conceptual-dictionary 0.1.1__py3-none-any.whl

conceptual_dictionary/__init__.py

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+# This file marks the conceptual_dictionary module.

conceptual_dictionary/conceptualdict.py

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+import yaml
+import json
+from typing import Any, Dict
+import numpy as np
+import string
+import random
+
+
+class ConceptualDict(dict):
+    def __init__(self, *args, **kwargs):
+        data = {"computational_sample": [], "workflow": []}
+        super().__init__(data, *args, **kwargs)
+
+    def generate_id(self, length=7):
+        """Generate a random alphanumeric ID of given length."""
+        chars = string.ascii_letters + string.digits
+        return "".join(random.choices(chars, k=length))
+
+    @staticmethod
+    def _clean_data(obj: Any) -> Any:
+        if isinstance(obj, dict):
+            return {k: ConceptualDict._clean_data(v) for k, v in obj.items()}
+        elif isinstance(obj, list):
+            return [ConceptualDict._clean_data(v) for v in obj]
+        elif isinstance(obj, np.ndarray):
+            return obj.tolist()
+        elif isinstance(obj, (np.floating, np.float32, np.float64)):
+            return float(obj)
+        elif isinstance(obj, (np.integer, np.int32, np.int64)):
+            return int(obj)
+        elif isinstance(obj, (np.bool_, bool)):
+            return bool(obj)
+        elif obj is None or isinstance(obj, (str, float, int)):
+            return obj
+        else:
+            return str(obj)
+
+    # --------------------
+    # YAML I/O
+    # --------------------
+    def to_yaml(self, filepath: str, sort_keys: bool = False) -> None:
+        clean_dict = ConceptualDict._clean_data(dict(self))
+        with open(filepath, "w") as f:
+            yaml.safe_dump(clean_dict, f, sort_keys=sort_keys, allow_unicode=True)
+
+    @classmethod
+    def from_yaml(cls, filepath: str) -> "ConceptualDict":
+        with open(filepath, "r") as f:
+            data = yaml.safe_load(f)
+        kg = cls()
+        kg.update(data)
+        return kg
+
+    # --------------------
+    # JSON I/O
+    # --------------------
+    def to_json(self, filepath: str, sort_keys: bool = False, indent: int = 2) -> None:
+        clean_dict = ConceptualDict._clean_data(dict(self))
+        with open(filepath, "w") as f:
+            json.dump(
+                clean_dict, f, sort_keys=sort_keys, indent=indent, ensure_ascii=False
+            )
+
+    @classmethod
+    def from_json(cls, filepath: str) -> "ConceptualDict":
+        with open(filepath, "r") as f:
+            data = json.load(f)
+        kg = cls()
+        kg.update(data)
+        return kg

conceptual_dictionary/templates.py

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+sample_template = {
+    "id": "sample1",
+    "material": {
+        "element_ratio": {},
+        "crystal_structure": {
+            "spacegroup_symbol": None,
+            "spacegroup_number": None,
+            "unit_cell": {
+                "bravais_lattice": None,
+                "lattice_parameter": None,
+                "angle": [],
+            },
+        },
+    },
+    "simulation_cell": {
+        "volume": {"value": None},
+        "number_of_atoms": None,
+        "length": [],
+        "vector": [],
+        "angle": [],
+        "repetitions": [],
+        "grain_size": None,
+        "number_of_grains": 0,
+    },
+    "atom_attribute": {
+        "position": None,
+        "species": None,
+    },
+}
+
+property_template = {
+    "basename": None,
+    "value": None,
+    "unit": None,
+    "associate_to_sample": [],
+}
+
+workflow_template = {
+    "algorithm": None,
+    "method": None,
+    "xc_functional": None,
+    "input_parameter": [],
+    "input_sample": [],
+    "output_sample": [],
+    "calculated_property": [],
+    "degrees_of_freedom": [],
+    "interatomic_potential": {
+        "potential_type": None,
+        "uri": None,
+    },
+    "software": {
+        "uri": None,
+        "version": None,
+        "label": None,
+    },
+    "workflow_manager": {
+        "uri": None,
+        "version": None,
+        "label": None,
+    },
+    "thermodynamic_ensemble": None,
+}

