genice3 3.0__tar.gz

genice3-3.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Masakazu Matsumoto
+
+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.

genice3-3.0/PKG-INFO

@@ -0,0 +1,176 @@
+Metadata-Version: 2.4
+Name: genice3
+Version: 3.0
+Summary: Generate ice-rule-compliant ice and clathrate hydrate structures for molecular simulation. This is the current GenIce.
+Author-email: Masakazu Matsumoto <vitroid@gmail.com>
+License: MIT
+Project-URL: Homepage, https://genice-dev.github.io/GenIce3
+Project-URL: Documentation, https://genice-dev.github.io/GenIce3
+Project-URL: Source, https://github.com/genice-dev/GenIce3
+Project-URL: Bug Tracker, https://github.com/genice-dev/GenIce3/issues
+Project-URL: Changelog, https://github.com/genice-dev/GenIce3/blob/main/CHANGELOG.md
+Project-URL: manual, https://genice-dev.github.io/GenIce3
+Keywords: GenIce,ice,clathrate hydrate,water,hydrogen disorder,ice rules,molecular simulation,molecular dynamics,crystal structure,structure generator,computational chemistry,GROMACS,LAMMPS
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+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
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: <4.0,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: networkx>=2.0.dev20160901144005
+Requires-Dist: numpy>=2.0
+Requires-Dist: pairlist>=1.0.0
+Requires-Dist: cycless>=0.7
+Requires-Dist: graphstat>=0.3.3
+Requires-Dist: yaplotlib>=0.1.2
+Requires-Dist: openpyscad>=0.5.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: jinja2>=3.1.4
+Requires-Dist: cif2ice<0.5.0,>=0.4.1
+Requires-Dist: genice-core<2.0.0,>=1.6.0
+Provides-Extra: web
+Requires-Dist: fastapi<0.136.0,>=0.135.3; extra == "web"
+Requires-Dist: uvicorn[standard]<0.45.0,>=0.44.0; extra == "web"
+Provides-Extra: mcp
+Requires-Dist: mcp<3,>=2.0; extra == "mcp"
+Provides-Extra: dev
+Requires-Dist: httpx>=0.27.0; extra == "dev"
+Requires-Dist: mkdocs>=1.5.0; extra == "dev"
+Requires-Dist: mkdocs-material>=9.0.0; extra == "dev"
+Requires-Dist: pymdown-extensions>=10.0; extra == "dev"
+Requires-Dist: toml>=0.10.2; extra == "dev"
+Requires-Dist: ipykernel>=6.27.1; extra == "dev"
+Requires-Dist: py3dmol>=2.0.4; extra == "dev"
+Requires-Dist: matplotlib>=3.8.2; extra == "dev"
+Requires-Dist: genice2-svg>=2.2; extra == "dev"
+Requires-Dist: plotly>=5.18.0; extra == "dev"
+Requires-Dist: nbformat>=5.9.2; extra == "dev"
+Requires-Dist: genice2-mdanalysis>=0.6.5; extra == "dev"
+Requires-Dist: requests>=2.31.0; extra == "dev"
+Requires-Dist: pytest>=8.1.1; extra == "dev"
+Requires-Dist: genice2-cif>=2.2.1; extra == "dev"
+Requires-Dist: watchdog>=4.0; extra == "dev"
+Dynamic: license-file
+
+![Logo](https://raw.githubusercontent.com/vitroid/GenIce/develop/logo/genice-v0.png)
+
+# GenIce3
+
+Generate ice-rule-compliant ice and clathrate hydrate structures for molecular simulation. This is the current GenIce.
+
+Successor of [GenIce 1](https://github.com/vitroid/GenIce) and [GenIce2](https://github.com/vitroid/GenIce2). Use this package for new work.
+
+```shell
+pip install genice3
+genice3 1h > ice.gro
+```
+
+Python 3.11 or later. Output obeys the ice rules and a chosen net polarization (default zero); it is not energy-minimized. Relax with the intended force field before a production run.
+
+**Manual:** [genice-dev.github.io/GenIce3](https://genice-dev.github.io/GenIce3)  
+**For AI assistants:** [for-ai-assistants](https://genice-dev.github.io/GenIce3/for-ai-assistants/) · [llms.txt](https://genice-dev.github.io/GenIce3/llms.txt)  
+**Agent skill (try it):** [skills.sh/genice-dev/GenIce3](https://skills.sh/genice-dev/GenIce3) · `npx skills add genice-dev/GenIce3`
+
+Version 3.0
+
+## New in GenIce3
+
+- **Command line**
+  - Option syntax is unified; hierarchical options and YAML config files (`-Y` / `--config`) replace many GenIce2-style flags.
+  - Polarization control uses `pol_loop_1` and `pol_loop_2` (replacing `depol_loop`).
+  - Package and entry points are `genice3` (PyPI: `genice3`); plugin groups use the `genice3.*` namespaces.
+- **API**
