From d0cdc73d3e8cd79cff26b47ee605033b3ffc8acd Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Thu, 28 May 2026 20:03:37 +0800 Subject: [PATCH 01/18] SOF-7915: implement primitive cell in the python interface --- .../mat3ra/made/{cell.py => cell/__init__.py} | 0 src/py/mat3ra/made/cell/primitive_cell.py | 149 ++++++++++++++++++ 2 files changed, 149 insertions(+) rename src/py/mat3ra/made/{cell.py => cell/__init__.py} (100%) create mode 100644 src/py/mat3ra/made/cell/primitive_cell.py diff --git a/src/py/mat3ra/made/cell.py b/src/py/mat3ra/made/cell/__init__.py similarity index 100% rename from src/py/mat3ra/made/cell.py rename to src/py/mat3ra/made/cell/__init__.py diff --git a/src/py/mat3ra/made/cell/primitive_cell.py b/src/py/mat3ra/made/cell/primitive_cell.py new file mode 100644 index 000000000..306c62038 --- /dev/null +++ b/src/py/mat3ra/made/cell/primitive_cell.py @@ -0,0 +1,149 @@ +""" +Routines for calculating primitive cell vectors from conventional cell Bravais parameters. +Python equivalent of src/js/cell/primitive_cell.ts. + +Following Setyawan, W., & Curtarolo, S. (2010). doi:10.1016/j.commatsci.2010.05.010 +""" + +import math +from typing import List + +from mat3ra.esse.models.properties_directory.structural.lattice import LatticeSchema + +Matrix3x3 = List[List[float]] + + +def _rhl(p: LatticeSchema) -> Matrix3x3: + a = p.a + alpha_rad = (p.alpha / 180) * math.pi + cos_alpha = math.cos(alpha_rad) + cos_half_alpha = math.sqrt((1 / 2) * (1 + cos_alpha)) + sin_half_alpha = math.sqrt((1 / 2) * (1 - cos_alpha)) + return [ + [a * cos_half_alpha, -a * sin_half_alpha, 0.0], + [a * cos_half_alpha, a * sin_half_alpha, 0.0], + [ + (a * cos_alpha) / cos_half_alpha, + 0.0, + a * math.sqrt(1 - (cos_alpha * cos_alpha) / (cos_half_alpha * cos_half_alpha)), + ], + ] + + +def _tri(p: LatticeSchema) -> Matrix3x3: + """ + Algorithm from pymatgen (from_params). + Mirrors the TRI case in primitive_cell.ts exactly. + """ + alpha = math.radians(p.alpha) + beta = math.radians(p.beta) + gamma = math.radians(p.gamma) + + cos_alpha = math.cos(alpha) + cos_beta = math.cos(beta) + cos_gamma = math.cos(gamma) + sin_alpha = math.sin(alpha) + sin_beta = math.sin(beta) + + acos_arg = (cos_alpha * cos_beta - cos_gamma) / (sin_alpha * sin_beta) + # Clamp to [-1, 1] to guard against floating-point drift + acos_arg = max(-1.0, min(1.0, acos_arg)) + + gamma_star = math.acos(acos_arg) + cos_gamma_star = math.cos(gamma_star) + sin_gamma_star = math.sin(gamma_star) + + a, b, c = p.a, p.b, p.c + return [ + [a * sin_beta, 0.0, a * cos_beta], + [-b * sin_alpha * cos_gamma_star, b * sin_alpha * sin_gamma_star, b * cos_alpha], + [0.0, 0.0, c], + ] + + +PRIMITIVE_CELLS = { + "CUB": lambda p: [ + [p.a, 0, 0], + [0, p.a, 0], + [0, 0, p.a], + ], + "FCC": lambda p: [ + [0.0, p.a / 2, p.a / 2], + [p.a / 2, 0.0, p.a / 2], + [p.a / 2, p.a / 2, 0.0], + ], + "BCC": lambda p: [ + [-p.a / 2, p.a / 2, p.a / 2], + [p.a / 2, -p.a / 2, p.a / 2], + [p.a / 2, p.a / 2, -p.a / 2], + ], + "TET": lambda p: [ + [p.a, 0, 0], + [0, p.a, 0], + [0, 0, p.c], + ], + "BCT": lambda p: [ + [-p.a / 2, p.a / 2, p.c / 2], + [p.a / 2, -p.a / 2, p.c / 2], + [p.a / 2, p.a / 2, -p.c / 2], + ], + "ORC": lambda p: [ + [p.a, 0, 0], + [0, p.b, 0], + [0, 0, p.c], + ], + "ORCF": lambda p: [ + [0, p.b / 2, p.c / 2], + [p.a / 2, 0, p.c / 2], + [p.a / 2, p.b / 2, 0], + ], + "ORCI": lambda p: [ + [-p.a / 2, p.b / 2, p.c / 2], + [p.a / 2, -p.b / 2, p.c / 2], + [p.a / 2, p.b / 2, -p.c / 2], + ], + "ORCC": lambda p: [ + [p.a / 2, p.b / 2, 0], + [-p.a / 2, p.b / 2, 0], + [0, 0, p.c], + ], + "HEX": lambda p: [ + [p.a / 2, -(p.a * math.sqrt(3)) / 2, 0], + [p.a / 2, (p.a * math.sqrt(3)) / 2, 0], + [0, 0, p.c], + ], + "RHL": lambda p: _rhl(p), + "MCL": lambda p: [ + [p.a, 0, 0], + [0, p.b, 0], + [0, p.c * math.cos(math.radians(p.alpha)), p.c * math.sin(math.radians(p.alpha))], + ], + "MCLC": lambda p: [ + [p.a / 2, p.b / 2, 0], + [-p.a / 2, p.b / 2, 0], + [0, p.c * math.cos(math.radians(p.alpha)), p.c * math.sin(math.radians(p.alpha))], + ], + "TRI": lambda p: _tri(p), +} + + +def get_primitive_lattice_vectors_from_config(lattice_config: LatticeSchema) -> Matrix3x3: + """ + Returns lattice vectors for a primitive cell for a given lattice config. + Python equivalent of getPrimitiveLatticeVectorsFromConfig() in primitive_cell.ts. + + Args: + lattice_config: LatticeSchema instance with fields: + type, a, b, c, alpha, beta, gamma. + + Returns: + 3x3 list of lists (rows = vectors a, b, c) in the same units as the + input lattice parameters (typically Angstroms). + """ + lattice_type = lattice_config.type or "TRI" + generator = PRIMITIVE_CELLS.get(lattice_type) + if generator is None: + raise ValueError( + f"Unsupported lattice type '{lattice_type}'. " f"Must be one of: {list(PRIMITIVE_CELLS.keys())}" + ) + return generator(lattice_config) From f80df56b6b404ce1d5482e6d850e60f10041a8f5 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Thu, 28 May 2026 21:08:14 +0800 Subject: [PATCH 02/18] fix lattice typ enum --- src/py/mat3ra/made/cell/primitive_cell.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/py/mat3ra/made/cell/primitive_cell.py b/src/py/mat3ra/made/cell/primitive_cell.py index 306c62038..122e6411d 100644 --- a/src/py/mat3ra/made/cell/primitive_cell.py +++ b/src/py/mat3ra/made/cell/primitive_cell.py @@ -140,7 +140,7 @@ def get_primitive_lattice_vectors_from_config(lattice_config: LatticeSchema) -> 3x3 list of lists (rows = vectors a, b, c) in the same units as the input lattice parameters (typically Angstroms). """ - lattice_type = lattice_config.type or "TRI" + lattice_type = lattice_config.type.value if lattice_config.type else "TRI" generator = PRIMITIVE_CELLS.get(lattice_type) if generator is None: raise ValueError( From 3314aded086071f47ebaeed16648f5cc71a4b127 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Thu, 28 May 2026 21:53:20 +0800 Subject: [PATCH 03/18] do not fail-fast for py tests --- .github/workflows/cicd.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 7712c2bf6..bfa8ee845 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -34,6 +34,7 @@ jobs: run-py-tests: needs: run-py-linter runs-on: ubuntu-24.04 + fail-fast: false strategy: matrix: python-version: From 190beb96c97d066396a5433b4a640442c49a73f9 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Thu, 28 May 2026 21:56:00 +0800 Subject: [PATCH 04/18] fix yaml --- .github/workflows/cicd.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index bfa8ee845..929848ec8 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -34,8 +34,8 @@ jobs: run-py-tests: needs: run-py-linter runs-on: ubuntu-24.04 - fail-fast: false strategy: + fail-fast: false matrix: python-version: - 3.10.x From 43869acba1131073620973b2bc8bea49155ce87e Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Tue, 2 Jun 2026 20:40:36 +0800 Subject: [PATCH 05/18] add py unit tests for primitive cell --- tests/py/unit/test_primitive_cell.py | 131 +++++++++++++++++++++++++++ 1 file changed, 131 insertions(+) create mode 100644 tests/py/unit/test_primitive_cell.py diff --git a/tests/py/unit/test_primitive_cell.py b/tests/py/unit/test_primitive_cell.py new file mode 100644 index 000000000..4427152b0 --- /dev/null +++ b/tests/py/unit/test_primitive_cell.py @@ -0,0 +1,131 @@ +import math +import pytest +from unittest.mock import MagicMock + +from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config + + +# Helper to mock LatticeSchema since it relies on mat3ra.esse +def create_mock_lattice(l_type=None, a=1.0, b=1.0, c=1.0, alpha=90.0, beta=90.0, gamma=90.0): + lattice = MagicMock() + if l_type is not None: + lattice.type.value = l_type + else: + lattice.type = None + + lattice.a = a + lattice.b = b + lattice.c = c + lattice.alpha = alpha + lattice.beta = beta + lattice.gamma = gamma + return lattice + + +def assert_matrix_almost_equal(mat1, mat2, abs=1e-5): + """Helper to assert that two 3x3 matrices are almost equal.""" + for row1, row2 in zip(mat1, mat2): + for val1, val2 in zip(row1, row2): + assert val1 == pytest.approx(val2, abs=abs) + + +class TestPrimitiveCell: + + def test_primitive_lattice_vectors_na4cl4(self): + """ + Replicates the TypeScript test for Na4Cl4 (CUB cell). + Translates from: tests/js/cell/primitive_cell.ts + """ + lattice = create_mock_lattice(l_type="CUB", a=5.691694) + + actual_primitive_cell = get_primitive_lattice_vectors_from_config(lattice) + expected_primitive_cell = [ + [5.691694, 0.0, 0.0], + [0.0, 5.691694, 0.0], + [0.0, 0.0, 5.691694], + ] + + assert_matrix_almost_equal(actual_primitive_cell, expected_primitive_cell) + + @pytest.mark.parametrize( + "l_type, kwargs, expected", + [ + # Cubic + ("CUB", {"a": 2.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]), + # Face-Centered Cubic + ("FCC", {"a": 2.0}, [[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 0.0]]), + # Body-Centered Cubic + ("BCC", {"a": 2.0}, [[-1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [1.0, 1.0, -1.0]]), + # Tetragonal + ("TET", {"a": 2.0, "c": 3.