try to fix mypy ci

Author: esoteric-ephemera

.pre-commit-config.yaml

@@ -52,4 +52,13 @@ repos:
         args:
           - --namespace-packages
           - --explicit-package-bases
-        additional_dependencies: ['types-requests','pydantic>=2.0.1']
+        additional_dependencies: ['types-requests','pydantic>=2.10.0']
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout
+        args:
+          - --drop-empty-cells
+          - --strip-init-cells
+          - --extra-keys=metadata.kernelspec

examples/using_validation_docs.ipynb

@@ -2,39 +2,43 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
-   "id": "b116c8b3-e927-401b-aed8-994fe5279b54",
+   "execution_count": null,
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
     "from __future__ import annotations\n",
     "\n",
-    "from emmet.core.tasks import TaskDoc\n",
+    "from monty.os.path import zpath\n",
     "from monty.serialization import loadfn\n",
     "import os\n",
+    "from pathlib import Path\n",
     "\n",
-    "from pymatgen.io.validation import ValidationDoc\n",
-    "from pymatgen.io.validation.check_potcar import CheckPotcar\n",
+    "from pymatgen.io.validation.validation import VaspValidator\n",
     "\n",
     "from pymatgen.io.vasp import PotcarSingle, Potcar"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 2,
-   "id": "80064515-1e98-43da-b075-5a4c41ede437",
+   "cell_type": "markdown",
+   "id": "1",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "\"\"\"\n",
     "For copyright reasons, the POTCAR for these calculations cannot be distributed with this file, but its summary stats can.\n",
-    "If you have the POTCAR resources set up in pymatgen, you can regenerate the POTCARs used here by enabling `regen_potcars`\n",
-    "\"\"\"\n",
     "\n",
+    "If you have the POTCAR resources set up in pymatgen, you can regenerate the POTCARs used here by enabling `regen_potcars`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "regen_potcars = True\n",
     "\n",
     "def get_potcar_from_spec(potcar_spec : dict) -> Potcar | None:\n",
-    "    potcar_checker = CheckPotcar()\n",
     "    \n",
     "    for functional in PotcarSingle._potcar_summary_stats:\n",
     "\n",
@@ -47,72 +51,83 @@
     "                \n",
     "            for stats in PotcarSingle._potcar_summary_stats[functional].get(titel_no_spc,[]):\n",
     "                \n",
-    "                if potcar_checker.compare_potcar_stats(spec[\"summary_stats\"], stats):\n",
+    "                if PotcarSingle.compare_potcar_stats(spec[\"summary_stats\"], stats):\n",
     "                    potcar.append(PotcarSingle.from_symbol_and_functional(symbol=symbol, functional=functional))\n",
     "                    matched[ispec] = True\n",
     "                    break\n",
     "                    \n",
     "            if all(matched):\n",
     "                return potcar\n",
     "    \n",
-    "def check_calc(calc_dir : str) -> ValidationDoc:\n",
+    "def check_calc(calc_dir : str | Path) -> VaspValidator:\n",
+    "\n",
+    "    calc_dir = Path(calc_dir)\n",
     "    potcar_filename = None\n",
     "    if regen_potcars:\n",
-    "        potcar = get_potcar_from_spec(loadfn(os.path.join(calc_dir,\"POTCAR.spec.gz\")))\n",
+    "        potcar = get_potcar_from_spec(loadfn(calc_dir / \"POTCAR.spec.gz\"))\n",
     "        if potcar:\n",
-    "            potcar_filename = os.path.join(calc_dir,\"POTCAR.gz\")\n",
+    "            potcar_filename = calc_dir / \"POTCAR.gz\"\n",
     "            potcar.write_file(potcar_filename)\n",
     "    \n",
-    "    valid_doc = ValidationDoc.from_directory(calc_dir, check_potcar=(regen_potcars and potcar))\n",
+    "    vasp_files = {\n",
+    "        k.lower().split(\".\")[0] : zpath(calc_dir / k) for k in (\n",
+    "            \"INCAR\",\"KPOINTS\",\"POSCAR\",\"POTCAR\",\"OUTCAR\", \"vasprun.xml\"\n",
+    "        )\n",
+    "    }\n",
     "    \n",
+    "    valid_doc = VaspValidator.from_vasp_input(\n",
+    "        vasp_file_paths={\n",
+    "            k : v for k,v in vasp_files.items() if Path(v).exists()\n",
+    "        },\n",
+    "        check_potcar=(regen_potcars and potcar)\n",
+    "    )\n",
+    "\n",
     "    if potcar_filename and potcar:\n",
