pesmaker 0.1.0__py3-none-any.whl

pesmaker/__init__.py

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+# Copyright 2026 Ting Liang and PESMaker development team
+# This file is part of PESMaker.
+#
+# PESMaker is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PESMaker is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with PESMaker. If not, see <https://www.gnu.org/licenses/>.
+"""PESMaker package public API."""
+
+from pesmaker.config.schema import PESMakerConfig
+
+__all__ = ["PESMakerConfig", "__contact__", "__version__"]
+__contact__ = "liangting.zj@gmail.com"
+__version__ = "0.1.0"

pesmaker/__main__.py

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+# Copyright 2026 Ting Liang and PESMaker development team
+# This file is part of PESMaker.
+#
+# PESMaker is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PESMaker is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with PESMaker. If not, see <https://www.gnu.org/licenses/>.
+"""Module entry point for `python -m pesmaker`."""
+
+from pesmaker.cli import main
+
+if __name__ == "__main__":
+    main()

pesmaker/artifacts.py

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+# Copyright 2026 Ting Liang and PESMaker development team
+# This file is part of PESMaker.
+#
+# PESMaker is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PESMaker is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with PESMaker. If not, see <https://www.gnu.org/licenses/>.
+
+"""Common manifest, input-discovery, and stage path helpers."""
+
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from typing import Any
+
+from pesmaker.config.schema import PESMakerConfig
+
+STRUCTURE_INPUT_SUFFIXES = {".cif", ".extxyz", ".poscar", ".vasp", ".xyz"}
+
+STRUCTURE_INPUT_NAMES = {"CONTCAR", "POSCAR"}
+
+
+def _section_output_dir(
+    config: PESMakerConfig,
+    options: dict[str, Any],
+    leaf: str,
+) -> Path:
+    value = options.get("output_dir")
+    return Path(str(value)) if value else Path("runs") / config.project / leaf
+
+
+def _load_input_records(
+    config: PESMakerConfig,
+    options: dict[str, Any],
+) -> list[dict[str, Any]]:
+    manifest = options.get("input_manifest")
+    if manifest:
+        manifest_path = Path(str(manifest))
+        return _mark_input_records(
+            _read_manifest(manifest_path),
+            input_dir=manifest_path.parent,
+            input_mode="input_manifest",
+        )
+    input_dir = options.get("input_dir")
+    if input_dir:
+        return _load_input_dir_records(Path(str(input_dir)), input_mode="input_dir")
+    generation_dir = _generated_structures_dir(config)
+    return _load_input_dir_records(generation_dir, input_mode="generated_dir")
+
+
+def _load_input_dir_records(
+    input_dir: Path, *, input_mode: str
+) -> list[dict[str, Any]]:
+    if not input_dir.exists():
+        raise ValueError(f"input structure directory does not exist: {input_dir}")
+    if not input_dir.is_dir():
+        raise ValueError(f"input structure path must be a directory: {input_dir}")
+
+    manifest_path = input_dir / "manifest.jsonl"
+    if manifest_path.exists():
+        return _mark_input_records(
+            _read_manifest(manifest_path),
+            input_dir=input_dir,
+            input_mode=f"{input_mode}_manifest",
+        )
+
+    paths = _discover_input_structure_files(input_dir)
+    if not paths:
+        raise ValueError(f"no structure files found in {input_dir}")
+    return [
+        {
+            "path": str(path),
+            "input_dir": str(input_dir),
+            "input_mode": f"{input_mode}_scan",
+            "input_relative_path": path.relative_to(input_dir).as_posix(),
+        }
+        for path in paths
+    ]
+
+
+def _mark_input_records(
+    records: list[dict[str, Any]],
+    *,
+    input_dir: Path,
+    input_mode: str,
+) -> list[dict[str, Any]]:
+    marked = []
+    for source_index, record in enumerate(records):
+        path = Path(str(record["path"]))
+        if not path.is_absolute() and not path.exists():
+            candidate = input_dir / path
+            if candidate.exists():
+                path = candidate
+        marked_record = {
+            **record,
+            "path": str(path),
+            "input_dir": str(input_dir),
+            "input_mode": input_mode,
+            "source_record_index": record.get("index", source_index),
+        }
+        try:
+            marked_record["input_relative_path"] = path.relative_to(
+                input_dir
+            ).as_posix()
+        except ValueError:
+            pass
+        marked.append(marked_record)
+    return marked
+
+
+def _discover_input_structure_files(input_dir: Path) -> list[Path]:
+    return sorted(
+        path
+        for path in input_dir.rglob("*")
+        if path.is_file() and _is_input_structure_file(path)
+    )
+
+
+def _is_input_structure_file(path: Path) -> bool:
+    if path.name.upper() in STRUCTURE_INPUT_NAMES:
+        return True
+    return path.suffix.lower() in STRUCTURE_INPUT_SUFFIXES
+
+
+def _generated_structures_dir(config: PESMakerConfig) -> Path:
+    if config.generation.output_dir:
+        return config.generation.output_dir
+    local_generated = Path("generated")
+    if local_generated.exists():
+        return local_generated
+    return Path("runs") / config.project / "generated"
+
+
+def _read_manifest(path: Path) -> list[dict[str, Any]]:
+    records = []
+    for line in path.read_text(encoding="utf-8").splitlines():
+        if line.strip():
+            record = json.loads(line)
+            if "path" in record:
+                record = {"path": str(record["path"]), **record}
+            records.append(record)
+    return records
+
+
+def _read_optional_file(value: Any, *, default: str) -> str:
+    if value:
+        return Path(str(value)).read_text(encoding="utf-8")
+    return default