Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[WIP] Autodoc typehints #350

Open
wants to merge 2 commits into
base: main
Choose a base branch
from
Open

[WIP] Autodoc typehints #350

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
8ceeefe
Add autodoc typehints module
oerc0122 Nov 8, 2024
5899452
Remove doc typehints in favour of signature
oerc0122 Nov 8, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 9 additions & 2 deletions docs/source/conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,16 +24,22 @@
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
"numpydoc",
# "numpydoc",
"sphinx.ext.autodoc",
"sphinx.ext.intersphinx",
"sphinx.ext.napoleon",
"sphinx.ext.mathjax",
"sphinx.ext.viewcode",
"sphinxcontrib.contentui",
"sphinx_copybutton",
"sphinx_autodoc_typehints",
]

numpydoc_validation_checks = {"all", "EX01", "SA01", "ES01"}
always_use_bars_union = True
napoleon_include_special_with_doc = True
napoleon_use_param = True

numpydoc_validation_checks = {"all", "EX01", "SA01", "ES01", "PR04"}
numpydoc_validation_exclude = {
r"\.__weakref__$",
r"\.__repr__$",
Expand Down Expand Up @@ -190,6 +196,7 @@

# Warnings to ignore when using the -n (nitpicky) option
# We should ignore any python built-in exception, for instance
nitpicky = True
nitpick_ignore = [
("py:class", "Logger"),
("py:class", "numpy.float64"),
Expand Down
72 changes: 36 additions & 36 deletions janus_core/calculations/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,48 +24,48 @@ class BaseCalculation(FileNameMixin):

Parameters
----------
calc_name : str
calc_name
Name of calculation being run, used for name of logger. Default is "base".
struct : MaybeSequence[Atoms] | None
struct
ASE Atoms structure(s) to simulate. Required if `struct_path` is None.
Default is None.
struct_path : PathLike | None
struct_path
Path of structure to simulate. Required if `struct` is None.
Default is None.
arch : Architectures
arch
MLIP architecture to use for calculations. Default is "mace_mp".
device : Devices
device
Device to run model on. Default is "cpu".
model_path : PathLike | None
model_path
Path to MLIP model. Default is `None`.
read_kwargs : ASEReadArgs
read_kwargs
Keyword arguments to pass to ase.io.read. Default is {}.
sequence_allowed : bool
sequence_allowed
Whether a sequence of Atoms objects is allowed. Default is True.
calc_kwargs : dict[str, Any] | None
calc_kwargs
Keyword arguments to pass to the selected calculator. Default is {}.
set_calc : bool | None
set_calc
Whether to set (new) calculators for structures. Default is None.
attach_logger : bool
attach_logger
Whether to attach a logger. Default is False.
log_kwargs : dict[str, Any] | None
log_kwargs
Keyword arguments to pass to `config_logger`. Default is {}.
track_carbon : bool
track_carbon
Whether to track carbon emissions of calculation. Default is True.
tracker_kwargs : dict[str, Any] | None
tracker_kwargs
Keyword arguments to pass to `config_tracker`. Default is {}.
file_prefix : PathLike | None
file_prefix
Prefix for output filenames. Default is None.
additional_prefix : str | None
additional_prefix
Component to add to default file_prefix (joined by hyphens). Default is None.
param_prefix : str | None
param_prefix
Additional parameters to add to default file_prefix. Default is None.

Attributes
----------
logger : logging.Logger | None
logger
Logger if log file has been specified.
tracker : OfflineEmissionsTracker | None
tracker
Tracker if logging is enabled.
"""

Expand Down Expand Up @@ -95,42 +95,42 @@ def __init__(

Parameters
----------
calc_name : str
calc_name
Name of calculation being run, used for name of logger. Default is "base".
struct : MaybeSequence[Atoms] | None
struct
ASE Atoms structure(s) to simulate. Required if `struct_path` is None.
Default is None.
struct_path : PathLike | None
struct_path
Path of structure to simulate. Required if `struct` is None. Default is
None.
arch : Architectures
arch
MLIP architecture to use for calculations. Default is "mace_mp".
device : Devices
device
Device to run MLIP model on. Default is "cpu".
model_path : PathLike | None
model_path
Path to MLIP model. Default is `None`.
read_kwargs : ASEReadArgs | None
read_kwargs
Keyword arguments to pass to ase.io.read. Default is {}.
sequence_allowed : bool
sequence_allowed
Whether a sequence of Atoms objects is allowed. Default is True.
calc_kwargs : dict[str, Any] | None
calc_kwargs
Keyword arguments to pass to the selected calculator. Default is {}.
set_calc : bool | None
set_calc
Whether to set (new) calculators for structures. Default is None.
attach_logger : bool
attach_logger
Whether to attach a logger. Default is False.
log_kwargs : dict[str, Any] | None
log_kwargs
Keyword arguments to pass to `config_logger`. Default is {}.
track_carbon : bool
track_carbon
Whether to track carbon emissions of calculation. Default is True.
tracker_kwargs : dict[str, Any] | None
tracker_kwargs
Keyword arguments to pass to `config_tracker`. Default is {}.
file_prefix : PathLike | None
file_prefix
Prefix for output filenames. Default is None.
additional_prefix : str | None
additional_prefix
Component to add to default file_prefix (joined by hyphens). Default is
None.
param_prefix : str | None
param_prefix
Additional parameters to add to default file_prefix. Default is None.
"""
(read_kwargs, calc_kwargs, log_kwargs, tracker_kwargs) = none_to_dict(
Expand Down
75 changes: 35 additions & 40 deletions janus_core/calculations/descriptors.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,49 +28,44 @@ class Descriptors(BaseCalculation):

