Change to pytest (#111)

* use pytest: unittest -> pytest translation

* use pytest: CI update & dependencies, including coverage

* pytest in dev dependencies

* empty tests/__init__.py

* Update .github/workflows/ci.yml

.github/workflows/ci.yml

@@ -1,32 +1,37 @@
 name: ci
 
-on: [push, pull_request]
+on: [ push, pull_request ]
 
 jobs:
 
   build:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: [ "3.9", "3.10", "3.11", "3.12" ]
 
     steps:
-    - uses: actions/checkout@v4
+      - uses: actions/checkout@v4
 
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
 
-    - name: Install poetry
-      run: pipx install poetry
+      - name: Install poetry
+        run: pipx install poetry
 
-    - name: Install python dependencies
-      run: |
-        poetry env use ${{ matrix.python-version }}
-        poetry install --with dev
+      - name: Install python dependencies
+        run: |
+          poetry env use ${{ matrix.python-version }}
+          poetry install --with dev
 
-    - name: Run unit tests
-      run: |
-        poetry run python -m unittest -v tests
+      - name: Run unit tests
+        run: |
+          poetry run pytest --cov=abcd --cov-report xml --cov-report term:skip-covered
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4.4.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 

pyproject.toml

@@ -3,7 +3,7 @@ name = "abcd"
 version = "0.6.0"
 description = "This is a package which helps to store and share atomistic data."
 authors = ["Adam Fekete", "Gabor Csanyi"]
-keywords=["ase", "database", "mongo", "flask", "opensearch"]
+keywords = ["ase", "database", "mongo", "flask", "opensearch"]
 readme = "README.md"
 homepage = "https://libatoms.github.io/abcd/"
 repository = "https://github.com/libatoms/abcd"
@@ -21,9 +21,11 @@ lark = "^1.1.9"
 
 [tool.poetry.group.dev.dependencies]
 mongomock = "^4.1.2"
+pytest = "^8.2.2"
+pytest-cov = "^5.0.0"
 
 [tool.poetry.extras]
-tests = ["mongomock"]
+tests = ["mongomock", "pytest", "pytest-cov"]
 mongo = ["pymongo"]
 http = ["requests"]
 server-api = ["flask"]

tests/__init__.py

@@ -1,9 +0,0 @@
-import unittest
-from tests.parsers import ParsingQueries, ParsingExtras
-from tests.database import Mongo
-
-import logging
-
-if __name__ == '__main__':
-    logging.basicConfig(level=logging.INFO)
-    unittest.main(verbosity=1, exit=False)

tests/test_database.py

@@ -0,0 +1,38 @@
+import pytest
+import mongomock
+
+from abcd import ABCD
+
+from io import StringIO
+from ase.io import read
+
+
+@pytest.fixture
+@mongomock.patch(servers=(('localhost', 27017),))
+def abcd_mongodb():
+    url = 'mongodb://localhost'
+    abcd = ABCD.from_url(url)
+    abcd.print_info()
+
+    return abcd
+
+
+def test_thing(abcd_mongodb):
+    print(abcd_mongodb.info())
+
+
+def test_push(abcd_mongodb):
+    xyz = StringIO("""2
+Properties=species:S:1:pos:R:3 s="sadf" _vtk_test="t e s t _ s t r" pbc="F F F"
+Si       0.00000000       0.00000000       0.00000000 
+Si       0.00000000       0.00000000       0.00000000 
+""")
+
+    atoms = read(xyz, format='extxyz')
+    atoms.set_cell([1, 1, 1])
+
+    abcd_mongodb.destroy()
+    abcd_mongodb.push(atoms)
+    new = list(abcd_mongodb.get_atoms())[0]
+
+    assert atoms == new