Merge utilities package

devtools/conda-envs/openeye-examples.yaml

@@ -16,7 +16,6 @@ dependencies:
   - openff-forcefields >=2023.11
   - openff-amber-ff-ports >=0.0.3
   - openff-units
-  - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
   - openff-nagl-base >=0.4.0
   - openff-nagl-models >=0.3.0

devtools/conda-envs/openeye.yaml

@@ -16,7 +16,6 @@ dependencies:
   - openff-forcefields >=2023.05.1
   - openff-units
   - openff-amber-ff-ports
-  - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
   - openff-nagl-base =0.4.0
   - openff-nagl-models >=0.3.0

devtools/conda-envs/rdkit-examples.yaml

@@ -15,7 +15,6 @@ dependencies:
   - openff-forcefields >=2023.11
   - openff-amber-ff-ports >=0.0.3
   - openff-units
-  - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
   - openff-nagl-base >=0.4.0
   - openff-nagl-models >=0.3.0

devtools/conda-envs/rdkit.yaml

@@ -15,7 +15,6 @@ dependencies:
   - openff-forcefields >=2023.05.1
   - openff-units
   - openff-amber-ff-ports
-  - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
   - openff-nagl-base >=0.4.0
   - openff-nagl-models >=0.3.0

devtools/conda-envs/test_env.yaml

@@ -16,7 +16,6 @@ dependencies:
   - openff-forcefields >=2023.05.1
   - openff-units
   - openff-amber-ff-ports
-  - openff-utilities >=0.1.5
   - openff-interchange-base >=0.5
   - openff-nagl-base >=0.4.0
   - openff-nagl-models >=0.3.0

docs/environment.yml

@@ -23,7 +23,6 @@ dependencies:
     - ambertools
     - packaging
     - openff-units
-    - openff-utilities
     - cachetools
     - python-constraint
     - mdtraj

openff/toolkit/_tests/test_interchange.py

@@ -1,6 +1,6 @@
 import pytest
-from openff.utilities import requires_package as requires_pkg
 
+from openff.toolkit._utilities import requires_package as requires_pkg
 from openff.toolkit.topology import Molecule
 from openff.toolkit.typing.engines.smirnoff.forcefield import ForceField
 

openff/toolkit/_tests/test_nagl.py

@@ -3,7 +3,6 @@
 
 import numpy
 import pytest
-from openff.utilities import has_package, skip_if_missing
 
 from openff.toolkit import Molecule, unit
 from openff.toolkit._tests.create_molecules import (
@@ -14,6 +13,7 @@
     create_reversed_ethanol,
 )
 from openff.toolkit._tests.utils import requires_openeye
+from openff.toolkit._utilities import has_package, skip_if_missing
 from openff.toolkit.utils import GLOBAL_TOOLKIT_REGISTRY
 from openff.toolkit.utils.exceptions import (
     ToolkitUnavailableException,

openff/toolkit/_tests/test_topology.py

@@ -16,7 +16,6 @@
 import openmm.unit
 import pytest
 from openff.units.openmm import from_openmm
-from openff.utilities import skip_if_missing
 
 from openff.toolkit import Molecule, Quantity, Topology, unit
 from openff.toolkit._tests.create_molecules import (
@@ -41,6 +40,7 @@
     requires_pkg,
     requires_rdkit,
 )
+from openff.toolkit._utilities import skip_if_missing
 from openff.toolkit.topology import (
     Atom,
     ImproperDict,

openff/toolkit/_tests/test_utilities/test_exceptions.py

@@ -0,0 +1,17 @@
+import pytest
+
+from openff.toolkit._utilities.exceptions import MissingOptionalDependencyError, OpenFFError
+
+
+def test_exceptions():
+    with pytest.raises(
+        MissingOptionalDependencyError,
+        match=r"The required foobar module could not be imported.*Try installing.*conda-forge.*",
+    ):
+        raise MissingOptionalDependencyError(library_name="foobar")
+
+    with pytest.raises(MissingOptionalDependencyError, match=r".*barbaz.*missing license."):
+        raise MissingOptionalDependencyError(library_name="barbaz", license_issue=True)
+
+    with pytest.raises(OpenFFError):
+        raise MissingOptionalDependencyError("numpy")