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]), + # Body-Centered Tetragonal + ("BCT", {"a": 2.0, "c": 3.0}, [[-1.0, 1.0, 1.5], [1.0, -1.0, 1.5], [1.0, 1.0, -1.5]]), + # Orthorhombic + ("ORC", {"a": 2.0, "b": 3.0, "c": 4.0}, [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]]), + # Face-Centered Orthorhombic + ("ORCF", {"a": 2.0, "b": 3.0, "c": 4.0}, [[0.0, 1.5, 2.0], [1.0, 0.0, 2.0], [1.0, 1.5, 0.0]]), + # Body-Centered Orthorhombic + ("ORCI", {"a": 2.0, "b": 3.0, "c": 4.0}, [[-1.0, 1.5, 2.0], [1.0, -1.5, 2.0], [1.0, 1.5, -2.0]]), + # Base-Centered Orthorhombic + ("ORCC", {"a": 2.0, "b": 3.0, "c": 4.0}, [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 0.0, 4.0]]), + # Hexagonal + ("HEX", {"a": 2.0, "c": 3.0}, [[1.0, -math.sqrt(3), 0.0], [1.0, math.sqrt(3), 0.0], [0.0, 0.0, 3.0]]), + # Rhombohedral (example angles) + ( + "RHL", + {"a": 2.0, "alpha": 60.0}, + [[1.7320508, -1.0, 0.0], [1.7320508, 1.0, 0.0], [1.1547005, 0.0, 1.6329931]], + ), + # Monoclinic + ( + "MCL", + {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0}, + [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 2.0, 3.4641016]], + ), + # Base-Centered Monoclinic + ( + "MCLC", + {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0}, + [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 2.0, 3.4641016]], + ), + # Triclinic + ( + "TRI", + {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 90.0, "beta": 90.0, "gamma": 90.0}, + [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]], + ), + ], + ) + def test_primitive_lattice_generators(self, l_type, kwargs, expected): + """ + Validates the math generators for all 14 Bravais lattice scenarios. + """ + lattice = create_mock_lattice(l_type=l_type, **kwargs) + result = get_primitive_lattice_vectors_from_config(lattice) + assert_matrix_almost_equal(result, expected) + + def test_fallback_to_tri_when_type_is_none(self): + """ + Tests the behavior when lattice_config.type is None. + Should default to the 'TRI' logic. + """ + # A pseudo-cubic configuration passed as TRI + lattice = create_mock_lattice(l_type=None, a=2.0, b=2.0, c=2.0, alpha=90.0, beta=90.0, gamma=90.0) + result = get_primitive_lattice_vectors_from_config(lattice) + expected = [ + [2.0, 0.0, 0.0], + [0.0, 2.0, 0.0], + [0.0, 0.0, 2.0], + ] + assert_matrix_almost_equal(result, expected) + + def test_unsupported_lattice_type_raises_value_error(self): + """ + Ensures a ValueError is raised for an unknown lattice type mapping. + """ + lattice = create_mock_lattice(l_type="INVALID_TYPE") + + with pytest.raises(ValueError) as exc_info: + get_primitive_lattice_vectors_from_config(lattice) + + assert "Unsupported lattice type 'INVALID_TYPE'" in str(exc_info.value) From 5ca41a01a2a4205a039c02ea92511e9c4d1b42de Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Tue, 2 Jun 2026 20:45:35 +0800 Subject: [PATCH 06/18] chore: pin actions to commit hash --- .github/workflows/build-wheel.yml | 6 +++--- .github/workflows/cicd.yml | 20 ++++++++++---------- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.github/workflows/build-wheel.yml b/.github/workflows/build-wheel.yml index 8d3bf4c20..e960a3827 100644 --- a/.github/workflows/build-wheel.yml +++ b/.github/workflows/build-wheel.yml @@ -17,10 +17,10 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 - name: Set up Python - uses: actions/setup-python@v5 + uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 with: python-version: ${{ github.event.inputs.python_version }} @@ -48,7 +48,7 @@ jobs: echo "${{ steps.get_filename.outputs.whl_name }}" > public/index.html - name: Publish to GitHub Pages - uses: peaceiris/actions-gh-pages@v4 + uses: peaceiris/actions-gh-pages@84c30a85c19949d7eee79c4ff27748b70285e453 # v4.1.0 with: github_token: ${{ secrets.GITHUB_TOKEN }} publish_dir: ./public diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 929848ec8..68e14f4d5 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -15,12 +15,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} @@ -46,12 +46,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} @@ -73,12 +73,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} @@ -105,10 +105,10 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 - name: Checkout actions repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} @@ -134,12 +134,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@v4 + uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} From 58dd0ddc33b7f4a3c0c33c581bae9d68ac7aafe1 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Tue, 2 Jun 2026 23:43:39 +0800 Subject: [PATCH 07/18] reuse assert_two_entities_deep_almost_equal --- tests/py/unit/test_primitive_cell.py | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/tests/py/unit/test_primitive_cell.py b/tests/py/unit/test_primitive_cell.py index 4427152b0..db2c58a9d 100644 --- a/tests/py/unit/test_primitive_cell.py +++ b/tests/py/unit/test_primitive_cell.py @@ -3,6 +3,7 @@ from unittest.mock import MagicMock from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config +from tests.py.unit.utils import assert_two_entities_deep_almost_equal # Helper to mock LatticeSchema since it relies on mat3ra.esse @@ -22,13 +23,6 @@ def create_mock_lattice(l_type=None, a=1.0, b=1.0, c=1.0, alpha=90.0, beta=90.0, return lattice -def assert_matrix_almost_equal(mat1, mat2, abs=1e-5): - """Helper to assert that two 3x3 matrices are almost equal.""" - for row1, row2 in zip(mat1, mat2): - for val1, val2 in zip(row1, row2): - assert val1 == pytest.approx(val2, abs=abs) - - class TestPrimitiveCell: def test_primitive_lattice_vectors_na4cl4(self): @@ -45,7 +39,7 @@ def test_primitive_lattice_vectors_na4cl4(self): [0.0, 0.0, 5.691694], ] - assert_matrix_almost_equal(actual_primitive_cell, expected_primitive_cell) + assert_two_entities_deep_almost_equal(actual_primitive_cell, expected_primitive_cell) @pytest.mark.parametrize( "l_type, kwargs, expected", @@ -102,7 +96,7 @@ def test_primitive_lattice_generators(self, l_type, kwargs, expected): """ lattice = create_mock_lattice(l_type=l_type, **kwargs) result = get_primitive_lattice_vectors_from_config(lattice) - assert_matrix_almost_equal(result, expected) + assert_two_entities_deep_almost_equal(result, expected) def test_fallback_to_tri_when_type_is_none(self): """ @@ -117,7 +111,7 @@ def test_fallback_to_tri_when_type_is_none(self): [0.0, 2.0, 0.0], [0.0, 0.0, 2.0], ] - assert_matrix_almost_equal(result, expected) + assert_two_entities_deep_almost_equal(result, expected) def test_unsupported_lattice_type_raises_value_error(self): """ From dc6cb0cce22e07e68fc1ef63c6a913a95314372e Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Tue, 2 Jun 2026 23:48:56 +0800 Subject: [PATCH 08/18] use Lattice class instead of MagicMock --- tests/py/unit/test_primitive_cell.py | 120 +++++++++++---------------- 1 file changed, 50 insertions(+), 70 deletions(-) diff --git a/tests/py/unit/test_primitive_cell.py b/tests/py/unit/test_primitive_cell.py index db2c58a9d..a989099aa 100644 --- a/tests/py/unit/test_primitive_cell.py +++ b/tests/py/unit/test_primitive_cell.py @@ -1,28 +1,11 @@ import math import pytest -from unittest.mock import MagicMock from mat3ra.made.cell.primitive_cell import get_primitive_lattice_vectors_from_config +from mat3ra.made.lattice import Lattice, LatticeTypeEnum from tests.py.unit.utils import assert_two_entities_deep_almost_equal -# Helper to mock LatticeSchema since it relies on mat3ra.esse -def create_mock_lattice(l_type=None, a=1.0, b=1.0, c=1.0, alpha=90.0, beta=90.0, gamma=90.0): - lattice = MagicMock() - if l_type is not None: - lattice.type.value = l_type - else: - lattice.type = None - - lattice.a = a - lattice.b = b - lattice.c = c - lattice.alpha = alpha - lattice.beta = beta - lattice.gamma = gamma - return lattice - - class TestPrimitiveCell: def test_primitive_lattice_vectors_na4cl4(self): @@ -30,7 +13,7 @@ def test_primitive_lattice_vectors_na4cl4(self): Replicates the TypeScript test for Na4Cl4 (CUB cell). Translates from: tests/js/cell/primitive_cell.ts """ - lattice = create_mock_lattice(l_type="CUB", a=5.691694) + lattice = Lattice(type=LatticeTypeEnum.CUB, a=5.691694) actual_primitive_cell = get_primitive_lattice_vectors_from_config(lattice) expected_primitive_cell = [ @@ -39,87 +22,84 @@ def test_primitive_lattice_vectors_na4cl4(self): [0.0, 0.0, 5.691694], ] - assert_two_entities_deep_almost_equal(actual_primitive_cell, expected_primitive_cell) + assert_two_entities_deep_almost_equal(expected_primitive_cell, actual_primitive_cell) @pytest.mark.parametrize( "l_type, kwargs, expected", [ - # Cubic - ("CUB", {"a": 2.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]), - # Face-Centered Cubic - ("FCC", {"a": 2.0}, [[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 0.0]]), - # Body-Centered Cubic - ("BCC", {"a": 2.0}, [[-1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [1.0, 1.0, -1.0]]), - # Tetragonal - ("TET", {"a": 2.0, "c": 3.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]), - # Body-Centered Tetragonal - ("BCT", {"a": 2.0, "c": 3.0}, [[-1.0, 1.0, 1.5], [1.0, -1.0, 1.5], [1.0, 1.0, -1.5]]), - # Orthorhombic - ("ORC", {"a": 2.0, "b": 3.0, "c": 4.0}, [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]]), - # Face-Centered Orthorhombic - ("ORCF", {"a": 2.0, "b": 3.0, "c": 4.0}, [[0.0, 1.5, 2.0], [1.0, 0.0, 2.0], [1.0, 1.5, 0.0]]), - # Body-Centered Orthorhombic - ("ORCI", {"a": 2.0, "b": 3.0, "c": 4.0}, [[-1.0, 1.5, 2.0], [1.0, -1.5, 2.0], [1.0, 1.5, -2.0]]), - # Base-Centered Orthorhombic - ("ORCC", {"a": 2.0, "b": 3.0, "c": 4.0}, [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 0.0, 4.0]]), - # Hexagonal - ("HEX", {"a": 2.0, "c": 3.0}, [[1.0, -math.sqrt(3), 0.0], [1.0, math.sqrt(3), 0.0], [0.0, 0.0, 3.0]]), - # Rhombohedral (example angles) + (LatticeTypeEnum.CUB, {"a": 2.