Latest versions of fancylog cause a crash with brainreg

[adamltyson]

The latest versions with the env logging have caused a bug in which there are some json errors. I've yanked the latest releases, but we should look into why this issue has arisen. There weren't any issues in #62 with my local testing or on CI.

[adamltyson]

Relevant stack trace:

File ~/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/superqt/utils/_qthreading.py:613, in create_worker.<locals>.reraise(e=JSONDecodeError('Expecting value: line 1 column 1 (char 0)'))
    612 def reraise(e):
--> 613     raise e
        e = JSONDecodeError('Expecting value: line 1 column 1 (char 0)')
File ~/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/superqt/utils/_qthreading.py:175, in WorkerBase.run(self=<napari._qt.qthreading.FunctionWorker object>)
    173     warnings.filterwarnings("always")
    174     warnings.showwarning = lambda *w: self.warned.emit(w)
--> 175     result = self.work()
        self = <napari._qt.qthreading.FunctionWorker object at 0x165735250>    176 if isinstance(result, Exception):
    177     if isinstance(result, RuntimeError):
    178         # The Worker object has likely been deleted.
    179         # A deleted wrapped C/C++ object may result in a runtime
    180         # error that will cause segfault if we try to do much other
    181         # than simply notify the user.

File ~/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/superqt/utils/_qthreading.py:354, in FunctionWorker.work(self=<napari._qt.qthreading.FunctionWorker object>)
    353 def work(self) -> _R:
--> 354     return self._func(*self._args, **self._kwargs)
        self._func = <function brainreg_register.<locals>.widget.<locals>.run at 0x15cac80e0>
        self = <napari._qt.qthreading.FunctionWorker object at 0x165735250>
        self._args = (2,)
        self._kwargs = {}
File ~/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/brainreg/napari/register.py:435, in brainreg_register.<locals>.widget.<locals>.run(n_free_cpus=2)
    432 args_namedtuple, args_dict = get_gui_logging_args()
    433 log_metadata(paths.metadata_path, args_dict)
--> 435 fancylog.start_logging(
        fancylog = <module 'fancylog.fancylog' from '/Users/k2366861/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/fancylog/fancylog.py'>
        paths = <brainreg.core.paths.Paths object at 0x1755a9580>
        paths.registration_output_folder = PosixPath('/Users/k2366861/SwcOpenSoftwareWeek')
        program_for_log = <module 'brainreg' from '/Users/k2366861/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/brainreg/__init__.py'>
        args_namedtuple = namespace(image_paths=None, backend='niftyreg', voxel_sizes=['50.0', '40.0', '40.0'], orientation='psl', data_orientation='psl', brain_geometry='geometry_keys.Full brain', save_original_orientation='False', atlas='allen_mouse_50um', atlas_key='atlas_key.allen_mouse_50um', registration_output_folder='/Users/k2366861/SwcOpenSoftwareWeek', affine_n_steps='4', affine_use_n_steps='5', freeform_n_steps='6', freeform_use_n_steps='4', bending_energy_weight='0.95', grid_spacing='-10', smoothing_sigma_reference='-1.0', smoothing_sigma_floating='-1.0', histogram_n_bins_floating='98.0', histogram_n_bins_reference='128.0', n_free_cpus='2', debug='False')
        niftyreg_args = NiftyregArgs(affine_n_steps=4, affine_use_n_steps=5, freeform_n_steps=6, freeform_use_n_steps=4, bending_energy_weight=0.95, grid_spacing=-10, smoothing_sigma_reference=-1.0, smoothing_sigma_floating=-1.0, histogram_n_bins_floating=98.0, histogram_n_bins_reference=128.0, debug=False)
        niftyreg_args.debug = False    436     str(paths.registration_output_folder),
    437     program_for_log,
    438     variables=args_namedtuple,
    439     verbose=niftyreg_args.debug,
    440     log_header="BRAINREG LOG",
    441     multiprocessing_aware=False,
    442 )
    444 voxel_sizes = z_pixel_um, x_pixel_um, y_pixel_um
    446 (
    447     n_free_cpus,
    448     n_processes,
   (...)    456     n_free_cpus=n_free_cpus,
    457 )