openff/toolkit/_tests/test_utilities/test_provenance.py

@@ -0,0 +1,54 @@
+import importlib
+
+import pytest
+
+from openff.toolkit._utilities.provenance import (
+    _get_conda_list_package_versions,
+    get_ambertools_version,
+)
+from openff.toolkit._utilities.warnings import CondaExecutableNotFoundWarning
+
+
+def mock_has_executable(executable_name: str) -> bool:
+    return False
+
+
+@pytest.mark.leaky
+def test_conda_unavailable_returns_empty_dict(monkeypatch):
+    """
+    Test that if `conda|etc. list` fails, with or without AmberTools (properly) installed,
+    get_ambertools_version returns `None`.
+
+    This test leaks! Do not run it alongside other tests! Select either it "pytest -m leaky"
+    or avoid it "pytest -m 'not leaky'"
+    """
+    with (
+        monkeypatch.context() as m,
+        pytest.warns(CondaExecutableNotFoundWarning, match="No .* executable found"),
+    ):
+        m.setenv("PIXI_IN_SHELL", "0")
+        m.setenv("CONDA_SHLVL", "0")
+
+        assert _get_conda_list_package_versions() == dict()
+
+
+def test_conda_available_get_ambertools_version_found():
+    # Skip if ambertools is not installed - sander would a better import test
+    # for AmberTools (since parmed could come from the standalone
+    # parmed package), however it's currently broken on ARM macs.
+    pytest.importorskip("parmed")
+
+    assert get_ambertools_version() is not None, (
+        f"note that len of package versions is {len(_get_conda_list_package_versions())}"
+    )
+
+
+def test_conda_available_get_ambertools_version_not_found():
+    try:
+        importlib.import_module("parmed")
+    except ImportError:
+        assert len(_get_conda_list_package_versions()) > 0
+        assert get_ambertools_version() is None
+        return
+
+    pytest.skip("only run when ambertools is not installed.")

openff/toolkit/_tests/test_utilities/test_testing_utilities.py

@@ -0,0 +1,16 @@
+import pytest
+
+from openff.toolkit._utilities.testing import skip_if_missing, skip_if_missing_exec
+
+
+def test_skips():
+    assert not skip_if_missing("pip").args[0]
+    assert skip_if_missing("numpynumpy").args[0]
+
+    assert not skip_if_missing_exec("python").args[0]
+    assert skip_if_missing_exec("python4").args[0]
+    assert not skip_if_missing_exec(["python", "python4"]).args[0]
+    assert skip_if_missing_exec(["python4", "python5"]).args[0]
+
+    with pytest.raises(ValueError, match=r"Bad type.*int"):
+        skip_if_missing_exec(0)

