emmet-builders 0.87.0.dev15__tar.gz → 0.87.0.dev16__tar.gz

{emmet_builders-0.87.0.dev15/emmet_builders.egg-info → emmet_builders-0.87.0.dev16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: emmet-builders
-Version: 0.87.0.dev15
+Version: 0.87.0.dev16
 Summary: Builders for the Emmet Library
 Author-email: The Materials Project <feedback@materialsproject.org>
 License-Expression: BSD-3-Clause-LBNL

emmet_builders-0.87.0.dev16/emmet/builders/materials/provenance.py

@@ -0,0 +1,188 @@
+"""Build provenance collection."""
+
+import logging
+from collections import defaultdict
+from itertools import chain, groupby
+from typing import Iterator
+
+from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
+
+from emmet.builders.base import BaseBuilderInput
+from emmet.builders.settings import EmmetBuildSettings
+from emmet.builders.utils import filter_map
+from emmet.core.connectors.analysis import parse_cif
+from emmet.core.connectors.icsd.client import IcsdClient
+from emmet.core.connectors.icsd.enums import IcsdSubset
+from emmet.core.provenance import DatabaseSNL, ProvenanceDoc
+
+SETTINGS = EmmetBuildSettings()
+structure_matcher = StructureMatcher(
+    ltol=SETTINGS.LTOL,
+    stol=SETTINGS.STOL,
+    comparator=ElementComparator(),
+    angle_tol=SETTINGS.ANGLE_TOL,
+    primitive_cell=True,
+    scale=True,
+    attempt_supercell=False,
+    allow_subset=False,
+)
+
+
+logger = logging.getLogger(__name__)
+
+
+def _get_snl_from_cif(cif_str: str, **kwargs) -> DatabaseSNL | None:
+    """Build a database SNL from a CIF plus its metadata.
+
+    NB: Only takes the first structure from a CIF.
+    While a CIF can technically contain many structures,
+    the ICSD usually only distributes CIFs with one structure
+    per file.
+
+    Parameters
+    -----------
+    cif_str : the CIF to parse
+    **kwargs to pass to `DatabaseSNL`
+    """
+    try:
+        structures, cif_parsing_remarks = parse_cif(cif_str)
+        remarks = kwargs.pop("remarks", None) or cif_parsing_remarks or None
+        snl = DatabaseSNL.from_structure(
+            meta_structure=structures[0],
+            structure=structures[0],
+            **kwargs,
+        )
+
+        snl.about.remarks = remarks
+
+    except Exception as e:
+        logger.warning(e)
+        snl = None
+
+    return snl
+
+
+def update_experimental_icsd_structures(**client_kwargs) -> list[DatabaseSNL]:
+    """Update the collection of ICSD SNLs.
+
+    Parameters
+    -----------
+    **client_kwargs to pass to `IcsdClient`
+
+    Returns
+    -----------
+    List of DatabaseSNL
+    """
+    data = []
+    with IcsdClient(use_document_model=False, **client_kwargs) as client:
+        for icsd_subset in (
+            IcsdSubset.EXPERIMENTAL_METALORGANIC,
+            IcsdSubset.EXPERIMENTAL_INORGANIC,
+        ):
+            data += client.search(
+                subset=icsd_subset,
+                space_group_number=(1, 230),
+                include_cif=False,
+                include_metadata=False,
+            )
+    return data
+
+    parsed = [
+        _get_snl_from_cif(
+            doc["cif"],
+            snl_id=f"icsd-{doc['collection_code']}",
+            tags=[doc["subset"].value],
+            source="icsd",
+        )
+        for doc in data
+    ]
