Merge branch 'master' into cleanup-test-files

.github/CODEOWNERS

@@ -2,3 +2,5 @@
 pymatgen/io/ase.py @Andrew-S-Rosen
 pymatgen/io/abinit/* @gmatteo
 pymatgen/io/lobster/* @JaGeo
+pymatgen/ext/* @ml-evs
+tests/ext/* @ml-evs

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.3.7
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]

pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -241,17 +241,16 @@ def __init__(
                 if links_data is None:
                     edge_data = None
 
+                elif (env_node1, env_node2, key) in links_data:
+                    edge_data = links_data[(env_node1, env_node2, key)]
+                elif (env_node2, env_node1, key) in links_data:
+                    edge_data = links_data[(env_node2, env_node1, key)]
+                elif (env_node1, env_node2) in links_data:
+                    edge_data = links_data[(env_node1, env_node2)]
+                elif (env_node2, env_node1) in links_data:
+                    edge_data = links_data[(env_node2, env_node1)]
                 else:
-                    if (env_node1, env_node2, key) in links_data:
-                        edge_data = links_data[(env_node1, env_node2, key)]
-                    elif (env_node2, env_node1, key) in links_data:
-                        edge_data = links_data[(env_node2, env_node1, key)]
-                    elif (env_node1, env_node2) in links_data:
-                        edge_data = links_data[(env_node1, env_node2)]
-                    elif (env_node2, env_node1) in links_data:
-                        edge_data = links_data[(env_node2, env_node1)]
-                    else:
-                        edge_data = None
+                    edge_data = None
 
                 if edge_data:
                     self._connected_subgraph.add_edge(env_node1, env_node2, key, **edge_data)

pymatgen/analysis/elasticity/stress.py

@@ -6,12 +6,15 @@
 from __future__ import annotations
 
 import math
+from typing import TYPE_CHECKING
 
 import numpy as np
-from typing_extensions import Self
 
 from pymatgen.core.tensors import SquareTensor
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 __author__ = "Joseph Montoya"
 __copyright__ = "Copyright 2012, The Materials Project"
 __credits__ = "Maarten de Jong, Mark Asta, Anubhav Jain"

pymatgen/core/__init__.py

@@ -1,4 +1,3 @@
-# ruff: noqa: PLC0414
 """This package contains core modules and classes for representing structures and operations on them."""
 
 from __future__ import annotations
@@ -10,25 +9,13 @@
 
 from ruamel.yaml import YAML
 
-from pymatgen.core.composition import Composition as Composition
-from pymatgen.core.lattice import Lattice as Lattice
-from pymatgen.core.operations import SymmOp as SymmOp
-from pymatgen.core.periodic_table import DummySpecie as DummySpecie
-from pymatgen.core.periodic_table import DummySpecies as DummySpecies
-from pymatgen.core.periodic_table import Element as Element
-from pymatgen.core.periodic_table import Species as Species
-from pymatgen.core.periodic_table import get_el_sp as get_el_sp
-from pymatgen.core.sites import PeriodicSite as PeriodicSite
-from pymatgen.core.sites import Site as Site
-from pymatgen.core.structure import IMolecule as IMolecule
-from pymatgen.core.structure import IStructure as IStructure
-from pymatgen.core.structure import Molecule as Molecule
-from pymatgen.core.structure import PeriodicNeighbor as PeriodicNeighbor
-from pymatgen.core.structure import SiteCollection as SiteCollection
-from pymatgen.core.structure import Structure as Structure
-from pymatgen.core.units import ArrayWithUnit as ArrayWithUnit
-from pymatgen.core.units import FloatWithUnit as FloatWithUnit
-from pymatgen.core.units import Unit as Unit
+from pymatgen.core.composition import Composition
+from pymatgen.core.lattice import Lattice
+from pymatgen.core.operations import SymmOp
+from pymatgen.core.periodic_table import DummySpecie, DummySpecies, Element, Species, get_el_sp
+from pymatgen.core.sites import PeriodicSite, Site
+from pymatgen.core.structure import IMolecule, IStructure, Molecule, PeriodicNeighbor, SiteCollection, Structure
+from pymatgen.core.units import ArrayWithUnit, FloatWithUnit, Unit
 
