Add unit tests for dic2owl CLI

.gitignore

@@ -10,3 +10,4 @@ __pycache__
 *.cif
 
 !test-cif/**/*.cif
+!tests/**/*.dic

dic2owl/requirements_dev.txt

@@ -2,3 +2,5 @@ bandit~=1.7.0
 mypy==0.910
 pre-commit>=2.14.0,<3
 pylint>=2.10.1,<3
+pytest>=6.2.4,<7
+pytest-cov>=2.12.1,<3

tests/dic2owl/conftest.py

@@ -0,0 +1,149 @@
+"""PyTest fixtures for `dic2owl`."""
+# pylint: disable=import-outside-toplevel,consider-using-with,too-many-branches
+# pylint: disable=redefined-outer-name,inconsistent-return-statements
+from enum import Enum
+from pathlib import Path
+from typing import List, Optional, TYPE_CHECKING, Union
+
+import pytest
+
+
+class CLI(Enum):
+    """Enumeration of CLIs."""
+
+    CIF2OWL = "cif2owl"
+    DIC2OWL = "dic2owl"
+
+
+if TYPE_CHECKING:
+    from subprocess import CompletedProcess
+    from typing import Callable
+
+    CLIRunner = Callable[
+        [
+            Optional[List[str]],
+            Optional[Union[CLI, str]],
+            Optional[str],
+            Optional[Union[Path, str]],
+        ],
+        CompletedProcess,
+    ]
+
+
+@pytest.fixture(scope="session")
+def clirunner() -> "CLIRunner":
+    """Call `dic2owl` CLI"""
+    from subprocess import run, CalledProcessError
+    from tempfile import TemporaryDirectory
+
+    def _clirunner(
+        options: Optional[List[str]] = None,
+        cli: Optional[Union[CLI, str]] = None,
+        expected_error: Optional[str] = None,
+        run_dir: Optional[Union[Path, str]] = None,
+    ) -> Union["CompletedProcess", CalledProcessError]:
+        """Call `dic2owl` CLI
+
+        Parameters:
+            options: Options with which to call `cli`, e.g., `--version`.
+            cli: The CLI to call, defaults to `dic2owl`.
+            expected_error: Sub-string expected in error output, if an error is
+                expected.
+            run_dir: The directory to use as current work directory when
+                running the CLI.
+
+        Returns:
+            The return class for a successful call to `subprocess.run()`.
+
+        """
+        options = options or []
+
+        if not isinstance(options, list):
+            try:
+                options = list(options)
+            except TypeError as exc:
+                raise TypeError("options must be a list of strings.") from exc
+
+        if cli is not None:
+            try:
+                cli = CLI(cli)
+            except ValueError as exc:
+                raise ValueError(
+                    f"{cli!r} is not a recognized CLI. Recognized CLIs: "
+                    f"{list(CLI.__members__)}"
+                ) from exc
+        else:
+            cli = CLI.DIC2OWL
+
+        if run_dir is None:
+            run_dir = TemporaryDirectory()
+        elif isinstance(run_dir, Path):
+            run_dir = run_dir.resolve()
+        else:
+            try:
+                run_dir = Path(run_dir).resolve()
+            except TypeError as exc:
+                raise TypeError(f"{run_dir} is not a valid path.") from exc
+
+        try:
+            output = run(
+                args=[cli.value] + options,
+                capture_output=True,
+                check=True,
+                cwd=run_dir.name
+                if isinstance(run_dir, TemporaryDirectory)
+                else run_dir,
+                text=True,
+            )
+            if expected_error:
+                pytest.fail(
+                    "Expected the CLI call to fail with an error containing "
+                    f"the sub-string: {expected_error}"
+                )
+        except CalledProcessError as error:
+            if expected_error:
+                if (
+                    expected_error in error.stdout
+                    or expected_error in error.stderr
+                ):
+                    # Expected error, found expected sub-string as well.
+                    return error
+
+                pytest.fail(
+                    "The CLI call failed as expected, but the expected "
+                    "error sub-string could not be found in stdout or "
+                    f"stderr. Sub-string: {expected_error}"
+                )
+            else:
+                pytest.fail(
+                    "The CLI call failed when it didn't expect to.\n"
+                    f"Information: {error}"
+                )
+        else:
+            return output
+        finally:
+            if isinstance(run_dir, TemporaryDirectory):
+                run_dir.cleanup()
+
+    return _clirunner
+
+
+@pytest.fixture(scope="session")
+def top_dir() -> Path:
+    """Return repository path."""
+    return Path(__file__).parent.parent.parent.resolve()
+
+
+@pytest.fixture(scope="session")
+def cif_ttl(top_dir: Path) -> str:
+    """Read and return CIF-Core minimized Turtle file (generated from the
+    accompanying dictionary).
+
+    NOTE: The commend conerning the file location has been removed manually
+        from this file.
+    """
+    with open(
+        top_dir / "tests/dic2owl/static/cif_core_minimized.ttl", "r"
+    ) as handle:
+        content = handle.read()
+    return content