+
+    return sorted(
+        [doc for doc in parsed if doc],
+        key=lambda doc: int(doc.snl_id.split("-", 1)[-1]),
+    )
+
+
+class ProvenanceBuilderInput(BaseBuilderInput):
+    formula_pretty: str
+
+
+def _match_against_snls(
+    inputs: tuple[list[ProvenanceBuilderInput], list[DatabaseSNL]],
+) -> list[ProvenanceDoc]:
+    """
+    Structure match a set of ProvenanceBuilderInputs against a group of DatabaseSNLs
+
+    Should be used in conjunction with ``build_provenance_docs`` to ensure inputs
+    are correctly grouped by 'formula_pretty'.
+    """
+    input_documents, snls = inputs
+
+    results = []
+    for input_doc in input_documents:
+        authors = [[SETTINGS.DEFAULT_AUTHOR]]
+        database_ids = defaultdict(list)
+        history = [[SETTINGS.DEFAULT_HISTORY]]
+        references = [SETTINGS.DEFAULT_REFERENCE]
+        theoretical = True
+
+        if snls:
+            for snl in snls:
+                if structure_matcher.fit(input_doc.structure, snl.structure):
+                    if snl.source and snl.source in {"icsd", "pauling"}:
+                        theoretical = False
+                        database_ids[snl.source].append(snl.snl_id)
+
+                    if snl.about:
+                        authors.append(snl.about.authors or [])
+                        history.append(snl.about.history or [])
+                        # `SNLAbout` uses string for `references`,
+                        # `ProvenanceDoc` uses list of str
+                        if snl.about.references:
+                            references.append(snl.about.references)
+
+        results.append(
+            ProvenanceDoc.from_structure(
+                meta_structure=input_doc.structure,
+                material_id=input_doc.material_id,
+                database_IDs=database_ids,
+                theoretical=theoretical,
+                authors=list(chain.from_iterable(authors)),
+                history=list(chain.from_iterable(history)),
+                references=references,
+            )
+        )
+
+    return results
+
+
+def build_provenance_docs(
+    input_documents: list[ProvenanceBuilderInput], snls: list[DatabaseSNL], **kwargs
+) -> Iterator[ProvenanceDoc]:
+    """
+    Groups input documents and SNLs by formula_pretty, performs structure matching
+    on each formula group, and constructs ProvenanceDocs for each group of
+    ProvenanceBuilderInputs with matching structures within each formula group.
+
+    Args:
+        input_documents: List of ProvenanceBuilderInput objects to process.
+        snls: List of DatabaseSNL objects for structure matching against.
+
+    Returns:
+        Iterator[ProvenanceDoc]
+    """
+
+    input_documents.sort(key=lambda x: x.formula_pretty)
+    snls.sort(key=lambda y: y.formula_pretty)
+
+    input_docs = dict()
+    for form, input_group in groupby(input_documents, key=lambda x: x.formula_pretty):
+        input_docs[form] = list(input_group)
+
+    snl_docs = dict()
+    for form, snl_group in groupby(snls, key=lambda y: y.formula_pretty):
+        snl_docs[form] = list(snl_group)
+
+    inputs = [(inp, snl_docs.get(form, [])) for form, inp in input_docs.items()]
+
+    return chain.from_iterable(filter_map(_match_against_snls, inputs, **kwargs))