File ~/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/fancylog/fancylog.py:108, in start_logging(output_dir='/Users/k2366861/SwcOpenSoftwareWeek', package=<module 'brainreg' from '/Users/k2366861/minifor...b/python3.12/site-packages/brainreg/__init__.py'>, variables=namespace(image_paths=None, backend='niftyreg', ...eference='128.0', n_free_cpus='2', debug='False'), verbose=False, file_log_level='DEBUG', filename='brainreg_2025-08-12_12-26-04', log_header='BRAINREG LOG', multiprocessing_aware=False, write_header=True, write_git=True, write_cli_args=True, write_python=True, write_env_packages=True, write_variables=True, log_to_file=True, log_to_console=True, timestamp=True, logger_name=None)
    105     logging_file = None
    107 if logging_file is not None:
--> 108     LoggingHeader(
        logging_file = '/Users/k2366861/SwcOpenSoftwareWeek/brainreg_2025-08-12_12-26-04.log'
        package = <module 'brainreg' from '/Users/k2366861/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/brainreg/__init__.py'>
        variables = namespace(image_paths=None, backend='niftyreg', voxel_sizes=['50.0', '40.0', '40.0'], orientation='psl', data_orientation='psl', brain_geometry='geometry_keys.Full brain', save_original_orientation='False', atlas='allen_mouse_50um', atlas_key='atlas_key.allen_mouse_50um', registration_output_folder='/Users/k2366861/SwcOpenSoftwareWeek', affine_n_steps='4', affine_use_n_steps='5', freeform_n_steps='6', freeform_use_n_steps='4', bending_energy_weight='0.95', grid_spacing='-10', smoothing_sigma_reference='-1.0', smoothing_sigma_floating='-1.0', histogram_n_bins_floating='98.0', histogram_n_bins_reference='128.0', n_free_cpus='2', debug='False')
        output_dir = '/Users/k2366861/SwcOpenSoftwareWeek'
        write_header = True
        write_git = True
        write_cli_args = True
        write_python = True
        write_env_packages = True
        write_variables = True
        log_header = 'BRAINREG LOG'    109         logging_file,
    110         package,
    111         variables,
    112         output_dir,
    113         write_header=write_header,
    114         write_git=write_git,
    115         write_cli_args=write_cli_args,
    116         write_python=write_python,
    117         write_env_packages=write_env_packages,
    118         write_variables=write_variables,
    119         log_header=log_header,
    120     )
    122 setup_logging(
    123     logging_file,
    124     print_level=print_log_level,
   (...)    128     logger_name=logger_name,
    129 )
    130 return logging_file

File ~/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/fancylog/fancylog.py:166, in LoggingHeader.__init__(self=<fancylog.fancylog.LoggingHeader object>, file='/Users/k2366861/SwcOpenSoftwareWeek/brainreg_2025-08-12_12-26-04.log', program=<module 'brainreg' from '/Users/k2366861/minifor...b/python3.12/site-packages/brainreg/__init__.py'>, variable_objects=namespace(image_paths=None, backend='niftyreg', ...eference='128.0', n_free_cpus='2', debug='False'), output_dir='/Users/k2366861/SwcOpenSoftwareWeek', write_header=True, write_git=True, write_cli_args=True, write_python=True, write_env_packages=True, write_variables=True, log_header='BRAINREG LOG')
    164     self.write_python_version()
    165 if write_env_packages:
--> 166     self.write_environment_packages()
        self = <fancylog.fancylog.LoggingHeader object at 0x1755ca990>    167 if write_variables and variable_objects:
    168     self.write_variables(variable_objects)

File ~/miniforge3/envs/brainglobe-env/lib/python3.12/site-packages/fancylog/fancylog.py:259, in LoggingHeader.write_environm
ent_packages(self=<fancylog.fancylog.LoggingHeader object>, header='ENVIRONMENT')

    254 conda_exe = os.environ["CONDA_EXE"]
    255 conda_list = subprocess.run(
    256     [conda_exe, "list", "--json"], capture_output=True, text=True
    257 )
--> 259 env_pkgs = json.loads(conda_list.stdout)
        conda_list = CompletedProcess(args=['/Users/k2366861/miniforge3/bin/conda', 'list', '--json'], returncode=1, stdout='', stderr='Traceback (most recent call last):\n  File "/Users/k2366861/miniforge3/bin/conda", line 12, in <module>\n    from conda.cli import main\nModuleNotFoundError: No module named \'conda\'\n')
        conda_list.stdout = ''    261 self.file.write(f"Conda environment: {conda_env}\n\n")
    262 self.file.write("Environment packages (conda):\n")

File ~/miniforge3/envs/brainglobe-env/lib/python3.12/json/__init__.py:346, in loads(s='', cls=None, object_hook=None, parse_float=None, parse_int=None, parse_constant=None, object_pairs_hook=None, **kw={})
    341     s = s.decode(detect_encoding(s), 'surrogatepass')
    343 if (cls is None and object_hook is None and
    344         parse_int is None and parse_float is None and
    345         parse_constant is None and object_pairs_hook is None and not kw):
--> 346     return _default_decoder.decode(s)
        s = ''
        _default_decoder = <json.decoder.JSONDecoder object at 0x10616b980>    347 if cls is None:
    348     cls = JSONDecoder

File ~/miniforge3/envs/brainglobe-env/lib/python3.12/json/decoder.py:338, in JSONDecoder.decode(self=<json.decoder.JSONDecoder object>, s='', _w=<built-in method match of re.Pattern object>)
    333 def decode(self, s, _w=WHITESPACE.match):
    334     """Return the Python representation of ``s`` (a ``str`` instance
    335     containing a JSON document).
    336
    337     """
--> 338     obj, end = self.raw_decode(s, idx=_w(s, 0).end())
        s = ''
        self = <json.decoder.JSONDecoder object at 0x10616b980>
        _w = <built-in method match of re.Pattern object at 0x10613df20>    339     end = _w(s, end).end()
    340     if end != len(s):

File ~/miniforge3/envs/brainglobe-env/lib/python3.12/json/decoder.py:356, in JSONDecoder.raw_decode(self=<json.decoder.JSONDecoder object>, s='', idx=0)
    354     obj, end = self.scan_once(s, idx)
    355 except StopIteration as err:
--> 356     raise JSONDecodeError("Expecting value", s, err.value) from None
        s = ''    357 return obj, end

JSONDecodeError: Expecting value: line 1 column 1 (char 0)

[adamltyson]

The latest versions have been yanked from PyPI and removed from conda. This issue should be addressed before making any further releases.