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Tests #21

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Dec 6, 2022
Merged

Tests #21

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1864e1d
added test modules
AntObi Dec 5, 2022
2861c30
test and requirements.txt added
AntObi Dec 6, 2022
42f478c
Added qa to Github actions
AntObi Dec 6, 2022
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27 changes: 27 additions & 0 deletions .github/workflows/ci.yml
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name: AtomicEmbeddings CI

on: [push]

jobs:

qa:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: pre-commit/action@v2.0.2

test:
needs: qa
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: Install dependencies
run: |
python -m pip install --upgrade pip wheel
pip install -r requirements.txt
- name: Run tests
run: python -m pytest -v
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -209,3 +209,4 @@ cython_debug/

# mkdocs
site/
examples/test.ipynb
Empty file added AtomicEmbeddings/tests/__init__.py
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233 changes: 233 additions & 0 deletions AtomicEmbeddings/tests/test_embeddings.py
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import unittest

import numpy as np

from AtomicEmbeddings import Atomic_Embeddings


class TestSequenceFunctions(unittest.TestCase):
# High Level functions

def test_Atomic_Embeddings_class_magpie(self):
magpie = Atomic_Embeddings.from_json("magpie")
# Check if the embeddings attribute is a dict
self.assertIsInstance(magpie.embeddings, dict)
# Check if the embedding vector is a numpy array
self.assertIsInstance(magpie.embeddings["H"], np.ndarray)
# Check if H is present in the embedding keys
self.assertIn("H", magpie.embeddings.keys())
# Check dimensions
self.assertEqual(magpie.dim, 21)
# Check that a list is returned
self.assertIsInstance(magpie.element_list, list)
# Check that the correct list is returned
el_list = [
"H",
"He",
"Li",
"Be",
"B",
"C",
"N",
"O",
"F",
"Ne",
"Na",
"Mg",
"Al",
"Si",
"P",
"S",
"Cl",
"Ar",
"K",
"Ca",
"Sc",
"Ti",
"V",
"Cr",
"Mn",
"Fe",
"Co",
"Ni",
"Cu",
"Zn",
"Ga",
"Ge",
"As",
"Se",
"Br",
"Kr",
"Rb",
"Sr",
"Y",
"Zr",
"Nb",
"Mo",
"Tc",
"Ru",
"Rh",
"Pd",
"Ag",
"Cd",
"In",
"Sn",
"Sb",
"Te",
"I",
"Xe",
"Cs",
"Ba",
"La",
"Ce",
"Pr",
"Nd",
"Pm",
"Sm",
"Eu",
"Gd",
"Tb",
"Dy",
"Ho",
"Er",
"Tm",
"Yb",
"Lu",
"Hf",
"Ta",
"W",
"Re",
"Os",
"Ir",
"Pt",
"Au",
"Hg",
"Tl",
"Pb",
"Bi",
"Po",
"At",
"Rn",
"Fr",
"Ra",
"Ac",
"Th",
"Pa",
"U",
"Np",
"Pu",
"Am",
"Cm",
"Bk",
]
self.assertEqual(magpie.element_list, el_list)
# Check that a dictionary is returned
self.assertIsInstance(magpie.element_groups_dict, dict)
# Check that the correct dictionary is returned
group_dict = {
"H": "Others",
"He": "Noble gas",
"Li": "Alkali",
"Be": "Alkaline",
"B": "Metalloid",
"C": "Others",
"N": "Others",
"O": "Chalcogen",
"F": "Halogen",
"Ne": "Noble gas",
"Na": "Alkali",
"Mg": "Alkaline",
"Al": "Post-TM",
"Si": "Metalloid",
"P": "Others",
"S": "Chalcogen",
"Cl": "Halogen",
"Ar": "Noble gas",
"K": "Alkali",
"Ca": "Alkaline",
"Sc": "TM",
"Ti": "TM",
"V": "TM",
"Cr": "TM",
"Mn": "TM",
"Fe": "TM",
"Co": "TM",
"Ni": "TM",
"Cu": "TM",
"Zn": "TM",
"Ga": "Post-TM",
"Ge": "Metalloid",
"As": "Metalloid",
"Se": "Chalcogen",
"Br": "Halogen",
"Kr": "Noble gas",
"Rb": "Alkali",
"Sr": "Alkaline",
"Y": "TM",
"Zr": "TM",
"Nb": "TM",
"Mo": "TM",
"Tc": "TM",
"Ru": "TM",
"Rh": "TM",
"Pd": "TM",
"Ag": "TM",
"Cd": "TM",
"In": "Post-TM",
"Sn": "Post-TM",
"Sb": "Metalloid",
"Te": "Chalcogen",
"I": "Halogen",
"Xe": "Noble gas",
"Cs": "Alkali",
"Ba": "Alkaline",
"La": "Lanthanoid",
"Ce": "Lanthanoid",
"Pr": "Lanthanoid",
"Nd": "Lanthanoid",
"Pm": "Lanthanoid",
"Sm": "Lanthanoid",
"Eu": "Lanthanoid",
"Gd": "Lanthanoid",
"Tb": "Lanthanoid",
"Dy": "Lanthanoid",
"Ho": "Lanthanoid",
"Er": "Lanthanoid",
"Tm": "Lanthanoid",
"Yb": "Lanthanoid",
"Lu": "Lanthanoid",
"Hf": "TM",
"Ta": "TM",
"W": "TM",
"Re": "TM",
"Os": "TM",
"Ir": "TM",
"Pt": "TM",
"Au": "TM",
"Hg": "TM",
"Tl": "Post-TM",
"Pb": "Post-TM",
"Bi": "Post-TM",
"Po": "Chalcogen",
"At": "Halogen",
"Rn": "Noble gas",
"Fr": "Alkali",
"Ra": "Alkaline",
"Ac": "Actinoid",
"Th": "Actinoid",
"Pa": "Actinoid",
"U": "Actinoid",
"Np": "Actinoid",
"Pu": "Actinoid",
"Am": "Actinoid",
"Cm": "Actinoid",
"Bk": "Actinoid",
}
self.assertEqual(magpie.element_groups_dict, group_dict)
# Check pair creation
self.assertEqual(
len(list(magpie.create_pairs())), 4753, "Incorrect number of pairs returned"
)

# TO-DO
# Create tests for checking dataframes and plotting functions
9 changes: 9 additions & 0 deletions requirements.txt
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numpy
scipy
pymatgen
seaborn
matplotlib
scikit-learn
pandas
pytest
pytest-subtests
3 changes: 3 additions & 0 deletions setup.py
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@@ -1,3 +1,5 @@
import unittest

from setuptools import find_packages, setup

VERSION = "0.0.3"
Expand All @@ -14,6 +16,7 @@
long_description=LONG_DESCRIPTION,
packages=find_packages(),
package_data={"AtomicEmbeddings": ["data/*.json", "data/*.csv"]},
test_suite="AtomicEmbeddings.tests.test",
install_requires=[
"numpy",
"scipy",
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