acellera-openff-utilities 0.1.16__tar.gz

acellera_openff_utilities-0.1.16/LICENSE

@@ -0,0 +1,22 @@
+
+MIT License
+
+Copyright (c) 2021 The Open Force Field Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

acellera_openff_utilities-0.1.16/MANIFEST.in

@@ -0,0 +1,6 @@
+include LICENSE
+include MANIFEST.in
+include CODE_OF_CONDUCT.md
+
+graft openff
+global-exclude *.py[cod] __pycache__ *.so

acellera_openff_utilities-0.1.16/PKG-INFO

@@ -0,0 +1,28 @@
+Metadata-Version: 2.4
+Name: acellera-openff-utilities
+Version: 0.1.16
+Summary: A collection of miscellaneous utility functions used throughout the OpenFF stack
+Author-email: Open Force Field Initiative <info@openforcefield.org>
+License: MIT
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+openff-utilities
+==============================
+[//]: # (Badges)
+[![GitHub Actions Build Status](https://github.com/openforcefield/openff-utilities/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-utilities/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/openforcefield/openff-utilities/branch/main/graph/badge.svg)](https://codecov.io/gh/openforcefield/openff-utilities/branch/main)
+
+
+A collection of miscellaneous utility functions used throughout the OpenFF stack
+
+### Copyright
+
+Copyright (c) 2021, The Open Force Field Initiative
+
+
+#### Acknowledgements
+
+Project based on the
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.5.

acellera_openff_utilities-0.1.16/README.md

@@ -0,0 +1,18 @@
+openff-utilities
+==============================
+[//]: # (Badges)
+[![GitHub Actions Build Status](https://github.com/openforcefield/openff-utilities/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-utilities/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/openforcefield/openff-utilities/branch/main/graph/badge.svg)](https://codecov.io/gh/openforcefield/openff-utilities/branch/main)
+
+
+A collection of miscellaneous utility functions used throughout the OpenFF stack
+
+### Copyright
+
+Copyright (c) 2021, The Open Force Field Initiative
+
+
+#### Acknowledgements
+
+Project based on the
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.5.

acellera_openff_utilities-0.1.16/acellera_openff_utilities.egg-info/PKG-INFO

@@ -0,0 +1,28 @@
+Metadata-Version: 2.4
+Name: acellera-openff-utilities
+Version: 0.1.16
+Summary: A collection of miscellaneous utility functions used throughout the OpenFF stack
+Author-email: Open Force Field Initiative <info@openforcefield.org>
+License: MIT
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+openff-utilities
+==============================
+[//]: # (Badges)
+[![GitHub Actions Build Status](https://github.com/openforcefield/openff-utilities/workflows/CI/badge.svg)](https://github.com/openforcefield/openff-utilities/actions?query=workflow%3ACI)
+[![codecov](https://codecov.io/gh/openforcefield/openff-utilities/branch/main/graph/badge.svg)](https://codecov.io/gh/openforcefield/openff-utilities/branch/main)
+
+
+A collection of miscellaneous utility functions used throughout the OpenFF stack
+
+### Copyright
+
+Copyright (c) 2021, The Open Force Field Initiative
+
+
+#### Acknowledgements
+
+Project based on the
+[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.5.

acellera_openff_utilities-0.1.16/acellera_openff_utilities.egg-info/SOURCES.txt

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+LICENSE
+MANIFEST.in
+README.md
+pyproject.toml
+acellera_openff_utilities.egg-info/PKG-INFO
+acellera_openff_utilities.egg-info/SOURCES.txt
+acellera_openff_utilities.egg-info/dependency_links.txt
+acellera_openff_utilities.egg-info/top_level.txt
+devtools/scripts/assert_openeye_not_found.py
+docs/conf.py
+openff/utilities/__init__.py
+openff/utilities/exceptions.py
+openff/utilities/provenance.py
+openff/utilities/py.typed
+openff/utilities/testing.py
+openff/utilities/utilities.py
+openff/utilities/warnings.py
+openff/utilities/_tests/__init__.py
+openff/utilities/_tests/test_exceptions.py
+openff/utilities/_tests/test_provenance.py
+openff/utilities/_tests/test_star_import.py
+openff/utilities/_tests/test_testing_utilities.py
+openff/utilities/_tests/test_utilities.py
+openff/utilities/data/data.dat
+openff/utilities/data/more/more.dat

acellera_openff_utilities-0.1.16/acellera_openff_utilities.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

acellera_openff_utilities-0.1.16/acellera_openff_utilities.egg-info/top_level.txt

