mp-api 0.46.3__tar.gz → 0.46.5__tar.gz

{mp_api-0.46.3 → mp_api-0.46.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mp-api
-Version: 0.46.3
+Version: 0.46.5
 Summary: API Client for the Materials Project
 Author-email: The Materials Project <feedback@materialsproject.org>
 License-Expression: BSD-3-Clause-LBNL
@@ -17,7 +17,7 @@ Requires-Dist: pymatgen>2024.2.20
 Requires-Dist: typing-extensions>=3.7.4.1
 Requires-Dist: requests>=2.23.0
 Requires-Dist: monty>=2024.12.10
-Requires-Dist: emmet-core<0.87.2,>=0.87.0
+Requires-Dist: emmet-core>=0.87.1
 Requires-Dist: boto3
 Requires-Dist: orjson<4,>=3.10
 Requires-Dist: pyarrow>=20.0.0
@@ -40,7 +40,7 @@ Requires-Dist: cachetools; extra == "contribs"
 Requires-Dist: pymongo; extra == "contribs"
 Provides-Extra: all
 Requires-Dist: custodian; extra == "all"
-Requires-Dist: emmet-core[all]<0.87.2,>=0.87.0; extra == "all"
+Requires-Dist: emmet-core[all]>=0.87.1; extra == "all"
 Requires-Dist: fastmcp; extra == "all"
 Requires-Dist: flask; extra == "all"
 Provides-Extra: test

{mp_api-0.46.3 → mp_api-0.46.5}/mp_api/client/mprester.py

@@ -1,11 +1,14 @@
 from __future__ import annotations
 
 import itertools
+import json
 import os
+import re
 import warnings
 from collections import defaultdict
 from functools import cache, lru_cache
 from typing import TYPE_CHECKING
+from urllib.parse import urlencode
 
 from emmet.core.band_theory import BSPathType
 from emmet.core.mpid import MPID, AlphaID
@@ -43,7 +46,7 @@ from mp_api.client.routes.materials import MATERIALS_RESTERS
 from mp_api.client.routes.molecules import MOLECULES_RESTERS
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
+    from collections.abc import Iterable, Sequence
     from typing import Any, Literal
 
     import numpy as np
@@ -88,6 +91,16 @@ TOP_LEVEL_RESTERS = [
 ]
 
 
+def _all_subchemsyses(elements: Iterable[str]) -> list[str]:
+    """Every chemical (sub)system spanned by `elements`, as sorted dash-joined strings."""
+    element_set = set(elements)
+    return [
+        "-".join(sorted(els))
+        for n in range(1, len(element_set) + 1)
+        for els in itertools.combinations(element_set, n)
+    ]
+
+
 class MPRester(_Rester):
     """Access the new Materials Project API."""
 
@@ -657,8 +670,10 @@ class MPRester(_Rester):
                     entry_dict["correction"] = 0.0
                     entry_dict["energy_adjustments"] = []
 
-                if property_data:
-                    entry_dict["data"] = {prop: doc[prop] for prop in property_data}
+                if (
+                    property_data
+                ):  # merge property_data, retaining entry data (e.g. `oxidation_states`)
+                    entry_dict["data"] |= {prop: doc[prop] for prop in property_data}
 
                 if conventional_unit_cell:
                     entry_struct = Structure.from_dict(entry_dict["structure"])
@@ -1054,6 +1069,26 @@ class MPRester(_Rester):
             **kwargs,
         )
 
+    def _get_unmixed_entries(
+        self, chemsyses: list[str], **kwargs
+    ) -> list[ComputedStructureEntry]:
+        """Get the GGA(+U) and r2SCAN entries for `chemsyses` as separate, un-mixed entries.
+
+        `MaterialsProjectDFTMixingScheme` needs both functionals side by side, as returned
+        by this helper function, while entries returned by the mixed thermo type cannot be
+        used with it.
+        """
+        return [
+            entry
+            for thermo_type in (ThermoType.GGA_GGA_U, ThermoType.R2SCAN)
+            for entry in self.get_entries(
+                chemsyses,
+                compatible_only=True,
+                additional_criteria={"thermo_types": [thermo_type.value]},
+                **kwargs,
+            )
+        ]
+
     def get_entries_in_chemsys(
         self,
         elements: str | list[str],
@@ -1073,6 +1108,14 @@ class MPRester(_Rester):
         Note that by default this returns mixed GGA/GGA+U/r2SCAN entries. For others,
         pass GGA/GGA+U, or R2SCAN as thermo_types in additional_criteria.
 