Parameters
----------
struct : MaybeSequence[Atoms] | None
struct
ASE Atoms structure(s) to calculate descriptors for. Required if `struct_path`
is None. Default is None.
struct_path : PathLike | None
struct_path
Path of structure to calculate descriptors for. Required if `struct` is None.
Default is None.
arch : Architectures
arch
MLIP architecture to use for calculations. Default is "mace_mp".
device : Devices
device
Device to run MLIP model on. Default is "cpu".
model_path : PathLike | None
model_path
Path to MLIP model. Default is `None`.
read_kwargs : ASEReadArgs | None
read_kwargs
Keyword arguments to pass to ase.io.read. By default,
read_kwargs["index"] is -1.
calc_kwargs : dict[str, Any] | None
calc_kwargs
Keyword arguments to pass to the selected calculator. Default is {}.
set_calc : bool | None
set_calc
Whether to set (new) calculators for structures. Default is None.
attach_logger : bool
attach_logger
Whether to attach a logger. Default is False.
log_kwargs : dict[str, Any] | None
log_kwargs
Keyword arguments to pass to `config_logger`. Default is {}.
track_carbon : bool
track_carbon
Whether to track carbon emissions of calculation. Default is True.
tracker_kwargs : dict[str, Any] | None
tracker_kwargs
Keyword arguments to pass to `config_tracker`. Default is {}.
invariants_only : bool
invariants_only
Whether only the invariant descriptors should be returned. Default is True.
calc_per_element : bool
calc_per_element
Whether to calculate mean descriptors for each element. Default is False.
calc_per_atom : bool
calc_per_atom
Whether to calculate descriptors for each atom. Default is False.
write_results : bool
write_results
True to write out structure with results of calculations. Default is False.
write_kwargs : ASEWriteArgs | None
write_kwargs
Keyword arguments to pass to ase.io.write if saving structure with
results of calculations. Default is {}.

Methods
-------
run()
Calculate descriptors for structure(s)
"""

def __init__(
Expand Down Expand Up @@ -98,42 +93,42 @@ def __init__(

Parameters
----------
struct : MaybeSequence[Atoms] | None
struct
ASE Atoms structure(s) to calculate descriptors for. Required if
`struct_path` is None. Default is None.
struct_path : PathLike | None
struct_path
Path of structure to calculate descriptors for. Required if `struct` is
None. Default is None.
arch : Architectures
arch
MLIP architecture to use for calculations. Default is "mace_mp".
device : Devices
device
Device to run MLIP model on. Default is "cpu".
model_path : PathLike | None
model_path
Path to MLIP model. Default is `None`.
read_kwargs : ASEReadArgs | None
read_kwargs
Keyword arguments to pass to ase.io.read. By default,
read_kwargs["index"] is -1.
calc_kwargs : dict[str, Any] | None
calc_kwargs
Keyword arguments to pass to the selected calculator. Default is {}.
set_calc : bool | None
set_calc
Whether to set (new) calculators for structures. Default is None.
attach_logger : bool
attach_logger
Whether to attach a logger. Default is False.
log_kwargs : dict[str, Any] | None
log_kwargs
Keyword arguments to pass to `config_logger`. Default is {}.
track_carbon : bool
track_carbon
Whether to track carbon emissions of calculation. Default is True.
tracker_kwargs : dict[str, Any] | None
tracker_kwargs
Keyword arguments to pass to `config_tracker`. Default is {}.
invariants_only : bool
invariants_only
Whether only the invariant descriptors should be returned. Default is True.
calc_per_element : bool
calc_per_element
Whether to calculate mean descriptors for each element. Default is False.
calc_per_atom : bool
calc_per_atom
Whether to calculate descriptors for each atom. Default is False.
write_results : bool
write_results
True to write out structure with results of calculations. Default is False.
write_kwargs : ASEWriteArgs | None
write_kwargs
Keyword arguments to pass to ase.io.write if saving structure with
results of calculations. Default is {}.
"""
Expand Down Expand Up @@ -225,7 +220,7 @@ def _calc_descriptors(self, struct: Atoms) -> None:

Parameters
----------
struct : Atoms
struct
Structure to calculate descriptors for.
"""
if "arch" in struct.calc.parameters:
Expand Down
Loading
Loading