port tests over from emmet

Author: esoteric-ephemera

.pre-commit-config.yaml

@@ -35,3 +35,12 @@ repos:
     rev: 25.9.0
     hooks:
       - id: black
+      
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.8.1
+    hooks:
+      - id: nbstripout
+        args:
+          - --drop-empty-cells
+          - --strip-init-cells
+          - --extra-keys=metadata.kernelspec

mpcontribs-lux/mpcontribs/lux/projects/esoteric_ephemera/__init__.py

@@ -1,6 +0,0 @@
-from mpcontribs.lux.projects.esoteric_ephemera.schemas.base import MLTrainDoc
-from mpcontribs.lux.projects.esoteric_ephemera.schemas.MatPES_2025_1 import MatPESTrainDoc
-from mpcontribs.lux.projects.esoteric_ephemera.schemas.MP_ALOE_2025 import MPAloeTrainDoc
-from mpcontribs.lux.projects.esoteric_ephemera.schemas.MPtrj_2022_9 import MPtrjTrainDoc
-
-__all__ = ["MLTrainDoc","MatPESTrainDoc","MPAloeTrainDoc","MPtrjTrainDoc"]

mpcontribs-lux/mpcontribs/lux/projects/esoteric_ephemera/schemas/MatPES_2025_1.py

@@ -45,7 +45,7 @@ class MatPESTrainDoc(MLTrainDoc):
     This schema is used in the data entries for MatPES v2025.1,
     which can be downloaded either:
         - On [MPContribs](https://materialsproject-contribs.s3.amazonaws.com/index.html#MatPES_2025_1/)
-        - or on [the site]
+        - or on [the site](https://matpes.ai)
     """
 
     matpes_id: str | None = Field(None, description="MatPES identifier.")

mpcontribs-lux/mpcontribs/lux/projects/esoteric_ephemera/schemas/__init__.py

@@ -0,0 +1,6 @@
+from mpcontribs.lux.projects.esoteric_ephemera.schemas.base import MLTrainDoc
+from mpcontribs.lux.projects.esoteric_ephemera.schemas.MatPES_2025_1 import MatPESTrainDoc
+from mpcontribs.lux.projects.esoteric_ephemera.schemas.MP_ALOE_2025 import MPAloeTrainDoc
+from mpcontribs.lux.projects.esoteric_ephemera.schemas.MPtrj_2022_9 import MPtrjTrainDoc
+
+__all__ = ["MLTrainDoc","MatPESTrainDoc","MPAloeTrainDoc","MPtrjTrainDoc"]

mpcontribs-lux/pyproject.toml

@@ -11,7 +11,7 @@ include-package-data = true
 
 [tool.setuptools.packages.find]
 where = ["."]
-exclude = ["tests"]
+exclude = ["tests","examples","test_data"]
 include = ["mpcontribs.lux"]
 
 

mpcontribs-lux/test_data/by_user/esoteric_ephemera/r2scan_task.json.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:32f19f1d06cadc8b33e995fd093d188484a26fbb70b7993d810e9f72b39dec79
+size 12200

mpcontribs-lux/tests/conftest.py

@@ -0,0 +1,23 @@
+"""Define common testing fixtures."""
+
+import os
+from pathlib import Path
+import shutil
+import tempfile
+
+import pytest
+
+@pytest.fixture(autouse=True)
+def test_dir():
+    """Same as clean_dir but is fresh for every test"""
+
+    old_cwd = os.getcwd()
+    new_path = tempfile.mkdtemp()
+    os.chdir(new_path)
+    yield
+    os.chdir(old_cwd)
+    shutil.rmtree(new_path)
+
+@pytest.fixture(scope="session")
+def test_data_dir() -> Path:
+    return (Path(__file__) / ".." / ".." / "test_data").resolve()

mpcontribs-lux/tests/projects/esoteric_ephemera/test_schemas.py

@@ -0,0 +1,53 @@
+"""Test schemas for user esoteric_ephemera."""
+
+import gzip
+import json
+from pathlib import Path
+
+import numpy as np
+import pytest
+
+from emmet.core.math import matrix_3x3_to_voigt
+from emmet.core.tasks import TaskDoc
+
+@pytest.fixture(scope="module")
+def task_doc(test_data_dir) -> TaskDoc:
+    with gzip.open(test_data_dir / "by_user" / "esoteric_ephemera" / "r2scan_task.json.gz","rt") as f:
+        return TaskDoc(**json.load(f))
+
+def test_matpes_doc_from_task_doc(test_dir, task_doc):
+
+    from mpcontribs.lux.projects.esoteric_ephemera.schemas import MatPESTrainDoc
+
+    matpes_train_docs = MatPESTrainDoc.from_task_doc(task_doc)
+
+    assert len(matpes_train_docs) == sum(
+        len(cr.output.ionic_steps) for cr in task_doc.calcs_reversed
+    )
+
+    ctr = 0
+    for cr in task_doc.calcs_reversed[::-1]:
+        for iistep, istep in enumerate(cr.output.ionic_steps):
+            assert matpes_train_docs[ctr].energy == pytest.approx(istep.e_0_energy)
+            assert np.allclose(matpes_train_docs[ctr].forces, istep.forces)
+
+            assert np.allclose(
+                matpes_train_docs[ctr].stress, matrix_3x3_to_voigt(istep.stress)
+            )
+
+            if iistep < len(cr.output.ionic_steps) - 1:
+                assert matpes_train_docs[ctr].bandgap is None
+                assert (
+                    matpes_train_docs[ctr].structure.site_properties.get("magmom")
+                    is None
+                )
+            else:
+                assert matpes_train_docs[ctr].bandgap == pytest.approx(
+                    cr.output.bandgap
+                )
+                assert np.allclose(
+                    matpes_train_docs[ctr].structure.site_properties.get("magmom"),
+                    cr.output.structure.site_properties.get("magmom"),
+                )
+
+            ctr += 1