Merge branch 'main' into add-types-module

.github/workflows/ci.yml

@@ -38,6 +38,8 @@ jobs:
       with:
         parallel: true
         flag-name: run-${{ matrix.python-version }}
+        file: coverage.xml
+        base-path: janus_core
 
   coverage:
     needs: tests

.gitignore

@@ -2,6 +2,7 @@
 *.pyc
 *.swo
 *.swp
+*.xml
 ~*
 *~
 .project

docs/Makefile

@@ -29,7 +29,7 @@ customdefault:
 all: html
 
 clean:
-	rm -r $(BUILDDIR)
+	rm -rf $(BUILDDIR)
 
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html

docs/source/apidoc/janus_core.rst

@@ -1,9 +1,29 @@
 janus\_core package
 ===================
 
+Module contents
+---------------
+
+.. automodule:: janus_core
+   :members:
+   :special-members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 ----------
 
+janus\_core.cli module
+----------------------
+
+.. automodule:: janus_core.cli
+   :members:
+   :special-members:
+   :private-members:
+   :undoc-members:
+   :show-inheritance:
+
 janus\_core.geom\_opt module
 ----------------------------
 
@@ -43,13 +63,3 @@ janus\_core.single\_point module
    :private-members:
    :undoc-members:
    :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: janus_core
-   :members:
-   :special-members:
-   :private-members:
-   :undoc-members:
-   :show-inheritance:

docs/source/conf.py

@@ -187,49 +187,6 @@
 
 # Warnings to ignore when using the -n (nitpicky) option
 # We should ignore any python built-in exception, for instance
-nitpick_ignore = [("py:class", "Logger"), ("py:class", "numpy.float64")]
-
-
-def run_apidoc(_):
-    """Runs sphinx-apidoc when building the documentation.
-
-    Needs to be done in conf.py in order to include the APIdoc in the
-    build on readthedocs.
-
-    See also https://github.com/rtfd/readthedocs.org/issues/1139
-    """
-    source_dir = os.path.abspath(os.path.dirname(__file__))
-    apidoc_dir = os.path.join(source_dir, "apidoc")
-    package_dir = os.path.join(source_dir, os.pardir, os.pardir, "janus_core")
-
-    # In #1139, they suggest the route below, but this ended up
-    # calling sphinx-build, not sphinx-apidoc
-    # from sphinx.apidoc import main
-    # main([None, '-e', '-o', apidoc_dir, package_dir, '--force'])
-
-    import subprocess
-
-    cmd_path = "sphinx-apidoc"
-    if hasattr(sys, "real_prefix"):  # Check to see if we are in a virtualenv
-        # If we are, assemble the path manually
-        cmd_path = os.path.abspath(os.path.join(sys.prefix, "bin", "sphinx-apidoc"))
-
-    options = [
-        "-o",
-        apidoc_dir,
-        package_dir,
-        "--private",
-        "--force",
-        "--no-toc",
-    ]
-
-    # See https://stackoverflow.com/a/30144019
-    env = os.environ.copy()
-    env["SPHINX_APIDOC_OPTIONS"] = (
-        "members,special-members,private-members,undoc-members,show-inheritance"
-    )
-    subprocess.check_call([cmd_path] + options, env=env)
-
-
-def setup(app):
-    app.connect("builder-inited", run_apidoc)
+nitpick_ignore = [
+    ("py:class", "Logger"),
+]