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]), + (LatticeTypeEnum.FCC, {"a": 2.0}, [[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 0.0]]), + (LatticeTypeEnum.BCC, {"a": 2.0}, [[-1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [1.0, 1.0, -1.0]]), + (LatticeTypeEnum.TET, {"a": 2.0, "c": 3.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]), + (LatticeTypeEnum.BCT, {"a": 2.0, "c": 3.0}, [[-1.0, 1.0, 1.5], [1.0, -1.0, 1.5], [1.0, 1.0, -1.5]]), + (LatticeTypeEnum.ORC, {"a": 2.0, "b": 3.0, "c": 4.0}, [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]]), + ( + LatticeTypeEnum.ORCF, + {"a": 2.0, "b": 3.0, "c": 4.0}, + [[0.0, 1.5, 2.0], [1.0, 0.0, 2.0], [1.0, 1.5, 0.0]], + ), + ( + LatticeTypeEnum.ORCI, + {"a": 2.0, "b": 3.0, "c": 4.0}, + [[-1.0, 1.5, 2.0], [1.0, -1.5, 2.0], [1.0, 1.5, -2.0]], + ), + ( + LatticeTypeEnum.ORCC, + {"a": 2.0, "b": 3.0, "c": 4.0}, + [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 0.0, 4.0]], + ), + ( + LatticeTypeEnum.HEX, + {"a": 2.0, "c": 3.0}, + [[1.0, -math.sqrt(3), 0.0], [1.0, math.sqrt(3), 0.0], [0.0, 0.0, 3.0]], + ), ( - "RHL", + LatticeTypeEnum.RHL, {"a": 2.0, "alpha": 60.0}, [[1.7320508, -1.0, 0.0], [1.7320508, 1.0, 0.0], [1.1547005, 0.0, 1.6329931]], ), - # Monoclinic ( - "MCL", + LatticeTypeEnum.MCL, {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0}, [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 2.0, 3.4641016]], ), - # Base-Centered Monoclinic ( - "MCLC", + LatticeTypeEnum.MCLC, {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0}, [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 2.0, 3.4641016]], ), - # Triclinic ( - "TRI", + LatticeTypeEnum.TRI, {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 90.0, "beta": 90.0, "gamma": 90.0}, [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]], ), ], ) def test_primitive_lattice_generators(self, l_type, kwargs, expected): - """ - Validates the math generators for all 14 Bravais lattice scenarios. - """ - lattice = create_mock_lattice(l_type=l_type, **kwargs) + """Validates the math generators for all 14 Bravais lattice scenarios.""" + lattice = Lattice(type=l_type, **kwargs) result = get_primitive_lattice_vectors_from_config(lattice) - assert_two_entities_deep_almost_equal(result, expected) + assert_two_entities_deep_almost_equal(expected, result) def test_fallback_to_tri_when_type_is_none(self): - """ - Tests the behavior when lattice_config.type is None. - Should default to the 'TRI' logic. - """ - # A pseudo-cubic configuration passed as TRI - lattice = create_mock_lattice(l_type=None, a=2.0, b=2.0, c=2.0, alpha=90.0, beta=90.0, gamma=90.0) + """Tests default fallback to 'TRI' when lattice_config.type is None.""" + lattice = Lattice(type=None, a=2.0, b=2.0, c=2.0, alpha=90.0, beta=90.0, gamma=90.0) result = get_primitive_lattice_vectors_from_config(lattice) - expected = [ - [2.0, 0.0, 0.0], - [0.0, 2.0, 0.0], - [0.0, 0.0, 2.0], - ] - assert_two_entities_deep_almost_equal(result, expected) + expected = [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]] + assert_two_entities_deep_almost_equal(expected, result) def test_unsupported_lattice_type_raises_value_error(self): - """ - Ensures a ValueError is raised for an unknown lattice type mapping. - """ - lattice = create_mock_lattice(l_type="INVALID_TYPE") + """Ensures a ValueError is raised for an unknown lattice type mapping.""" + + # Using a MagicMock specifically here to force an invalid type value + # since LatticeTypeEnum won't allow arbitrary strings + class InvalidLatticeMock: + class MockType: + value = "INVALID_TYPE" + + type = MockType() with pytest.raises(ValueError) as exc_info: - get_primitive_lattice_vectors_from_config(lattice) + get_primitive_lattice_vectors_from_config(InvalidLatticeMock()) assert "Unsupported lattice type 'INVALID_TYPE'" in str(exc_info.value) From adb44eb05140a10b9bca65133051c14736a8f779 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Wed, 3 Jun 2026 00:00:15 +0800 Subject: [PATCH 09/18] fix type of Lattice --- tests/py/unit/test_primitive_cell.py | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/tests/py/unit/test_primitive_cell.py b/tests/py/unit/test_primitive_cell.py index a989099aa..48d5be8b4 100644 --- a/tests/py/unit/test_primitive_cell.py +++ b/tests/py/unit/test_primitive_cell.py @@ -83,9 +83,17 @@ def test_primitive_lattice_generators(self, l_type, kwargs, expected): def test_fallback_to_tri_when_type_is_none(self): """Tests default fallback to 'TRI' when lattice_config.type is None.""" - lattice = Lattice(type=None, a=2.0, b=2.0, c=2.0, alpha=90.0, beta=90.0, gamma=90.0) + # Use a simple dummy class to bypass Pydantic's strict validation + # and simulate a malformed or incomplete Lattice config. + class MockLattice: + type = None + a, b, c = 2.0, 2.0, 2.0 + alpha, beta, gamma = 90.0, 90.0, 90.0 + + lattice = MockLattice() result = get_primitive_lattice_vectors_from_config(lattice) expected = [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]] + assert_two_entities_deep_almost_equal(expected, result) def test_unsupported_lattice_type_raises_value_error(self): @@ -93,13 +101,18 @@ def test_unsupported_lattice_type_raises_value_error(self): # Using a MagicMock specifically here to force an invalid type value # since LatticeTypeEnum won't allow arbitrary strings - class InvalidLatticeMock: - class MockType: - value = "INVALID_TYPE" + class MockType: + value = "INVALID_TYPE" + class MockLattice: type = MockType() + # Provide dummy parameters just in case + a, b, c = 2.0, 2.0, 2.0 + alpha, beta, gamma = 90.0, 90.0, 90.0 + + lattice = MockLattice() with pytest.raises(ValueError) as exc_info: - get_primitive_lattice_vectors_from_config(InvalidLatticeMock()) + get_primitive_lattice_vectors_from_config(lattice) assert "Unsupported lattice type 'INVALID_TYPE'" in str(exc_info.value) From e5fa168b942f73623fed986dde7a5ba55c6f9821 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Wed, 3 Jun 2026 23:24:42 +0800 Subject: [PATCH 10/18] use dev branch of utils --- package-lock.json | 11 ++++++----- package.json | 2 +- pyproject.toml | 2 +- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/package-lock.json b/package-lock.json index 1be3365c0..2194b0b8f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -34,7 +34,7 @@ "@mat3ra/code": "2026.5.27-0", "@mat3ra/esse": "2026.5.27-0", "@mat3ra/tsconfig": "2024.6.3-0", - "@mat3ra/utils": "2025.4.14-0", + "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#3a0c91bae49b39a926891c25dddd3b264eb33144", "@types/crypto-js": "^4.2.2", "@typescript-eslint/eslint-plugin": "^5.9.1", "@typescript-eslint/parser": "^5.9.1", @@ -3661,10 +3661,11 @@ } }, "node_modules/@mat3ra/utils": { - "version": "2025.4.14-0", - "resolved": "https://registry.npmjs.org/@mat3ra/utils/-/utils-2025.4.14-0.tgz", - "integrity": "sha512-0ON8w7O57zAeWYiQf+0oXrR6srtlLaEfpKKT7879pIWYcFXvUIlbfiEvgEOJKvNrr2LRui9RieASwNQW5R/mQQ==", + "version": "0.0.0", + "resolved": "git+ssh://git@github.com/exabyte-io/utils.git#3a0c91bae49b39a926891c25dddd3b264eb33144", + "integrity": "sha512-fczSYG4O5BGBUyTw+NpAclCyybH2pGb1keIR/hGo5x8UX1JfYYgYsNsTO1ixIu4ouED4MPcrhVRS7OBIee9pFg==", "dev": true, + "license": "ISC", "dependencies": { "@babel/cli": "7.16.0", "@babel/core": "7.24.1", @@ -3687,7 +3688,7 @@ "uuid": "8.3.2" }, "engines": { - "node": ">=14.0.0" + "node": ">=20.0.0" } }, "node_modules/@mat3ra/utils/node_modules/@babel/cli": { diff --git a/package.json b/package.json index 08638dd35..751698478 100644 --- a/package.json +++ b/package.json @@ -37,7 +37,7 @@ "@mat3ra/code": "2026.5.27-0", "@mat3ra/esse": "2026.5.27-0", "@mat3ra/tsconfig": "2024.6.3-0", - "@mat3ra/utils": "2025.4.14-0", + "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#3a0c91bae49b39a926891c25dddd3b264eb33144", "@types/crypto-js": "^4.2.2", "@typescript-eslint/eslint-plugin": "^5.9.1", "@typescript-eslint/parser": "^5.9.1", diff --git a/pyproject.toml b/pyproject.toml index ae35d94e6..c914e369d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ dependencies = [ # add requirements here # new verison of numpy==2.0.0 is not handled by pymatgen yet "numpy<=1.26.4", - "mat3ra-utils", + "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@3a0c91bae49b39a926891c25dddd3b264eb33144", "mat3ra-esse", "mat3ra-code" ] From 9f24bff67b63dc5d4c55c0c89509e72743ad1258 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Wed, 3 Jun 2026 23:54:08 +0800 Subject: [PATCH 11/18] update utils --- package-lock.json | 4 ++-- package.json | 2 +- pyproject.toml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index 2194b0b8f..25391c40c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -34,7 +34,7 @@ "@mat3ra/code": "2026.5.27-0", "@mat3ra/esse": "2026.5.27-0", "@mat3ra/tsconfig": "2024.6.3-0", - "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#3a0c91bae49b39a926891c25dddd3b264eb33144", + "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#0582b104400fc2464aeebb126213acdec7d2fce9", "@types/crypto-js": "^4.2.2", "@typescript-eslint/eslint-plugin": "^5.9.1", "@typescript-eslint/parser": "^5.9.1", @@ -3662,7 +3662,7 @@ }, "node_modules/@mat3ra/utils": { "version": "0.0.0", - "resolved": "git+ssh://git@github.com/exabyte-io/utils.git#3a0c91bae49b39a926891c25dddd3b264eb33144", + "resolved": "git+ssh://git@github.com/exabyte-io/utils.git#0582b104400fc2464aeebb126213acdec7d2fce9", "integrity": "sha512-fczSYG4O5BGBUyTw+NpAclCyybH2pGb1keIR/hGo5x8UX1JfYYgYsNsTO1ixIu4ouED4MPcrhVRS7OBIee9pFg==", "dev": true, "license": "ISC", diff --git a/package.json b/package.json index 751698478..c817303fe 100644 --- a/package.json +++ b/package.json @@ -37,7 +37,7 @@ "@mat3ra/code": "2026.5.27-0", "@mat3ra/esse": "2026.5.27-0", "@mat3ra/tsconfig": "2024.6.3-0", - "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#3a0c91bae49b39a926891c25dddd3b264eb33144", + "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#0582b104400fc2464aeebb126213acdec7d2fce9", "@types/crypto-js": "^4.2.2", "@typescript-eslint/eslint-plugin": "^5.9.1", "@typescript-eslint/parser": "^5.9.1", diff --git a/pyproject.toml b/pyproject.toml index c914e369d..d8dd99832 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ dependencies = [ # add requirements here # new verison of numpy==2.0.0 is not handled by pymatgen yet "numpy<=1.26.4", - "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@3a0c91bae49b39a926891c25dddd3b264eb33144", + "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@0582b104400fc2464aeebb126213acdec7d2fce9", "mat3ra-esse", "mat3ra-code" ] From 97cd8a9a9f9898446ebffc5881919ef236849a1b Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Thu, 4 Jun 2026 17:35:21 +0800 Subject: [PATCH 12/18] update utils x2 --- package-lock.json | 4 ++-- package.json | 2 +- pyproject.toml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/package-lock.json b/package-lock.json index 25391c40c..6c27f3efd 100644 --- a/package-lock.json +++ b/package-lock.json @@ -34,7 +34,7 @@ "@mat3ra/code": "2026.5.27-0", "@mat3ra/esse": "2026.5.27-0", "@mat3ra/tsconfig": "2024.6.3-0", - "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#0582b104400fc2464aeebb126213acdec7d2fce9", + "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#1574df23cb9b0f249ee589e2c338546c4b83a97a", "@types/crypto-js": "^4.2.2", "@typescript-eslint/eslint-plugin": "^5.9.1", "@typescript-eslint/parser": "^5.9.1", @@ -3662,7 +3662,7 @@ }, "node_modules/@mat3ra/utils": { "version": "0.0.0", - "resolved": "git+ssh://git@github.com/exabyte-io/utils.git#0582b104400fc2464aeebb126213acdec7d2fce9", + "resolved": "git+ssh://git@github.com/exabyte-io/utils.git#1574df23cb9b0f249ee589e2c338546c4b83a97a", "integrity": "sha512-fczSYG4O5BGBUyTw+NpAclCyybH2pGb1keIR/hGo5x8UX1JfYYgYsNsTO1ixIu4ouED4MPcrhVRS7OBIee9pFg==", "dev": true, "license": "ISC", diff --git a/package.json b/package.json index c817303fe..909c4c91c 100644 --- a/package.json +++ b/package.json @@ -37,7 +37,7 @@ "@mat3ra/code": "2026.5.27-0", "@mat3ra/esse": "2026.5.27-0", "@mat3ra/tsconfig": "2024.6.3-0", - "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#0582b104400fc2464aeebb126213acdec7d2fce9", + "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#1574df23cb9b0f249ee589e2c338546c4b83a97a", "@types/crypto-js": "^4.2.2", "@typescript-eslint/eslint-plugin": "^5.9.1", "@typescript-eslint/parser": "^5.9.1", diff --git a/pyproject.toml b/pyproject.toml index d8dd99832..ddad02a98 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ dependencies = [ # add requirements here # new verison of numpy==2.0.0 is not handled by pymatgen yet "numpy<=1.26.4", - "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@0582b104400fc2464aeebb126213acdec7d2fce9", + "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@1574df23cb9b0f249ee589e2c338546c4b83a97a", "mat3ra-esse", "mat3ra-code" ] From d4a1f9af5b1aa12cbf6bc81f4d42d3c8a45ce0c0 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Sat, 6 Jun 2026 01:16:41 +0800 Subject: [PATCH 13/18] chore: bump npm dependencies --- dist/js/cell/conventional_cell.js | 4 +- dist/js/cell/primitive_cell.js | 3 +- dist/js/lattice/lattice.js | 24 +- dist/js/lattice/lattice_types.js | 2 +- dist/js/lattice/reciprocal/symmetry_points.js | 3 +- dist/js/material.d.ts | 30 +- dist/js/parsers/poscar.js | 3 +- dist/js/parsers/xyz.js | 4 +- dist/js/parsers/xyz_combinatorial_basis.d.ts | 3 +- dist/js/parsers/xyz_combinatorial_basis.js | 24 +- package-lock.json | 6877 ++++++++++------- package.json | 70 +- 12 files changed, 4026 insertions(+), 3021 deletions(-) diff --git a/dist/js/cell/conventional_cell.js b/dist/js/cell/conventional_cell.js index 9a7e1f4aa..a03c7fc0f 100644 --- a/dist/js/cell/conventional_cell.js +++ b/dist/js/cell/conventional_cell.js @@ -1,6 +1,7 @@ "use strict"; Object.defineProperty(exports, "__esModule", { value: true }); -exports.isConventionalCellSameAsPrimitiveForLatticeType = exports.PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES = exports.PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS = void 0; +exports.PRIMITIVE_TO_CONVENTIONAL_CELL_LATTICE_TYPES = exports.PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS = void 0; +exports.isConventionalCellSameAsPrimitiveForLatticeType = isConventionalCellSameAsPrimitiveForLatticeType; /** * Routines for calculating conventional cell vectors from primitive cell Bravais parameters. * Following Setyawan, W., & Curtarolo, S. (2010). doi:10.1016/j.commatsci.2010.05.010 @@ -77,4 +78,3 @@ function isConventionalCellSameAsPrimitiveForLatticeType(latticeType) { const multiplier = exports.PRIMITIVE_TO_CONVENTIONAL_CELL_MULTIPLIERS[latticeType || "TRI"]; return multiplier === unitMatrix; } -exports.isConventionalCellSameAsPrimitiveForLatticeType = isConventionalCellSameAsPrimitiveForLatticeType; diff --git a/dist/js/cell/primitive_cell.js b/dist/js/cell/primitive_cell.js index ebda53e28..3f9d954dd 100644 --- a/dist/js/cell/primitive_cell.js +++ b/dist/js/cell/primitive_cell.js @@ -1,6 +1,6 @@ "use strict"; Object.defineProperty(exports, "__esModule", { value: true }); -exports.getPrimitiveLatticeVectorsFromConfig = void 0; +exports.getPrimitiveLatticeVectorsFromConfig = getPrimitiveLatticeVectorsFromConfig; const math_1 = require("@mat3ra/code/dist/js/math"); /** * Routines for calculating primitive cell vectors from conventional cell Bravais parameters. @@ -143,4 +143,3 @@ function getPrimitiveLatticeVectorsFromConfig(latticeConfig) { const [vectorA, vectorB, vectorC] = primitiveCellGenerator(latticeConfig); return [vectorA, vectorB, vectorC]; } -exports.getPrimitiveLatticeVectorsFromConfig = getPrimitiveLatticeVectorsFromConfig; diff --git a/dist/js/lattice/lattice.js b/dist/js/lattice/lattice.js index da86b14d3..79e89773f 100644 --- a/dist/js/lattice/lattice.js +++ b/dist/js/lattice/lattice.js @@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? ( }) : function(o, v) { o["default"] = v; }); -var __importStar = (this && this.__importStar) || function (mod) { - if (mod && mod.__esModule) return mod; - var result = {}; - if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k); - __setModuleDefault(result, mod); - return result; -}; +var __importStar = (this && this.__importStar) || (function () { + var ownKeys = function(o) { + ownKeys = Object.getOwnPropertyNames || function (o) { + var ar = []; + for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k; + return ar; + }; + return ownKeys(o); + }; + return function (mod) { + if (mod && mod.__esModule) return mod; + var result = {}; + if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]); + __setModuleDefault(result, mod); + return result; + }; +})(); Object.defineProperty(exports, "__esModule", { value: true }); exports.Lattice = exports.LatticeVectors = exports.nonPeriodicLatticeScalingFactor = void 0; const constants_1 = require("@mat3ra/code/dist/js/constants"); diff --git a/dist/js/lattice/lattice_types.js b/dist/js/lattice/lattice_types.js index 2a5a91f0c..50f74a2a1 100644 --- a/dist/js/lattice/lattice_types.js +++ b/dist/js/lattice/lattice_types.js @@ -27,7 +27,7 @@ var LatticeTypeExtended; LatticeTypeExtended["TRI_1a"] = "TRI_1a"; LatticeTypeExtended["TRI_2a"] = "TRI_2a"; LatticeTypeExtended["TRI_1b"] = "TRI_1b"; -})(LatticeTypeExtended = exports.LatticeTypeExtended || (exports.LatticeTypeExtended = {})); +})(LatticeTypeExtended || (exports.LatticeTypeExtended = LatticeTypeExtended = {})); exports.DEFAULT_LATTICE_UNITS = { // by default lattice vectors shall be measured in angstrom, angles - in degrees length: { diff --git a/dist/js/lattice/reciprocal/symmetry_points.js b/dist/js/lattice/reciprocal/symmetry_points.js index d5ea776b8..73d57b9ed 100644 --- a/dist/js/lattice/reciprocal/symmetry_points.js +++ b/dist/js/lattice/reciprocal/symmetry_points.js @@ -1,6 +1,6 @@ "use strict"; Object.defineProperty(exports, "__esModule", { value: true }); -exports.symmetryPoints = void 0; +exports.symmetryPoints = symmetryPoints; const POINTS = { CUB: () => { return [ @@ -863,4 +863,3 @@ function symmetryPoints(lattice) { }, ].concat(POINTS[lattice.type](lattice) || []); } -exports.symmetryPoints = symmetryPoints; diff --git a/dist/js/material.d.ts b/dist/js/material.d.ts index e9c84d04f..40841b3d3 100644 --- a/dist/js/material.d.ts +++ b/dist/js/material.d.ts @@ -37,34 +37,34 @@ declare class Material extends InMemoryEntity implements Schema { * @summary Returns the specific derived property (as specified by name) for a material. */ getDerivedPropertyByName(name: string): { - name?: "volume" | undefined; - units?: "angstrom^3" | undefined; + name?: "volume"; + units?: "angstrom^3"; value: number; } | { - name?: "density" | undefined; - units?: "g/cm^3" | undefined; + name?: "density"; + units?: "g/cm^3"; value: number; } | { - pointGroupSymbol?: string | undefined; - spaceGroupSymbol?: string | undefined; + pointGroupSymbol?: string; + spaceGroupSymbol?: string; tolerance?: { - units?: "angstrom" | undefined; + units?: "angstrom"; value: number; - } | undefined; - name?: "symmetry" | undefined; + }; + name?: "symmetry"; } | { - name?: "elemental_ratio" | undefined; + name?: "elemental_ratio"; value: number; - element?: string | undefined; + element?: string; } | { - name?: "p-norm" | undefined; - degree?: number | undefined; + name?: "p-norm"; + degree?: number; value: number; } | { - name?: "inchi" | undefined; + name?: "inchi"; value: string; } | { - name?: "inchi_key" | undefined; + name?: "inchi_key"; value: string; } | undefined; /** diff --git a/dist/js/parsers/poscar.js b/dist/js/parsers/poscar.js index 0ed0393d8..200b045e9 100644 --- a/dist/js/parsers/poscar.js +++ b/dist/js/parsers/poscar.js @@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) { return (mod && mod.