+  - Python API redesigned around `GenIce3` and `DependencyEngine`: specify what you need and dependent quantities recompute automatically.
+  - Embed protonic defects (H₃O⁺, OH⁻) and Bjerrum topological defects from Python (see the [API examples](https://genice-dev.github.io/GenIce3/api-examples/) in the manual).
+  - Setter-style configuration and expanded notebooks/examples (`API.ipynb`, `examples/api/`).
+- **Algorithm and core**
+  - Ice-rule and depolarization logic delegated to **genice-core** (≥1.6.0); GenIce3 focuses on unit cells, guests, ions, and exporters.
+  - Reactive pipeline: `@reactive` properties and explicit dependency tracking replace ad-hoc recalculation.
+- **Unit cells and structures**
+  - Lattice plugins moved to `genice3.unitcell`; many GenIce2 structures ported with identity comparison tests.
+  - CIF-derived unit cells branch on whether hydrogen positions are supplied; `partial_order` removed.
+  - New or updated structures include auxiliary ices, `YKD`, `ice21` (and aliases), and cylindrical **prism** ice (API).
+- **Clathrates, ions, and defects**
+  - Cage assessment: GenIce2's `--assess_cages` removed — use exporter `cage_survey` (JSON). Default max cage ring count is 16 (override via exporter options).
+  - Spot ions use `-A` / `-C` (spot anion/cation; **not** the old cage-assessment flag). Group guests and spot-cation cage reporting extended; unit-cell ion suboptions (e.g. `--group`) in YAML.
+- **Exporters and visualization**
+  - Built-in and plugin exporters (GROMACS, CIF, LAMMPS, yaplot, plotly, py3Dmol, etc.); format functions and option parsing refined.
+  - Optional **Web API** (`genice3[web]` / `genice3-web`) and **stdio MCP** (`genice3[mcp]` / `genice3-mcp`); shared `genice3.service` layer.
+- **Documentation and tooling**
+  - Manual on GitHub Pages; plugin tables and citations generated from the repo (`make docs`, `make README.md`).
+  - For a narrative of the GenIce3 development period and compatibility notes, see [RELEASE_NOTE.md](https://github.com/genice-dev/GenIce3/blob/main/RELEASE_NOTE.md) in the repository.
+
+**Example — cage survey (formerly `--assess_cages`):**
+
+```shell
+genice3 CS2 -e cage_survey > cages.json
+```
+
+## Demo
+
+[Try GenIce3 on Google Colaboratory](https://colab.research.google.com/github/genice-dev/GenIce3/blob/main/API.ipynb).
+
+Coding agents (Cursor, Claude Code, Codex, …): open [skills.sh/genice-dev/GenIce3](https://skills.sh/genice-dev/GenIce3) or install in one step:
+
+```shell
+npx skills add genice-dev/GenIce3
+```
+
+Optional **MCP** (chat tool calls into GenIce3): `pip install "genice3[mcp]"`, then add `genice3-mcp` to the client’s MCP config. Setup: [MCP](https://genice-dev.github.io/GenIce3/mcp/).
+
+## Requirements
+
+- networkx >=2.0.dev20160901144005
+- numpy >=2.0
+- pairlist >=1.0.0
+- cycless >=0.7
+- graphstat >=0.3.3
+- yaplotlib >=0.1.2
+- openpyscad >=0.5.0
+- pyyaml >=6.0
+- jinja2 >=3.1.4
+- cif2ice (>=0.4.1,<0.5.0)
+- genice-core (>=1.6.0,<2.0.0)
+
+
+## Installation
+
+GenIce3 is on [PyPI](https://pypi.org/project/genice3/). Install with pip:
+
+```shell
+pip install genice3
+```
+
+## Uninstallation
+
+```shell
+pip uninstall genice3
+```
+
+## References
+
+See the [manual → References](https://genice-dev.github.io/GenIce3/references.html) for the full reference list (generated from `citations.yaml`).
+
+## Citation
+
+If you use GenIce in your work, please cite as in [CITATION.cff](CITATION.cff) or:
+
+> M. Matsumoto, T. Yagasaki, and H. Tanaka, "GenIce: Hydrogen-Disordered Ice Generator", _J. Comput. Chem._ **39**, 61-64 (2017). [DOI: 10.1002/jcc.25077](http://doi.org/10.1002/jcc.25077)
+
+> M. Matsumoto, T. Yagasaki, and H. Tanaka, "GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures.", _J. Chem. Phys._ **160**, 094101 (2024). [DOI:10.1063/5.0198056](https://doi.org/10.1063/5.0198056)
+
+## How to contribute
+
+GenIce is developed on GitHub (https://github.com/genice-dev/GenIce3). Feedback, bug fixes, and contributions are welcome.
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.