conceptual_dictionary-0.1.1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: conceptual-dictionary
+Version: 0.1.1
+Summary: A Python dictionary template for storing serializable metadata
+Author: Sarath Menon, Abril Azocar Guzman
+License: MIT License
+        
+        Copyright (c) 2025 pyscal
+        
+        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/pyscal/conceptual_dictionary
+Project-URL: Bug Tracker, https://github.com/pyscal/conceptual_dictionary/issues
+Keywords: dictionary,metadata,serialization,conceptual
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pyyaml
+Dynamic: license-file
+
+# conceptual_dictionary
+
+A Python dictionary template for storing serializable metadata.
+
+## Installation
+
+Install from source:
+
+```bash
+pip install -e .
+```
+
+## Usage
+
+### Using Templates
+
+Import and use predefined dictionary templates:
+
+```python
+from conceptual_dictionary.templates import sample_template, property_template, workflow_template
+
+# Use a template directly
+my_data = sample_template.copy()
+my_data['material']['element_ratio'] = {'Fe': 0.7, 'C': 0.3}
+my_data['simulation_cell']['volume']['value'] = 1000
+```
+
+### Using ConceptualDict Class
+
+Work with conceptual dictionaries using the ConceptualDict class:
+
+```python
+from conceptual_dictionary.conceptualdict import ConceptualDict
+
+# Create a new conceptual dictionary
+cd = ConceptualDict()
+
+# Set values using dot notation
+cd.set("material.element_ratio.Fe", 0.7)
+cd.set("material.element_ratio.C", 0.3)
+cd.set("simulation_cell.volume.value", 1000)
+
+# Get values
+fe_ratio = cd.get("material.element_ratio.Fe")
+volume = cd.get("simulation_cell.volume.value")
+
+# Convert to standard dictionary
+data = cd.to_dict()
+
+# Serialize to JSON
+json_str = cd.to_json(indent=2)
+
+# Save to file
+cd.save("my_conceptual.json")
+
+# Load from file
+cd_loaded = ConceptualDict.from_json("my_conceptual.json")
+```
+
+## Available Templates
+
+- **sample_template**: Standard template with metadata, content, and schema sections
+- **property_template**: Template for defining properties with values and units
+- **workflow_template**: Template for describing workflows, including algorithms and methods
+
+## License
+
+MIT License

conceptual_dictionary-0.1.1.dist-info/RECORD

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+conceptual_dictionary/__init__.py,sha256=Gtthpv5dXjBPbhDviJsLqf7ui_CMQH7KqOqsA2kmooY,52
+conceptual_dictionary/conceptualdict.py,sha256=uU_1zbZVCAseXhO-y-j8HdulFQtBZvUAlHOqUa2YQzE,2357
+conceptual_dictionary/templates.py,sha256=cJf4ItGZa74W9lLXLzTD16Dr35Q-LqdgEe1iI_kRlV4,1375
+conceptual_dictionary-0.1.1.dist-info/licenses/LICENSE,sha256=Cz67nMihKnofYU66OZOzm0k5gCBMC56w6wWV-AuffKw,1063
+conceptual_dictionary-0.1.1.dist-info/METADATA,sha256=Tx8qkFb0DVGH20YqdTb3Djtc1bNv6BWGMlFPd40Inzw,3837
+conceptual_dictionary-0.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+conceptual_dictionary-0.1.1.dist-info/top_level.txt,sha256=YuqFwcFZvCKBgG1-2CqVjzFCcE135GEmwMZWEz5yf6w,22
+conceptual_dictionary-0.1.1.dist-info/RECORD,,

conceptual_dictionary-0.1.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

conceptual_dictionary-0.1.1.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2025 pyscal
+
+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.

conceptual_dictionary-0.1.1.dist-info/top_level.txt

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+conceptual_dictionary