tests/dic2owl/static/cif_core_minimized.dic

@@ -0,0 +1,185 @@
+#\#CIF_2.0
+##########################################################################
+#                                                                        #
+#  CIF CORE DICTIONARY                                                   #
+#                                                                        #
+##########################################################################
+
+data_CORE_DIC
+
+    _dictionary.title             CORE_DIC
+    _dictionary.class             Instance
+    _dictionary.version           3.1.0
+    _dictionary.date              2021-08-18
+    _dictionary.uri
+        https://raw.githubusercontent.com/COMCIFS/cif_core/master/cif_core.dic
+    _dictionary.ddl_conformance   4.0.1
+    _dictionary.namespace         CifCore
+    _description.text
+;
+    The CIF_CORE dictionary records all the CORE data items defined
+    and used with in the Crystallographic Information Framework (CIF).
+;
+
+save_CIF_CORE
+
+    _definition.id                CIF_CORE
+    _definition.scope             Category
+    _definition.class             Head
+    _definition.update            2014-06-18
+    _description.text
+;
+    The CIF_CORE group contains the definitions of data items that
+    are common to all domains of crystallographic studies.
+;
+    _name.category_id             CORE_DIC
+    _name.object_id               CIF_CORE
+
+save_
+
+save_DIFFRACTION
+
+    _definition.id                DIFFRACTION
+    _definition.scope             Category
+    _definition.class             Set
+    _definition.update            2012-11-26
+    _description.text
+;
+    The DICTIONARY group encompassing the CORE DIFFRACTION data items defined
+    and used with in the Crystallographic Information Framework (CIF).
+;
+    _name.category_id             CIF_CORE
+    _name.object_id               DIFFRACTION
+
+save_
+
+save_DIFFRN
+
+    _definition.id                DIFFRN
+    _definition.scope             Category
+    _definition.class             Set
+    _definition.update            2012-12-13
+    _description.text
+;
+    The CATEGORY of data items used to describe the diffraction experiment.
+;
+    _name.category_id             DIFFRACTION
+    _name.object_id               DIFFRN
+
+save_
+
+save_diffrn.ambient_environment
+
+    _definition.id                '_diffrn.ambient_environment'
+    _alias.definition_id          '_diffrn_ambient_environment'
+    _definition.update            2012-11-26
+    _description.text
+;
+    The gas or liquid environment of the crystal sample, if not air.
+;
+    _name.category_id             diffrn
+    _name.object_id               ambient_environment
+    _type.purpose                 Describe
+    _type.source                  Recorded
+    _type.container               Single
+    _type.contents                Text
+
+    loop_
+      _description_example.case
+         'He'
+         'vacuum'
+         'mother liquor'
+
+save_
+
+save_diffrn.ambient_pressure
+
+    _definition.id                '_diffrn.ambient_pressure'
+    _alias.definition_id          '_diffrn_ambient_pressure'
+    _definition.update            2012-11-26
+    _description.text
+;
+    Mean hydrostatic  pressure at which intensities were measured.
+;
+    _name.category_id             diffrn
+    _name.object_id               ambient_pressure
+    _type.purpose                 Measurand
+    _type.source                  Recorded
+    _type.container               Single
+    _type.contents                Real
+    _enumeration.range            0.0:
+    _units.code                   kilopascals
+
+save_
+
+save_diffrn.ambient_pressure_su
+
+    _definition.id                '_diffrn.ambient_pressure_su'
+
+    loop_
+      _alias.definition_id
+         '_diffrn_ambient_pressure_su'
+         '_diffrn.ambient_pressure_esd'
+
+    _definition.update            2021-03-03
+    _description.text
+;
+    Standard uncertainty of the mean hydrostatic pressure
+    at which intensities were measured.
+;
+    _name.category_id             diffrn
+    _name.object_id               ambient_pressure_su
+    _name.linked_item_id          '_diffrn.ambient_pressure'
+    _type.purpose                 SU
+    _type.source                  Recorded
+    _type.container               Single
+    _type.contents                Real
+    _units.code                   kilopascals
+
+save_
+
+save_diffrn.ambient_pressure_gt
+
+    _definition.id                '_diffrn.ambient_pressure_gt'
+    _alias.definition_id          '_diffrn_ambient_pressure_gt'
+    _definition.update            2012-12-13
+    _description.text
+;
+    Mean hydrostatic pressure above which intensities were measured.
+    These items allow for a pressure range to be given.
+    _diffrn.ambient_pressure should be used in preference to this
+    item when possible.
+;
+    _name.category_id             diffrn
+    _name.object_id               ambient_pressure_gt
+    _type.purpose                 Number
+    _type.source                  Recorded
+    _type.container               Single
+    _type.contents                Real
+    _enumeration.range            0.0:
+    _units.code                   kilopascals
+
+save_
+
+save_diffrn.ambient_pressure_lt
+
+    _definition.id                '_diffrn.ambient_pressure_lt'
+    _alias.definition_id          '_diffrn_ambient_pressure_lt'
+    _definition.update            2012-12-13
+    _description.text
+;
+    Mean hydrostatic pressure below which intensities were measured.
+    These items allow for a pressure range to be given.
+    _diffrn.ambient_pressure should be used in preference to this
+    item when possible.
+;
+    _name.category_id             diffrn
+    _name.object_id               ambient_pressure_lt
+    _type.purpose                 Number
+    _type.source                  Recorded
+    _type.container               Single
+    _type.contents                Real
+    _enumeration.range            0.0:
+    _units.code                   kilopascals
+
+save_