     "        os.remove(potcar_filename)\n",
     "        \n",
     "    return valid_doc\n",
     "    "
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "3",
+   "metadata": {},
+   "source": [
+    "An example of an MP-compatible r2SCAN static calculation for GaAs is located in the `MP_compliant` directory."
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "id": "0f660f54-ca8a-466c-b382-2f0fac46d8bf",
+   "execution_count": null,
+   "id": "4",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "True\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "\"\"\"\n",
-    "An example of an MP-compatible r2SCAN static calculation for GaAs is located in the `MP_compliant` directory.\n",
-    "\"\"\"\n",
     "mp_compliant_doc = check_calc(\"MP_compliant\")\n",
-    "print(mp_compliant_doc.valid)"
+    "print(mp_compliant_doc.is_valid)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5",
+   "metadata": {},
+   "source": [
+    "We also include `TaskDoc` objects generated with `atomate2`, the workflow software currently used by the Materials Project (MP) for high-throughput calculations. A `TaskDoc` is also the document schema for the MP `task` collection.\n",
+    "\n",
+    "If you have `emmet-core` (this is the software used to build Materials Project data) or `atomate2` installed, you can load a `TaskDoc` like this:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "id": "25b85de2",
+   "execution_count": null,
+   "id": "6",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "True\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
-    "\"\"\"\n",
-    "TaskDocs for these calculations (generated with atomate2) are also saved in these directories.\n",
-    "You can load in the TaskDocs like so:\n",
-    "\"\"\"\n",
+    "from emmet.core.tasks import TaskDoc\n",
+    "from pymatgen.io.validation.emmet_validation import ValidationDoc\n",
+    "\n",
     "compliant_task_doc = TaskDoc(\n",
     "    **loadfn(os.path.join(\"MP_compliant\",\"MP_compatible_GaAs_r2SCAN_static.json.gz\"))\n",
     ")\n",
@@ -121,59 +136,31 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": 5,
-   "id": "c919fedd-38ef-4cf7-a2ed-54544eec8d82",
+   "cell_type": "markdown",
+   "id": "7",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "False\n",
-      "INPUT SETTINGS --> KPOINTS or KSPACING: 64 kpoints were used, but it should have been at least 194.\n",
-      "INPUT SETTINGS --> ENAUG: is 900.0, but should be >= 1360.\n",
-      "INPUT SETTINGS --> ENCUT: is 450.0, but should be >= 680.\n",
-      "False\n",
-      "True\n"
-     ]
-    }
-   ],
    "source": [
-    "\"\"\"\n",
-    "An example of an MP incompatible r2SCAN static calculation for GaAs is located in the `MP_non_compliant` directory.\n",
+    "An example of an MP incompatible r<sup>2</sup>SCAN static calculation for GaAs is located in the `MP_non_compliant` directory.\n",
     "\n",
     "This calculation uses a lower ENCUT, ENAUG, and k-point density (larger KSPACING) than is permitted by the appropriate input set, `pymatgen.io.vasp.sets.MPScanStaticSet`.\n",
-    "These reasons are reflected transparently in the output reasons.\n",
-    "\"\"\"\n",
-    "mp_non_compliant_doc = check_calc(\"MP_non_compliant\")\n",
-    "print(mp_non_compliant_doc.valid)\n",
-    "for reason in mp_non_compliant_doc.reasons:\n",
-    "    print(reason)\n",
-    "\n",
-    "non_compliant_task_doc = TaskDoc(\n",
-    "    **loadfn(os.path.join(\"MP_non_compliant\",\"MP_incompatible_GaAs_r2SCAN_static.json.gz\"))\n",
-    ")\n",
-    "mp_non_compliant_doc_from_taskdoc = ValidationDoc.from_task_doc(non_compliant_task_doc)\n",
-    "print(mp_non_compliant_doc_from_taskdoc.valid)\n",
-    "print(mp_non_compliant_doc_from_taskdoc.reasons == mp_non_compliant_doc_from_taskdoc.reasons)"
+    "These reasons are reflected transparently in the output reasons."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "128e49d1",
+   "id": "8",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "mp_non_compliant_doc = check_calc(\"MP_non_compliant\")\n",
+    "print(mp_non_compliant_doc.is_valid)\n",
+    "for reason in mp_non_compliant_doc.reasons:\n",
+    "    print(reason)"
+   ]
   }
  ],
  "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",

