@mat3ra/made 2026.8.7-0 → 2026.8.18-0

package/tests/py/conftest.py

@@ -1,34 +0,0 @@
-## To avoid the following problem with spglib
-# .venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115
-# tests/py/unit/test_tools_build_defect.py::test_create_island
-# tests/py/unit/test_tools_build_slab.py::test_build_slab
-#   /Users/mat3ra/code/GREEN/stack/lib/made/.venv-3.11.2/lib/python3.11/site-packages/spglib/spglib.py:115:
-#   DeprecationWarning: dict interface (SpglibDataset['rotations']) is deprecated.
-#   Use attribute interface ({self.__class__.__name__}.{key}) instead
-#     warnings.warn(
-#
-# -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
-##
-
-import warnings
-
-
-def pytest_configure(config):
-    warnings.filterwarnings("ignore", category=DeprecationWarning, module="spglib.*")
-
-
-_orig_warn = warnings.warn
-
-
-def custom_warn(message, category=None, *args, **kwargs):
-    # spglib emits DeprecationWarnings without using `stacklevel`,
-    # so pytest and warning filters can't suppress them properly.
-    # These warnings always appear to come from inside spglib itself.
-    # This patch intercepts `warnings.warn` to ignore only those specific messages.
-
-    if isinstance(message, str) and "SpglibDataset" in message and category is DeprecationWarning:
-        return  # suppress
-    return _orig_warn(message, category, *args, **kwargs)
-
-
-warnings.warn = custom_warn

package/tests/py/mat3ra/debug_utils.py

@@ -1,75 +0,0 @@
-import os
-import tempfile
-import time
-import webbrowser
-
-# Use a default div id
-default_div_id = "wave-div"
-default_width = 1200
-default_height = 1200
-
-
-def get_wave_html(div_id=default_div_id, width=default_width, height=default_height, title="Material"):
-    size = min(width, height)  # Make it square using the smaller dimension
-    return f"""
-    <h2>{title}</h2>
-    <div id="{div_id}" style="width:{size}px; height:{size}px; border:1px solid #333;"></div>
-    """
-
-
-def get_wave_js(material_json, div_id=default_div_id):
-    return (
-        f"""
-    const materialConfig = {material_json};
-    const container = document.getElementById('{div_id}');
-        """
-        + """
-    (async function() {
-        const module = await import('https://exabyte-io.github.io/wave.js/main.js');
-        window.renderThreeDEditor(materialConfig, container);
-    })();
-    document.head.insertAdjacentHTML(
-        'beforeend',
-        '<link rel="stylesheet" href="https://exabyte-io.github.io/wave.js/main.css"/>'
-    );
-    """
-    )
-
-
-def debug_visualize_material(material, width=default_width, height=default_height, title="Material"):
-    """
-    Generates a temporary HTML file that uses Wave.js to visualize the material,
-    and opens it in the default browser.
-
-    Call this function from the PyCharm debugger (e.g., via Evaluate Expression).
-    """
-    # Convert your material to JSON.
-    # (Assuming material.to_json() returns a JSON-serializable object)
-    material_json = material.to_json()
-    title = material.name if hasattr(material, "name") else title
-    # Generate a unique div id so multiple calls don't conflict
-    div_id = f"wave-{int(time.time())}"
-
-    # Create HTML content that includes our working code
-    html_content = f"""
-    <!DOCTYPE html>
-    <html>
-    <head>
-      <meta charset="UTF-8">
-      <title>Wave.js Debug Viewer</title>
-    </head>
-    <body>
-      {get_wave_html(div_id, width, height, title)}
-      <script type="module">
-        {get_wave_js(material_json, div_id)}
-      </script>
-    </body>
-    </html>
-    """
-
-    # Write the HTML to a temporary file and open it in the default browser
-    fd, file_path = tempfile.mkstemp(suffix=".html", prefix="wave_debug_")
-    with os.fdopen(fd, "w", encoding="utf-8") as f:
-        f.write(html_content)
-
-    webbrowser.open("file://" + file_path)