genice3-3.0/README.md

@@ -0,0 +1,114 @@
+![Logo](https://raw.githubusercontent.com/vitroid/GenIce/develop/logo/genice-v0.png)
+
+# GenIce3
+
+Generate ice-rule-compliant ice and clathrate hydrate structures for molecular simulation. This is the current GenIce.
+
+Successor of [GenIce 1](https://github.com/vitroid/GenIce) and [GenIce2](https://github.com/vitroid/GenIce2). Use this package for new work.
+
+```shell
+pip install genice3
+genice3 1h > ice.gro
+```
+
+Python 3.11 or later. Output obeys the ice rules and a chosen net polarization (default zero); it is not energy-minimized. Relax with the intended force field before a production run.
+
+**Manual:** [genice-dev.github.io/GenIce3](https://genice-dev.github.io/GenIce3)  
+**For AI assistants:** [for-ai-assistants](https://genice-dev.github.io/GenIce3/for-ai-assistants/) · [llms.txt](https://genice-dev.github.io/GenIce3/llms.txt)  
+**Agent skill (try it):** [skills.sh/genice-dev/GenIce3](https://skills.sh/genice-dev/GenIce3) · `npx skills add genice-dev/GenIce3`
+
+Version 3.0
+
+## New in GenIce3
+
+- **Command line**
+  - Option syntax is unified; hierarchical options and YAML config files (`-Y` / `--config`) replace many GenIce2-style flags.
+  - Polarization control uses `pol_loop_1` and `pol_loop_2` (replacing `depol_loop`).
+  - Package and entry points are `genice3` (PyPI: `genice3`); plugin groups use the `genice3.*` namespaces.
+- **API**
+  - Python API redesigned around `GenIce3` and `DependencyEngine`: specify what you need and dependent quantities recompute automatically.
+  - Embed protonic defects (H₃O⁺, OH⁻) and Bjerrum topological defects from Python (see the [API examples](https://genice-dev.github.io/GenIce3/api-examples/) in the manual).
+  - Setter-style configuration and expanded notebooks/examples (`API.ipynb`, `examples/api/`).
+- **Algorithm and core**
+  - Ice-rule and depolarization logic delegated to **genice-core** (≥1.6.0); GenIce3 focuses on unit cells, guests, ions, and exporters.
+  - Reactive pipeline: `@reactive` properties and explicit dependency tracking replace ad-hoc recalculation.
+- **Unit cells and structures**
+  - Lattice plugins moved to `genice3.unitcell`; many GenIce2 structures ported with identity comparison tests.
+  - CIF-derived unit cells branch on whether hydrogen positions are supplied; `partial_order` removed.
+  - New or updated structures include auxiliary ices, `YKD`, `ice21` (and aliases), and cylindrical **prism** ice (API).
+- **Clathrates, ions, and defects**
+  - Cage assessment: GenIce2's `--assess_cages` removed — use exporter `cage_survey` (JSON). Default max cage ring count is 16 (override via exporter options).
+  - Spot ions use `-A` / `-C` (spot anion/cation; **not** the old cage-assessment flag). Group guests and spot-cation cage reporting extended; unit-cell ion suboptions (e.g. `--group`) in YAML.
+- **Exporters and visualization**
+  - Built-in and plugin exporters (GROMACS, CIF, LAMMPS, yaplot, plotly, py3Dmol, etc.); format functions and option parsing refined.
+  - Optional **Web API** (`genice3[web]` / `genice3-web`) and **stdio MCP** (`genice3[mcp]` / `genice3-mcp`); shared `genice3.service` layer.
+- **Documentation and tooling**
+  - Manual on GitHub Pages; plugin tables and citations generated from the repo (`make docs`, `make README.md`).
+  - For a narrative of the GenIce3 development period and compatibility notes, see [RELEASE_NOTE.md](https://github.com/genice-dev/GenIce3/blob/main/RELEASE_NOTE.md) in the repository.
+
+**Example — cage survey (formerly `--assess_cages`):**
+
+```shell
+genice3 CS2 -e cage_survey > cages.json
+```
+
+## Demo
+
+[Try GenIce3 on Google Colaboratory](https://colab.research.google.com/github/genice-dev/GenIce3/blob/main/API.ipynb).
+
+Coding agents (Cursor, Claude Code, Codex, …): open [skills.sh/genice-dev/GenIce3](https://skills.sh/genice-dev/GenIce3) or install in one step:
+
+```shell
+npx skills add genice-dev/GenIce3
+```
+
+Optional **MCP** (chat tool calls into GenIce3): `pip install "genice3[mcp]"`, then add `genice3-mcp` to the client’s MCP config. Setup: [MCP](https://genice-dev.github.io/GenIce3/mcp/).
+
+## Requirements
+
+- networkx >=2.0.dev20160901144005
+- numpy >=2.0
+- pairlist >=1.0.0
+- cycless >=0.7
+- graphstat >=0.3.3
+- yaplotlib >=0.1.2
+- openpyscad >=0.5.0
+- pyyaml >=6.0
+- jinja2 >=3.1.4
+- cif2ice (>=0.4.1,<0.5.0)
+- genice-core (>=1.6.0,<2.0.0)
+
+
+## Installation
+
+GenIce3 is on [PyPI](https://pypi.org/project/genice3/). Install with pip:
+
+```shell
+pip install genice3
+```
+
+## Uninstallation
+
+```shell
+pip uninstall genice3
+```
+
+## References
+
+See the [manual → References](https://genice-dev.github.io/GenIce3/references.html) for the full reference list (generated from `citations.yaml`).
+
+## Citation
+
+If you use GenIce in your work, please cite as in [CITATION.cff](CITATION.cff) or:
+
+> M. Matsumoto, T. Yagasaki, and H. Tanaka, "GenIce: Hydrogen-Disordered Ice Generator", _J. Comput. Chem._ **39**, 61-64 (2017). [DOI: 10.1002/jcc.25077](http://doi.org/10.1002/jcc.25077)
+
+> M. Matsumoto, T. Yagasaki, and H. Tanaka, "GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures.", _J. Chem. Phys._ **160**, 094101 (2024). [DOI:10.1063/5.0198056](https://doi.org/10.1063/5.0198056)
+
+## How to contribute
+
+GenIce is developed on GitHub (https://github.com/genice-dev/GenIce3). Feedback, bug fixes, and contributions are welcome.
+
+## License
+
+MIT License. See [LICENSE](LICENSE) for details.

