Update docs (#340)

* Fix documentation link

* Update type hints

docs/source/developer_guide/get_started.rst

@@ -64,7 +64,7 @@ Rules enforced by ruff are currently set up to be comparable to:
 - `isort <https://pycqa.github.io/isort/>`_ (import sorter)
 - `flake8-bugbear <https://pypi.org/project/flake8-bugbear/>`_ (bug finder)
 
-The full set of `ruff rules <https://docs.astral.sh/ruff/rules/>`_ are specified by the ``[tool.ruff]]`` sections of `pyproject.toml <https://github.com/stfc/janus-core/blob/main/pyproject.toml>`
+The full set of `ruff rules <https://docs.astral.sh/ruff/rules/>`_ are specified by the ``[tool.ruff]`` sections of `pyproject.toml <https://github.com/stfc/janus-core/blob/main/pyproject.toml>`_.
 
 
 Building the documentation

janus_core/calculations/md.py

@@ -509,7 +509,7 @@ def __init__(
 
         self._parse_correlations()
 
-    def _set_info(self):
+    def _set_info(self) -> None:
         """Set time in fs, current dynamics step, and density to info."""
         time = (self.offset * self.timestep + self.dyn.get_time()) / units.fs
         step = self.offset + self.dyn.nsteps
@@ -631,7 +631,7 @@ def _optimize_structure(self) -> None:
             optimizer = GeomOpt(self.struct, **self.minimize_kwargs)
             optimizer.run()
 
-    def _set_param_prefix(self, file_prefix: Optional[PathLike] = None):
+    def _set_param_prefix(self, file_prefix: Optional[PathLike] = None) -> str:
         """
         Set ensemble parameters for output files.
 
@@ -1205,7 +1205,7 @@ def __init__(
             **ensemble_kwargs,
         )
 
-    def _set_param_prefix(self, file_prefix: Optional[PathLike] = None):
+    def _set_param_prefix(self, file_prefix: Optional[PathLike] = None) -> str:
         """
         Set ensemble parameters for output files.
 

janus_core/cli/descriptors.py

@@ -57,7 +57,7 @@ def descriptors(
     write_kwargs: WriteKwargs = None,
     log: LogPath = None,
     summary: Summary = None,
-):
+) -> None:
     """
     Calculate MLIP descriptors for the given structure(s).
 

janus_core/cli/eos.py

@@ -73,7 +73,7 @@ def eos(
     ] = None,
     log: LogPath = None,
     summary: Summary = None,
-):
+) -> None:
     """
     Calculate equation of state and write out results.
 

janus_core/cli/geomopt.py

@@ -147,7 +147,7 @@ def geomopt(
     write_kwargs: WriteKwargs = None,
     log: LogPath = None,
     summary: Summary = None,
-):
+) -> None:
     """
     Perform geometry optimization and save optimized structure to file.
 

janus_core/cli/md.py

@@ -171,7 +171,7 @@ def md(
     ] = None,
     log: LogPath = None,
     summary: Summary = None,
-):
+) -> None:
     """
     Run molecular dynamics simulation, and save trajectory and statistics.
 

janus_core/cli/phonons.py

@@ -101,7 +101,7 @@ def phonons(
     ] = None,
     log: LogPath = None,
     summary: Summary = None,
-):
+) -> None:
     """
     Perform phonon calculations and write out results.
 

janus_core/cli/singlepoint.py

@@ -54,7 +54,7 @@ def singlepoint(
     write_kwargs: WriteKwargs = None,
     log: LogPath = None,
     summary: Summary = None,
-):
+) -> None:
     """
     Perform single point calculations and save to file.
 

janus_core/cli/train.py

@@ -26,7 +26,7 @@ def train(
             )
         ),
     ] = Path("train-summary.yml"),
-):
+) -> None:
     """
     Run training for MLIP by passing a configuration file to the MLIP's CLI.
 

janus_core/cli/types.py

@@ -41,7 +41,7 @@ class TyperDict:
         Value of string representing a dictionary.
     """
 
-    def __init__(self, value: str):
+    def __init__(self, value: str) -> None:
         """
         Initialise class.
 
@@ -52,7 +52,7 @@ def __init__(self, value: str):
         """
         self.value = value
 
-    def __str__(self):
+    def __str__(self) -> str:
         """
         Return string representation of class.
 

janus_core/helpers/correlator.py

@@ -23,7 +23,7 @@ class Correlator:
         Averaging window per block level.
     """
 
-    def __init__(self, *, blocks: int, points: int, averaging: int):
+    def __init__(self, *, blocks: int, points: int, averaging: int) -> None:
         """
         Initialise an empty Correlator.
 
@@ -50,7 +50,7 @@ def __init__(self, *, blocks: int, points: int, averaging: int):
         self._correlation = np.zeros((self._blocks, self._points))
         self._count_correlated = np.zeros((self._blocks, self._points), dtype=int)
 
-    def update(self, a: float, b: float):
+    def update(self, a: float, b: float) -> None:
         """
         Update the correlation, <ab>, with new values a and b.
 
@@ -63,7 +63,7 @@ def update(self, a: float, b: float):
         """
         self._propagate(a, b, 0)
 
-    def _propagate(self, a: float, b: float, block: int):
+    def _propagate(self, a: float, b: float, block: int) -> None:
         """
         Propagate update down block hierarchy.
 
@@ -203,7 +203,7 @@ def __init__(
         points: int,
         averaging: int,
         update_frequency: int,
-    ):
+    ) -> None:
         """
         Initialise a correlation.
 
@@ -252,7 +252,7 @@ def update_frequency(self) -> int:
         """
         return self._update_frequency
 
-    def update(self, atoms: Atoms):
+    def update(self, atoms: Atoms) -> None:
         """
         Update a correlation.
 

janus_core/helpers/observables.py

@@ -15,7 +15,7 @@ class Stress:
         Calculate with the ideal gas contribution.
     """
 
-    def __init__(self, component: str, *, include_ideal_gas: bool = True):
+    def __init__(self, component: str, *, include_ideal_gas: bool = True) -> None:
         """
         Initialise the observables from a symbolic str component.
 

janus_core/helpers/utils.py

@@ -67,7 +67,7 @@ def __init__(
         struct_path: Optional[PathLike],
         file_prefix: Optional[PathLike],
         *additional,
-    ):
+    ) -> None:
         """
         Provide mixin functions for standard filename handling.
 
@@ -643,7 +643,7 @@ def _dump_ascii(
     header: list[str],
     columns: dict[str, Sequence[Any]],
     formats: Sequence[str],
-):
+) -> None:
     """
     Dump data as an ASCII style table.
 
@@ -675,7 +675,7 @@ def _dump_csv(
     header: list[str],
     columns: dict[str, Sequence[Any]],
     formats: Sequence[str],
-):
+) -> None:
     """
     Dump data as a csv style table.