+        Mixed entries are taken from the MP-built phase diagram for the whole chemical
+        system, so they share one energy scale and reproduce the hull shown on
+        https://materialsproject.org. Narrowing the query with `additional_criteria`,
+        or passing ``compatible_only = False``, cannot be served that way and returns
+        entries that are *not* immediately suitable for constructing a phase diagram;
+        ``property_data`` and ``conventional_unit_cell`` re-apply the mixing scheme here
+        instead, which can differ slightly from MP. Warnings are thrown for these cases.
+
         Args:
             elements (str or [str]): Parent chemical system string comprising element
                 symbols separated by dashes, e.g., "Li-Fe-O" or List of element
@@ -1114,11 +1157,7 @@ class MPRester(_Rester):
                 "or identify a subset of relevant chemical systems to query first."
             )
 
-        all_chemsyses = [
-            "-".join(sorted(els))
-            for i in range(len(elements_set))
-            for els in itertools.combinations(elements_set, i + 1)
-        ]
+        all_chemsyses = _all_subchemsyses(elements_set)
 
         if additional_criteria is None:
             warnings.warn(
@@ -1131,15 +1170,79 @@ class MPRester(_Rester):
                 stacklevel=2,
             )
 
-        entries = self.get_entries(
-            all_chemsyses,
-            compatible_only=compatible_only,
-            property_data=property_data,
-            conventional_unit_cell=conventional_unit_cell,
-            additional_criteria=additional_criteria or DEFAULT_THERMOTYPE_CRITERIA,
-            **kwargs,
+        additional_criteria = {
+            **DEFAULT_THERMOTYPE_CRITERIA,
+            **(additional_criteria or {}),
+        }  # default thermo type unless the caller explicitly overrides
+
+        # The mixing correction stored on a mixed GGA(+U)/r2SCAN entry is referenced to the hull
+        # of the one chemical system that entry's thermo doc was built for, so the served entries
+        # cannot be pooled _across subsystems_ -- they end up on different absolute energy scales
+        # (issue #1104). Thus we serve MP's phase diagram; built with mixing applied across the
+        # full system, thus self-consistent by construction and identical to the MP website:
+        mixed = set(additional_criteria["thermo_types"]) == {"GGA_GGA+U_R2SCAN"}
+        consistent = (
+            mixed and compatible_only and set(additional_criteria) == {"thermo_types"}
         )
 