__esModule) ? mod : { "default": mod }; }; Object.defineProperty(exports, "__esModule", { value: true }); -exports.atomsCount = void 0; +exports.atomsCount = atomsCount; const math_1 = require("@mat3ra/code/dist/js/math"); const underscore_string_1 = __importDefault(require("underscore.string")); const constrained_basis_1 = require("../basis/constrained_basis"); @@ -61,7 +61,6 @@ function atomsCount(poscarFileContent) { const atomsLine = poscarFileContent.split("\n")[6].split(/\s+/); return atomsLine.map((x) => parseInt(x, 10)).reduce((a, b) => a + b); } -exports.atomsCount = atomsCount; /** * Parses POSCAR file into a Material config object. * @param fileContent - POSCAR file content. diff --git a/dist/js/parsers/xyz.js b/dist/js/parsers/xyz.js index 4bcf03c80..f8a7d8d64 100644 --- a/dist/js/parsers/xyz.js +++ b/dist/js/parsers/xyz.js @@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) { return (mod && mod.__esModule) ? mod : { "default": mod }; }; Object.defineProperty(exports, "__esModule", { value: true }); -exports.validate = exports.XYZ_COORDINATE_PRECISION = void 0; +exports.XYZ_COORDINATE_PRECISION = void 0; +exports.validate = validate; const lodash_1 = require("lodash"); const underscore_string_1 = __importDefault(require("underscore.string")); const constrained_basis_1 = require("../basis/constrained_basis"); @@ -43,7 +44,6 @@ function validate(xyzTxt) { .filter((x) => x.trim() !== "") .forEach(validateLine); } -exports.validate = validate; /** * Parses XYZ line and returns an object. * @param line - line of text diff --git a/dist/js/parsers/xyz_combinatorial_basis.d.ts b/dist/js/parsers/xyz_combinatorial_basis.d.ts index 1a57caa1f..b8ed5f405 100644 --- a/dist/js/parsers/xyz_combinatorial_basis.d.ts +++ b/dist/js/parsers/xyz_combinatorial_basis.d.ts @@ -1,3 +1,4 @@ +import { BasisSchema } from "@mat3ra/esse/dist/js/types"; import { ElementsAndCoordinatesConfig } from "../basis/basis"; import { AtomicCoordinateValue } from "../basis/coordinates"; import { AtomicElementValue } from "../basis/elements"; @@ -37,7 +38,7 @@ export declare class CombinatorialBasis { * @return {String[]} */ get uniqueElements(): any[]; - static toBasisConfigForElementsAndCoordinates(array: ElementWithCoordinate[], units?: "crystal" | "cartesian" | undefined, cell?: Cell): ElementsAndCoordinatesConfig; + static toBasisConfigForElementsAndCoordinates(array: ElementWithCoordinate[], units?: BasisSchema["units"], cell?: Cell): ElementsAndCoordinatesConfig; /** * Returns array of regular bases extracted from current combinatorial basis. * @return {Basis[]|Object[]} diff --git a/dist/js/parsers/xyz_combinatorial_basis.js b/dist/js/parsers/xyz_combinatorial_basis.js index fa36d4c5e..3e8e4276b 100644 --- a/dist/js/parsers/xyz_combinatorial_basis.js +++ b/dist/js/parsers/xyz_combinatorial_basis.js @@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? ( }) : function(o, v) { o["default"] = v; }); -var __importStar = (this && this.__importStar) || function (mod) { - if (mod && mod.__esModule) return mod; - var result = {}; - if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k); - __setModuleDefault(result, mod); - return result; -}; +var __importStar = (this && this.__importStar) || (function () { + var ownKeys = function(o) { + ownKeys = Object.getOwnPropertyNames || function (o) { + var ar = []; + for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k; + return ar; + }; + return ownKeys(o); + }; + return function (mod) { + if (mod && mod.__esModule) return mod; + var result = {}; + if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]); + __setModuleDefault(result, mod); + return result; + }; +})(); Object.defineProperty(exports, "__esModule", { value: true }); exports.CombinatorialBasis = exports.WrongBasisFormat = void 0; const math_1 = require("@mat3ra/code/dist/js/math"); diff --git a/package-lock.json b/package-lock.json index 6c27f3efd..d114deebe 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,55 +9,55 @@ "version": "0.0.0", "license": "Apache-2.0", "dependencies": { - "@babel/core": "7.24.1", - "@exabyte-io/periodic-table.js": "2022.5.28-0", - "@types/chai": "^4.3.5", + "@babel/core": "^7.29.7", + "@exabyte-io/periodic-table.js": "^2023.12.23-3", + "@types/chai": "^4.3.20", "@types/chai-almost": "^1.0.3", - "@types/mocha": "^10.0.1", - "@types/node": "^20.4.2", - "@types/underscore.string": "^0.0.40", + "@types/mocha": "^10.0.10", + "@types/node": "^20.19.41", + "@types/underscore.string": "^0.0.42", "array-almost-equal": "^1.0.0", - "crypto-js": "4.2.0", - "lodash": "^4.17.*", - "ts-node": "^10.9.1", - "typescript": "^4.5.5", - "underscore.string": "^3.3.4" + "crypto-js": "^4.2.0", + "lodash": "^4.18.*", + "ts-node": "^10.9.2", + "typescript": "^5.9.3", + "underscore.string": "^3.3.6" }, "devDependencies": { - "@babel/eslint-parser": "^7.16.3", - "@babel/plugin-proposal-class-properties": "^7.16.0", - "@babel/preset-env": "^7.16.4", - "@babel/preset-react": "^7.16.7", - "@babel/register": "^7.22.15", - "@babel/runtime-corejs3": "^7.16.8", - "@exabyte-io/eslint-config": "2025.5.13-0", - "@mat3ra/code": "2026.5.27-0", - "@mat3ra/esse": "2026.5.27-0", - "@mat3ra/tsconfig": "2024.6.3-0", + "@babel/eslint-parser": "^7.29.7", + "@babel/plugin-proposal-class-properties": "^7.18.6", + "@babel/preset-env": "^7.29.7", + "@babel/preset-react": "^7.29.7", + "@babel/register": "^7.29.7", + "@babel/runtime-corejs3": "^7.29.7", + "@exabyte-io/eslint-config": "^2025.5.13-0", + "@mat3ra/code": "^2026.5.27-0", + "@mat3ra/esse": "^2026.6.5-0", + "@mat3ra/tsconfig": "^2024.6.3-0", "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#1574df23cb9b0f249ee589e2c338546c4b83a97a", "@types/crypto-js": "^4.2.2", - "@typescript-eslint/eslint-plugin": "^5.9.1", - "@typescript-eslint/parser": "^5.9.1", - "chai": "^4.3.4", + "@typescript-eslint/eslint-plugin": "^5.62.0", + "@typescript-eslint/parser": "^5.62.0", + "chai": "^4.5.0", "chai-almost": "^1.0.1", "eslint": "^7.32.0", - "eslint-config-airbnb": "^19.0.2", - "eslint-config-prettier": "^8.5.0", + "eslint-config-airbnb": "^19.0.4", + "eslint-config-prettier": "^8.10.2", "eslint-import-resolver-exports": "^1.0.0-beta.5", "eslint-import-resolver-meteor": "^0.4.0", - 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"@babel/helper-plugin-utils": "^7.28.6", - "@babel/traverse": "^7.28.6" + "@babel/helper-plugin-utils": "^7.29.7", + "@babel/traverse": "^7.29.7" }, "engines": { "node": ">=6.9.0" @@ -696,6 +696,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-async-generator-functions/-/plugin-proposal-async-generator-functions-7.20.7.tgz", "integrity": "sha512-xMbiLsn/8RK7Wq7VeVytytS2L6qE69bXPB10YCmMdDZbKF4okCqY74pI/jJQ/8U0b/F6NrT2+14b8/P9/3AMGA==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-async-generator-functions instead.", + "license": "MIT", "dependencies": { "@babel/helper-environment-visitor": "^7.18.9", "@babel/helper-plugin-utils": "^7.20.2", @@ -715,6 +716,7 @@ "integrity": "sha512-cumfXOF0+nzZrrN8Rf0t7M+tF6sZc7vhQwYQck9q1/5w2OExlD+b4v4RpMJFaV1Z7WcDRgO6FqvxqxGlwo+RHQ==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-class-properties instead.", "dev": true, + "license": "MIT", "dependencies": { "@babel/helper-create-class-features-plugin": "^7.18.6", "@babel/helper-plugin-utils": "^7.18.6" @@ -731,6 +733,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-class-static-block/-/plugin-proposal-class-static-block-7.21.0.tgz", "integrity": "sha512-XP5G9MWNUskFuP30IfFSEFB0Z6HzLIUcjYM4bYOPHXl7eiJ9HFv8tWj6TXTN5QODiEhDZAeI4hLok2iHFFV4hw==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-class-static-block instead.", + "license": "MIT", "dependencies": { "@babel/helper-create-class-features-plugin": "^7.21.0", "@babel/helper-plugin-utils": "^7.20.2", @@ -748,6 +751,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-dynamic-import/-/plugin-proposal-dynamic-import-7.18.6.tgz", "integrity": "sha512-1auuwmK+Rz13SJj36R+jqFPMJWyKEDd7lLSdOj4oJK0UTgGueSAtkrCvz9ewmgyU/P941Rv2fQwZJN8s6QruXw==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-dynamic-import