pymatgen/io/validation/common.py

@@ -7,7 +7,7 @@
 import os
 from pathlib import Path
 from pydantic import BaseModel, Field, model_serializer, PrivateAttr
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, Optional
 
 from pymatgen.core import Structure
 from pymatgen.io.vasp import Incar, Kpoints, Poscar, Potcar, Outcar, Vasprun
@@ -55,8 +55,8 @@ class _PotcarSummaryStatsNames(BaseModel):
         header: _PotcarSummaryStatsNames = Field(description="The keywords in the POTCAR header.")
         data: _PotcarSummaryStatsNames = Field(description="The keywords in the POTCAR body.")
 
-    keywords: _PotcarSummaryStatsKeywords | None = None
-    stats: _PotcarSummaryStatsStats | None = None
+    keywords: Optional[_PotcarSummaryStatsKeywords] = None
+    stats: Optional[_PotcarSummaryStatsStats] = None
     titel: str
     lexch: str
 
@@ -73,8 +73,8 @@ def from_file(cls, potcar_path: os.PathLike | Potcar) -> list[Self]:
 class LightOutcar(BaseModel):
     """Schematic of pymatgen's Outcar."""
 
-    drift: list[list[float]] | None = Field(None, description="The drift forces.")
-    magnetization: list[dict[str, float]] | None = Field(
+    drift: Optional[list[list[float]]] = Field(None, description="The drift forces.")
+    magnetization: Optional[list[dict[str, float]]] = Field(
         None, description="The on-site magnetic moments, possibly with orbital resolution."
     )
 
@@ -89,7 +89,7 @@ class LightVasprun(BaseModel):
     kpoints: Kpoints = Field(description="The actual k-points used in the calculation.")
     parameters: dict[str, Any] = Field(description="The default-padded input parameters interpreted by VASP.")
     bandgap: float = Field(description="The bandgap - note that this field is derived from the Vasprun object.")
-    potcar_symbols: list[str] | None = Field(
+    potcar_symbols: Optional[list[str]] = Field(
         None,
         description="Optional: if a POTCAR is unavailable, this is used to determine the functional used in the calculation.",
     )
@@ -107,10 +107,10 @@ class VaspInputSafe(BaseModel):
 
     incar: Incar = Field(description="The INCAR used in the calculation.")
     structure: Structure = Field(description="The structure associated with the calculation.")
-    kpoints: Kpoints | None = Field(None, description="The optional KPOINTS or IBZKPT file used in the calculation.")
-    potcar: list[PotcarSummaryStats] | None = Field(None, description="The optional POTCAR used in the calculation.")
-    potcar_functional: str | None = Field(None, description="The pymatgen-labelled POTCAR library release.")
-    _pmg_vis: VaspInputSet | None = PrivateAttr(None)
+    kpoints: Optional[Kpoints] = Field(None, description="The optional KPOINTS or IBZKPT file used in the calculation.")
+    potcar: Optional[list[PotcarSummaryStats]] = Field(None, description="The optional POTCAR used in the calculation.")
+    potcar_functional: Optional[str] = Field(None, description="The pymatgen-labelled POTCAR library release.")
+    _pmg_vis: Optional[VaspInputSet] = PrivateAttr(None)
 
     @model_serializer
     def deserialize_objects(self) -> dict[str, Any]:
@@ -155,8 +155,8 @@ class VaspFiles(BaseModel):
     """Define required and optional files for validation."""
 
     user_input: VaspInputSafe = Field(description="The VASP input set used in the calculation.")
-    outcar: LightOutcar | None = None
-    vasprun: LightVasprun | None = None
+    outcar: Optional[LightOutcar] = None
+    vasprun: Optional[LightVasprun] = None
 
     @property
     def actual_kpoints(self) -> Kpoints | None:

pymatgen/io/validation/vasp_defaults.py

@@ -1,7 +1,7 @@
 """Define VASP defaults and input categories to check."""
 
 from __future__ import annotations
-from typing import Any, Literal
+from typing import Any, Literal, Optional
 import math
 from pathlib import Path
 from pydantic import BaseModel, Field, field_validator
@@ -70,16 +70,16 @@ class VaspParam(BaseModel):
     tag: str = Field(
         description="the general category of input the tag belongs to. Used only to properly update INCAR fields in the same way VASP does."
     )
-    operation: str | list[str] | tuple[str] | None = Field(
+    operation: Optional[str | list[str] | tuple[str]] = Field(
         None, description="One or more of VALID_OPERATIONS to apply in validating this parameter."
     )
-    alias: str | None = Field(
+    alias: Optional[str] = Field(
         None,
         description="If a str, an alternate name for a parameter to use when reporting invalid values, e.g., ENMAX instead of ENCUT.",
     )
     tolerance: float = Field(1e-4, description="The tolerance used when evaluating approximate float equality.")
-    comment: str | None = Field(None, description="Additional information to pass to the user if a check fails.")
-    warning: str | None = Field(None, description="Additional warnings to pass to the user if a check fails.")
+    comment: Optional[str] = Field(None, description="Additional information to pass to the user if a check fails.")
+    warning: Optional[str] = Field(None, description="Additional warnings to pass to the user if a check fails.")
     severity: Literal["reason", "warning"] = Field("reason", description="The severity of failing this check.")
 
     @staticmethod
@@ -449,7 +449,7 @@ def format_val(val: Any) -> Any:
     ),
     VaspParam(
         name="IBRION",
-        value=0,
+        value=-1,
         operation="in",
         alias="IBRION",
         tag="ionic",

pyproject.toml

@@ -80,6 +80,7 @@ select = "C, E, F, W, B, B950"
 explicit_package_bases = true
 namespace_packages = true
 ignore_missing_imports = true
+no_strict_optional = true
 plugins = ["pydantic.mypy"]
 
 [tool.coverage.run]

requirements-dev.txt

@@ -6,3 +6,4 @@ pydocstyle==6.1.1
 flake8==7.1.1
 pylint==3.3.1
 black==24.8.0
+pydantic==2.11.3

requirements.txt

@@ -1,9 +1,7 @@
-pymatgen==2024.11.13
+pymatgen==2025.4.17
 emmet-core==0.84.5
-pydantic==2.4.2
-pydantic-core==2.10.1
-pydantic-settings==2.2.1
+pydantic==2.11.3
 typing-extensions==4.12.2
-monty==2025.1.9
+monty==2025.3.3
 numpy==1.26.1
 requests==2.32.3