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+devtools
+docs
+openff

acellera_openff_utilities-0.1.16/devtools/scripts/assert_openeye_not_found.py

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+try:
+    from openeye import oechem
+
+    raise Exception("OpenEye Toolkits ARE installed")
+except ModuleNotFoundError:
+    pass

acellera_openff_utilities-0.1.16/docs/conf.py

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+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/stable/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+# Incase the project was not installed
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath(".."))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "openff-utilities"
+copyright = (
+    "2021, The Open Force Field Initiative. Project structure based on the "
+    "Computational Molecular Science Python Cookiecutter version 1.5"
+)
+author = "The Open Force Field Initiative"
+
+# The short X.Y version
+version = ""
+# The full version, including alpha/beta/rc tags
+release = ""
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autosummary",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.extlinks",
+]
+
+autosummary_generate = True
+napoleon_google_docstring = False
+napoleon_use_param = False
+napoleon_use_ivar = True
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "default"
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "openffdoc"
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, "openff.tex", "openff-utilities Documentation", "openff", "manual"),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "openff", "openff-utilities Documentation", [author], 1)]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "openff",
+        "openff-utilities Documentation",
+        author,
+        "openff",
+        "A collection of miscellaneous utility functions used throughout the OpenFF stack",
+        "Miscellaneous",
+    ),
+]
+
+
+# -- Extension configuration -------------------------------------------------

acellera_openff_utilities-0.1.16/openff/utilities/__init__.py

@@ -0,0 +1,30 @@
+from importlib.metadata import version
+
+from openff.utilities.exceptions import MissingOptionalDependencyError
+from openff.utilities.provenance import get_ambertools_version
+from openff.utilities.testing import skip_if_missing, skip_if_missing_exec
+from openff.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",
+)
+
+__version__ = version("openff.utilities")

acellera_openff_utilities-0.1.16/openff/utilities/_tests/test_exceptions.py

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

acellera_openff_utilities-0.1.16/openff/utilities/_tests/test_provenance.py

@@ -0,0 +1,54 @@
+import importlib
+
+import pytest
+
+from openff.utilities.provenance import (
+    _get_conda_list_package_versions,
+    get_ambertools_version,
+)
+from openff.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.")

acellera_openff_utilities-0.1.16/openff/utilities/_tests/test_star_import.py

@@ -0,0 +1 @@
+from openff.utilities import *  # noqa: F403

acellera_openff_utilities-0.1.16/openff/utilities/_tests/test_testing_utilities.py

@@ -0,0 +1,16 @@
+import pytest
+
+from openff.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="Bad type.*int"):
+        skip_if_missing_exec(0)

acellera_openff_utilities-0.1.16/openff/utilities/_tests/test_utilities.py

@@ -0,0 +1,181 @@
+import os
+
+import pytest
+
+from openff.utilities.exceptions import MissingOptionalDependencyError
+from openff.utilities.testing import skip_if_missing
+from openff.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.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.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.utilities")
+
+    # Test that a file directory raises NotaDirectoryError
+    with pytest.raises(NotADirectoryError):
+        get_data_dir_path("data/data.dat", package_name="openff.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.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.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.utilities")
+
+    # Test that a directory raises FileNotFoundError
+    with pytest.raises(FileNotFoundError):
+        get_data_file_path("data/", package_name="openff.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)