instead.", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.18.6", "@babel/plugin-syntax-dynamic-import": "^7.8.3" @@ -764,6 +768,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-export-namespace-from/-/plugin-proposal-export-namespace-from-7.18.9.tgz", "integrity": "sha512-k1NtHyOMvlDDFeb9G5PhUXuGj8m/wiwojgQVEhJ/fsVsMCpLyOP4h0uGEjYJKrRI+EVPlb5Jk+Gt9P97lOGwtA==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-export-namespace-from instead.", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.18.9", "@babel/plugin-syntax-export-namespace-from": "^7.8.3" @@ -780,6 +785,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-json-strings/-/plugin-proposal-json-strings-7.18.6.tgz", "integrity": "sha512-lr1peyn9kOdbYc0xr0OdHTZ5FMqS6Di+H0Fz2I/JwMzGmzJETNeOFq2pBySw6X/KFL5EWDjlJuMsUGRFb8fQgQ==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-json-strings instead.", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.18.6", "@babel/plugin-syntax-json-strings": "^7.8.3" @@ -796,6 +802,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-logical-assignment-operators/-/plugin-proposal-logical-assignment-operators-7.20.7.tgz", "integrity": "sha512-y7C7cZgpMIjWlKE5T7eJwp+tnRYM89HmRvWM5EQuB5BoHEONjmQ8lSNmBUwOyy/GFRsohJED51YBF79hE1djug==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-logical-assignment-operators instead.", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.20.2", "@babel/plugin-syntax-logical-assignment-operators": "^7.10.4" @@ -812,6 +819,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-nullish-coalescing-operator/-/plugin-proposal-nullish-coalescing-operator-7.18.6.tgz", "integrity": "sha512-wQxQzxYeJqHcfppzBDnm1yAY0jSRkUXR2z8RePZYrKwMKgMlE8+Z6LUno+bd6LvbGh8Gltvy74+9pIYkr+XkKA==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-nullish-coalescing-operator instead.", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.18.6", "@babel/plugin-syntax-nullish-coalescing-operator": "^7.8.3" @@ -828,6 +836,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-numeric-separator/-/plugin-proposal-numeric-separator-7.18.6.tgz", "integrity": "sha512-ozlZFogPqoLm8WBr5Z8UckIoE4YQ5KESVcNudyXOR8uqIkliTEgJ3RoketfG6pmzLdeZF0H/wjE9/cCEitBl7Q==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-numeric-separator instead.", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.18.6", "@babel/plugin-syntax-numeric-separator": "^7.10.4" @@ -844,6 +853,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-object-rest-spread/-/plugin-proposal-object-rest-spread-7.20.7.tgz", "integrity": "sha512-d2S98yCiLxDVmBmE8UjGcfPvNEUbA1U5q5WxaWFUGRzJSVAZqm5W6MbPct0jxnegUZ0niLeNX+IOzEs7wYg9Dg==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-object-rest-spread instead.", + "license": "MIT", "dependencies": { "@babel/compat-data": "^7.20.5", "@babel/helper-compilation-targets": "^7.20.7", @@ -863,6 +873,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-optional-catch-binding/-/plugin-proposal-optional-catch-binding-7.18.6.tgz", "integrity": "sha512-Q40HEhs9DJQyaZfUjjn6vE8Cv4GmMHCYuMGIWUnlxH6400VGxOuwWsPt4FxXxJkC/5eOzgn0z21M9gMT4MOhbw==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-optional-catch-binding instead.", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.18.6", "@babel/plugin-syntax-optional-catch-binding": "^7.8.3" @@ -879,6 +890,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-optional-chaining/-/plugin-proposal-optional-chaining-7.21.0.tgz", "integrity": "sha512-p4zeefM72gpmEe2fkUr/OnOXpWEf8nAgk7ZYVqqfFiyIG7oFfVZcCrU64hWn5xp4tQ9LkV4bTIa5rD0KANpKNA==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-optional-chaining instead.", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.20.2", "@babel/helper-skip-transparent-expression-wrappers": "^7.20.0", @@ -896,6 +908,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-private-methods/-/plugin-proposal-private-methods-7.18.6.tgz", "integrity": "sha512-nutsvktDItsNn4rpGItSNV2sz1XwS+nfU0Rg8aCx3W3NOKVzdMjJRu0O5OkgDp3ZGICSTbgRpxZoWsxoKRvbeA==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-private-methods instead.", + "license": "MIT", "dependencies": { "@babel/helper-create-class-features-plugin": "^7.18.6", "@babel/helper-plugin-utils": "^7.18.6" @@ -912,6 +925,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-private-property-in-object/-/plugin-proposal-private-property-in-object-7.21.0-placeholder-for-preset-env.2.tgz", "integrity": "sha512-SOSkfJDddaM7mak6cPEpswyTRnuRltl429hMraQEglW+OkovnCzsiszTmsrlY//qLFjCpQDFRvjdm2wA5pPm9w==", "dev": true, + "license": "MIT", "engines": { "node": ">=6.9.0" }, @@ -924,6 +938,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-unicode-property-regex/-/plugin-proposal-unicode-property-regex-7.18.6.tgz", "integrity": "sha512-2BShG/d5yoZyXZfVePH91urL5wTG6ASZU9M4o03lKK8u8UW1y08OMttBSOADTcJrnPMpvDXRG3G8fyLh4ovs8w==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-unicode-property-regex instead.", + "license": "MIT", "dependencies": { "@babel/helper-create-regexp-features-plugin": "^7.18.6", "@babel/helper-plugin-utils": "^7.18.6" @@ -939,6 +954,7 @@ "version": "7.8.4", "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-async-generators/-/plugin-syntax-async-generators-7.8.4.tgz", "integrity": "sha512-tycmZxkGfZaxhMRbXlPXuVFpdWlXpir2W4AMhSJgRKzk/eDlIXOhb2LHWoLpDF7TEHylV5zNhykX6KAgHJmTNw==", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.8.0" }, @@ -950,6 +966,7 @@ "version": "7.12.13", "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-class-properties/-/plugin-syntax-class-properties-7.12.13.tgz", "integrity": "sha512-fm4idjKla0YahUNgFNLCB0qySdsoPiZP3iQE3rky0mBUtMZ23yDJ9SJdg6dXTSDnulOVqiF3Hgr9nbXvXTQZYA==", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.12.13" }, @@ -961,6 +978,7 @@ "version": "7.14.5", "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-class-static-block/-/plugin-syntax-class-static-block-7.14.5.tgz", "integrity": "sha512-b+YyPmr6ldyNnM6sqYeMWE+bgJcJpO6yS4QD7ymxgH34GBPNDM/THBh8iunyvKIZztiwLH4CJZ0RxTk9emgpjw==", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.14.5" }, @@ -975,6 +993,7 @@ "version": "7.8.3", "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-dynamic-import/-/plugin-syntax-dynamic-import-7.8.3.tgz", "integrity": "sha512-5gdGbFon+PszYzqs83S3E5mpi7/y/8M9eC90MRTZfduQOYW76ig6SOSPNe41IG5LoP3FGBn2N0RjVDSQiS94kQ==", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.8.0" }, @@ -986,6 +1005,7 @@ "version": "7.8.3", "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-export-namespace-from/-/plugin-syntax-export-namespace-from-7.8.3.tgz", "integrity": "sha512-MXf5laXo6c1IbEbegDmzGPwGNTsHZmEy6QGznu5Sh2UCWvueywb2ee+CCE4zQiZstxU9BMoQO9i6zUFSY0Kj0Q==", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.8.3" }, @@ -994,13 +1014,13 @@ } }, "node_modules/@babel/plugin-syntax-import-assertions": { - "version": "7.28.6", - "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-import-assertions/-/plugin-syntax-import-assertions-7.28.6.tgz", - "integrity": "sha512-pSJUpFHdx9z5nqTSirOCMtYVP2wFgoWhP0p3g8ONK/4IHhLIBd0B9NYqAvIUAhq+OkhO4VM1tENCt0cjlsNShw==", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-import-assertions/-/plugin-syntax-import-assertions-7.29.7.tgz", + "integrity": "sha512-/An1OCBN93thpBAGyfsK2pcf0jvju1SAtKkL2Ny++B5Sy6sqgzXDQH1cZxWbF96Wuk+bn41MDA9bLd4VVAw6rw==", "dev": true, "license": "MIT", "dependencies": { - "@babel/helper-plugin-utils": "^7.28.6" + "@babel/helper-plugin-utils": "^7.29.7" }, "engines": { "node": ">=6.9.0" @@ -1010,13 +1030,13 @@ } }, "node_modules/@babel/plugin-syntax-import-attributes": { - "version": "7.28.6", - "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-import-attributes/-/plugin-syntax-import-attributes-7.28.6.tgz", - "integrity": "sha512-jiLC0ma9XkQT3TKJ9uYvlakm66Pamywo+qwL+oL8HJOvc6TWdZXVfhqJr8CCzbSGUAbDOzlGHJC1U+vRfLQDvw==", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-import-attributes/-/plugin-syntax-import-attributes-7.29.7.tgz", + "integrity": "sha512-zGYcYfq/WmZ4V+kBIXQon9dSSc8ircGZqw9ZaNhhGj9nZkeBu1jHLBDQqYYi5WA9uawvA2sIMbry2nCFhf5Djg==", "dev": true, "license": "MIT", "dependencies": { - "@babel/helper-plugin-utils": "^7.28.6" + "@babel/helper-plugin-utils": "^7.29.7" }, "engines": { "node": ">=6.9.0" @@ -1029,6 +1049,7 @@ "version": "7.8.3", "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-json-strings/-/plugin-syntax-json-strings-7.8.3.tgz", "integrity": "sha512-lY6kdGpWHvjoe2vk4WrAapEuBR69EMxZl+RoGRhrFGNYVK8mOPAW8VfbT/ZgrFbXlDNiiaxQnAtgVCZ6jv30EA==", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.8.0" }, @@ -1037,12 +1058,13 @@ } }, "node_modules/@babel/plugin-syntax-jsx": { - "version": "7.27.1", - "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-jsx/-/plugin-syntax-jsx-7.27.1.tgz", - "integrity": "sha512-y8YTNIeKoyhGd9O0Jiyzyyqk8gdjnumGTQPsz0xOZOQ2RmkVJeZ1vmmfIvFEKqucBG6axJGBZDE/7iI5suUI/w==", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/plugin-syntax-jsx/-/plugin-syntax-jsx-7.29.7.tgz", + "integrity": "sha512-TSu8+mHCoEaaCDEZ0I3+6mvTBYR4PCxQwf2z9/r5Tbztv6NaLR3B9thGTTxX2WGuGHJqRiAbKPeGTJ5XWXVg6A==", "dev": true, + "license": "MIT", "dependencies": { - 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Please use @babel/plugin-transform-class-properties instead.", + "license": "MIT", "dependencies": { "@babel/helper-create-class-features-plugin": "^7.16.0", "@babel/helper-plugin-utils": "^7.14.5" @@ -2634,6 +2649,7 @@ "resolved": "https://registry.npmjs.org/@babel/plugin-proposal-private-property-in-object/-/plugin-proposal-private-property-in-object-7.21.11.tgz", "integrity": "sha512-0QZ8qP/3RLDVBwBFoWAwCtgcDZJVwA5LUJRZU8x2YFfKNuFq161wK3cuGrALu5yiPu+vzwTAg/sMWVNeWeNyaw==", "deprecated": "This proposal has been merged to the ECMAScript standard and thus this plugin is no longer maintained. Please use @babel/plugin-transform-private-property-in-object instead.", + "license": "MIT", "dependencies": { "@babel/helper-annotate-as-pure": "^7.18.6", "@babel/helper-create-class-features-plugin": "^7.21.0", @@ -2651,6 +2667,7 @@ "version": "7.16.4", "resolved": "https://registry.npmjs.org/@babel/preset-env/-/preset-env-7.16.4.tgz", "integrity": "sha512-v0QtNd81v/xKj4gNKeuAerQ/azeNn/G1B1qMLeXOcV8+4TWlD2j3NV1u8q29SDFBXx/NBq5kyEAO+0mpRgacjA==", + "license": "MIT", "dependencies": { "@babel/compat-data": "^7.16.4", "@babel/helper-compilation-targets": "^7.16.3", @@ -2738,6 +2755,7 @@ "version": "0.1.6", "resolved": "https://registry.npmjs.org/@babel/preset-modules/-/preset-modules-0.1.6.tgz", "integrity": "sha512-ID2yj6K/4lKfhuU3+EX4UvNbIt7eACFbHmNUjzA+ep+B5971CknnA/9DEWKbRokfbbtblxxxXFJJrH47UEAMVg==", + "license": "MIT", "dependencies": { "@babel/helper-plugin-utils": "^7.0.0", "@babel/plugin-proposal-unicode-property-regex": "^7.4.4", @@ -2753,6 +2771,7 @@ "version": "7.16.0", "resolved": "https://registry.npmjs.org/@babel/register/-/register-7.16.0.tgz", "integrity": "sha512-lzl4yfs0zVXnooeLE0AAfYaT7F3SPA8yB2Bj4W1BiZwLbMS3MZH35ZvCWSRHvneUugwuM+Wsnrj7h0F7UmU3NQ==", + "license": "MIT", "dependencies": { "clone-deep": "^4.0.1", "find-cache-dir": "^2.0.0", @@ -2771,6 +2790,7 @@ "version": "0.3.3", "resolved": "https://registry.npmjs.org/babel-plugin-polyfill-corejs2/-/babel-plugin-polyfill-corejs2-0.3.3.tgz", "integrity": "sha512-8hOdmFYFSZhqg2C/JgLUQ+t52o5nirNwaWM2B9LWteozwIvM14VSwdsCAUET10qT+kmySAlseadmfeeSWFCy+Q==", + "license": "MIT", "dependencies": { "@babel/compat-data": "^7.17.7", "@babel/helper-define-polyfill-provider": "^0.3.3", @@ -2784,6 +2804,7 @@ "version": "0.4.0", "resolved": "https://registry.npmjs.org/babel-plugin-polyfill-corejs3/-/babel-plugin-polyfill-corejs3-0.4.0.tgz", "integrity": "sha512-YxFreYwUfglYKdLUGvIF2nJEsGwj+RhWSX/ije3D2vQPOXuyMLMtg/cCGMDpOA7Nd+MwlNdnGODbd2EwUZPlsw==", + "license": "MIT", "dependencies": { "@babel/helper-define-polyfill-provider": "^0.3.0", "core-js-compat": "^3.18.0" @@ -2796,6 +2817,7 @@ "version": "0.3.1", "resolved": "https://registry.npmjs.org/babel-plugin-polyfill-regenerator/-/babel-plugin-polyfill-regenerator-0.3.1.tgz", "integrity": "sha512-Y2B06tvgHYt1x0yz17jGkGeeMr5FeKUu+ASJ+N6nB5lQ8Dapfg42i0OVrf8PNGJ3zKL4A23snMi1IRwrqqND7A==", + "license": "MIT", "dependencies": { "@babel/helper-define-polyfill-provider": "^0.3.1" }, @@ -2806,34 +2828,15 @@ "node_modules/@exabyte-io/periodic-table.js/node_modules/convert-source-map": { "version": "1.9.0", "resolved": "https://registry.npmjs.org/convert-source-map/-/convert-source-map-1.9.0.tgz", - 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"@babel/eslint-parser": "^7.16.3", - "@babel/plugin-proposal-class-properties": "^7.16.0", - "@babel/preset-env": "^7.16.4", - "@babel/preset-react": "^7.16.7", - "@babel/register": "^7.22.15", - "@babel/runtime-corejs3": "^7.16.8", - "@exabyte-io/eslint-config": "2025.5.13-0", - "@mat3ra/code": "2026.5.27-0", - "@mat3ra/esse": "2026.5.27-0", - "@mat3ra/tsconfig": "2024.6.3-0", + "@babel/eslint-parser": "^7.29.7", + "@babel/plugin-proposal-class-properties": "^7.18.6", + "@babel/preset-env": "^7.29.7", + "@babel/preset-react": "^7.29.7", + "@babel/register": "^7.29.7", + "@babel/runtime-corejs3": "^7.29.7", + "@exabyte-io/eslint-config": "^2025.5.13-0", + "@mat3ra/code": "^2026.5.27-0", + "@mat3ra/esse": "^2026.6.5-0", + "@mat3ra/tsconfig": "^2024.6.3-0", "@mat3ra/utils": "git+https://github.com/exabyte-io/utils.git#1574df23cb9b0f249ee589e2c338546c4b83a97a", "@types/crypto-js": "^4.2.2", - "@typescript-eslint/eslint-plugin": "^5.9.1", - "@typescript-eslint/parser": "^5.9.1", - "chai": "^4.3.4", + "@typescript-eslint/eslint-plugin": "^5.62.0", + "@typescript-eslint/parser": "^5.62.0", + "chai": "^4.5.0", "chai-almost": "^1.0.1", "eslint": "^7.32.0", - "eslint-config-airbnb": "^19.0.2", - "eslint-config-prettier": "^8.5.0", + "eslint-config-airbnb": "^19.0.4", + "eslint-config-prettier": "^8.10.2", "eslint-import-resolver-exports": "^1.0.0-beta.5", "eslint-import-resolver-meteor": "^0.4.0", - "eslint-import-resolver-node": "^0.3.9", - "eslint-plugin-import": "^2.25.3", - "eslint-plugin-jsdoc": "^37.1.0", - "eslint-plugin-jsx-a11y": "^6.5.1", + "eslint-import-resolver-node": "^0.3.10", + "eslint-plugin-import": "^2.32.0", + "eslint-plugin-jsdoc": "^37.9.7", + "eslint-plugin-jsx-a11y": "^6.10.2", "eslint-plugin-mui-path-imports": "0.0.15", - "eslint-plugin-prettier": "^4.2.1", - "eslint-plugin-react": "^7.30.0", + "eslint-plugin-prettier": "^4.2.5", + "eslint-plugin-react": "^7.37.5", "eslint-plugin-simple-import-sort": "^7.0.0", "husky": "^7.0.4", - "lint-staged": "^12.1.2", - "mocha": "10.3.0", - "prettier": "^2.5.1", + "lint-staged": "^12.5.0", + "mocha": "10.8.2", + "prettier": "^2.8.8", "nyc": "^15.1.0" }, "dependencies": { - "@babel/core": "7.24.1", - "@exabyte-io/periodic-table.js": "2022.5.28-0", - "@types/chai": "^4.3.5", + "@babel/core": "^7.29.7", + "@exabyte-io/periodic-table.js": "^2023.12.23-3", + "@types/chai": "^4.3.20", "@types/chai-almost": "^1.0.3", - "@types/mocha": "^10.0.1", - "@types/node": "^20.4.2", - "@types/underscore.string": "^0.0.40", + "@types/mocha": "^10.0.10", + "@types/node": "^20.19.41", + "@types/underscore.string": "^0.0.42", "array-almost-equal": "^1.0.0", - "crypto-js": "4.2.0", - "lodash": "^4.17.*", - "ts-node": "^10.9.1", - "typescript": "^4.5.5", - "underscore.string": "^3.3.4" + "crypto-js": "^4.2.0", + "lodash": "^4.18.*", + "ts-node": "^10.9.2", + "typescript": "^5.9.3", + "underscore.string": "^3.3.6" }, "peerDependencies": { "@mat3ra/code": "*", From 774c0c2c54c5f175291ea026411de1ee8405d825 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Fri, 12 Jun 2026 22:06:52 +0800 Subject: [PATCH 14/18] bump utils in pyproject.toml --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 6eebc8cf5..ad2b07fb2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ dependencies = [ # add requirements here # new verison of numpy==2.0.0 is not handled by pymatgen yet "numpy<=1.26.4", - "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@1574df23cb9b0f249ee589e2c338546c4b83a97a", + "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@c88d62c22bbd4203875183194677af03476e0f1a", "mat3ra-esse", "mat3ra-code" ] From 1b18d807cea0d34b4551baa1da6cc2827298193b Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Sat, 13 Jun 2026 12:49:44 +0800 Subject: [PATCH 15/18] bump utils --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ad2b07fb2..842476ee9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ dependencies = [ # add requirements here # new verison of numpy==2.0.0 is not handled by pymatgen yet "numpy<=1.26.4", - "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@c88d62c22bbd4203875183194677af03476e0f1a", + "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@01b7a69314fac1b6202d9263089c6962dadc85fb", "mat3ra-esse", "mat3ra-code" ] From 073ac27ef5027f98967601b64ddeec90bca58fb4 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Fri, 19 Jun 2026 18:01:08 +0800 Subject: [PATCH 16/18] change unittest class to pytest functions --- pyproject.toml | 2 +- tests/py/unit/test_primitive_cell.py | 222 +++++++++++++-------------- 2 files changed, 112 insertions(+), 112 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index df6441fed..d6892f5b9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ dependencies = [ # add requirements here # new verison of numpy==2.0.0 is not handled by pymatgen yet "numpy<=1.26.4", - "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@01b7a69314fac1b6202d9263089c6962dadc85fb", + "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@4ad29b7081b2c613dbde3a63427bc273adf2507e", "mat3ra-esse", "mat3ra-code" ] diff --git a/tests/py/unit/test_primitive_cell.py b/tests/py/unit/test_primitive_cell.py index 48d5be8b4..5a823d05e 100644 --- a/tests/py/unit/test_primitive_cell.py +++ b/tests/py/unit/test_primitive_cell.py @@ -5,114 +5,114 @@ from mat3ra.made.lattice import Lattice, LatticeTypeEnum from tests.py.unit.utils import assert_two_entities_deep_almost_equal - -class TestPrimitiveCell: - - def test_primitive_lattice_vectors_na4cl4(self): - """ - Replicates the TypeScript test for Na4Cl4 (CUB cell). - Translates from: tests/js/cell/primitive_cell.ts - """ - lattice = Lattice(type=LatticeTypeEnum.CUB, a=5.691694) - - actual_primitive_cell = get_primitive_lattice_vectors_from_config(lattice) - expected_primitive_cell = [ - [5.691694, 0.0, 0.0], - [0.0, 5.691694, 0.0], - [0.0, 0.0, 5.691694], - ] - - assert_two_entities_deep_almost_equal(expected_primitive_cell, actual_primitive_cell) - - @pytest.mark.parametrize( - "l_type, kwargs, expected", - [ - (LatticeTypeEnum.CUB, {"a": 2.