package/tests/py/unit/fixtures/adatom.py

@@ -1,60 +0,0 @@
-SLAB_Si_3_ADATOMS = {
-    "name": "Si(001), termination Si_P4/mmm_2, Slab, C, N, Si Adatom",
-    "basis": {
-        "elements": [
-            {"id": 0, "value": "Si"},
-            {"id": 1, "value": "Si"},
-            {"id": 2, "value": "Si"},
-            {"id": 3, "value": "Si"},
-            {"id": 4, "value": "Si"},
-            {"id": 5, "value": "Si"},
-            {"id": 6, "value": "Si"},
-            {"id": 7, "value": "Si"},
-            {"id": 8, "value": "Si"},
-            {"id": 9, "value": "Si"},
-            {"id": 10, "value": "Si"},
-            {"id": 11, "value": "Si"},
-            {"id": 12, "value": "Si"},
-            {"id": 13, "value": "Si"},
-            {"id": 14, "value": "Si"},
-            {"id": 15, "value": "Si"},
-            {"id": 16, "value": "Si"},
-            {"id": 17, "value": "C"},
-            {"id": 18, "value": "N"},
-        ],
-        "coordinates": [
-            {"id": 0, "value": [0.5, 0, 0.204677904]},
-            {"id": 1, "value": [0.25, 0.25, 0.136452118]},
-            {"id": 2, "value": [0.5, 0.5, 0.068226332]},
-            {"id": 3, "value": [0.25, 0.75, 5.46e-7]},
-            {"id": 4, "value": [0, 0, 0.068226332]},
-            {"id": 5, "value": [0.75, 0.25, 5.46e-7]},
-            {"id": 6, "value": [0, 0.5, 0.204677904]},
-            {"id": 7, "value": [0.75, 0.75, 0.136452118]},
-            {"id": 8, "value": [0.5, 0, 0.477581049]},
-            {"id": 9, "value": [0.25, 0.25, 0.409355263]},
-            {"id": 10, "value": [0.5, 0.5, 0.341129477]},
-            {"id": 11, "value": [0.25, 0.75, 0.272903691]},
-            {"id": 12, "value": [0, 0, 0.341129477]},
-            {"id": 13, "value": [0.75, 0.25, 0.272903691]},
-            {"id": 14, "value": [0, 0.5, 0.477581049]},
-            {"id": 15, "value": [0.75, 0.75, 0.409355263]},
-            {"id": 16, "value": [0.5, 0.5, 0.577390366]},
-            {"id": 17, "value": [0.25, 0.25, 0.552439285]},
-            {"id": 18, "value": [0.75, 0.75, 0.527488203]},
-        ],
-        "units": "crystal",
-        "labels": [],
-        "constraints": [],
-    },
-    "lattice": {
-        "a": 5.468763846,
-        "b": 5.468763846,
-        "c": 20.03921150886921,
-        "alpha": 90,
-        "beta": 90,
-        "gamma": 90,
-        "units": {"length": "angstrom", "angle": "degree"},
-        "type": "TRI",
-    },
-}