{emmet_builders-0.87.0.dev15 → emmet_builders-0.87.0.dev16/emmet_builders.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: emmet-builders
-Version: 0.87.0.dev15
+Version: 0.87.0.dev16
 Summary: Builders for the Emmet Library
 Author-email: The Materials Project <feedback@materialsproject.org>
 License-Expression: BSD-3-Clause-LBNL

emmet_builders-0.87.0.dev15/emmet/builders/materials/provenance.py

@@ -1,151 +0,0 @@
-"""Build provenance collection."""
-
-import logging
-
-from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
-
-from emmet.builders.base import BaseBuilderInput
-from emmet.builders.settings import EmmetBuildSettings
-from emmet.builders.utils import filter_map
-from emmet.core.connectors.analysis import parse_cif
-from emmet.core.connectors.icsd.client import IcsdClient
-from emmet.core.connectors.icsd.enums import IcsdSubset
-from emmet.core.provenance import DatabaseSNL, ProvenanceDoc
-
-SETTINGS = EmmetBuildSettings()
-structure_matcher = StructureMatcher(
-    ltol=SETTINGS.LTOL,
-    stol=SETTINGS.STOL,
-    comparator=ElementComparator(),
-    angle_tol=SETTINGS.ANGLE_TOL,
-    primitive_cell=True,
-    scale=True,
-    attempt_supercell=False,
-    allow_subset=False,
-)
-
-
-logger = logging.getLogger(__name__)
-
-
-def _get_snl_from_cif(cif_str: str, **kwargs) -> DatabaseSNL | None:
-    """Build a database SNL from a CIF plus its metadata.
-
-    NB: Only takes the first structure from a CIF.
-    While a CIF can technically contain many structures,
-    the ICSD usually only distributes CIFs with one structure
-    per file.
-
-    Parameters
-    -----------
-    cif_str : the CIF to parse
-    **kwargs to pass to `DatabaseSNL`
-    """
-    try:
-        structures, cif_parsing_remarks = parse_cif(cif_str)
-        remarks = kwargs.pop("remarks", None) or cif_parsing_remarks or None
-        snl = DatabaseSNL.from_structure(
-            meta_structure=structures[0],
-            structure=structures[0],
-            **kwargs,
-        )
-
-        snl.about.remarks = remarks
-
-    except Exception as e:
-        logger.warning(e)
-        snl = None
-
-    return snl
-
-
-def update_experimental_icsd_structures(**client_kwargs) -> list[DatabaseSNL]:
-    """Update the collection of ICSD SNLs.
-
-    Parameters
-    -----------
-    **client_kwargs to pass to `IcsdClient`
-
-    Returns
-    -----------
-    List of DatabaseSNL
-    """
-    data = []
-    with IcsdClient(use_document_model=False, **client_kwargs) as client:
-        for icsd_subset in (
-            IcsdSubset.EXPERIMENTAL_METALORGANIC,
-            IcsdSubset.EXPERIMENTAL_INORGANIC,
-        ):
-            data += client.search(
-                subset=IcsdSubset.EXPERIMENTAL_INORGANIC,
-                space_group_number=(1, 230),
-                include_cif=True,
-                include_metadata=False,
-            )
-
-    parsed = [
-        _get_snl_from_cif(
-            doc["cif"],
-            snl_id=f"icsd-{doc['collection_code']}",
-            tags=[doc["subset"].value],
-            source="icsd",
-        )
-        for doc in data
-    ]
-
-    return sorted(
-        [doc for doc in parsed if doc],
-        key=lambda doc: int(doc.snl_id.split("-", 1)[-1]),
-    )
-
-
-def match_against_snls(
-    input_doc: BaseBuilderInput,
-    snls: list[DatabaseSNL],
-):
-    """Match a single document against the SNL collection."""
-    database_ids = {}
-    authors = [SETTINGS.DEFAULT_AUTHOR]
-    history = [SETTINGS.DEFAULT_HISTORY]
-    references = [SETTINGS.DEFAULT_REFERENCE]
-    theoretical = True
-
-    for snl in [
-        doc
-        for doc in snls
-        if doc.chemsys
-        == (
-            "-".join(sorted(input_doc.structure.composition.chemical_system.split("-")))
-        )
-    ]:
-        if structure_matcher.fit(input_doc.structure, snl.structure):
-
-            if snl.source and snl.source in {"icsd", "pauling"}:
-                theoretical = False
-                database_ids[snl.source].append(snl.snl_id)
-
-            if snl.about:
-                authors.extend(snl.about.authors or [])
-                history.extend(snl.about.history or [])
-                # `SNLAbout` uses string for `references`,
-                # `ProvenanceDoc` uses list of str
-                if snl.about.references:
-                    references.append(snl.about.references)
-
-    return ProvenanceDoc.from_structure(
-        meta_structure=input_doc.structure,
-        material_id=input_doc.material_id,
-        database_IDs=database_ids,
-        theoretical=theoretical,
-        authors=authors,
-        history=history,
-        references=references,
-    )
-
-
-def build_provenance_docs(
-    input_documents: list[BaseBuilderInput], snls: list[DatabaseSNL], **kwargs
-) -> list[ProvenanceDoc]:
-    """Build the provenance collection."""
-
-    return list(filter_map(match_against_snls, input_documents, snls=snls, **kwargs))