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]), - (LatticeTypeEnum.FCC, {"a": 2.0}, [[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 0.0]]), - (LatticeTypeEnum.BCC, {"a": 2.0}, [[-1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [1.0, 1.0, -1.0]]), - (LatticeTypeEnum.TET, {"a": 2.0, "c": 3.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]), - (LatticeTypeEnum.BCT, {"a": 2.0, "c": 3.0}, [[-1.0, 1.0, 1.5], [1.0, -1.0, 1.5], [1.0, 1.0, -1.5]]), - (LatticeTypeEnum.ORC, {"a": 2.0, "b": 3.0, "c": 4.0}, [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]]), - ( - LatticeTypeEnum.ORCF, - {"a": 2.0, "b": 3.0, "c": 4.0}, - [[0.0, 1.5, 2.0], [1.0, 0.0, 2.0], [1.0, 1.5, 0.0]], - ), - ( - LatticeTypeEnum.ORCI, - {"a": 2.0, "b": 3.0, "c": 4.0}, - [[-1.0, 1.5, 2.0], [1.0, -1.5, 2.0], [1.0, 1.5, -2.0]], - ), - ( - LatticeTypeEnum.ORCC, - {"a": 2.0, "b": 3.0, "c": 4.0}, - [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 0.0, 4.0]], - ), - ( - LatticeTypeEnum.HEX, - {"a": 2.0, "c": 3.0}, - [[1.0, -math.sqrt(3), 0.0], [1.0, math.sqrt(3), 0.0], [0.0, 0.0, 3.0]], - ), - ( - LatticeTypeEnum.RHL, - {"a": 2.0, "alpha": 60.0}, - [[1.7320508, -1.0, 0.0], [1.7320508, 1.0, 0.0], [1.1547005, 0.0, 1.6329931]], - ), - ( - LatticeTypeEnum.MCL, - {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0}, - [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 2.0, 3.4641016]], - ), - ( - LatticeTypeEnum.MCLC, - {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0}, - [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 2.0, 3.4641016]], - ), - ( - LatticeTypeEnum.TRI, - {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 90.0, "beta": 90.0, "gamma": 90.0}, - [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]], - ), - ], - ) - def test_primitive_lattice_generators(self, l_type, kwargs, expected): - """Validates the math generators for all 14 Bravais lattice scenarios.""" - lattice = Lattice(type=l_type, **kwargs) - result = get_primitive_lattice_vectors_from_config(lattice) - assert_two_entities_deep_almost_equal(expected, result) - - def test_fallback_to_tri_when_type_is_none(self): - """Tests default fallback to 'TRI' when lattice_config.type is None.""" - # Use a simple dummy class to bypass Pydantic's strict validation - # and simulate a malformed or incomplete Lattice config. - class MockLattice: - type = None - a, b, c = 2.0, 2.0, 2.0 - alpha, beta, gamma = 90.0, 90.0, 90.0 - - lattice = MockLattice() - result = get_primitive_lattice_vectors_from_config(lattice) - expected = [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]] - - assert_two_entities_deep_almost_equal(expected, result) - - def test_unsupported_lattice_type_raises_value_error(self): - """Ensures a ValueError is raised for an unknown lattice type mapping.""" - - # Using a MagicMock specifically here to force an invalid type value - # since LatticeTypeEnum won't allow arbitrary strings - class MockType: - value = "INVALID_TYPE" - - class MockLattice: - type = MockType() - # Provide dummy parameters just in case - a, b, c = 2.0, 2.0, 2.0 - alpha, beta, gamma = 90.0, 90.0, 90.0 - - lattice = MockLattice() - - with pytest.raises(ValueError) as exc_info: - get_primitive_lattice_vectors_from_config(lattice) - - assert "Unsupported lattice type 'INVALID_TYPE'" in str(exc_info.value) +EXPECTED_PRIMITIVE_CELL_NA4CL4 = [ + [5.691694, 0.0, 0.0], + [0.0, 5.691694, 0.0], + [0.0, 0.0, 5.691694], +] + + +def test_primitive_lattice_vectors_na4cl4(): + """ + Replicates the TypeScript test for Na4Cl4 (CUB cell). + Translates from: tests/js/cell/primitive_cell.ts + """ + lattice = Lattice(type=LatticeTypeEnum.CUB, a=5.691694) + actual_primitive_cell = get_primitive_lattice_vectors_from_config(lattice) + + assert_two_entities_deep_almost_equal(EXPECTED_PRIMITIVE_CELL_NA4CL4, actual_primitive_cell) + + +@pytest.mark.parametrize( + "l_type, kwargs, expected", + [ + (LatticeTypeEnum.CUB, {"a": 2.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]]), + (LatticeTypeEnum.FCC, {"a": 2.0}, [[0.0, 1.0, 1.0], [1.0, 0.0, 1.0], [1.0, 1.0, 0.0]]), + (LatticeTypeEnum.BCC, {"a": 2.0}, [[-1.0, 1.0, 1.0], [1.0, -1.0, 1.0], [1.0, 1.0, -1.0]]), + (LatticeTypeEnum.TET, {"a": 2.0, "c": 3.0}, [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 3.0]]), + (LatticeTypeEnum.BCT, {"a": 2.0, "c": 3.0}, [[-1.0, 1.0, 1.5], [1.0, -1.0, 1.5], [1.0, 1.0, -1.5]]), + (LatticeTypeEnum.ORC, {"a": 2.0, "b": 3.0, "c": 4.0}, [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]]), + ( + LatticeTypeEnum.ORCF, + {"a": 2.0, "b": 3.0, "c": 4.0}, + [[0.0, 1.5, 2.0], [1.0, 0.0, 2.0], [1.0, 1.5, 0.0]], + ), + ( + LatticeTypeEnum.ORCI, + {"a": 2.0, "b": 3.0, "c": 4.0}, + [[-1.0, 1.5, 2.0], [1.0, -1.5, 2.0], [1.0, 1.5, -2.0]], + ), + ( + LatticeTypeEnum.ORCC, + {"a": 2.0, "b": 3.0, "c": 4.0}, + [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 0.0, 4.0]], + ), + ( + LatticeTypeEnum.HEX, + {"a": 2.0, "c": 3.0}, + [[1.0, -math.sqrt(3), 0.0], [1.0, math.sqrt(3), 0.0], [0.0, 0.0, 3.0]], + ), + ( + LatticeTypeEnum.RHL, + {"a": 2.0, "alpha": 60.0}, + [[1.7320508, -1.0, 0.0], [1.7320508, 1.0, 0.0], [1.1547005, 0.0, 1.6329931]], + ), + ( + LatticeTypeEnum.MCL, + {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0}, + [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 2.0, 3.4641016]], + ), + ( + LatticeTypeEnum.MCLC, + {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 60.0}, + [[1.0, 1.5, 0.0], [-1.0, 1.5, 0.0], [0.0, 2.0, 3.4641016]], + ), + ( + LatticeTypeEnum.TRI, + {"a": 2.0, "b": 3.0, "c": 4.0, "alpha": 90.0, "beta": 90.0, "gamma": 90.0}, + [[2.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 4.0]], + ), + ], +) +def test_primitive_lattice_generators(l_type, kwargs, expected): + """Validates the math generators for all 14 Bravais lattice scenarios.""" + lattice = Lattice(type=l_type, **kwargs) + result = get_primitive_lattice_vectors_from_config(lattice) + assert_two_entities_deep_almost_equal(expected, result) + + +def test_fallback_to_tri_when_type_is_none(): + """Tests default fallback to 'TRI' when lattice_config.type is None.""" + # Use a simple dummy class to bypass Pydantic's strict validation + # and simulate a malformed or incomplete Lattice config. + class MockLattice: + type = None + a, b, c = 2.0, 2.0, 2.0 + alpha, beta, gamma = 90.0, 90.0, 90.0 + + lattice = MockLattice() + result = get_primitive_lattice_vectors_from_config(lattice) + expected = [[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 2.0]] + + assert_two_entities_deep_almost_equal(expected, result) + + +def test_unsupported_lattice_type_raises_value_error(): + """Ensures a ValueError is raised for an unknown lattice type mapping.""" + # Using a MagicMock specifically here to force an invalid type value + # since LatticeTypeEnum won't allow arbitrary strings + class MockType: + value = "INVALID_TYPE" + + class MockLattice: + type = MockType() + # Provide dummy parameters just in case + a, b, c = 2.0, 2.0, 2.0 + alpha, beta, gamma = 90.0, 90.0, 90.0 + + lattice = MockLattice() + + with pytest.raises(ValueError) as exc_info: + get_primitive_lattice_vectors_from_config(lattice) + + assert "Unsupported lattice type 'INVALID_TYPE'" in str(exc_info.value) From 35674b9a63b2171c96f37d6d7c9628a14d6244e5 Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Fri, 19 Jun 2026 18:11:32 +0800 Subject: [PATCH 17/18] chore: bump gh actions --- .github/workflows/build-wheel.yml | 2 +- .github/workflows/cicd.yml | 20 ++++++++++---------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/.github/workflows/build-wheel.yml b/.github/workflows/build-wheel.yml index e960a3827..8d831e1c9 100644 --- a/.github/workflows/build-wheel.yml +++ b/.github/workflows/build-wheel.yml @@ -17,7 +17,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 - name: Set up Python uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0 diff --git a/.github/workflows/cicd.yml b/.github/workflows/cicd.yml index 68e14f4d5..ca059daeb 100644 --- a/.github/workflows/cicd.yml +++ b/.github/workflows/cicd.yml @@ -15,12 +15,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} @@ -46,12 +46,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} @@ -73,12 +73,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} @@ -105,10 +105,10 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 - name: Checkout actions repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} @@ -134,12 +134,12 @@ jobs: steps: - name: Checkout this repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: lfs: true - name: Checkout actions repository - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2 + uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0 with: repository: Exabyte-io/actions token: ${{ secrets.BOT_GITHUB_TOKEN }} From bdfa37a451f0364cee1602bcec723fb878fdfc0a Mon Sep 17 00:00:00 2001 From: Pranab Das <31024886+pranabdas@users.noreply.github.com> Date: Fri, 19 Jun 2026 18:13:39 +0800 Subject: [PATCH 18/18] update utils --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index d6892f5b9..93e606c6a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ dependencies = [ # add requirements here # new verison of numpy==2.0.0 is not handled by pymatgen yet "numpy<=1.26.4", - "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@4ad29b7081b2c613dbde3a63427bc273adf2507e", + "mat3ra-utils @ git+https://github.com/exabyte-io/utils.git@5675929ed0b7bc9c7c574d8080cc82d41e74d24d", "mat3ra-esse", "mat3ra-code" ]