janus_core/cli.py

@@ -0,0 +1,144 @@
+"""Set up commandline interface."""
+
+import ast
+from typing import Annotated
+
+import typer
+
+from janus_core.single_point import SinglePoint
+
+app = typer.Typer()
+
+
+class TyperDict:  #  pylint: disable=too-few-public-methods
+    """
+    Custom dictionary for typer.
+
+    Parameters
+    ----------
+    value : str
+        Value of string representing a dictionary.
+    """
+
+    def __init__(self, value: str):
+        """
+        Initialise class.
+
+        Parameters
+        ----------
+        value : str
+            Value of string representing a dictionary.
+        """
+        self.value = value
+
+    def __str__(self):
+        """
+        String representation of class.
+
+        Returns
+        -------
+        str
+            Class name and value of string representing a dictionary.
+        """
+        return f"<TyperDict: value={self.value}>"
+
+
+def parse_dict_class(value: str):
+    """
+    Convert string input into a dictionary.
+
+    Parameters
+    ----------
+    value : str
+        String representing dictionary to be parsed.
+
+    Returns
+    -------
+    TyperDict
+        Parsed string as a dictionary.
+    """
+    return TyperDict(ast.literal_eval(value))
+
+
+@app.command()
+def singlepoint(
+    structure: Annotated[
+        str, typer.Option(help="Path to structure to perform calculations")
+    ],
+    architecture: Annotated[
+        str, typer.Option("--arch", help="MLIP architecture to use for calculations")
+    ] = "mace_mp",
+    device: Annotated[str, typer.Option(help="Device to run calculations on")] = "cpu",
+    properties: Annotated[
+        list[str],
+        typer.Option(
+            "--property",
+            help="Properties to calculate. If not specified, 'energy', 'forces', \
+                and 'stress' will be returned.",
+        ),
+    ] = None,
+    read_kwargs: Annotated[
+        TyperDict,
+        typer.Option(
+            parser=parse_dict_class,
+            help="Keyword arguments to pass to ase.io.read  [default: {}]",
+            metavar="DICT",
+        ),
+    ] = None,
+    calc_kwargs: Annotated[
+        TyperDict,
+        typer.Option(
+            parser=parse_dict_class,
+            help="Keyword arguments to pass to selected calculator  [default: {}]",
+            metavar="DICT",
+        ),
+    ] = None,
+):
+    """
+    Perform single point calculations.
+
+    Parameters
+    ----------
+    structure : str
+        Structure to simulate.
+    architecture : Optional[str]
+        MLIP architecture to use for single point calculations.
+        Default is "mace_mp".
+    device : Optional[str]
+        Device to run model on. Default is "cpu".
+    properties : Optional[str]
+        Physical properties to calculate. Default is "energy".
+    read_kwargs : Optional[dict[str, Any]]
+        Keyword arguments to pass to ase.io.read. Default is {}.
+    calc_kwargs : Optional[dict[str, Any]]
+        Keyword arguments to pass to the selected calculator. Default is {}.
+    """
+    read_kwargs = read_kwargs.value if read_kwargs else {}
+    calc_kwargs = calc_kwargs.value if calc_kwargs else {}
+
+    if not isinstance(read_kwargs, dict):
+        raise ValueError("read_kwargs must be a dictionary")
+    if not isinstance(calc_kwargs, dict):
+        raise ValueError("calc_kwargs must be a dictionary")
+
+    s_point = SinglePoint(
+        structure=structure,
+        architecture=architecture,
+        device=device,
+        read_kwargs=read_kwargs,
+        calc_kwargs=calc_kwargs,
+    )
+    print(s_point.run_single_point(properties=properties))
+
+
+@app.command()
+def test(name: str):
+    """
+    Dummy alternative CLI command.
+
+    Parameters
+    ----------
+    name : str
+        Name of person.
+    """
+    print(f"Hello, {name}!")

janus_core/mlip_calculators.py

@@ -55,15 +55,15 @@ def choose_calculator(
         from mace.calculators import mace_mp
 
         kwargs.setdefault("default_dtype", "float64")
-        kwargs.setdefault("model", "small")
+        kwargs["model"] = kwargs.pop("model_paths", "small")
         calculator = mace_mp(**kwargs)
 
     elif architecture == "mace_off":
         from mace import __version__
         from mace.calculators import mace_off
 
         kwargs.setdefault("default_dtype", "float64")
-        kwargs.setdefault("model", "small")
+        kwargs["model"] = kwargs.pop("model_paths", "small")
         calculator = mace_off(**kwargs)
 
     elif architecture == "m3gnet":