+        entries: list[ComputedStructureEntry] | None = None
+        if consistent:
+            if not (property_data or conventional_unit_cell):
+                phase_diagram = self.materials.thermo.get_phase_diagram_from_chemsys(
+                    "-".join(sorted(elements_set)),
+                    thermo_type=additional_criteria["thermo_types"][0],
+                )  # default, mixed thermotype; takes a single type, not a list
+                if phase_diagram is not None:
+                    entries = list(phase_diagram.all_entries)
+
+            if entries is None:
+                # MP has no pre-built diagram for this system, or the entries need reshaping
+                # first, so redo the mixing here as MP does when building PDs. Mixing scheme
+                # is chemical-system dependent, so this can anchor on a different hull than
+                # MP did/would, and it drops entries it cannot place:
+                from pymatgen.entries.mixing_scheme import (
+                    MaterialsProjectDFTMixingScheme,
+                )
+
+                warnings.warn(
+                    "Reconstructing a common energy scale for these entries with the "
+                    "GGA(+U)/r2SCAN mixing scheme, as the Materials Project has no pre-built "
+                    "phase diagram to serve for this query. Energies and hull distances may "
+                    "differ slightly from https://materialsproject.org, and entries the mixing "
+                    "scheme cannot place are dropped.",
+                    category=MPRestWarning,
+                    stacklevel=2,
+                )
+                entries = MaterialsProjectDFTMixingScheme().process_entries(
+                    self._get_unmixed_entries(
+                        all_chemsyses,
+                        property_data=property_data,
+                        conventional_unit_cell=conventional_unit_cell,
+                        **kwargs,
+                    )
+                )
+        else:  # non-consistent
+            if mixed:
+                warnings.warn(
+                    "Mixed GGA(+U)/r2SCAN entries can only be placed on a common energy scale "
+                    "when the whole chemical system is retrieved with `compatible_only = True`, "
+                    "so these entries are not suitable for constructing a phase diagram. Either "
+                    "drop the extra `additional_criteria` (and filter the returned entries "
+                    "instead), or request a single functional with "
+                    '`additional_criteria = {"thermo_types": ["GGA_GGA+U"]}`.',
+                    category=MPRestWarning,
+                    stacklevel=2,
+                )
+
+            entries = self.get_entries(
+                all_chemsyses,
+                compatible_only=compatible_only,
+                property_data=property_data,
+                conventional_unit_cell=conventional_unit_cell,
+                additional_criteria=additional_criteria,
+                **kwargs,
+            )
+
         if use_gibbs:
             # replace the entries with GibbsComputedStructureEntry
             from pymatgen.entries.computed_entries import GibbsComputedStructureEntry
@@ -1365,45 +1468,66 @@ class MPRester(_Rester):
                 if calc_types and calc_type not in calc_types:
                     continue
                 mp_id = doc["material_id"]
-                meta[mp_id].append({"task_id": task_id, "calc_type": calc_type})
+                meta[mp_id].append(
+                    {
+                        "task_id": str(AlphaID(task_id, prefix="mp").formatted),
+                        "task_id_as_alpha": task_id,
+                        "calc_type": calc_type,
+                    }
+                )
 
         if not meta:
             raise ValueError(f"No tasks found for material id {material_ids}.")
 
         # return a list of URLs for NoMaD Downloads containing the list of files
         # for every external_id in `task_ids`
-        # For reference, please visit https://nomad-lab.eu/prod/rae/api/
+        # For reference, please visit https://nomad-lab.eu/prod/v1/api/v1/extensions/docs#/entries/raw
 
         # check if these task ids exist on NOMAD
-        prefix = "https://nomad-lab.eu/prod/rae/api/repo/?"
-        if file_patterns is not None:
-            for file_pattern in file_patterns:
-                prefix += f"file_pattern={file_pattern}&"
-        prefix += "external_id="
+        nomad_check_endpoint = "https://nomad-lab.eu/prod/v1/api/v1/entries/rawdir"
+        nomad_download_endpoint = "https://nomad-lab.eu/prod/v1/api/v1/entries/raw"
 
         task_ids = [t["task_id"] for tl in meta.values() for t in tl]
+        task_id_query_params: list[tuple[str, dict]] = [
+            (tid, {"json_query": json.dumps({"external_id": tid})}) for tid in task_ids
+        ]
+
         nomad_exist_task_ids = self._check_get_download_info_url_by_task_id(
-            prefix=prefix, task_ids=task_ids
+            prefix=nomad_check_endpoint, task_ids=task_id_query_params
         )
+
         if len(nomad_exist_task_ids) != len(task_ids):
             self._print_help_message(
-                nomad_exist_task_ids, task_ids, file_patterns, calc_types
+                [pair[0] for pair in nomad_exist_task_ids],
+                task_ids,
+                file_patterns,
+                calc_types,
             )
 
         # generate download links for those that exist
-        prefix = "https://nomad-lab.eu/prod/rae/api/raw/query?"
         if file_patterns is not None:
-            for file_pattern in file_patterns:
-                prefix += f"file_pattern={file_pattern}&"
-        prefix += "external_id="
+            if len(file_patterns) == 1:
+                for _, json_query in nomad_exist_task_ids:
+                    json_query["glob_pattern"] = file_patterns[0]
+            else:
+                re_pattern = "|".join(re.escape(pattern) for pattern in file_patterns)
+                for _, json_query in nomad_exist_task_ids:
+                    json_query["re_pattern"] = re_pattern
+
+        urls = [
+            f"{nomad_download_endpoint}?{urlencode(json_query)}"
+            for _, json_query in nomad_exist_task_ids
+        ]
 
-        urls = [prefix + tids for tids in nomad_exist_task_ids]
         return meta, urls
 