package/tests/py/unit/fixtures/bulk.py

@@ -1,162 +0,0 @@
-from typing import Any, Dict
-
-from mat3ra.standata.materials import Materials
-
-BULK_SrTiO3 = Materials.get_by_name_first_match("SrTiO3")
-BULK_GRAPHITE = Materials.get_by_name_first_match("Graphite")
-BULK_SiO2 = Materials.get_by_name_first_match("SiO2")
-BULK_Hf2O_MCL = Materials.get_by_name_first_match("Hafnium IV Oxide, MCL")
-BULK_TiN = Materials.get_by_name_first_match("TiN")
-BULK_Ni_PRIMITIVE = Materials.get_by_name_first_match("Nickel")
-BULK_GRAPHENE = Materials.get_by_name_first_match("Graphene")
-
-BULK_Si_PRIMITIVE: Dict[str, Any] = {
-    "name": "Silicon FCC",
-    "basis": {
-        "constraints": [],
-        "coordinates": [{"id": 0, "value": [0.0, 0.0, 0.0]}, {"id": 1, "value": [0.25, 0.25, 0.25]}],
-        "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
-        "labels": [],
-        "units": "crystal",
-    },
-    "lattice": {
-        "a": 3.867,
-        "alpha": 60.0,
-        "b": 3.867,
-        "beta": 60.0,
-        "c": 3.867,
-        "gamma": 60.0,
-        "type": "FCC",
-        "units": {"angle": "degree", "length": "angstrom"},
-    },
-}
-
-BULK_Si_PRIMITIVIZED = {
-    "metadata": {"build": [], "boundaryConditions": {"type": "pbc", "offset": 0}},
-    "name": "Si2",
-    "basis": {
-        "elements": [{"id": 0, "value": "Si"}, {"id": 1, "value": "Si"}],
-        "coordinates": [{"id": 0, "value": [0.5, 0.5, 0.5]}, {"id": 1, "value": [0.75, 0.75, 0.75]}],
-        "units": "crystal",
-        "labels": [],
-        "constraints": [],
-    },
-    "lattice": {
-        "a": 3.867,
-        "b": 3.867,
-        "c": 3.867,
-        "alpha": 60.0,
-        "beta": 60.0,
-        "gamma": 60.0,
-        "units": {"length": "angstrom", "angle": "degree"},
-        "type": "TRI",
-    },
-}
-
-
-BULK_Si_CONVENTIONAL: Dict[str, Any] = {
-    "name": "Si8",
-    "basis": {
-        "elements": [
-            {"id": 0, "value": "Si"},
-            {"id": 1, "value": "Si"},
-            {"id": 2, "value": "Si"},
-            {"id": 3, "value": "Si"},
-            {"id": 4, "value": "Si"},
-            {"id": 5, "value": "Si"},
-            {"id": 6, "value": "Si"},
-            {"id": 7, "value": "Si"},
-        ],
-        "coordinates": [
-            {"id": 0, "value": [0.5, 0.0, 0.0]},
-            {"id": 1, "value": [0.25, 0.25, 0.75]},
-            {"id": 2, "value": [0.5, 0.5, 0.5]},
-            {"id": 3, "value": [0.25, 0.75, 0.25]},
-            {"id": 4, "value": [0.0, 0.0, 0.5]},
-            {"id": 5, "value": [0.75, 0.25, 0.25]},
-            {"id": 6, "value": [0.0, 0.5, 0.0]},
-            {"id": 7, "value": [0.75, 0.75, 0.75]},
-        ],
-        "units": "crystal",
-        "constraints": [],
-        "labels": [],
-    },
-    "lattice": {
-        "a": 5.468763846,
-        "b": 5.468763846,
-        "c": 5.468763846,
-        "alpha": 90.0,
-        "beta": 90.0,
-        "gamma": 90.0,
-        "units": {"length": "angstrom", "angle": "degree"},
-        "type": "TRI",
-    },
-    "isNonPeriodic": False,
-    "metadata": {"boundaryConditions": {"type": "pbc", "offset": 0}},
-}
-
-BULK_Si_CONVENTIONAL_FILTERED: Dict[str, Any] = {
-    "name": "Si",
-    "basis": {
-        "elements": [
-            {"id": 0, "value": "Si"},
-            {"id": 2, "value": "Si"},
-        ],
-        "coordinates": [
-            {"id": 0, "value": [0.5, 0.0, 0.0]},
-            {"id": 2, "value": [0.5, 0.5, 0.5]},
-        ],
-        "units": "crystal",
-        "labels": [],
-        "constraints": [],
-    },
-    "lattice": {
-        "a": 5.468763846,
-        "b": 5.468763846,
-        "c": 5.468763846,
-        "alpha": 90.0,
-        "beta": 90.0,
-        "gamma": 90.0,
-        "units": {"length": "angstrom", "angle": "degree"},
-        "type": "TRI",
-    },
-}
-
-BULK_Ge_CONVENTIONAL: Dict[str, Any] = {
-    "name": "Germanium FCC",
-    "basis": {
-        "units": "crystal",
-        "elements": [
-            {"id": 0, "value": "Ge"},
-            {"id": 1, "value": "Ge"},
-            {"id": 2, "value": "Ge"},
-            {"id": 3, "value": "Ge"},
-            {"id": 4, "value": "Ge"},
-            {"id": 5, "value": "Ge"},
-            {"id": 6, "value": "Ge"},
-            {"id": 7, "value": "Ge"},
-        ],
-        "coordinates": [
-            {"id": 0, "value": [0, 0, 0]},
-            {"id": 1, "value": [0.5, 0.5, 0]},
-            {"id": 2, "value": [0.5, 0, 0.5]},
-            {"id": 3, "value": [0, 0.5, 0.5]},
-            {"id": 4, "value": [0.25, 0.25, 0.25]},
-            {"id": 5, "value": [0.75, 0.75, 0.25]},
-            {"id": 6, "value": [0.75, 0.25, 0.75]},
-            {"id": 7, "value": [0.25, 0.75, 0.75]},
-        ],
-        "constraints": [],
-    },
-    "lattice": {
-        "a": 5.67099638511611,
-        "b": 5.67099638511611,
-        "c": 5.67099638511611,
-        "alpha": 90,
-        "beta": 90,
-        "gamma": 90,
-        "units": {"length": "angstrom", "angle": "degree"},
-        "type": "CUB",
-        "vectors": {"a": [5.671, 0, 0], "b": [0, 5.671, 0], "c": [0, 0, 5.671], "alat": 1, "units": "angstrom"},
-    },
-}