acellera_openff_utilities-0.1.16/openff/utilities/data/data.dat

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

acellera_openff_utilities-0.1.16/openff/utilities/exceptions.py

@@ -0,0 +1,52 @@
+class OpenFFError(BaseException):
+    """The base exception from which most custom exceptions in openff-utilities should inherit."""
+
+
+class MissingOptionalDependencyError(OpenFFError, ImportError):
+    """An exception raised when an optional dependency is required
+    but cannot be found.
+
+    Attributes
+    ----------
+    library_name
+        The name of the missing library.
+    license_issue
+        Whether the library was importable but was unusable due
+        to a missing license.
+    """
+
+    def __init__(self, library_name: str, license_issue: bool = False):
+        """
+
+        Parameters
+        ----------
+        library_name
+            The name of the missing library.
+        license_issue
+            Whether the library was importable but was unusable due
+            to a missing license.
+        """
+
+        message = f"The required {library_name} module could not be imported."
+
+        if license_issue:
+            message = f"{message} This is due to a missing license."
+
+        library_name_corrected = library_name.replace(".", "-")
+
+        if "openeye" not in library_name:
+            message = (
+                f"{message} Try installing the package by running "
+                f"`conda install -c conda-forge {library_name_corrected}`"
+            )
+
+        super().__init__(message)
+
+        self.library_name = library_name
+        self.license_issue = license_issue
+
+
+class CondaExecutableNotFoundError(OpenFFError):
+    """
+    A conda (or mamba/micromamba) executable is not found.
+    """

acellera_openff_utilities-0.1.16/openff/utilities/provenance.py

@@ -0,0 +1,66 @@
+import functools
+import json
+import os
+import subprocess
+import warnings
+from typing import Optional
+
+
+@functools.lru_cache
+def _get_conda_list_package_versions() -> dict[str, str]:
+    """
+    Returns the versions of any packages found while executing `conda list`.
+    If no conda executable is found, emits CondaExecutableNotFoundWarning
+    """
+    from openff.utilities.warnings import CondaExecutableNotFoundWarning
+
+    if os.environ.get("PIXI_IN_SHELL") == "1" and os.environ.get("PIXI_EXE"):
+        conda_command = "{} list --json --manifest-path {}".format(
+            os.environ["PIXI_EXE"], os.environ["PIXI_PROJECT_MANIFEST"]
+        )
+    elif os.environ.get("CONDA_SHLVL", "0") != "0" and os.environ.get("CONDA_EXE"):
+        conda_command = "{} list --json".format(os.environ["CONDA_EXE"])
+    elif os.environ.get("CONDA_SHLVL", "0") != "0" and os.environ.get("MAMBA_EXE"):
+        conda_command = "{} list --json".format(os.environ["MAMBA_EXE"])
+    else:
+        warnings.warn(
+            "No conda/mamba/micromamba executable found. Unable to determine package versions.",
+            CondaExecutableNotFoundWarning,
+        )
+        return dict()
+
+    output = json.loads(subprocess.check_output(conda_command.split()).decode())
+
+    package_versions = {}
+    for _package in output:
+        package_versions[_package["name"]] = _package["version"]
+
+    return package_versions
+
+
+def get_ambertools_version() -> Optional[str]:
+    """
+    Attempts to retrieve the version of the currently installed AmberTools.
+
+    There are two soft failure modes, each of which cause this function to return `None`:
+        1. If there is a failure calling `{conda|mamba|etc.} list`, the user is
+            warned by `_get_conda_list_package_versions` and this function returns `None`.
+        2. If there is a failure calling `{conda|mamba|etc.} list`, this function
+            still returns `None`, but without a warning associated with the above failure.
+    """
+
+    try:
+        return _get_conda_list_package_versions().get("ambertools", None)
+    except (
+        ValueError,  # Issue 98
+        subprocess.CalledProcessError,  # Issue 101
+    ):
+        from openff.utilities.warnings import CondaExecutableNotFoundWarning
+
+        warnings.warn(
+            "Something went wrong parsing the output of `conda list` or similar. Unable to "
+            "determine AmberTools version, returning None.",
+            CondaExecutableNotFoundWarning,
+        )
+
+        return None

