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dpdata
/
docs
/
make_format.py
dpdata
/
docs
/
make_format.py
make_format.py 13.26 KB
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Han Wang 提交于 2025年01月17日 10:53 +08:00 . breaking: drop python 3.7 (#783)
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from __future__ import annotations
import csv
import os
from collections import defaultdict
from inspect import Parameter, Signature, cleandoc, signature
from typing import Literal
from numpydoc.docscrape import Parameter as numpydoc_Parameter
from numpydoc.docscrape_sphinx import SphinxDocString
from dpdata.bond_order_system import BondOrderSystem
# ensure all plugins are loaded!
from dpdata.driver import Driver, Minimizer
from dpdata.format import Format
from dpdata.system import LabeledSystem, MultiSystems, System
def get_formats() -> dict:
formats = defaultdict(list)
for kk, ff in Format.get_formats().items():
formats[ff].append(kk)
return formats
def get_driver() -> dict:
drivers = defaultdict(list)
for kk, ff in Driver.get_drivers().items():
drivers[ff].append(kk)
return drivers
def get_minimizer() -> dict:
minimizers = defaultdict(list)
for kk, ff in Minimizer.get_minimizers().items():
minimizers[ff].append(kk)
return minimizers
def detect_overridden(cls: Format, method: str) -> bool:
"""Check whether a method is override.
Parameters
----------
cls : Format
a format
method : str
method name
Returns
-------
bool
whether a method is overridden
"""
return method in cls.__dict__
def get_cls_link(cls: object) -> str:
"""Returns class link.
Parameters
----------
cls : object
the class
Returns
-------
str
the link of a class
"""
return ":class:`{} <{}>`".format(
cls.__name__, ".".join([cls.__module__, cls.__name__])
)
def check_supported(fmt: Format):
methods = {}
for mtd in [
"from_system",
"to_system",
"from_labeled_system",
"to_labeled_system",
"from_bond_order_system",
"to_bond_order_system",
"from_multi_systems",
"to_multi_systems",
]:
if detect_overridden(fmt, mtd):
methods[mtd] = None
if mtd == "to_system":
methods["to_labeled_system"] = None
if fmt.MultiMode != fmt.MultiModes.NotImplemented:
methods["from_multi_systems"] = None
methods["to_multi_systems"] = None
return list(methods.keys())
method_links = {
"from_system": ":ref:`System() <{}_{}>`",
"to_system": ":ref:`System.to() <{}_{}>`",
"from_labeled_system": ":ref:`LabeledSystem() <{}_{}>`",
"to_labeled_system": ":ref:`LabeledSystem.to() <{}_{}>`",
"from_bond_order_system": ":ref:`BondOrderSystem() <{}_{}>`",
"to_bond_order_system": ":ref:`BondOrderSystem.to() <{}_{}>`",
"from_multi_systems": ":ref:`MultiSystems.load_systems_from_file() <{}_{}>`",
"to_multi_systems": ":ref:`MultiSystems.to() <{}_{}>`",
}
method_classes = {
"from_system": "System",
"to_system": "System",
"from_labeled_system": "LabeledSystem",
"to_labeled_system": "LabeledSystem",
"from_bond_order_system": "BondOrderSystem",
"to_bond_order_system": "BondOrderSystem",
"from_multi_systems": "MultiSystems",
"to_multi_systems": "MultiSystems",
}
method_cls_obj = {
"from_system": System,
"to_system": System,
"from_labeled_system": LabeledSystem,
"to_labeled_system": LabeledSystem,
"from_bond_order_system": BondOrderSystem,
"to_bond_order_system": BondOrderSystem,
"from_multi_systems": MultiSystems,
"to_multi_systems": MultiSystems,
}
def generate_sub_format_pages(formats: dict):
"""Generate sub format pages."""
os.makedirs("formats", exist_ok=True)
for format, alias in formats.items():
# format: Format, alias: list[str]
buff = []
buff.append(f".. _{format.__name__}:")
buff.append("")
for aa in alias:
buff.append(f"{aa} format")
buff.append("=" * len(buff[-1]))
buff.append("")
buff.append(f"Class: {get_cls_link(format)}")
buff.append("")
docstring = format.__doc__
if docstring is not None:
docstring = cleandoc(docstring)
rst = str(SphinxDocString(docstring))
buff.append(rst)
buff.append("")
buff.append("Conversions")
buff.append("-----------")
methods = check_supported(format)
for method in methods:
buff.append("")
buff.append(f".. _{format.__name__}_{method}:")
buff.append("")
if method.startswith("from_"):
buff.append(f"Convert from this format to {method_classes[method]}")
buff.append("`" * len(buff[-1]))
elif method.startswith("to_"):
buff.append(f"Convert from {method_classes[method]} to this format")
buff.append("`" * len(buff[-1]))
buff.append("")
method_obj = getattr(format, method)
if (
method == "to_labeled_system"
and method not in format.__dict__
and "to_system" in format.__dict__
):
method_obj = getattr(format, "to_system")
docstring = method_obj.__doc__
if docstring is not None:
docstring = cleandoc(docstring)
sig = signature(method_obj)
parameters = dict(sig.parameters)
return_annotation = sig.return_annotation
# del self
del parameters[list(parameters)[0]]
# del data
if method.startswith("to_"):
del parameters[list(parameters)[0]]
if "args" in parameters:
del parameters["args"]
if "kwargs" in parameters:
del parameters["kwargs"]
if method == "to_multi_systems" or method.startswith("from_"):
sig = Signature(
list(parameters.values()), return_annotation=method_cls_obj[method]
)
else:
sig = Signature(
list(parameters.values()), return_annotation=return_annotation
)
sig = str(sig)
if method.startswith("from_"):
if method != "from_multi_systems":
for aa in alias:
parameters["fmt"] = Parameter(
"fmt",
Parameter.POSITIONAL_OR_KEYWORD,
default=None,
annotation=Literal[aa],
)
sig_fmt = Signature(
list(parameters.values()),
return_annotation=method_cls_obj[method],
)
sig_fmt = str(sig_fmt)
buff.append(
f""".. py:function:: dpdata.{method_classes[method]}{sig_fmt}"""
)
buff.append(""" :noindex:""")
for aa in alias:
buff.append(
""".. py:function:: dpdata.{}.from_{}{}""".format(
method_classes[method],
aa.replace("/", "_").replace(".", ""),
sig,
)
)
buff.append(""" :noindex:""")
buff.append("")
if docstring is None or method not in format.__dict__:
docstring = f""" Convert this format to :class:`{method_classes[method]}`."""
