[Feat] Add type hints #251

fjosw · 2024-12-25T10:28:13Z

As a first step towards adding type hints, I added automatic type hints with monkeytype. Hints for the more complicated methods will need additional manual work but for the simpler methods this seems to have worked quite well.

compatability

fjosw · 2025-01-03T18:16:25Z

Not quite done but already in decent shape for a review @s-kuberski @jkuhl-uni:

Most of the changes are just type annotations
I changed a few lines to help mypy with understanding the type annotations
I fixed a few smaller bugs in which explicit type checks were not consistent or did not cover certain edge cases

For now I ignored the input/* modules and most of correlators.py, the remaining modules only raise a few smaller mypy errors which I wasn't able to fix right away.

s-kuberski · 2025-01-05T14:32:54Z

Great, thanks a lot for all of your work! I'll have a look in the upcoming week.

jkuhl-uni · 2025-01-09T09:32:26Z

pyerrors/correlators.py

    __slots__ = ["content", "N", "T", "tag", "prange"]

-    def __init__(self, data_input, padding=[0, 0], prange=None):
+    def __init__(self, data_input: Any, padding: list[int]=[0, 0], prange: Optional[list[int]]=None):


Shouldn't this be list[Obs]? Alternatively, in the list, there could be something Obs-like, I suppose, such as list[CObs]?

jkuhl-uni · 2025-01-09T09:54:35Z

Hey @fjosw,
thanks for all the work, I am looking through it right now, it looks excellent to me. I hope it was okay that I pushed a few small changes. If not, feel free to revert them, as you please :)

jkuhl-uni · 2025-11-04T10:24:58Z

Hi,
I looked through the code again and made mainly small changes, as to improve some type hints.
The PR looks good to me otherwise.

jkuhl-uni · 2025-01-09T12:57:08Z

pyerrors/obs.py

+    N_sigma_dict: dict[str, int] = {}

-    def __init__(self, samples, names, idl=None, **kwargs):
+    def __init__(self, samples: list[Union[ndarray, list[Any]]], names: list[str], idl: Optional[Union[list[list[int]], list[Union[list[int], range]], list[range]]]=None, **kwargs):


Could one make this more concrete? Is this Union[None, float, int]?
Or if this used as we also allow np types?

jkuhl-uni · 2025-11-14T09:03:23Z

pyerrors/input/hadrons.py



-def read_ExternalLeg_hd5(path, filestem, ens_id, idl=None):
+def read_ExternalLeg_hd5(path: str, filestem: str, ens_id: str, idl: Optional[range]=None):


Suggested change

def read_ExternalLeg_hd5(path: str, filestem: str, ens_id: str, idl: Optional[range]=None):

def read_ExternalLeg_hd5(path: str, filestem: str, ens_id: str, idl: Optional[Union[list, range]]=None):

jkuhl-uni · 2025-11-14T09:03:50Z

pyerrors/input/hadrons.py



-def extract_t0_hd5(path, filestem, ens_id, obs='Clover energy density', fit_range=5, idl=None, **kwargs):
+def extract_t0_hd5(path: str, filestem: str, ens_id: str, obs='Clover energy density', fit_range: int=5, idl: Optional[range]=None, **kwargs):


Suggested change

def extract_t0_hd5(path: str, filestem: str, ens_id: str, obs='Clover energy density', fit_range: int=5, idl: Optional[range]=None, **kwargs):

def extract_t0_hd5(path: str, filestem: str, ens_id: str, obs='Clover energy density', fit_range: int=5, idl: Optional[Union[list, range]]=None, **kwargs):

jkuhl-uni · 2025-11-14T09:04:17Z

pyerrors/input/hadrons.py



-def read_meson_hd5(path, filestem, ens_id, meson='meson_0', idl=None, gammas=None):
+def read_meson_hd5(path: str, filestem: str, ens_id: str, meson: str='meson_0', idl: Optional[range]=None, gammas: Optional[tuple[str, ...]]=None):


Suggested change

def read_meson_hd5(path: str, filestem: str, ens_id: str, meson: str='meson_0', idl: Optional[range]=None, gammas: Optional[tuple[str, ...]]=None):

def read_meson_hd5(path: str, filestem: str, ens_id: str, meson: str='meson_0', idl: Optional[Union[list, range]]=None, gammas: Optional[tuple[str, ...]]=None):

jkuhl-uni · 2025-11-14T09:04:44Z

pyerrors/input/hadrons.py



-def read_hd5(filestem, ens_id, group, attrs=None, idl=None, part="real"):
+def read_hd5(filestem: str, ens_id: str, group: str, attrs: Optional[Union[dict, int]]=None, idl=None, part="real") -> Corr:


Suggested change

def read_hd5(filestem: str, ens_id: str, group: str, attrs: Optional[Union[dict, int]]=None, idl=None, part="real") -> Corr:

def read_hd5(filestem: str, ens_id: str, group: str, attrs: Optional[Union[dict, int]]=None, idl:Optional[Union[list, range]]=None, part="real") -> Corr:

jkuhl-uni · 2025-11-14T09:05:36Z

pyerrors/input/hadrons.py



-def read_Fourquark_hd5(path, filestem, ens_id, idl=None, vertices=["VA", "AV"]):
+def read_Fourquark_hd5(path: str, filestem: str, ens_id: str, idl: Optional[range]=None, vertices: list[str]=["VA", "AV"]):


Suggested change

def read_Fourquark_hd5(path: str, filestem: str, ens_id: str, idl: Optional[range]=None, vertices: list[str]=["VA", "AV"]):

def read_Fourquark_hd5(path: str, filestem: str, ens_id: str, idl: Optional[Union[list, range]]=None, vertices: list[str]=["VA", "AV"]):

jkuhl-uni · 2025-11-14T09:21:29Z

pyerrors/misc.py

+    path = kwargs.get('path')
+    if path is not None:
+        if not isinstance(path, str):
+            raise Exception("Path has to be a string.")
+        file_name = path + '/' + name + '.p'
    else:
        file_name = name + '.p'


Suggested change

path = kwargs.get('path')

if path is not None:

if not isinstance(path, str):

raise Exception("Path has to be a string.")

file_name = path + '/' + name + '.p'

else:

file_name = name + '.p'

path = kwargs.get('path', '.')

if not isinstance(path, str):

raise Exception("Path has to be a string.")

file_name = path + '/' + name + '.p'

jkuhl-uni · 2025-11-14T09:39:43Z

pyerrors/input/sfcf.py

                            intern[name]["spec"][quarks][off][w][w2]["pattern"] = _make_pattern(version, name, off, w, w2, intern[name]['b2b'], quarks)
                    else:
                        intern[name]["spec"][quarks][off][w]["0"] = {}
                        intern[name]["spec"][quarks][off][w]["0"]["pattern"] = _make_pattern(version, name, off, w, 0, intern[name]['b2b'], quarks)


Suggested change

intern[name]["spec"][quarks][off][w]["0"]["pattern"] = _make_pattern(version, name, off, w, 0, intern[name]['b2b'], quarks)

intern[name]["spec"][quarks][off][w]["0"]["pattern"] = _make_pattern(version, name, off, w, "0", intern[name]['b2b'], quarks)

jkuhl-uni · 2025-11-14T09:40:37Z

pyerrors/input/sfcf.py



-def _make_pattern(version, name, noffset, wf, wf2, b2b, quarks):
+def _make_pattern(version: str, name: str, noffset: str, wf: str, wf2: Union[str, int], b2b: bool, quarks: str) -> str:


Suggested change

def _make_pattern(version: str, name: str, noffset: str, wf: str, wf2: Union[str, int], b2b: bool, quarks: str) -> str:

def _make_pattern(version: str, name: str, noffset: str, wf: str, wf2: str, b2b: bool, quarks: str) -> str:

jkuhl-uni · 2025-11-14T10:05:15Z

pyerrors/obs.py

+        path = kwargs.get('path')
+        if path is not None:
+            if not isinstance(path, str):
+                raise TypeError('path has to be a string.')
+            file_name = path + '/' + filename
        else:
            file_name = filename


Suggested change

path = kwargs.get('path')

if path is not None:

if not isinstance(path, str):

raise TypeError('path has to be a string.')

file_name = path + '/' + filename

else:

file_name = filename

path = kwargs.get('path', '.')

if not isinstance(path, str):

raise TypeError('path has to be a string.')

file_name = path + '/' + filename

fjosw added 12 commits December 25, 2024 11:09

[Feat] Add type hints to pyerrors modules

3db8eb2

[Feat] Added type hints to input modules

9fe375a

[Feat] Fixed a few type hints manually

8d86295

[Fix] Fix ruff errors and a few type annotations

2d34b35

[Fix] Fix type annotations for first part of obs.py

a9e082c

[Fix] Fixed most type annotations in obs.py

0198256

[CI] Add typing extension package to pytest run for pytthon 3.9

9389ad6

[Fix] Fix type hints in misc.py and remove strict zips for python 3.9

23d4f4c

compatability

[Fix] Start fixing remaining type hints

1916de1

[Fix] Removed unused imports

3654635

[CI] Add E252 to flake8 exceptions

4f1606d

[Fix] Fixed remaining flake8 errors

d45b43e

fjosw marked this pull request as ready for review January 3, 2025 18:12

fjosw requested review from jkuhl-uni and s-kuberski as code owners January 3, 2025 18:12