acellera_openff_utilities-0.1.16/openff/utilities/testing.py

@@ -0,0 +1,54 @@
+from typing import TYPE_CHECKING, Optional, Union
+
+from openff.utilities.utilities import has_executable, has_package
+
+if TYPE_CHECKING:
+    from _pytest.mark.structures import MarkDecorator
+
+
+def skip_if_missing(package_name: str, reason: Optional[str] = None) -> "MarkDecorator":
+    """
+    Helper function to generate a pytest.mark.skipif decorator
+    for any package. This allows tests to be skipped if some
+    optional dependency is not found.
+
+    Parameters
+    ----------
+    package_name : str
+        The name of the package that is required for a test(s)
+    reason : str, optional
+        Explanation of why the skipped it to be tested
+
+    Returns
+    -------
+    requires_package : _pytest.mark.structures.MarkDecorator
+        A pytest decorator that will skip tests if the package is not available
+    """
+    import pytest
+
+    if not reason:
+        reason = f"Package {package_name} is required, but was not found."
+    requires_package = pytest.mark.skipif(not has_package(package_name), reason=reason)
+    return requires_package
+
+
+def skip_if_missing_exec(exec: Union[str, list[str]]) -> "MarkDecorator":
+    """Helper function to generate a pytest.mark.skipif decorator
+    if an executable(s) is not found."""
+    import pytest
+
+    execs: list[str]
+    if isinstance(exec, str):
+        execs = [exec]
+    elif isinstance(exec, list):
+        execs = exec
+    else:
+        raise ValueError(f"Bad type passed to skip_if_missing_exec. Found type {type(exec)}")
+
+    found_exec = False
+    for exec_ in execs:
+        found_exec = found_exec or has_executable(exec_)
+
+    reason = f"Package {exec!s} is required, but was not found."
+    mark = pytest.mark.skipif(not found_exec, reason=reason)
+    return mark