-    def _check_get_download_info_url_by_task_id(self, prefix, task_ids) -> list[str]:
-        prefix = prefix.replace("/raw/query", "/repo/")
+    def _check_get_download_info_url_by_task_id(
+        self, prefix, task_ids
+    ) -> list[tuple[str, dict]]:
         return [
-            task_id for task_id in task_ids if self._check_nomad_exist(prefix + task_id)
+            pair
+            for pair in task_ids
+            if self._check_nomad_exist(url=f"{prefix}?{urlencode(pair[1])}")
         ]
 
     @staticmethod
@@ -1411,7 +1535,7 @@ class MPRester(_Rester):
         response = get(url=url)
         if response.status_code != 200:
             return False
-        return load_json(response.text)["pagination"]["total"] != 0
+        return response.json()["pagination"]["total"] != 0
 
     @staticmethod
     def _print_help_message(nomad_exist_task_ids, task_ids, file_patterns, calc_types):
@@ -1650,8 +1774,14 @@ class MPRester(_Rester):
 
         joint_entries: Sequence[ComputedEntry | ComputedStructureEntry | PDEntry] = [
             *entries,
-            *pd.all_entries,
-        ]
+            *(
+                self._get_unmixed_entries(_all_subchemsyses(str(el) for el in chemsys))
+                if thermo_type_valid_str == ThermoType.GGA_GGA_U_R2SCAN.value
+                else pd.all_entries
+            ),  # `pd.all_entries` for a mixed hull hold one already-mixed entry per material,
+        ]  # which the mixing scheme cannot re-process (needs the GGA(+U) and r2SCAN entries
+        # side by side), and silently drops every entry it cannot pair up -- so we fetch
+        # separately in the mixed case
 
         new_pd = PhaseDiagram(
             corrector.process_entries(joint_entries)  # type: ignore[arg-type]

{mp_api-0.46.3 → mp_api-0.46.5}/mp_api.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mp-api
-Version: 0.46.3
+Version: 0.46.5
 Summary: API Client for the Materials Project
 Author-email: The Materials Project <feedback@materialsproject.org>
 License-Expression: BSD-3-Clause-LBNL
@@ -17,7 +17,7 @@ Requires-Dist: pymatgen>2024.2.20
 Requires-Dist: typing-extensions>=3.7.4.1
 Requires-Dist: requests>=2.23.0
 Requires-Dist: monty>=2024.12.10
-Requires-Dist: emmet-core<0.87.2,>=0.87.0
+Requires-Dist: emmet-core>=0.87.1
 Requires-Dist: boto3
 Requires-Dist: orjson<4,>=3.10
 Requires-Dist: pyarrow>=20.0.0
@@ -40,7 +40,7 @@ Requires-Dist: cachetools; extra == "contribs"
 Requires-Dist: pymongo; extra == "contribs"
 Provides-Extra: all
 Requires-Dist: custodian; extra == "all"
-Requires-Dist: emmet-core[all]<0.87.2,>=0.87.0; extra == "all"
+Requires-Dist: emmet-core[all]>=0.87.1; extra == "all"
 Requires-Dist: fastmcp; extra == "all"
 Requires-Dist: flask; extra == "all"
 Provides-Extra: test

{mp_api-0.46.3 → mp_api-0.46.5}/mp_api.egg-info/SOURCES.txt

@@ -26,6 +26,8 @@ mp_api.egg-info/SOURCES.txt
 mp_api.egg-info/dependency_links.txt
 mp_api.egg-info/entry_points.txt
 mp_api.egg-info/requires.txt
+mp_api.egg-info/scm_file_list.json
+mp_api.egg-info/scm_version.json
 mp_api.egg-info/top_level.txt
 mp_api/client/__init__.py
 mp_api/client/_server_utils.py

{mp_api-0.46.3 → mp_api-0.46.5}/mp_api.egg-info/requires.txt

@@ -2,7 +2,7 @@ pymatgen>2024.2.20
 typing-extensions>=3.7.4.1
 requests>=2.23.0
 monty>=2024.12.10
-emmet-core<0.87.2,>=0.87.0
+emmet-core>=0.87.1
 boto3
 orjson<4,>=3.10
 pyarrow>=20.0.0
@@ -10,7 +10,7 @@ deltalake<1.6.0,>=1.4.0
 
