Test all backends together in CI (#118)

* move backend tests

* avoid cached parametrization

* remove conda configs

* make all tests work

* remove mols in favour of fixtures

* make molecules fixtures

* avoid graph-tool on windows

* simplify ci

* mention pip explicitly

* reset backend for good measure

* try no space

* windows

* changelog

* reset backend for every test

* add warning test

* Apply suggestions from code review

* format

.github/workflows/pytest.yml

@@ -26,15 +26,16 @@ jobs:
         os: [macOS-latest, ubuntu-latest, windows-latest]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         chemlib: [obabel, rdkit]
-        graphlib: [nx, gt, rx, all]
+        graphlib: [nogt, all]
         exclude:
-        # graph-tools does not work on Windows
-        - {os: "windows-latest", graphlib: "gt"}
-        - {os: "windows-latest", graphlib: "all"}
-        - {graphlib: "all", chemlib: "obabel"}
+          # graph-tool does not work on Windows
+          - {os: "windows-latest", graphlib: "all"}
+          # Don't run without graph-tool on Ubuntu and macOS
+          - {os: "ubuntu-latest", graphlib: "nogt"}
+          - {os: "macOS-latest", graphlib: "nogt"}
         include:
-        - {os: "macOS-14", graphlib: "gt", chemlib: "obabel", python-version: "3.12"}
-        - {os: "macOS-14", graphlib: "nx", chemlib: "rdkit", python-version: "3.12"}
+          - {os: "macOS-14", graphlib: "all", chemlib: "obabel", python-version: "3.12"}
+          - {os: "macOS-14", graphlib: "all", chemlib: "rdkit", python-version: "3.12"}
 
     steps:
     - uses: actions/checkout@v3

CHANGELOG.md

@@ -8,10 +8,24 @@
 Date:            XX/YY/ZZZZ
 Contributors:    @RMeli
 
+### Added
+
+* Warnings filter for tests of multiple backends [PR #118 | @RMeli]
+* Parametrized fixture to run tests with all available backends [PR #118 | @RMeli]
+
 ### Improved
 
 * Test IDs [PR #117 | @RMeli]
 
+### Changed
+
+* Location of backend tests to standalone file [PR #118 | @RMeli]
+
+### Removed
+
+* Many CI configurations in favour of running tests for all available backends [PR #118 | @RMeli]
+* `tests/molecule.py` in favour of fixtures [PR #118 | @RMeli]
+
 ## Version 0.7.0
 
 Date:            05/04/2024

devtools/conda-envs/spyrmsd-test-obabel-gt.yaml → devtools/conda-envs/spyrmsd-test-obabel-all.yaml

@@ -4,12 +4,15 @@ channels:
 dependencies:
   # Base
   - python
+  - pip
   - setuptools
 
   # Maths
   - numpy
   - scipy
   - graph-tool
+  - networkx>=2
+  - rustworkx
 
   # Chemistry
   - openbabel

devtools/conda-envs/spyrmsd-test-obabel-nx.yaml → devtools/conda-envs/spyrmsd-test-obabel-nogt.yaml

@@ -4,12 +4,14 @@ channels:
 dependencies:
   # Base
   - python
+  - pip
   - setuptools
 
   # Maths
   - numpy
   - scipy
   - networkx>=2
+  - rustworkx
 
   # Chemistry
   - openbabel

devtools/conda-envs/spyrmsd-test-rdkit-all.yaml

@@ -5,6 +5,7 @@ channels:
 dependencies:
   # Base
   - python
+  - pip
   - setuptools
 
   # Maths

devtools/conda-envs/spyrmsd-test-rdkit-nx.yaml → devtools/conda-envs/spyrmsd-test-rdkit-nogt.yaml

@@ -5,12 +5,14 @@ channels:
 dependencies:
   # Base
   - python
+  - pip
   - setuptools
 
   # Maths
   - numpy
   - scipy
   - networkx>=2
+  - rustworkx
 
   # Chemistry
   - rdkit

tests/conftest.py

@@ -5,9 +5,18 @@
     https://docs.pytest.org/en/latest/example/simple.html
 """
 
+import os
+import warnings
+from collections import namedtuple
+
 import numpy as np
 import pytest
 
+import spyrmsd
+from spyrmsd import io
+
+Mol = namedtuple("Mol", ["mol", "name", "n_atoms", "n_bonds", "n_h"])
+
 
 def pytest_addoption(parser):
     parser.addoption(
@@ -69,3 +78,91 @@ def pytest_generate_tests(metafunc):
         n = metafunc.config.getoption("--n-tests")
 
         metafunc.parametrize("idx", np.random.randint(0, pytest.n_systems, size=n))
+
+
+@pytest.fixture(autouse=True, params=spyrmsd.available_backends)
+def set_backend(request):
+    # Capture warning when trying to switch to the same backend
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        spyrmsd.set_backend(request.param)
+
+
+@pytest.fixture(scope="session")
+def molpath():
+    fdir = os.path.dirname(os.path.abspath(__file__))
+    return os.path.join(fdir, f"data{os.sep}molecules")
+
+
+@pytest.fixture
+def benzene(molpath):
+    mol = io.loadmol(os.path.join(molpath, "benzene.sdf"))
+    return Mol(mol, "benzene", 12, 12, 6)
+
+
+@pytest.fixture
+def pyridine(molpath):
+    mol = io.loadmol(os.path.join(molpath, "pyridine.sdf"))
+    return Mol(mol, "pyridine", 11, 11, 5)
+
+
+@pytest.fixture(
+    params=[
+        # (name, n_atoms, n_bonds, n_h)
+        ("benzene", 12, 12, 6),
+        ("ethanol", 9, 8, 6),
+        ("pyridine", 11, 11, 5),
+        ("dialanine", 23, 22, 12),
+    ]
+)
+def mol(request, molpath):
+    """
+    Load molecule as sPyRMSD molecule.
+    """
+
+    name, n_atoms, n_bonds, n_h = request.param
+
+    mol = io.loadmol(os.path.join(molpath, f"{name}.sdf"))
+
+    return Mol(mol, name, n_atoms, n_bonds, n_h)
+
+
+@pytest.fixture
+def rawmol(mol, molpath):
+    """
+    Load molecule as a molecule of the current molecular I/O library.
+    """
+
+    RawMol = namedtuple(
+        "RawMol", ["mol", "rawmol", "name", "n_atoms", "n_bonds", "n_h"]
+    )
+
+    rawmol = io.load(os.path.join(molpath, f"{mol.name}.sdf"))
+
+    return RawMol(mol.mol, rawmol, mol.name, mol.n_atoms, mol.n_bonds, mol.n_h)
+
+
+@pytest.fixture
+def trps(molpath):
+    trp_list = []
+    for i in range(6):
+        trp_list.append(io.loadmol(os.path.join(molpath, f"trp{i}.pdb")))
+
+    return trp_list
+
+
+@pytest.fixture
+def docking_2viz(molpath):
+    mols = {}  # Dictionary (pose, molecule)
+    for i in [1, 2, 3]:
+        mols[i] = io.loadmol(os.path.join(molpath, f"2viz_{i}.sdf"))
+
+    return mols
+
+
+@pytest.fixture
+def docking_1cbr(molpath):
+    return [
+        io.loadmol(os.path.join(molpath, "1cbr_ligand.mol2")),
+        *io.loadallmols(os.path.join(molpath, "1cbr_docking.sdf")),
+    ]