openff/toolkit/_tests/test_utilities/test_utilities.py

@@ -0,0 +1,181 @@
+import os
+
+import pytest
+
+from openff.toolkit._utilities.exceptions import MissingOptionalDependencyError
+from openff.toolkit._utilities.testing import skip_if_missing
+from openff.toolkit._utilities.utilities import (
+    get_data_dir_path,
+    get_data_file_path,
+    has_executable,
+    has_package,
+    requires_oe_module,
+    requires_package,
+    temporary_cd,
+)
+
+
+def compare_paths(path_1: str, path_2: str) -> bool:
+    """Checks whether two paths are the same.
+
+    Parameters
+    ----------
+    path_1
+        The first path.
+    path_2
+        The second path.
+
+    Returns
+    -------
+    True if the paths are equivalent.
+    """
+    return os.path.normpath(path_1) == os.path.normpath(path_2)
+
+
+def test_get_data_dir_path():
+    """Tests that the `get_data_dir_path` can correctly find
+    data directories.
+    """
+
+    # Test a path which should exist.
+    data_file_path = get_data_dir_path("data/more", package_name="openff.toolkit._utilities")
+    assert os.path.isdir(data_file_path)
+
+    # Ensure a double-checking through data/ takes place
+    data_file_path = get_data_dir_path("more", package_name="openff.toolkit._utilities")
+    assert os.path.isdir(data_file_path)
+
+    # Test a path which should not exist.
+    with pytest.raises(NotADirectoryError):
+        get_data_dir_path("missing", package_name="openff.toolkit._utilities")
+
+    # Test that a file directory raises NotaDirectoryError
+    with pytest.raises(NotADirectoryError):
+        get_data_dir_path("data/data.dat", package_name="openff.toolkit._utilities")
+
+
+def test_get_data_file_path():
+    """Tests that the `get_data_file_path` can correctly find
+    data files.
+    """
+
+    # Test a path which should exist.
+    data_file_path = get_data_file_path("data/data.dat", package_name="openff.toolkit._utilities")
+    assert os.path.isfile(data_file_path)
+
+    # Ensure a double-checking through data/ takes place
+    data_file_path = get_data_file_path("data.dat", package_name="openff.toolkit._utilities")
+    assert os.path.isfile(data_file_path)
+
+    # Test a path which should not exist.
+    with pytest.raises(FileNotFoundError):
+        get_data_file_path("missing.file", package_name="openff.toolkit._utilities")
+
+    # Test that a directory raises FileNotFoundError
+    with pytest.raises(FileNotFoundError):
+        get_data_file_path("data/", package_name="openff.toolkit._utilities")
+
+
+def test_temporary_cd():
+    """Tests that temporary cd works as expected"""
+
+    original_directory = os.getcwd()
+
+    # Move to the parent directory
+    with temporary_cd(os.pardir):
+        current_directory = os.getcwd()
+        expected_directory = os.path.abspath(os.path.join(original_directory, os.pardir))
+
+        assert compare_paths(current_directory, expected_directory)
+
+    assert compare_paths(os.getcwd(), original_directory)
+
+    # Move to a temporary directory
+    with temporary_cd():
+        assert not compare_paths(os.getcwd(), original_directory)
+
+    assert compare_paths(os.getcwd(), original_directory)
+
+    # Move to the same directory
+    with temporary_cd(""):
+        assert compare_paths(os.getcwd(), original_directory)
+
+    assert compare_paths(os.getcwd(), original_directory)
+
+    with temporary_cd(os.curdir):
+        assert compare_paths(os.getcwd(), original_directory)
+
+    assert compare_paths(os.getcwd(), original_directory)
+
+
+def test_has_package():
+    assert has_package("os")
+    assert has_package("pytest")
+    assert not has_package("nummmmmmpy")
+
+
+def test_has_executable():
+    assert has_executable("pwd")
+    assert has_executable("pytest")
+
+    assert has_executable("/usr/bin/whoami")
+
+    assert not has_package("pyyyyython")
+
+
+def test_requires_package():
+    """Tests that the ``requires_package`` utility behaves as expected."""
+
+    def dummy_function():
+        pass
+
+    # sys should always be found so this should not raise an exception.
+    requires_package("sys")(dummy_function)()
+
+    with pytest.raises(MissingOptionalDependencyError) as error_info:
+        requires_package("fake-lib")(dummy_function)()
+
+    assert error_info.value.library_name == "fake-lib"
+
+
+@skip_if_missing("openeye.oechem")
+@pytest.mark.skipif("OE_LICENSE" not in os.environ, reason="Requires an OpenEye license is NOT set up")
+def test_requires_oe_module():
+    """Tests that the ``requires_package`` utility behaves as expected when an OpenEye license is set up."""
+
+    def dummy_function():
+        pass
+
+    requires_oe_module("oechem")(dummy_function)()
+
+
+@pytest.mark.parametrize("oe_module", ["oechem", "oeiupac", "oeomega", "oequacpac", "oedepict"])
+@skip_if_missing("openeye")
+@pytest.mark.skipif("OE_LICENSE" in os.environ, reason="Requires an OpenEye license is NOT set up")
+def test_requires_oe_module_installed_missing_license(oe_module):
+    """Tests that the ``requires_package`` utility behaves as expected while OpenEye toolkits are
+    installed but no OpenEye license is set up."""
+
+    def dummy_function():
+        pass
+
+    with pytest.raises(MissingOptionalDependencyError) as error_info:
+        requires_oe_module(oe_module)(dummy_function)()
+
+    assert oe_module in str(error_info.value)
+    assert "conda-forge" not in str(error_info.value)
+
+
+@pytest.mark.skipif(has_package("openeye.oechem"), reason="Requires OpenEye toolkits are NOT installed")
+def test_requires_oe_module_not_installed():
+    """Tests that the ``requires_package`` utility behaves as expected while OpenEye toolkits are
+    installed."""
+
+    def dummy_function():
+        pass
+
+    with pytest.raises(MissingOptionalDependencyError) as error_info:
+        requires_oe_module("oechem")(dummy_function)()
+
+    assert "oechem" in str(error_info.value)
+    assert "conda-forge" not in str(error_info.value)

openff/toolkit/_tests/test_utils_serialization.py

@@ -5,8 +5,8 @@
 
 import numpy as np
 import pytest
-from openff.utilities import requires_package as requires_pkg
 
+from openff.toolkit._utilities import requires_package as requires_pkg
 from openff.toolkit.utils.serialization import Serializable
 from openff.toolkit.utils.utils import deserialize_numpy, serialize_numpy
 

openff/toolkit/_utilities/__init__.py

@@ -0,0 +1,26 @@
+from openff.toolkit._utilities.exceptions import MissingOptionalDependencyError
+from openff.toolkit._utilities.provenance import get_ambertools_version
+from openff.toolkit._utilities.testing import skip_if_missing, skip_if_missing_exec
+from openff.toolkit._utilities.utilities import (
+    get_data_dir_path,
+    get_data_file_path,
+    has_executable,
+    has_package,
+    requires_oe_module,
+    requires_package,
+    temporary_cd,
+)
+
+__all__ = (
+    "MissingOptionalDependencyError",
+    "get_ambertools_version",
+    "get_data_dir_path",
+    "get_data_file_path",
+    "has_executable",
+    "has_package",
+    "requires_oe_module",
+    "requires_package",
+    "skip_if_missing",
+    "skip_if_missing_exec",
+    "temporary_cd",
+)

openff/toolkit/_utilities/data/data.dat

@@ -0,0 +1,2 @@
+1 0
+0 1