 [all]
 custodian
-emmet-core[all]<0.87.2,>=0.87.0
+emmet-core[all]>=0.87.1
 fastmcp
 flask
 

mp_api-0.46.5/mp_api.egg-info/scm_file_list.json

@@ -0,0 +1,142 @@
+{
+  "files": [
+    ".coveragerc",
+    ".github/workflows/lint.yml",
+    ".github/workflows/release.yml",
+    ".github/workflows/testing.yml",
+    ".github/workflows/upgrade_dependencies.yml",
+    ".gitignore",
+    ".pre-commit-config.yaml",
+    "CODE_OF_CONDUCT.md",
+    "LICENSE",
+    "README.md",
+    "dev/generate_mcp_tools.py",
+    "dev/inspect_mcp.sh",
+    "docs/Makefile",
+    "docs/_templates/custom-class-template.rst",
+    "docs/_templates/custom-module-template.rst",
+    "docs/conf.py",
+    "docs/index.rst",
+    "docs/make.bat",
+    "docs/modules.rst",
+    "mp_api/__init__.py",
+    "mp_api/_test_utils.py",
+    "mp_api/client/__init__.py",
+    "mp_api/client/_server_utils.py",
+    "mp_api/client/contribs/__init__.py",
+    "mp_api/client/contribs/_logger.py",
+    "mp_api/client/contribs/_types.py",
+    "mp_api/client/contribs/_units.py",
+    "mp_api/client/contribs/client.py",
+    "mp_api/client/contribs/schemas.py",
+    "mp_api/client/contribs/settings.py",
+    "mp_api/client/contribs/utils.py",
+    "mp_api/client/core/__init__.py",
+    "mp_api/client/core/_oxygen_evolution.py",
+    "mp_api/client/core/client.py",
+    "mp_api/client/core/exceptions.py",
+    "mp_api/client/core/schemas.py",
+    "mp_api/client/core/settings.py",
+    "mp_api/client/core/utils.py",
+    "mp_api/client/mprester.py",
+    "mp_api/client/routes/__init__.py",
+    "mp_api/client/routes/_server.py",
+    "mp_api/client/routes/materials/__init__.py",
+    "mp_api/client/routes/materials/absorption.py",
+    "mp_api/client/routes/materials/alloys.py",
+    "mp_api/client/routes/materials/bonds.py",
+    "mp_api/client/routes/materials/chemenv.py",
+    "mp_api/client/routes/materials/dielectric.py",
+    "mp_api/client/routes/materials/doi.py",
+    "mp_api/client/routes/materials/elasticity.py",
+    "mp_api/client/routes/materials/electrodes.py",
+    "mp_api/client/routes/materials/electronic_structure.py",
+    "mp_api/client/routes/materials/eos.py",
+    "mp_api/client/routes/materials/grain_boundaries.py",
+    "mp_api/client/routes/materials/magnetism.py",
+    "mp_api/client/routes/materials/materials.py",
+    "mp_api/client/routes/materials/oxidation_states.py",
+    "mp_api/client/routes/materials/phonon.py",
+    "mp_api/client/routes/materials/piezo.py",
+    "mp_api/client/routes/materials/provenance.py",
+    "mp_api/client/routes/materials/robocrys.py",
+    "mp_api/client/routes/materials/similarity.py",
+    "mp_api/client/routes/materials/substrates.py",
+    "mp_api/client/routes/materials/summary.py",
+    "mp_api/client/routes/materials/surface_properties.py",
+    "mp_api/client/routes/materials/synthesis.py",
+    "mp_api/client/routes/materials/tasks.py",
+    "mp_api/client/routes/materials/thermo.py",
+    "mp_api/client/routes/materials/xas.py",
+    "mp_api/client/routes/molecules/__init__.py",
+    "mp_api/client/routes/molecules/jcesr.py",
+    "mp_api/client/routes/molecules/molecules.py",
+    "mp_api/client/routes/molecules/summary.py",
+    "mp_api/mcp/__init__.py",
+    "mp_api/mcp/_schemas.py",
+    "mp_api/mcp/mp_mcp.py",
+    "mp_api/mcp/server.py",
+    "mp_api/mcp/tools.py",
+    "mp_api/mcp/utils.py",
+    "mp_api/py.typed",
+    "pyproject.toml",