acellera_openff_utilities-0.1.16/openff/utilities/utilities.py

@@ -0,0 +1,261 @@
+import errno
+import importlib
+import os
+from collections.abc import Generator
+from contextlib import contextmanager
+from functools import wraps
+from importlib.resources import as_file, files
+from tempfile import TemporaryDirectory
+from typing import Any, Callable, Literal, Optional, TypeVar
+
+from openff.utilities.exceptions import MissingOptionalDependencyError
+
+# https://mypy.readthedocs.io/en/stable/generics.html#declaring-decorators
+
+F = TypeVar("F", bound=Callable[..., Any])
+
+
+def has_package(package_name: str) -> bool:
+    """
+    Helper function to generically check if a Python package is installed.
+    Intended to be used to check for optional dependencies.
+
+    Parameters
+    ----------
+    package_name : str
+        The name of the Python package to check the availability of
+
+    Returns
+    -------
+    package_available : bool
+        Boolean indicator if the package is available or not
+
+    Examples
+    --------
+    >>> has_numpy = has_package('numpy')
+    >>> has_numpy
+    True
+    >>> has_foo = has_package('other_non_installed_package')
+    >>> has_foo
+    False
+    """
+    try:
+        importlib.import_module(package_name)
+    except ModuleNotFoundError:
+        return False
+    return True
+
+
+def requires_package(package_name: str) -> Callable[..., Any]:
+    """
+    Helper function to denote that a funciton requires some optional
+    dependency. A function decorated with this decorator will raise
+    `MissingOptionalDependencyError` if the package is not found by
+    `importlib.import_module()`.
+
+    Parameters
+    ----------
+    package_name : str
+        The name of the module to be imported.
+
+    Raises
+    ------
+    MissingOptionalDependencyError
+
+    """
+
+    def inner_decorator(function: F) -> F:
+        @wraps(function)
+        def wrapper(*args, **kwargs):  # type: ignore[no-untyped-def]
+            import importlib
+
+            try:
+                importlib.import_module(package_name)
+            except ImportError:
+                raise MissingOptionalDependencyError(library_name=package_name)
+            except Exception as e:
+                raise e
+
+            return function(*args, **kwargs)
+
+        return wrapper  # type: ignore[return-value]
+
+    return inner_decorator
+
+
+def requires_oe_module(
+    module_name: Literal["oechem", "oeomega", "oequacpac", "oeiupac", "oedepict"],
+) -> Callable[..., Any]:
+    """
+    Helper function to denote that a funciton requires a particular OpenEye library.
+    A function decorated with this decorator will raise `MissingOptionalDependencyError` if
+    the module is not found by @requires_package or the module is not found to be
+    licensed.
+
+    Parameters
+    ----------
+    module_name : str
+        The name of the OpenEye module to be imported.
+
+    Raises
+    ------
+    MissingOptionalDependencyError
+    """
+
+    def inner_decorator(function: F) -> F:
+        @requires_package(f"openeye.{module_name}")
+        @wraps(function)
+        def wrapper(*args, **kwargs):  # type: ignore[no-untyped-def]
+            oe_module = importlib.import_module(f"openeye.{module_name}")
+
+            license_functions = {
+                "oechem": "OEChemIsLicensed",
+                "oequacpac": "OEQuacPacIsLicensed",
+                "oeiupac": "OEIUPACIsLicensed",
+                "oeomega": "OEOmegaIsLicensed",
+                "oedepict": "OEDepictIsLicensed",
+            }
+
+            is_licensed = getattr(oe_module, license_functions[module_name])()
+
+            if not is_licensed:
+                raise MissingOptionalDependencyError(library_name=f"openeye.{module_name}", license_issue=True)
+
+            return function(*args, **kwargs)
+
+        return wrapper  # type: ignore
+
+    return inner_decorator
+
+
+def has_executable(program_name: str) -> bool:
+    import os
+
+    def _is_executable(fpath: str) -> bool:
+        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+    fpath, fname = os.path.split(program_name)
+    if fpath:
+        if _is_executable(program_name):
+            return True
+    else:
+        for path in os.environ["PATH"].split(os.pathsep):
+            path = path.strip('"')
+            exe_file = os.path.join(path, program_name)
+            if _is_executable(exe_file):
+                return True
+
+    return False
+
+
+@contextmanager
+def temporary_cd(directory_path: Optional[str] = None) -> Generator[None, None, None]:
+    """Temporarily move the current working directory to the path
+    specified. If no path is given, a temporary directory will be
+    created, moved into, and then destroyed when the context manager
+    is closed.
+
+    Parameters
+    ----------
+    directory_path: str, optional
+
+    Returns
+    -------
+
+    """
+
+    if directory_path is not None and len(directory_path) == 0:
+        yield
+        return
+
+    old_directory = os.getcwd()
+
+    try:
+        if directory_path is None:
+            with TemporaryDirectory() as new_directory:
+                os.chdir(new_directory)
+                yield
+
+        else:
+            os.chdir(directory_path)
+            yield
+
+    finally:
+        os.chdir(old_directory)
+
+
+def get_data_dir_path(relative_path: str, package_name: str) -> str:
+    """Get the full path to a directory within a module's tree.
+
+    If no directory is found at `relative_path`, a second attempt will be made
+    with `data/` preprended. If no directory is found at path, a NotADirectoryError
+    is raised.
+
+    Parameters
+    ----------
+    relative_path : str
+        The relative path of the file to load.
+    package_name : str
+        The name of the package in which a file is to be loaded, i.e. "openff.toolkit" or "openff.evaluator".
+
+    Returns
+    -------
+        The absolute path to the file.
+
+    Raises
+    ------
+    NotADirectoryError
+
+    See Also
+    --------
+    get_data_file_path, for getting the path to a particular file in a data directory.
+
+    """
+    with as_file(files(package_name) / relative_path) as dir_path:
+        if dir_path.is_dir():
+            return dir_path.as_posix()
+
+    with as_file(files(package_name) / "data" / relative_path) as dir_path:
+        if dir_path.is_dir():
+            return dir_path.as_posix()
+
+    raise NotADirectoryError(f"Directory {relative_path} not found in {package_name}.")
+
+
+def get_data_file_path(relative_path: str, package_name: str) -> str:
+    """Get the full path to one of the files in the data directory.
+
+    If no file is found at `relative_path`, a second attempt will be made
+    with `data/` preprended. If no files exist at either path, a FileNotFoundError
+    is raised.
+
+    Parameters
+    ----------
+    relative_path : str
+        The relative path of the file to load.
+    package_name : str
+        The name of the package in which a file is to be loaded, i.e.
+        "openff.toolkit" or "openff.evaluator"
+
+    Returns
+    -------
+        The absolute path to the file.
+
+    Raises
+    ------
+    FileNotFoundError
+
+    See Also
+    --------
+    get_data_dir_path, for getting the path to a directory instead of an individual file.
+
+    """
+    with as_file(files(package_name) / relative_path) as file_path:
+        if file_path.is_file():
+            return file_path.as_posix()
+
+    with as_file(files(package_name) / "data" / relative_path) as file_path:
+        if file_path.is_file():
+            return file_path.as_posix()
+
+    raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), file_path)

