17078564745

Committed 19 Aug 2025 06:33PM UTC coverage: 92.755% (-0.6%) from 93.337%

Build # 17078564745

Build Type

push

github

Committed by

web-flow

Commit Message

Refactoring and low hanging fruits (#49)

* feat: add from_dict contructors for job data objects

* chore: pass linter

* fix: several issues

* fix: linting

* fix: fully linted and sorted

* fix: tests after linting

* Apply suggestion from @troycomi

Co-authored-by: Troy Comi <troycomi@gmail.com>

* fix: removing unused functions

* addressing Tryoy's comments

* fix: final linting

---------

Co-authored-by: Troy Comi <troycomi@gmail.com>

Run Details

136 of 150 branches covered (90.67%)

Branch coverage included in aggregate %.

314 of 355 new or added lines in 20 files covered. (88.45%)

4 existing lines in 3 files now uncovered.

1490 of 1603 relevant lines covered (92.95%)

1.86 hits per line

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0.0

/tests/utils.py

import os

import h5py


def print_hdf5(h5py_obj, level=-1, print_full_name: bool = False, print_attrs: bool = True) -> None:
    """Prints the name and shape of datasets in a H5py HDF5 file.

    Parameters
    ----------
    h5py_obj: [h5py.File, h5py.Group]
        the h5py.File or h5py.Group object
    level: int
        What level of the file tree you are in
    print_full_name
        If True, the full tree will be printed as the name, e.g. /group0/group1/group2/dataset: ...
        If False, only the current node will be printed, e.g. dataset:
    print_attrs
        If True: print all attributes in the file
    Returns
    -------
    None

    """

    def is_group(f):
        return isinstance(f, h5py._hl.group.Group)

    def is_dataset(f):
        return isinstance(f, h5py._hl.dataset.Dataset)

    def print_level(level, n_spaces=5) -> str:
        if level == -1:
            return ""
        prepend = "|" + " " * (n_spaces - 1)
        prepend *= level
        tree = "|" + "-" * (n_spaces - 2) + " "
        return prepend + tree

    for key in h5py_obj.keys():
        entry = h5py_obj[key]
        name = entry.name if print_full_name else os.path.basename(entry.name)
        if is_group(entry):
            print(f"{print_level(level)}{name}")
            print_hdf5(entry, level + 1, print_full_name=print_full_name)
        elif is_dataset(entry):
            shape = entry.shape
            dtype = entry.dtype
            print(f"{print_level(level)}{name}: {shape} {dtype} {entry[()]}")
    if level == -1 and print_attrs:
        print("attrs: ")
        for key, value in h5py_obj.attrs.items():
            print(f" {key}: {value}")

1	import os	×
2
3	import h5py	×
4
5
NEW 6	def print_hdf5(h5py_obj, level=-1, print_full_name: bool = False, print_attrs: bool = True) -> None:	×
7	"""Prints the name and shape of datasets in a H5py HDF5 file.
8
9	Parameters
10	----------
11	h5py_obj: [h5py.File, h5py.Group]
12	the h5py.File or h5py.Group object
13	level: int
14	What level of the file tree you are in
15	print_full_name
16	If True, the full tree will be printed as the name, e.g. /group0/group1/group2/dataset: ...
17	If False, only the current node will be printed, e.g. dataset:
18	print_attrs
19	If True: print all attributes in the file
20	Returns
21	-------
22	None
23
24	"""
25
26	def is_group(f):	×
NEW 27	return isinstance(f, h5py._hl.group.Group)	×
28
29	def is_dataset(f):	×
NEW 30	return isinstance(f, h5py._hl.dataset.Dataset)	×
31
32	def print_level(level, n_spaces=5) -> str:	×
33	if level == -1:	×
34	return ""	×
35	prepend = "\|" + " " * (n_spaces - 1)	×
36	prepend *= level	×
37	tree = "\|" + "-" * (n_spaces - 2) + " "	×
38	return prepend + tree	×
39
40	for key in h5py_obj.keys():	×
41	entry = h5py_obj[key]	×
42	name = entry.name if print_full_name else os.path.basename(entry.name)	×
43	if is_group(entry):	×
44	print(f"{print_level(level)}{name}")	×
45	print_hdf5(entry, level + 1, print_full_name=print_full_name)	×
46	elif is_dataset(entry):	×
47	shape = entry.shape	×
48	dtype = entry.dtype	×
49	print(f"{print_level(level)}{name}: {shape} {dtype} {entry[()]}")	×
NEW 50	if level == -1 and print_attrs:	×
NEW 51	print("attrs: ")	×
NEW 52	for key, value in h5py_obj.attrs.items():	×
NEW 53	print(f" {key}: {value}")	×

PrincetonUniversity / slurmise / 17078564745

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