"]
+
+[tool.coverage.report]
+fail_under = 80
+show_missing = true

orca_auto-6.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

orca_auto-6.0.0/src/orca_auto/__init__.py

@@ -0,0 +1,11 @@
+"""Shared namespace package for the chemistry automation monorepo."""
+
+from pkgutil import extend_path
+
+# Core owns this initializer; separately installed extensions own subpackages.
+# Never discover sibling checkout sources unless they were explicitly installed.
+__path__ = extend_path(__path__, __name__)
+
+from ._version import __version__
+
+__all__ = ["__version__"]

orca_auto-6.0.0/src/orca_auto/_process_evidence.py

@@ -0,0 +1,60 @@
+"""Process-local provenance used by the systemd freshness check."""
+
+from __future__ import annotations
+
+import os
+import sys
+from importlib import import_module
+from pathlib import Path
+
+PROCESS_IMPORT_SOURCE_ENV = "ORCA_AUTO_PROCESS_IMPORT_SOURCE"
+PROCESS_WORKFLOW_IMPORT_SOURCE_ENV = "ORCA_AUTO_PROCESS_WORKFLOW_IMPORT_SOURCE"
+
+
+def _workflow_worker_requested(argv: list[str]) -> bool:
+    return "--app=workflow" in argv or any(
+        flag == "--app" and value == "workflow" for flag, value in zip(argv, argv[1:], strict=False)
+    )
+
+
+def exec_with_import_source_evidence() -> None:
+    """Re-exec the module CLI once with its actual imported source in environ.
+
+    ``/proc/<pid>/environ`` exposes only the environment installed by ``exec``;
+    mutating ``os.environ`` after Python starts is not reliable process evidence.
+    Re-exec preserves the systemd MainPID and kernel process start identity while
+    making the source path observable without a sidecar state file.
+    """
+
+    if sys.argv[1:3] != ["queue", "worker"]:
+        return
+    import_source = str(Path(__file__).resolve(strict=False))
+    environment = os.environ.copy()
+    environment[PROCESS_IMPORT_SOURCE_ENV] = import_source
+    if _workflow_worker_requested(sys.argv[3:]):
+        from orca_auto.core.extensions import require_workflows
+
+        require_workflows()
+        workflow_module = import_module("orca_auto.flow")
+        workflow_source = workflow_module.__file__
+        if workflow_source is None:
+            raise ValueError("workflow import source is unavailable")
+        environment[PROCESS_WORKFLOW_IMPORT_SOURCE_ENV] = str(
+            Path(workflow_source).resolve(strict=True)
+        )
+    else:
+        environment.pop(PROCESS_WORKFLOW_IMPORT_SOURCE_ENV, None)
+    if environment == os.environ:
+        return
+    os.execve(
+        sys.executable,
+        [sys.executable, "-m", "orca_auto.cli", *sys.argv[1:]],
+        environment,
+    )
+
+
+__all__ = [
+    "PROCESS_IMPORT_SOURCE_ENV",
+    "PROCESS_WORKFLOW_IMPORT_SOURCE_ENV",
+    "exec_with_import_source_evidence",
+]

orca_auto-6.0.0/src/orca_auto/_version.py

@@ -0,0 +1,45 @@
+from __future__ import annotations
+
+import tomllib
+from importlib import metadata
+from pathlib import Path
+
+
+def package_version() -> str:
+    try:
+        return metadata.version("orca_auto")
+    except metadata.PackageNotFoundError:
+        return "0.0.0+unknown"
+
+
+def _source_pyproject_version(source_root: Path) -> str | None:
+    try:
+        with open(source_root / "pyproject.toml", "rb") as fh:
+            project = tomllib.load(fh)["project"]
+        if project["name"] != "orca_auto":
+            return None
+        return str(project["version"])
+    except (OSError, tomllib.TOMLDecodeError, KeyError, TypeError):
+        return None
+
+
+def installed_version_drift(source_root: Path | None = None) -> tuple[str, str] | None:
+    """Report `(installed, source)` when the two disagree, else `None`.
+
+    An editable install freezes its distribution metadata at install time while
+    the interpreter keeps importing the checkout, so a live deployment can run
+    one version's code and declare another until someone reruns the install.
+    Returns `None` when there is no source `pyproject.toml` to compare against,
+    which is the normal shape of a wheel install rather than a drift verdict.
+    """
+    root = source_root if source_root is not None else Path(__file__).resolve().parents[2]
+    source = _source_pyproject_version(root)
+    if source is None:
+        return None
+    installed = package_version()
+    return None if installed == source else (installed, source)
+
+
+__version__ = package_version()
+
+__all__ = ["__version__", "installed_version_drift", "package_version"]