Expand test matrix to macOS (#32)

* expand test matrix

* change directory for tempfile

* fix python versions list

* tempfile in current dir with os module

* fix noxfile linting

* revert change in noxfile

* try to use tempdirs instead of tempfiles

* remove temporary files

* fix linting

* fix linting

* try to remove pytype

* add back pytype

* remove windows from ci matrix

Signed-off-by: Rocco Meli <rocco.meli@biodtp.ox.ac.uk>

Author: RMeli

.github/workflows/tests.yml

@@ -1,13 +1,22 @@
 # .github/workflows/tests.yml
 name: Tests
-on: push
+
+on:
+  push:
+    branches:
+      - "master"
+  pull_request:
+    branches:
+      - "*"
+
 jobs:
   tests:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.7', '3.8']
-    name: Python ${{ matrix.python-version }}
+        os: [ubuntu-latest, macOS-latest]
+        python-version: ['3.7', '3.8', '3.9']
+    name: Python ${{ matrix.python-version }} OS ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v2
     - uses: actions/setup-python@v1

.gitignore

@@ -17,6 +17,7 @@ pip-log.txt
 .coverage
 .tox
 .pytest_cache
+.pytype
 
 .DS_Store
 .idea/*

noxfile.py

@@ -1,5 +1,6 @@
 # noxfile.py
 
+import os
 import tempfile
 
 import nox
@@ -10,7 +11,10 @@
 locations = "src", "tests", "noxfile.py"
 
 
-@nox.session(python=["3.8", "3.7"])
+python_versions = ["3.9", "3.8", "3.7"]
+
+
+@nox.session(python=python_versions)
 def tests(session: Session) -> None:
     args = session.posargs or ["--cov", "-m", "not e2e"]
     session.run("poetry", "install", "--no-dev", external=True)
@@ -20,7 +24,7 @@ def tests(session: Session) -> None:
     session.run("pytest", *args)
 
 
-@nox.session(python=["3.8", "3.7"])
+@nox.session(python=python_versions)
 def lint(session: Session) -> None:
     args = session.posargs or locations
     install_with_constraints(
@@ -43,21 +47,26 @@ def black(session: Session) -> None:
 
 @nox.session(python="3.8")
 def safety(session: Session) -> None:
-    with tempfile.NamedTemporaryFile() as requirements:
+    with tempfile.TemporaryDirectory() as tmpdirname:
         session.run(
             "poetry",
             "export",
             "--dev",
             "--format=requirements.txt",
             "--without-hashes",
-            f"--output={requirements.name}",
+            f"--output={os.path.join(tmpdirname, 'poetry-export.out')}",
             external=True,
         )
         install_with_constraints(session, "safety")
-        session.run("safety", "check", f"--file={requirements.name}", "--full-report")
+        session.run(
+            "safety",
+            "check",
+            f"--file={os.path.join(tmpdirname, 'safety-check.out')}",
+            "--full-report",
+        )
 
 
-@nox.session(python=["3.8", "3.7"])
+@nox.session(python=python_versions)
 def mypy(session: Session) -> None:
     args = session.posargs or locations
     install_with_constraints(session, "mypy")
@@ -81,14 +90,18 @@ def coverage(session: Session) -> None:
 
 
 def install_with_constraints(session: Session, *args, **kwargs) -> None:
-    with tempfile.NamedTemporaryFile() as requirements:
+    with tempfile.TemporaryDirectory() as tmpdirname:
         session.run(
             "poetry",
             "export",
             "--dev",
             "--format=requirements.txt",
             "--without-hashes",
-            f"--output={requirements.name}",
+            f"--output={os.path.join(tmpdirname, 'poetry-export.out')}",
             external=True,
         )
-        session.install(f"--constraint={requirements.name}", *args, **kwargs)
+        session.install(
+            f"--constraint={os.path.join(tmpdirname, 'poetry-export.out')}",
+            *args,
+            **kwargs,
+        )

tests/conftest.py

@@ -1,9 +1,13 @@
 # tests/conftest.py
 
+import os
+
 import pytest
 
 from tests.store import acetylene, iridiumCatalyst, pyridine
 
+s = os.linesep
+
 
 @pytest.fixture(scope="session")
 def pyridine_xyz(tmpdir_factory):
@@ -48,3 +52,81 @@ def iridiumcat_xyz(tmpdir_factory):
     mol.writeMolecule(name=name, path=dn)
 