doc_obj = SphinxDocString(docstring)
if len(doc_obj["Parameters"]) > 0:
doc_obj["Parameters"] = [
xx
for xx in doc_obj["Parameters"]
if xx.name not in ("*args", "**kwargs")
]
else:
if method == "from_multi_systems":
doc_obj["Parameters"] = [
numpydoc_Parameter(
"directory",
"str",
["directory of systems"],
)
]
doc_obj["Yields"] = []
doc_obj["Returns"] = [
numpydoc_Parameter("", method_classes[method], ["converted system"])
]
rst = " " + str(doc_obj)
buff.append(rst)
buff.append("")
elif method.startswith("to_"):
for aa in alias:
parameters = {
"fmt": Parameter(
"fmt",
Parameter.POSITIONAL_OR_KEYWORD,
annotation=Literal[aa],
),
**parameters,
}
if method == "to_multi_systems":
sig_fmt = Signature(
list(parameters.values()),
return_annotation=method_cls_obj[method],
)
else:
sig_fmt = Signature(
list(parameters.values()),
return_annotation=return_annotation,
)
sig_fmt = str(sig_fmt)
buff.append(
f""".. py:function:: dpdata.{method_classes[method]}.to{sig_fmt}"""
)
buff.append(""" :noindex:""")
for aa in alias:
buff.append(
""".. py:function:: dpdata.{}.to_{}{}""".format(
method_classes[method],
aa.replace("/", "_").replace(".", ""),
sig,
)
)
buff.append(""" :noindex:""")
buff.append("")
if docstring is None or (
method not in format.__dict__
and not (
method == "to_labeled_system"
and method not in format.__dict__
and "to_system" in format.__dict__
)
):
docstring = (
f"Convert :class:`{method_classes[method]}` to this format."
)
doc_obj = SphinxDocString(docstring)
if len(doc_obj["Parameters"]) > 0:
doc_obj["Parameters"] = [
xx
for xx in doc_obj["Parameters"][1:]
if xx.name not in ("*args", "**kwargs")
]
else:
if method == "to_multi_systems":
doc_obj["Parameters"] = [
numpydoc_Parameter(
"directory",
"str",
["directory to save systems"],
)
]
if method == "to_multi_systems":
doc_obj["Yields"] = []
doc_obj["Returns"] = [
numpydoc_Parameter("", method_classes[method], ["this system"])
]
rst = " " + str(doc_obj)
buff.append(rst)
buff.append("")
buff.append("")
buff.append("")
with open(f"formats/{format.__name__}.rst", "w") as rstfile:
rstfile.write("\n".join(buff))
if __name__ == "__main__":
formats = get_formats()
with open("formats.csv", "w", newline="") as csvfile:
fieldnames = [
"Format",
"Alias",
"Supported Conversions",
]
writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
writer.writeheader()
for kk, vv in formats.items():
writer.writerow(
{
"Format": f":ref:`{kk.__name__}`",
"Alias": "\n".join(f"``{vvv}``" for vvv in vv),
"Supported Conversions": "\n".join(
method_links[mtd].format(kk.__name__, mtd)
for mtd in check_supported(kk)
),
}
)
drivers = get_driver()
with open("drivers.csv", "w", newline="") as csvfile:
fieldnames = [
"Class",
"Alias",
]
writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
writer.writeheader()
for kk, vv in drivers.items():
writer.writerow(
{
"Class": get_cls_link(kk),
"Alias": "\n".join(f"``{vvv}``" for vvv in vv),
}
)
minimizers = get_minimizer()
with open("minimizers.csv", "w", newline="") as csvfile:
fieldnames = [
"Class",
"Alias",
]
writer = csv.DictWriter(csvfile, fieldnames=fieldnames)
writer.writeheader()
for kk, vv in minimizers.items():
writer.writerow(
{
"Class": get_cls_link(kk),
"Alias": "\n".join(f"``{vvv}``" for vvv in vv),
}
)
generate_sub_format_pages(formats)
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