genice3-3.0/dependency_engine/__init__.py

@@ -0,0 +1,218 @@
+"""
+Dependency-resolution engine for reactive pipelines.
+
+Executes only the tasks needed to reach a given goal, working backwards
+from the target. May be split into a separate package in the future.
+"""
+
+import inspect
+from logging import getLogger
+import time
+
+# @reactive でデコレートされた関数を (モジュール名, 関数) で保持。
+# 利用側が _register_tasks で get_reactive_tasks(__name__) により自モジュール分だけ登録する。
+_REACTIVE_REGISTRY = []
+
+# Sentinel: Input に default も default_factory もない。
+_MISSING = object()
+
+
+class UnsetInputError(Exception):
+    """Raised when a required ``Input`` has not been assigned."""
+
+
+def reactive(func=None, *, public=False):
+    """Marker decorator to register a function as a DependencyEngine task.
+
+    The decorated function name becomes the reactive property name
+    (for example, ``genice.cages``). Names should be nouns.
+
+    Args:
+        public: If True, the task is part of the public API listing.
+
+    Side effect: the function is registered in ``_REACTIVE_REGISTRY``.
+    Use ``get_reactive_tasks(module_name)`` to obtain the task list for a module.
+    """
+
+    def decorate(fn):
+        fn._reactive_public = public
+        _REACTIVE_REGISTRY.append((fn.__module__, fn))
+        return fn
+
+    if func is None:
+        return decorate
+    return decorate(func)
+
+
+def get_reactive_tasks(module_name: str):
+    """Return functions decorated with ``@reactive`` in the given module."""
+    return [f for mod, f in _REACTIVE_REGISTRY if mod == module_name]
+
+
+class Input:
+    """Descriptor for a DAG root (settable reactive input).
+
+    Assignment stores the value, optionally coerces it (same kind of object),
+    runs ``on_set``, and clears ``obj.engine.cache``. Getter and
+    ``collect_inputs`` are derived from the class-level declaration.
+
+    Do not use ``coerce`` to change the public type (for example str to a
+    constructed object). Keep a separate factory method for that.
+    """
+
+    def __init__(
+        self,
+        *,
+        default=_MISSING,
+        default_factory=None,
+        public=False,
+        required=False,
+        coerce=None,
+        on_set=None,
+        unset_error=None,
+        doc=None,
+    ):
+        if required and (default is not _MISSING or default_factory is not None):
+            raise TypeError("required Input cannot have a default")
+        if default is not _MISSING and default_factory is not None:
+            raise TypeError("specify default or default_factory, not both")
+        self.default = default
+        self.default_factory = default_factory
+        self.public = public
+        self.required = required
+        self.coerce = coerce
+        self.on_set = on_set
+        self.unset_error = unset_error
+        self.name = None
+        self.private_name = None
+        if doc is not None:
+            self.__doc__ = doc
+
+    def __set_name__(self, owner, name):
+        self.name = name
+        self.private_name = f"_{name}"
+        if "_input_fields" not in owner.__dict__:
+            owner._input_fields = {}
+        owner._input_fields[name] = self
+
+    def is_set(self, obj) -> bool:
+        """Return True if this input has been assigned on ``obj``."""
+        return self.private_name in obj.__dict__
+
+    def __get__(self, obj, objtype=None):
+        if obj is None:
+            return self
+        if self.private_name in obj.__dict__:
+            return obj.__dict__[self.private_name]
+        if self.required:
