Merge pull request #5 from ap--/packaging-changes

Packaging changes

.github/workflows/run_pytests.yaml

@@ -0,0 +1,39 @@
+name: scikit_mol ci
+
+on: [push, pull_request]
+
+jobs:
+  # run pytests for scikit_mol
+  tests:
+    name: pytest ${{ matrix.os }}::py${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 6
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.10"]
+        include:
+          # test python version compatibility on linux only
+          - os: ubuntu-latest
+            python-version: 3.9
+          - os: ubuntu-latest
+            python-version: 3.8
+          - os: ubuntu-latest
+            python-version: 3.7
+    steps:
+      - name: Checkout scikit_mol
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install scikit_mol
+        run: python -m pip install -e .[dev]
+      - name: Cache tests/data
+        uses: actions/cache@v3
+        with:
+          path: tests/data
+          key: ${{ runner.os }}-${{ hashFiles('tests/conftest.py') }}
+      - name: Run Tests
+        run: pytest --cov=./scikit_mol .

.gitignore

@@ -132,3 +132,9 @@ dmypy.json
 scikit-mol.code-workspace
 notebooks/25747817
 *.ipynb
+
+# test data
+tests/data/
+
+# setuptools_scm version
+scikit_mol/_version.py

MANIFEST.in

@@ -0,0 +1,3 @@
+prune .github
+exclude .git*
+

pyproject.toml

@@ -0,0 +1,27 @@
+[build-system]
+requires = [
+  "setuptools >= 64",
+  "setuptools_scm[toml]>=6.2",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "scikit_mol/_version.py"
+version_scheme = "post-release"
+
+[tool.pytest.ini_options]
+addopts = [
+  "-v",
+]
+
+[tool.coverage.run]
+source = ["scikit_mol"]
+
+[tool.coverage.report]
+exclude_lines = [
+  "pragma: no cover",
+  "raise NotImplementedError",
+  "if TYPE_CHECKING:",
+  "if MYPY:",
+  "^\\s+[.][.][.]$",
+]

scikit_mol/__init__.py

@@ -0,0 +1,4 @@
+try:
+    from scikit_mol._version import __version__
+except ImportError:  # pragma: no cover
+    __version__ = "not-installed"

setup.cfg

@@ -0,0 +1,45 @@
+[metadata]
+name = scikit_mol
+url = https://github.com/EBjerrum/scikit-mol
+download_url = https://github.com/EBjerrum/scikit-mol
+license = Apache-2.0
+license_file = LICENSE
+description = scikit-learn classes for molecule transformation
+long_description = file: README.md
+long_description_content_type = text/markdown
+author = Esben Jannik Bjerrum
+author_email = esben@cheminformania.com
+classifiers =
+    Development Status :: 3 - Alpha
+    Intended Audience :: Science/Research
+    License :: OSI Approved :: Apache Software License
+    Programming Language :: Python
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Programming Language :: Python :: 3.10
+    Topic :: Scientific/Engineering
+    Topic :: Utilities
+    Operating System :: Microsoft :: Windows
+    Operating System :: POSIX
+    Operating System :: Unix
+    Operating System :: MacOS
+
+[options]
+packages = find:
+python_requires = >=3.7
+install_requires =
+    rdkit
+    numpy
+    pandas
+    scikit-learn
+
+[options.packages.find]
+exclude =
+    tests/*
+
+[options.extras_require]
+dev =
+    pytest>=6
+    pytest-cov

tests/conftest.py

@@ -0,0 +1,47 @@
+import hashlib
+import shutil
+from pathlib import Path
+from pathlib import PurePath
+from urllib.parse import urlsplit
+from urllib.request import urlopen
+
+import pandas as pd
+import pytest
+
+
+TEST_DATA_URL = "https://ndownloader.figshare.com/files/25747817"
+TEST_DATA_MD5 = "1ec89bde544c3c4bc400d5b75315921e"
+
+
+def md5(fn):
+    m = hashlib.md5()
+    with open(fn, "rb") as f:
+        for chunk in iter(lambda: f.read(4096), b""):
+            m.update(chunk)
+    return m.hexdigest()
+
+
+@pytest.fixture(scope="session")
+def data_pth(tmp_path_factory) -> Path:
+    """download the smallest aperio test image svs or use local"""
+    filename = PurePath(urlsplit(TEST_DATA_URL).path).name
+    data_dir = Path(__file__).parent / "data"
+    data_dir.mkdir(parents=True, exist_ok=True)
+    data_fn = data_dir / filename
+
+    if not data_fn.is_file():
+        # download svs from openslide test images
+        with urlopen(TEST_DATA_URL) as response, open(
+            data_fn, "wb"
+        ) as out_file:
+            shutil.copyfileobj(response, out_file)
+
+        if md5(data_fn) != TEST_DATA_MD5:  # pragma: no cover
+            shutil.rmtree(data_fn)
+            pytest.fail("incorrect md5")
+
+    yield data_fn.absolute()
+
+@pytest.fixture()
+def data(data_pth) -> pd.DataFrame:
+    yield pd.read_csv(data_pth)

tests/test_scikit_mol.py

@@ -0,0 +1,4 @@
+
+def test_load_data(data):
+    assert len(data) > 0
+