fjosw added 4 commits January 3, 2025 22:43

[Fix] Simplify type hints

1c6053e

[Fix] Fix type annotations in json.py

b8700ef

[Fix] Simplify type annotations in input modules

6d5a9b9

[Fix] Fix ruff

6a990c1

fjosw mentioned this pull request Jan 3, 2025

ens_name not correctly set in sfcf module #252

Closed

fjosw and others added 5 commits January 5, 2025 16:30

[Fix] Correct type hints in fits.py

9c960ae

[Fix] Further type fixes in fits and sfcf

5376a8a

[Fix] More type hint fixing

336117c

Merge branch 'develop' into feat/typehints

dba277f

add typehints for other util functions

52b91d8

jkuhl-uni reviewed Jan 9, 2025

View reviewed changes

make deriv structure like second_deriv

cb9d942

fjosw requested a review from jkuhl-uni May 7, 2025 15:28

fjosw and others added 17 commits June 23, 2025 21:36

[Chore] Simplify flaot typehints

356a396

Merge branch 'develop' into feat/typehints

54a8e02

correct typo

a4525be

small type corrections

1a77122

simplify internal method for read_rwms

33be7c2

fix types for r_start and r_stop, also for postfix

c822811

lint

b8ee9ec

allow all as tag

eb94260

simplify read_flow_obs names handling

5bad13f

small renamings

e2649b3

better steps from kwargs in read flow obs

4f09fc7

small switch of lines

1e00caf

lint

4f8567a

simplify r_start and r_stop in read_pbp

fb7ba0c

renameing in read_hd5 for less confisuion

dddaaa4

typehints for hadron read functions

53192d3

lint

9827899

jkuhl-uni mentioned this pull request Nov 3, 2025

Missing return statement in _import_array() #276

Open

jkuhl-uni added 9 commits November 3, 2025 17:09

add typehints for bdio

38692d2

being a bit more concrete with literals

dcf6a1f

cast epsilon tensors to int

dd6a2dc

undo import change

e116e74

add some typecasts

c9cef8f

rename some internal functions

898551d

small renaming for type consistency

38df833

undo signature change in linalg

51b9d2f

slight typechange in cov_Obs

8d9a136

jkuhl-uni requested changes Nov 14, 2025

View reviewed changes



		def read_ExternalLeg_hd5(path, filestem, ens_id, idl=None):
		def read_ExternalLeg_hd5(path: str, filestem: str, ens_id: str, idl: Optional[range]=None):



		def extract_t0_hd5(path, filestem, ens_id, obs='Clover energy density', fit_range=5, idl=None, **kwargs):
		def extract_t0_hd5(path: str, filestem: str, ens_id: str, obs='Clover energy density', fit_range: int=5, idl: Optional[range]=None, **kwargs):



		def read_meson_hd5(path, filestem, ens_id, meson='meson_0', idl=None, gammas=None):
		def read_meson_hd5(path: str, filestem: str, ens_id: str, meson: str='meson_0', idl: Optional[range]=None, gammas: Optional[tuple[str, ...]]=None):



		def read_hd5(filestem, ens_id, group, attrs=None, idl=None, part="real"):
		def read_hd5(filestem: str, ens_id: str, group: str, attrs: Optional[Union[dict, int]]=None, idl=None, part="real") -> Corr:



		def read_Fourquark_hd5(path, filestem, ens_id, idl=None, vertices=["VA", "AV"]):
		def read_Fourquark_hd5(path: str, filestem: str, ens_id: str, idl: Optional[range]=None, vertices: list[str]=["VA", "AV"]):

	intern[name]["spec"][quarks][off][w]["0"]["pattern"] = _make_pattern(version, name, off, w, 0, intern[name]['b2b'], quarks)
	intern[name]["spec"][quarks][off][w]["0"]["pattern"] = _make_pattern(version, name, off, w, "0", intern[name]['b2b'], quarks)



		def _make_pattern(version, name, noffset, wf, wf2, b2b, quarks):
		def _make_pattern(version: str, name: str, noffset: str, wf: str, wf2: Union[str, int], b2b: bool, quarks: str) -> str:

[Feat] Add type hints #251

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fjosw commented Dec 25, 2024

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jkuhl-uni commented Jan 9, 2025

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fjosw commented Jan 3, 2025 •

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jkuhl-uni Jan 9, 2025 •

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