+            if self.unset_error is not None:
+                err = self.unset_error
+                raise err() if callable(err) else err
+            raise UnsetInputError(
+                f"{type(obj).__name__}.{self.name} is not set."
+            )
+        if self.default_factory is not None:
+            return self.default_factory()
+        if self.default is not _MISSING:
+            return self.default
+        raise UnsetInputError(f"{type(obj).__name__}.{self.name} is not set.")
+
+    def __set__(self, obj, value):
+        if self.coerce is not None:
+            value = self.coerce(value)
+        obj.__dict__[self.private_name] = value
+        logger = getattr(obj, "logger", None)
+        if logger is not None:
+            logger.debug("  %s=%r", self.name, value)
+        if self.on_set is not None:
+            self.on_set(obj, value)
+        engine = getattr(obj, "engine", None)
+        if engine is not None:
+            engine.cache.clear()
+
+
+def input_fields(cls) -> dict:
+    """Return ``{name: Input}`` declared on ``cls`` (including bases)."""
+    fields = {}
+    for base in reversed(cls.__mro__):
+        fields.update(getattr(base, "_input_fields", {}))
+    return fields
+
+
+def collect_inputs(obj) -> dict:
+    """Return a dict of all ``Input`` values on ``obj`` for ``engine.resolve``."""
+    return {name: getattr(obj, name) for name in input_fields(type(obj))}
+
+
+class DependencyEngine:
+    """Engine that back-solves dependencies and runs only needed tasks."""
+
+    logger = getLogger("dependency_engine")
+
+    def __init__(self):
+        self.registry = {}  # { 'output_name': function }
+        self.cache = {}
+
+    def task(self, func):
+        """Decorator to register a task with ``func.__name__`` as its output name."""
+        self.registry[func.__name__] = func
+        return func
+
+    def resolve(self, target: str, inputs: dict):
+        """Resolve ``target`` by recursively computing its dependencies."""
+
+        # 1. 既に計算済み or 入力として与えられているならそれを返す
+        if target in inputs:
+            return inputs[target]
+        if target in self.cache:
+            return self.cache[target]
+
+        # 2. 生成ルール（関数）を探す
+        if target not in self.registry:
+            raise ValueError(f"Don't know how to make '{target}'")
+
+        func = self.registry[target]
+
+        # 3. その関数の引数（依存先）を調べて、再帰的に解決する
+        sig = inspect.signature(func)
+        dependencies = {}
+        for param_name in sig.parameters:
+            dependencies[param_name] = self.resolve(param_name, inputs)
+
+        # 4. 実行して結果を保存（所要時間は JSON ログの duration_ms にも載せる）
+        now = time.time()
+        result = func(**dependencies)
+        delta_ms = (time.time() - now) * 1000.0
+        self.logger.info(
+            "Executing: %s",
+            target,
+            extra={
+                "event": "task.execute",
+                "task": target,
+                "duration_ms": round(delta_ms, 3),
+            },
+        )
+        self.cache[target] = result
+        return result
+
+
+def _demo():
+    """Package self-test demo (run with ``python -m dependency_engine``)."""
+    engine = DependencyEngine()
+
+    @engine.task
+    def reaction_A(raw_material: int):
+        return raw_material * 2
+
+    @engine.task
+    def reaction_B(reaction_A: int, catalyst: int):
+        return reaction_A + catalyst
+
+    result = engine.resolve(
+        target="reaction_B", inputs={"raw_material": 10, "catalyst": 5}
+    )
+    print(result)
+
+
+if __name__ == "__main__":
+    _demo()