 __author__ = "Pymatgen Development Team"
 __email__ = "pymatgen@googlegroups.com"

pymatgen/electronic_structure/cohp.py

@@ -772,57 +772,52 @@ def from_file(
                     # LMTO COHPs have 5 significant figures
                     avg_data[i].update({spin: np.array([round_to_sigfigs(a, 5) for a in avg], dtype=float)})
             avg_cohp = Cohp(efermi, energies, avg_data["COHP"], icohp=avg_data["ICOHP"])
+        elif not are_multi_center_cobis:
+            avg_cohp = Cohp(
+                efermi,
+                energies,
+                cohp_data["average"]["COHP"],
+                icohp=cohp_data["average"]["ICOHP"],
+                are_coops=are_coops,
+                are_cobis=are_cobis,
+                are_multi_center_cobis=are_multi_center_cobis,
+            )
+            del cohp_data["average"]
         else:
-            if not are_multi_center_cobis:
-                avg_cohp = Cohp(
-                    efermi,
-                    energies,
-                    cohp_data["average"]["COHP"],
-                    icohp=cohp_data["average"]["ICOHP"],
-                    are_coops=are_coops,
-                    are_cobis=are_cobis,
-                    are_multi_center_cobis=are_multi_center_cobis,
-                )
-                del cohp_data["average"]
-            else:
-                # only include two-center cobis in average
-                # do this for both spin channels
-                cohp = {}
-                cohp[Spin.up] = np.array(
-                    [np.array(c["COHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
+            # only include two-center cobis in average
+            # do this for both spin channels
+            cohp = {}
+            cohp[Spin.up] = np.array(
+                [np.array(c["COHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
+            ).mean(axis=0)
+            try:
+                cohp[Spin.down] = np.array(
+                    [np.array(c["COHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
+                ).mean(axis=0)
+            except KeyError:
+                pass
+            try:
+                icohp = {}
+                icohp[Spin.up] = np.array(
+                    [np.array(c["ICOHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
                 ).mean(axis=0)
                 try:
-                    cohp[Spin.down] = np.array(
-                        [np.array(c["COHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
+                    icohp[Spin.down] = np.array(
+                        [np.array(c["ICOHP"][Spin.down]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
                     ).mean(axis=0)
                 except KeyError:
                     pass
-                try:
-                    icohp = {}
-                    icohp[Spin.up] = np.array(
-                        [np.array(c["ICOHP"][Spin.up]) for c in cohp_file.cohp_data.values() if len(c["sites"]) <= 2]
-                    ).mean(axis=0)
-                    try:
-                        icohp[Spin.down] = np.array(
-                            [
-                                np.array(c["ICOHP"][Spin.down])
-                                for c in cohp_file.cohp_data.values()
-                                if len(c["sites"]) <= 2
-                            ]
-                        ).mean(axis=0)
-                    except KeyError:
-                        pass
-                except KeyError:
-                    icohp = None
-                avg_cohp = Cohp(
-                    efermi,
-                    energies,
-                    cohp,
-                    icohp=icohp,
-                    are_coops=are_coops,
-                    are_cobis=are_cobis,
-                    are_multi_center_cobis=are_multi_center_cobis,
-                )
+            except KeyError:
+                icohp = None
+            avg_cohp = Cohp(
+                efermi,
+                energies,
+                cohp,
+                icohp=icohp,
+                are_coops=are_coops,
+                are_cobis=are_cobis,
+                are_multi_center_cobis=are_multi_center_cobis,
+            )
 
         cohp_dict = {
             key: Cohp(

pymatgen/ext/optimade.py

@@ -5,16 +5,19 @@
 import logging
 import sys
 from collections import namedtuple
+from typing import TYPE_CHECKING
 from urllib.parse import urljoin, urlparse
 
 import requests
 from tqdm import tqdm
-from typing_extensions import Self
 
 from pymatgen.core import DummySpecies, Structure
 from pymatgen.util.due import Doi, due
 from pymatgen.util.provenance import StructureNL
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 # TODO: importing optimade-python-tool's data structures will make more sense
 Provider = namedtuple("Provider", ["name", "base_url", "description", "homepage", "prefix"])
 