     return fn
+
+
+@pytest.fixture(scope="session")
+def fluoromethane_coord(tmpdir_factory):
+    fn = tmpdir_factory.mktemp("data").join("fluoromethane.coord")
+
+    with open(fn, mode="w+", encoding="utf-8") as f:
+        f.write("$coord" + s)
+        f.write("  1.87167924 -0.101043656  0.1596818582  c" + s)
+        f.write("  4.43543289 -0.101043656  0.1596818582  f" + s)
+        f.write("  1.20847986 -1.386321988  1.6312493924  h" + s)
+        f.write("  1.20847986 -0.732816897 -1.6891694984  h" + s)
+        f.write("  1.20846096  1.816007916  0.5369845779  h" + s)
+        f.write("$end")
+        f.flush()
+
+    return fn
+
+
+@pytest.fixture(scope="session")
+def lithium_hydride_coord(tmpdir_factory):
+    fn = tmpdir_factory.mktemp("data").join("lithium_hydride.coord")
+
+    with open(fn, mode="w+", encoding="utf-8") as f:
+        f.write("$coord" + s)
+        f.write("0 0 0 li" + s)
+        f.write("0 0 2 h" + s)
+        f.write("0 0 4 h" + s)
+        f.write("$end")
+        f.flush()
+
+    return fn
+
+
+@pytest.fixture(scope="session")
+def ch_coord(tmpdir_factory):
+    fn = tmpdir_factory.mktemp("data").join("ch.coord")
+
+    with open(fn, mode="w+", encoding="utf-8") as f:
+        f.write("$coord" + s)
+        f.write("0.00000000000000 0.00000000000000 -1.06176434496059 c" + s)
+        f.write("0.00000000000000 0.00000000000000  1.06176434496059 h" + s)
+        f.write("$end")
+        f.flush()
+
+    return fn
+
+
+@pytest.fixture(scope="session")
+def ch_coord_2(tmpdir_factory):
+    fn = tmpdir_factory.mktemp("data").join("ch-2.coord")
+
+    with open(fn, mode="w+", encoding="utf-8") as f:
+        f.write("test" + s)
+        f.write("test" + s)
+        f.write("$coord" + s)
+        f.write("0.00000000000000 0.00000000000000 -1.06176434496059 c" + s)
+        f.write("0.00000000000000 0.00000000000000  1.06176434496059 h" + s)
+        f.write("$end")
+        f.flush()
+
+    return fn
+
+
+@pytest.fixture(scope="session")
+def ch_coord_ignore(tmpdir_factory):
+    fn = tmpdir_factory.mktemp("data").join("ch_ignore.coord")
+
+    with open(fn, mode="w+", encoding="utf-8") as f:
+        f.write("test" + s)
+        f.write("$coord" + s)
+        f.write("0.00000000000000 0.00000000000000 -1.06176434496059 c" + s)
+        f.write("0.00000000000000 0.00000000000000  1.06176434496059 h" + s)
+        f.write("$end")
+        f.write("0.00000000000000 0.00000000000000  2.06176434496059 h" + s)
+        f.flush()
+
+    return fn

tests/test_molecule.py

@@ -1,7 +1,6 @@
 # tests/test_molecule.py
 
 import os
-import tempfile
 
 import numpy as np
 import pytest
@@ -20,41 +19,25 @@
 
 
 # turbomole coord files can be read
-def test_a_user_can_compute_coordination_numbers_for_molecule():
-    with tempfile.NamedTemporaryFile(mode="w+", encoding="utf-8") as f:
-        f.write("$coord" + s)
-        f.write("  1.87167924 -0.101043656  0.1596818582  c" + s)
-        f.write("  4.43543289 -0.101043656  0.1596818582  f" + s)
-        f.write("  1.20847986 -1.386321988  1.6312493924  h" + s)
-        f.write("  1.20847986 -0.732816897 -1.6891694984  h" + s)
-        f.write("  1.20846096  1.816007916  0.5369845779  h" + s)
-        f.write("$end")
-        f.flush()
-        fileObject = open(f.name, "r+")
-        atoms = ksr.read(fileObject)
-        molecule = Molecule(symbols=atoms)
-        cns = molecule.get_cns(cntype="exp")
-        c1 = np.around(cns, decimals=1)
-        got = c1[0]
-        want = 4.0
-        assert got == want
-
-
-def test_user_can_calculate_eeq_atomic_charges():
-    with tempfile.NamedTemporaryFile(mode="w+", encoding="utf-8") as f:
-        f.write("$coord" + s)
-        f.write("0 0 0 li" + s)
-        f.write("0 0 2 h" + s)
-        f.write("0 0 4 h" + s)
-        f.write("$end")
-        f.flush()
-        fileObject = open(f.name, "r+")
-        atoms = ksr.read(fileObject)
-        molecule = Molecule(symbols=atoms)
-        eeq = molecule.get_eeq(charge=0)
-        want = [0.51925854, -0.35007273, -0.16918582]
-        difference = sum([a - b for a, b in zip(want, eeq)])
-        assert difference < 1e-6
+def test_a_user_can_compute_coordination_numbers_for_molecule(fluoromethane_coord):
+    fileObject = open(fluoromethane_coord, "r+")
+    atoms = ksr.read(fileObject)
+    molecule = Molecule(symbols=atoms)
+    cns = molecule.get_cns(cntype="exp")
+    c1 = np.around(cns, decimals=1)
+    got = c1[0]
+    want = 4.0
+    assert got == want
+
+
+def test_user_can_calculate_eeq_atomic_charges(lithium_hydride_coord):
+    fileObject = open(lithium_hydride_coord, "r+")
+    atoms = ksr.read(fileObject)
+    molecule = Molecule(symbols=atoms)
+    eeq = molecule.get_eeq(charge=0)
+    want = [0.51925854, -0.35007273, -0.16918582]
+    difference = sum([a - b for a, b in zip(want, eeq)])
+    assert difference < 1e-6
 
 
 def test_user_can_pass_information_from_mol_to_mol():