acellera_openff_utilities-0.1.16/openff/utilities/warnings.py

@@ -0,0 +1,4 @@
+class CondaExecutableNotFoundWarning(UserWarning):
+    """
+    A conda (or mamba/micromamba) executable is not found.
+    """

acellera_openff_utilities-0.1.16/pyproject.toml

@@ -0,0 +1,85 @@
+[build-system]
+requires = [
+    "setuptools",
+    "versioningit",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "acellera-openff-utilities"
+description = "A collection of miscellaneous utility functions used throughout the OpenFF stack"
+readme = "README.md"
+authors = [{name = "Open Force Field Initiative", email = "info@openforcefield.org"}]
+license = {text = "MIT"}
+dynamic = ["version"]
+
+[tool.setuptools.packages]
+find = {}
+
+[tool.versioningit]
+
+[tool.ruff]
+line-length = 119
+namespace-packages = ["openff/utilities/"]
+
+[tool.ruff.lint]
+select = ["F", "E", "W", "NPY", "UP", "RUF", "I"]
+
+[tool.ruff.lint.per-file-ignores]
+"openff/utilities/__init__.py" = ["F401"]
+
+[tool.mypy]
+exclude="openff/utilities/_tests"
+python_version = "3.12"
+warn_unused_configs = true
+warn_unused_ignores = true
+show_error_codes = true
+strict = true
+
+[tool.pytest.ini_options]
+markers = [
+    "leaky: run leaky tests",
+]
+addopts = "--cov=openff/utilities --cov-report=xml -m \"not leaky\""
+
+[tool.coverage.run]
+omit = [
+    "*/*/_tests/*",
+]
+
+[tool.coverage.report]
+exclude_lines = [
+    "pragma: no cover",
+    "if TYPE_CHECKING:",
+    "raise NotImplementedError",
+    "@overload",
+]
+
+[tool.pixi.project]
+channels = ["conda-forge", "openeye"]
+platforms = ["linux-64", "osx-64", "osx-arm64"]
+
+[tool.pixi.dependencies]
+python = "*"
+pip = "*"
+versioningit = "*"
+pytest = "*"
+pytest-cov = "*"
+pytest-xdist = "*"
+pytest-randomly = "*"
+nbval = "*"
+mypy = "*"
+types-setuptools = "*"
+types-toml = "*"
+
+[tool.pixi.pypi-dependencies]
+openff-utilities = { path = ".", editable = true }
+
+[tool.pixi.feature.py311.dependencies]
+python = "3.11.*"
+[tool.pixi.feature.py312.dependencies]
+python = "3.12.*"
+
+[tool.pixi.environments]
+py311 = ["py311"]
+py312 = ["py312"]

acellera_openff_utilities-0.1.16/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+