package/tests/py/unit/fixtures/cuts.py

@@ -1,118 +0,0 @@
-FULL_MATERIAL = {
-    "basis": {
-        "constraints": [],
-        "coordinates": [
-            {"id": 0, "value": [0.0, 0.0, 0.0]},
-            {"id": 1, "value": [0.0, 0.5, 0.5]},
-            {"id": 2, "value": [0.5, 0.0, 0.5]},
-            {"id": 3, "value": [0.5, 0.5, 0.0]},
-        ],
-        "elements": [
-            {"id": 0, "value": "Ni"},
-            {"id": 1, "value": "Ni"},
-            {"id": 2, "value": "Ni"},
-            {"id": 3, "value": "Ni"},
-        ],
-        "labels": [],
-        "units": "crystal",
-    },
-    "consistencyChecks": None,
-    "derivedProperties": None,
-    "description": None,
-    "descriptionObject": None,
-    "external": None,
-    "field_id": None,
-    "formula": None,
-    "icsdId": None,
-    "isDefault": False,
-    "isNonPeriodic": False,
-    "lattice": {
-        "a": 3.52,
-        "alpha": 90.0,
-        "b": 3.52,
-        "beta": 90.0,
-        "c": 3.52,
-        "gamma": 90.0,
-        "type": "TRI",
-        "units": {"angle": "degree", "length": "angstrom"},
-    },
-    "metadata": {"boundaryConditions": {"offset": 0, "type": "pbc"}},
-    "name": "",
-    "scaledHash": None,
-    "schemaVersion": "2022.8.16",
-    "slug": None,
-    "src": None,
-    "systemName": None,
-    "unitCellFormula": None,
-}
-
-CAVITY_MATERIAL_BASIS = {
-    "basis": {
-        "constraints": [],
-        "coordinates": [
-            {"id": 1, "value": [0.0, 0.5, 0.5]},
-            {"id": 2, "value": [0.5, 0.0, 0.5]},
-            {"id": 4, "value": [0.5, 0.5, 0.0]},
-        ],
-        "elements": [{"id": 1, "value": "Ni"}, {"id": 2, "value": "Ni"}, {"id": 4, "value": "Au"}],
-        "labels": [],
-        "units": "crystal",
-    }
-}
-
-
-SECTION_MATERIAL_BASIS = {
-    "basis": {
-        "constraints": [],
-        "coordinates": [{"id": 0, "value": [0.0, 0.0, 0.0]}, {"id": 3, "value": [0.5, 0.5, 0.0]}],
-        "elements": [{"id": 0, "value": "Ni"}, {"id": 3, "value": "Ni"}],
-        "labels": [],
-        "units": "crystal",
-    }
-}
-
-SECTION_MATERIAL_BASIS_EXTRA_ATOM = {
-    "basis": {
-        "constraints": [],
-        "coordinates": [
-            {"id": 0, "value": [0.0, 0.0, 0.0]},
-            {"id": 3, "value": [0.5, 0.5, 0.0]},
-            {"id": 4, "value": [0.51, 0.51, 0.0]},  # Extra atom collides with Au in cavity material
-        ],
-        "elements": [{"id": 0, "value": "Ni"}, {"id": 3, "value": "Ni"}, {"id": 4, "value": "O"}],
-        "labels": [],
-        "units": "crystal",
-    }
-}
-
-MERGED_SECTION_CAVITY_BASIS = {
-    "elements": [
-        {"id": 0, "value": "Ni"},
-        {"id": 1, "value": "Ni"},
-        {"id": 2, "value": "Ni"},
-        {"id": 4, "value": "Au"},
-    ],
-    "coordinates": [
-        {"id": 0, "value": [0.0, 0.0, 0.0]},
-        {"id": 1, "value": [0.0, 0.5, 0.5]},
-        {"id": 2, "value": [0.5, 0.0, 0.5]},
-        {"id": 4, "value": [0.5, 0.5, 0.0]},
-    ],
-    "labels": [],
-}
-
-MERGED_CAVITY_SECTION_BASIS = {
-    "elements": [
-        {"id": 1, "value": "Ni"},
-        {"id": 2, "value": "Ni"},
-        {"id": 0, "value": "Ni"},
-        {"id": 3, "value": "Ni"},
-    ],
-    "coordinates": [
-        {"id": 1, "value": [0.0, 0.5, 0.5]},
-        {"id": 2, "value": [0.5, 0.0, 0.5]},
-        {"id": 0, "value": [0.0, 0.0, 0.0]},
-        {"id": 3, "value": [0.5, 0.5, 0.0]},
-    ],
-    "labels": [],
-}