genice3-3.0/dependency_engine/__main__.py

@@ -0,0 +1,4 @@
+"""python -m dependency_engine でデモを実行"""
+from dependency_engine import _demo
+
+_demo()

genice3-3.0/genice3/__init__.py

@@ -0,0 +1,22 @@
+# -*- coding: utf-8 -*-
+from logging import getLogger
+
+from genice3.logging_config import setup_logging as _setup_logging_impl
+
+
+class ConfigurationError(Exception):
+    """設定に関するエラーを表す例外"""
+
+    pass
+
+
+def _setup_logging(debug: bool = False, fmt: str | None = None) -> str:
+    """ルートロガーの設定を統一する（:func:`genice3.logging_config.setup_logging` への薄いラップ）。"""
+    return _setup_logging_impl(debug=debug, fmt=fmt)
+
+
+# API利用時にも明示的な呼び出しなしでINFOログが出るよう、
+# ハンドラ未設定の場合だけデフォルト設定を適用する。
+# （ユーザーが事前に basicConfig 等を呼んでいる場合はそちらを尊重する）
+if not getLogger().handlers:
+    _setup_logging(debug=False)

genice3-3.0/genice3/_build.py

@@ -0,0 +1,43 @@
+"""
+カスタムビルドフック: symlinkを実際のファイルにコピーする
+"""
+import os
+import shutil
+from pathlib import Path
+from setuptools.command.build_py import build_py as _build_py
+
+
+class BuildPy(_build_py):
+    """symlinkを実際のファイルにコピーするカスタムビルドコマンド"""
+
+    def copy_file(self, src, dst, preserve_mode=True, preserve_times=True, link=None, level=1):
+        """ファイルをコピーする際に、symlinkの場合は実際のファイルをコピー"""
+        # symlinkの場合は、ターゲットファイルをコピー
+        if os.path.islink(src):
+            # symlinkのターゲットを取得
+            target = os.readlink(src)
+            
+            # 相対パスの場合は、srcのディレクトリからの相対パスとして解決
+            if not os.path.isabs(target):
+                src_dir = os.path.dirname(src)
+                target_path = os.path.normpath(os.path.join(src_dir, target))
+            else:
+                target_path = target
+            
+            # ターゲットファイルが存在する場合のみコピー
+            if os.path.exists(target_path):
+                # ターゲットファイルをコピー（再帰的に呼び出し）
+                return super().copy_file(
+                    target_path, dst, preserve_mode, preserve_times, link, level
+                )
+            else:
+                # ターゲットが見つからない場合は警告を出してスキップ
+                print(f"Warning: symlink target not found: {src} -> {target_path}")
+                return dst, False
+        
+        # 通常のファイルの場合は親クラスのメソッドを呼び出す
+        return super().copy_file(src, dst, preserve_mode, preserve_times, link, level)
+
+
+
+