+    "requirements/requirements-ubuntu-latest_py3.11.txt",
+    "requirements/requirements-ubuntu-latest_py3.11_extras.txt",
+    "requirements/requirements-ubuntu-latest_py3.12.txt",
+    "requirements/requirements-ubuntu-latest_py3.12_extras.txt",
+    "requirements/requirements-ubuntu-latest_py3.13.txt",
+    "requirements/requirements-ubuntu-latest_py3.13_extras.txt",
+    "requirements/requirements-ubuntu-latest_py3.14.txt",
+    "requirements/requirements-ubuntu-latest_py3.14_extras.txt",
+    "test_files/Si_mp_149.cif",
+    "tests/__init__.py",
+    "tests/client/__init__.py",
+    "tests/client/contribs/conftest.py",
+    "tests/client/contribs/test_client.py",
+    "tests/client/contribs/test_contribs_schemas.py",
+    "tests/client/contribs/test_contribs_utils.py",
+    "tests/client/contribs/test_types.py",
+    "tests/client/core/test_oxygen_evolution.py",
+    "tests/client/core/test_schemas.py",
+    "tests/client/core/test_utils.py",
+    "tests/client/materials/__init__.py",
+    "tests/client/materials/test_absorption.py",
+    "tests/client/materials/test_alloys.py",
+    "tests/client/materials/test_bonds.py",
+    "tests/client/materials/test_chemenv.py",
+    "tests/client/materials/test_dielectric.py",
+    "tests/client/materials/test_doi.py",
+    "tests/client/materials/test_elasticity.py",
+    "tests/client/materials/test_electrodes.py",
+    "tests/client/materials/test_electronic_structure.py",
+    "tests/client/materials/test_eos.py",
+    "tests/client/materials/test_grain_boundary.py",
+    "tests/client/materials/test_magnetism.py",
+    "tests/client/materials/test_materials.py",
+    "tests/client/materials/test_oxidation_states.py",
+    "tests/client/materials/test_phonon.py",
+    "tests/client/materials/test_piezo.py",
+    "tests/client/materials/test_provenance.py",
+    "tests/client/materials/test_robocrys.py",
+    "tests/client/materials/test_similarity.py",
+    "tests/client/materials/test_substrates.py",
+    "tests/client/materials/test_summary.py",
+    "tests/client/materials/test_surface_properties.py",
+    "tests/client/materials/test_synthesis.py",
+    "tests/client/materials/test_tasks.py",
+    "tests/client/materials/test_thermo.py",
+    "tests/client/materials/test_xas.py",
+    "tests/client/molecules/__init__.py",
+    "tests/client/molecules/test_jcesr.py",
+    "tests/client/molecules/test_molecules.py",
+    "tests/client/molecules/test_summary.py",
+    "tests/client/test_client.py",
+    "tests/client/test_core_client.py",
+    "tests/client/test_heartbeat.py",
+    "tests/client/test_mprester.py",
+    "tests/mcp/__init__.py",
+    "tests/mcp/test_server.py",
+    "tests/mcp/test_tools.py",
+    "tests/mcp/test_utils.py"
+  ]
+}

mp_api-0.46.5/mp_api.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "0.46.5",
+  "distance": 0,
+  "node": "ge114cc193551f421ed5cf10bf8854bf474cf6a7e",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-08-18"
+}

{mp_api-0.46.3 → mp_api-0.46.5}/pyproject.toml

@@ -24,7 +24,7 @@ dependencies = [
   "typing-extensions>=3.7.4.1",
   "requests>=2.23.0",
   "monty>=2024.12.10",
-  "emmet-core>=0.87.0,<0.87.2",
+  "emmet-core>=0.87.1",
   "boto3",
   "orjson >= 3.10,<4",
   "pyarrow >= 20.0.0",
@@ -50,7 +50,7 @@ contribs = [
 ]
 all = [
   "custodian",
-  "emmet-core[all]>=0.87.0,<0.87.2",
+  "emmet-core[all]>=0.87.1",
   "fastmcp",
   "flask",
 ]