@@ -49,7 +52,9 @@ class OptimadeRester:
     # these aliases are provided as a convenient shortcut for users of the OptimadeRester class
     aliases = {
         "aflow": "http://aflow.org/API/optimade/",
-        "alexandria": "https://alexandria.odbx.science",
+        "alexandria": "https://alexandria.icams.rub.de/pbe",
+        "alexandria.pbe": "https://alexandria.icams.rub.de/pbe",
+        "alexandria.pbesol": "https://alexandria.icams.rub.de/pbesol",
         "cod": "https://www.crystallography.net/cod/optimade",
         "cmr": "https://cmr-optimade.fysik.dtu.dk",
         "mcloud.mc3d": "https://aiida.materialscloud.org/mc3d/optimade",
@@ -68,6 +73,7 @@ class OptimadeRester:
         "nmd": "https://nomad-lab.eu/prod/rae/optimade/",
         "odbx": "https://optimade.odbx.science",
         "odbx.odbx_misc": "https://optimade-misc.odbx.science",
+        "odbx.gnome": "https://optimade-gnome.odbx.science",
         "omdb.omdb_production": "http://optimade.openmaterialsdb.se",
         "oqmd": "http://oqmd.org/optimade/",
         "jarvis": "https://jarvis.nist.gov/optimade/jarvisdft",
@@ -127,6 +133,11 @@ def __init__(
         # and values as the corresponding URL
         self.resources = {}
 
+        # preprocess aliases to ensure they have a trailing slash where appropriate
+        for alias, url in self.aliases.items():
+            if urlparse(url).path is not None and not url.endswith("/"):
+                self.aliases[alias] += "/"
+
         if not aliases_or_resource_urls:
             aliases_or_resource_urls = list(self.aliases)
             _logger.warning(
@@ -436,6 +447,10 @@ def _validate_provider(self, provider_url) -> Provider | None:
         TODO: careful reading of OPTIMADE specification required
         TODO: add better exception handling, intentionally permissive currently
         """
+        # Add trailing slash to all URLs if missing; prevents urljoin from scrubbing
+        # sections of the path
+        if urlparse(provider_url).path is not None and not provider_url.endswith("/"):
+            provider_url += "/"
 
         def is_url(url) -> bool:
             """Basic URL validation thanks to https://stackoverflow.com/a/52455972."""
@@ -486,6 +501,9 @@ def _parse_provider(self, provider: str, provider_url: str) -> dict[str, Provide
             A dictionary of keys (in format of "provider.database") to
             Provider objects.
         """
+        # Add trailing slash to all URLs if missing; prevents urljoin from scrubbing
+        if urlparse(provider_url).path is not None and not provider_url.endswith("/"):
+            provider_url += "/"
         try:
             url = urljoin(provider_url, "v1/links")
             provider_link_json = self._get_json(url)
@@ -546,6 +564,11 @@ def refresh_aliases(self, providers_url="https://providers.optimade.org/provider
 
         self.aliases = {alias: provider.base_url for alias, provider in structure_providers.items()}
 
+        # Add missing trailing slashes to any aliases with a path that need them
+        for alias, url in self.aliases.items():
+            if urlparse(url).path is not None and not url.endswith("/"):
+                self.aliases[alias] += "/"
+
     # TODO: revisit context manager logic here and in MPRester
     def __enter__(self) -> Self:
         """Support for "with" context."""

pymatgen/io/abinit/netcdf.py

@@ -7,18 +7,21 @@
 import logging
 import os.path
 import warnings
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.collections import AttrDict
 from monty.dev import requires
 from monty.functools import lazy_property
 from monty.string import marquee
-from typing_extensions import Self
 
 from pymatgen.core.structure import Structure
 from pymatgen.core.units import ArrayWithUnit
 from pymatgen.core.xcfunc import XcFunc
 
+if TYPE_CHECKING:
+    from typing_extensions import Self
+
 try:
     import netCDF4
 except ImportError:

pymatgen/io/aims/sets/bs.py

@@ -45,9 +45,8 @@ def prepare_band_input(structure: Structure, density: float = 20):
                 current_segment["length"] += 1
                 lines_and_labels.append(current_segment)
                 current_segment = None
-        else:
-            if current_segment is not None:
-                current_segment["length"] += 1
+        elif current_segment is not None:
+            current_segment["length"] += 1
 
     bands = []
     for segment in lines_and_labels: