Closed aloboa closed 5 months ago
guiwitz
commented
5 months ago The tiling option was only added recently in the separate plugin handling the ML annotation. Maybe you can try to do pip install napari-convpaint -U to update it and see if that works.
aloboa
commented
5 months ago Unfortunately not. After a succesful upgrading with
(sediment) alobo@pop-os:~$ pip install napari-convpaint -U
.../...
Downloading napari_convpaint-0.4.0-py3-none-any.whl (29 kB)
Installing collected packages: napari-convpaint
Attempting uninstall: napari-convpaint
Found existing installation: napari-convpaint 0.3.0
Uninstalling napari-convpaint-0.3.0:
Successfully uninstalled napari-convpaint-0.3.0
Successfully installed napari-convpaint-0.4.0As soon as I select Plugins/napari Sediment/Sediment (or any other component), I get:
RuntimeError: Failed to import command at 'napari_sediment.sediment_widget:SedimentWidget': module 'numpy' has no attribute 'complex'.
`np.complex` was a deprecated alias for the builtin `complex`. To avoid this error in existing code, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
and a very long traceback output in the console:
AttributeError Traceback (most recent call last)
~/miniconda3/envs/sediment/lib/python3.9/site-packages/npe2/_command_registry.py in resolve(self=CommandHandler(id='napari-sediment.make_qwidget'...'napari_sediment.sediment_widget:SedimentWidget'))
31 try:
---> 32 self.function = utils.import_python_name(self.python_name)
self.function = None
global utils.import_python_name = <function import_python_name at 0x73231c7d9a60>
self.python_name = 'napari_sediment.sediment_widget:SedimentWidget'
33 except Exception as e:
~/miniconda3/envs/sediment/lib/python3.9/site-packages/npe2/manifest/utils.py in import_python_name(python_name='napari_sediment.sediment_widget:SedimentWidget')
253
--> 254 mod = import_module(module_name)
mod = undefined
global import_module = <function import_module at 0x7323729df820>
module_name = 'napari_sediment.sediment_widget'
255 return getattr(mod, funcname)
~/miniconda3/envs/sediment/lib/python3.9/importlib/__init__.py in import_module(name='napari_sediment.sediment_widget', package=None)
126 level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)
global _bootstrap._gcd_import = <function _gcd_import at 0x732373c61310>
name = 'napari_sediment.sediment_widget'
level = 0
package = None
128
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _gcd_import(name='napari_sediment.sediment_widget', package=None, level=0)
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _find_and_load(name='napari_sediment.sediment_widget', import_=<function _gcd_import>)
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _find_and_load_unlocked(name='napari_sediment.sediment_widget', import_=<function _gcd_import>)
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _call_with_frames_removed(f=<function _gcd_import>, *args=('napari_sediment',), **kwds={})
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _gcd_import(name='napari_sediment', package=None, level=0)
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _find_and_load(name='napari_sediment', import_=<function _gcd_import>)
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _find_and_load_unlocked(name='napari_sediment', import_=<function _gcd_import>)
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _load_unlocked(spec=ModuleSpec(name='napari_sediment', loader=<_froz...nt/lib/python3.9/site-packages/napari_sediment']))
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap_external.py in exec_module(self=<_frozen_importlib_external.SourceFileLoader object>, module=<module 'napari_sediment' from '/home/alobo/mini...on3.9/site-packages/napari_sediment/__init__.py'>)
~/miniconda3/envs/sediment/lib/python3.9/importlib/_bootstrap.py in _call_with_frames_removed(f=<built-in function exec>, *args=(<code object <module> at 0x7322e2bd4190, file "/...te-packages/napari_sediment/__init__.py", line 2>, {'__builtins__': {'ArithmeticError': <class 'ArithmeticError'>, 'AssertionError': <class 'AssertionError'>, 'AttributeError': <class 'AttributeError'>, 'BaseException': <class 'BaseException'>, 'BlockingIOError': <class 'BlockingIOError'>, 'BrokenPipeError': <class 'BrokenPipeError'>, 'BufferError': <class 'BufferError'>, 'BytesWarning': <class 'BytesWarning'>, 'ChildProcessError': <class 'ChildProcessError'>, 'ConnectionAbortedError': <class 'ConnectionAbortedError'>, ...}, '__cached__': '/home/alobo/miniconda3/envs/sediment/lib/python3...pari_sediment/__pycache__/__init__.cpython-39.pyc', '__doc__': None, '__file__': '/home/alobo/miniconda3/envs/sediment/lib/python3.9/site-packages/napari_sediment/__init__.py', '__loader__': <_frozen_importlib_external.SourceFileLoader object>, '__name__': 'napari_sediment', '__package__': 'napari_sediment', '__path__': ['/home/alobo/miniconda3/envs/sediment/lib/python3.9/site-packages/napari_sediment'], '__spec__': ModuleSpec(name='napari_sediment', loader=<_froz...nt/lib/python3.9/site-packages/napari_sediment']), '__version__': '0.1.dev309+g5655932', ...}), **kwds={})
~/miniconda3/envs/sediment/lib/python3.9/site-packages/napari_sediment/__init__.py in <module>
7 from ._reader import napari_get_reader
----> 8 from .sediment_widget import SedimentWidget
global sediment_widget = undefined
global SedimentWidget = undefined
9
~/miniconda3/envs/sediment/lib/python3.9/site-packages/napari_sediment/sediment_widget.py in <module>
41 from .images import save_rgb_tiff_image
---> 42 from .widgets.rgb_widget import RGBWidget
global widgets.rgb_widget = undefined
global RGBWidget = undefined
43 from .utils import update_contrast_on_layer
~/miniconda3/envs/sediment/lib/python3.9/site-packages/napari_sediment/widgets/rgb_widget.py in <module>
9
---> 10 from ..utils import update_contrast_on_layer
global utils = undefined
global update_contrast_on_layer = undefined
11
~/miniconda3/envs/sediment/lib/python3.9/site-packages/napari_sediment/utils.py in <module>
1 import numpy as np
----> 2 import colour
global colour = undefined
3
~/.local/lib/python3.9/site-packages/colour/__init__.py in <module>
66 table_interpolation, lagrange_coefficients)
---> 67 from .colorimetry import (
global colorimetry = undefined
global BANDPASS_CORRECTION_METHODS = undefined
global CCS_ILLUMINANTS = undefined
global CCS_LIGHT_SOURCES = undefined
global LIGHTNESS_METHODS = undefined
global LUMINANCE_METHODS = undefined
global MSDS_CMFS = undefined
global MSDS_TO_XYZ_METHODS = undefined
global MultiSpectralDistributions = undefined
global SDS_ILLUMINANTS = undefined
global SDS_LEFS = undefined
global SDS_LIGHT_SOURCES = undefined
global SD_GAUSSIAN_METHODS = undefined
global SD_MULTI_LEDS_METHODS = undefined
global SD_SINGLE_LED_METHODS = undefined
global SD_TO_XYZ_METHODS = undefined
global SPECTRAL_SHAPE_ASTME308 = undefined
global SPECTRAL_SHAPE_DEFAULT = undefined
global SpectralDistribution = undefined
global SpectralShape = undefined
global TVS_ILLUMINANTS_HUNTERLAB = undefined
global WHITENESS_METHODS = undefined
global YELLOWNESS_METHODS = undefined
global bandpass_correction = undefined
global colorimetric_purity = undefined
global complementary_wavelength = undefined
global dominant_wavelength = undefined
global excitation_purity = undefined
global lightness = undefined
global luminance = undefined
global luminous_efficacy = undefined
global luminous_efficiency = undefined
global luminous_flux = undefined
global msds_constant = undefined
global msds_ones = undefined
global msds_zeros = undefined
global msds_to_XYZ = undefined
global sd_CIE_illuminant_D_series = undefined
global sd_CIE_standard_illuminant_A = undefined
global sd_blackbody = undefined
global sd_constant = undefined
global sd_gaussian = undefined
global sd_mesopic_luminous_efficiency_function = undefined
global sd_multi_leds = undefined
global sd_ones = undefined
global sd_single_led = undefined
global sd_to_XYZ = undefined
global sd_zeros = undefined
global wavelength_to_XYZ = undefined
global whiteness = undefined
global yellowness = undefined
68 BANDPASS_CORRECTION_METHODS, CCS_ILLUMINANTS, CCS_LIGHT_SOURCES,
~/.local/lib/python3.9/site-packages/colour/colorimetry/__init__.py in <module>
9
---> 10 from .spectrum import (SpectralShape, SPECTRAL_SHAPE_DEFAULT,
global spectrum = undefined
global SpectralShape = undefined
global SPECTRAL_SHAPE_DEFAULT = undefined
global SpectralDistribution = undefined
global MultiSpectralDistributions = undefined
global sds_and_msds_to_sds = undefined
global sds_and_msds_to_msds = undefined
11 SpectralDistribution, MultiSpectralDistributions,
~/.local/lib/python3.9/site-packages/colour/colorimetry/spectrum.py in <module>
486
--> 487 SPECTRAL_SHAPE_DEFAULT = SpectralShape(360, 780, 1)
global SPECTRAL_SHAPE_DEFAULT = undefined
global SpectralShape = <class 'colour.colorimetry.spectrum.SpectralShape'>
488 """
~/.local/lib/python3.9/site-packages/colour/colorimetry/spectrum.py in __init__(self=SpectralShape(None, None, None), start=360, end=780, interval=1)
99 self._interval = None
--> 100 self.start = start
self.start = None
start = 360
101 self.end = end
~/.local/lib/python3.9/site-packages/colour/colorimetry/spectrum.py in start(self=SpectralShape(None, None, None), value=360)
128 if value is not None:
--> 129 assert is_numeric(value), (
global is_numeric = <function is_numeric at 0x7322cb35c430>
value.format = undefined
value = 360
130 '"{0}" attribute: "{1}" is not a "numeric"!'.format(
~/.local/lib/python3.9/site-packages/colour/utilities/common.py in is_numeric(a=360)
612 list(integer_types) +
--> 613 [float, complex, np.integer, np.floating, np.complex]))
global float = undefined
global complex = undefined
global np.integer = <class 'numpy.integer'>
global np.floating = <class 'numpy.floating'>
global np.complex = undefined
614
~/miniconda3/envs/sediment/lib/python3.9/site-packages/numpy/__init__.py in __getattr__(attr='complex')
323 if attr in __former_attrs__:
--> 324 raise AttributeError(__former_attrs__[attr])
global AttributeError = undefined
global __former_attrs__ = {'object': "module 'numpy' has no attribute 'object'.\n`np.object` was a deprecated alias for the builtin `object`. To avoid this error in existing code, use `object` by itself. Doing this will not modify any behavior and is safe. \nThe aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:\n https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations", 'bool': "module 'numpy' has no attribute 'bool'.\n`np.bool` was a deprecated alias for the builtin `bool`. To avoid this error in existing code, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.\nThe aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:\n https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations", 'float': "module 'numpy' has no attribute 'float'.\n`np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here.\nThe aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:\n https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations", 'complex': "module 'numpy' has no attribute 'complex'.\n`np.complex` was a deprecated alias for the builtin `complex`. To avoid this error in existing code, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.\nThe aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:\n https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations", 'str': "module 'numpy' has no attribute 'str'.\n`np.str` was a deprecated alias for the builtin `str`. To avoid this error in existing code, use `str` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.str_` here.\nThe aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:\n https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations", 'int': "module 'numpy' has no attribute 'int'.\n`np.int` was a deprecated alias for the builtin `int`. To avoid this error in existing code, use `int` by itself. Doing this will not modify any behavior and is safe. When replacing `np.int`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.\nThe aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:\n https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations"}
attr = 'complex'
325
AttributeError: module 'numpy' has no attribute 'complex'.
`np.complex` was a deprecated alias for the builtin `complex`. To avoid this error in existing code, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
The above exception was the direct cause of the following exception:
RuntimeError Traceback (most recent call last)
~/miniconda3/envs/sediment/lib/python3.9/site-packages/napari/_qt/menus/plugins_menu.py in _add_toggle_widget(key=('napari-sediment', 'Sediment'), hook_type='dock')
103
104 if hook_type == 'dock':
--> 105 self._win.add_plugin_dock_widget(*key)
global self._win.add_plugin_dock_widget = undefined
key = ('napari-sediment', 'Sediment')
106 else:
107 self._win._add_plugin_function_widget(*key)
~/miniconda3/envs/sediment/lib/python3.9/site-packages/napari/_qt/qt_main_window.py in add_plugin_dock_widget(self=<napari._qt.qt_main_window.Window object>, plugin_name='napari-sediment', widget_name='Sediment', tabify=False)
874 dock_kwargs = {}
875
--> 876 if result := _npe2.get_widget_contribution(plugin_name, widget_name):
result = undefined
_npe2.get_widget_contribution = <function get_widget_contribution at 0x7323152989d0>
plugin_name = 'napari-sediment'
widget_name = 'Sediment'
877 Widget, widget_name = result
878
~/miniconda3/envs/sediment/lib/python3.9/site-packages/napari/plugins/_npe2.py in get_widget_contribution(plugin_name='napari-sediment', widget_name='Sediment')
134 if contrib.plugin_name == plugin_name:
135 if not widget_name or contrib.display_name == widget_name:
--> 136 return contrib.get_callable(), contrib.display_name
contrib.get_callable = <bound method WidgetContribution.get_callable of WidgetContribution(command='napari-sediment.make_qwidget', display_name='Sediment', autogenerate=False)>
contrib.display_name = 'Sediment'
137 widgets_seen.add(contrib.display_name)
138 if widget_name and widgets_seen:
~/miniconda3/envs/sediment/lib/python3.9/site-packages/npe2/manifest/contributions/_widgets.py in get_callable(self=WidgetContribution(command='napari-sediment.make...et', display_name='Sediment', autogenerate=False), _registry=None)
47 self, _registry: Optional[CommandRegistry] = None
48 ) -> Callable[..., Widget]:
---> 49 func = super().get_callable()
func = undefined
global super.get_callable = undefined
50 if self.autogenerate:
51 try:
~/miniconda3/envs/sediment/lib/python3.9/site-packages/npe2/manifest/utils.py in get_callable(self=WidgetContribution(command='napari-sediment.make...et', display_name='Sediment', autogenerate=False), _registry=<npe2._command_registry.CommandRegistry object>)
69
70 _registry = PluginManager.instance().commands
---> 71 return _registry.get(self.command)
_registry.get = <bound method CommandRegistry.get of <npe2._command_registry.CommandRegistry object at 0x732315fc97c0>>
self.command = 'napari-sediment.make_qwidget'
72
73 @property
~/miniconda3/envs/sediment/lib/python3.9/site-packages/npe2/_command_registry.py in get(self=<npe2._command_registry.CommandRegistry object>, id='napari-sediment.make_qwidget')
136 if id not in self._commands: # sourcery skip
137 raise KeyError(f"command {id!r} not registered")
--> 138 return self._commands[id].resolve()
self._commands = {'napari-sediment.get_reader': CommandHandler(id='napari-sediment.get_reader', function=None, python_name='napari_sediment._reader:napari_get_reader'), 'napari-sediment.make_qwidget': CommandHandler(id='napari-sediment.make_qwidget', function=None, python_name='napari_sediment.sediment_widget:SedimentWidget'), 'napari-sediment.make_hyperwidget': CommandHandler(id='napari-sediment.make_hyperwidget', function=None, python_name='napari_sediment.hyperanalysis_widget:HyperAnalysisWidget'), 'napari-sediment.make_spectralindexwidget': CommandHandler(id='napari-sediment.make_spectralindexwidget', function=None, python_name='napari_sediment.spectral_indices_widget:SpectralIndexWidget'), 'napari-sediment.make_batchwidget': CommandHandler(id='napari-sediment.make_batchwidget', function=None, python_name='napari_sediment.batch_indices:BatchIndexWidget'), 'napari-sediment.make_preproc_batchwidget': CommandHandler(id='napari-sediment.make_preproc_batchwidget', function=None, python_name='napari_sediment.batch_preproc:BatchPreprocWidget'), 'napari-sediment.make_convertwidget': CommandHandler(id='napari-sediment.make_convertwidget', function=None, python_name='napari_sediment.convert_widget:ConvertWidget')}
id.resolve = undefined
139
140 def execute(self, id: str, args=(), kwargs=None) -> Any:
~/miniconda3/envs/sediment/lib/python3.9/site-packages/npe2/_command_registry.py in resolve(self=CommandHandler(id='napari-sediment.make_qwidget'...'napari_sediment.sediment_widget:SedimentWidget'))
32 self.function = utils.import_python_name(self.python_name)
33 except Exception as e:
---> 34 raise RuntimeError(
global RuntimeError = undefined
e = undefined
35 f"Failed to import command at {self.python_name!r}: {e}"
36 ) from e
RuntimeError: Failed to import command at 'napari_sediment.sediment_widget:SedimentWidget': module 'numpy' has no attribute 'complex'.
`np.complex` was a deprecated alias for the builtin `complex`. To avoid this error in existing code, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
(sediment) alobo@pop-os:~$
Can you post the output of conda list for that environment? I think you have a very outdated version of the the color-science package which produces this message and I don't know why.
aloboa
commented
5 months ago I had not realized that Convpaint was outside napari Sediment in the plugin list. Convpaint starts up with no problems. I can display an RGB image.
Can you post the output of conda list for that environment?
I do not see color-science listed. My napari-sediment version is 0.1.dev309+g5655932
(sediment) alobo@pop-os:~$ conda list
# packages in environment at /home/alobo/miniconda3/envs/sediment:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alabaster 0.7.16 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.10 hd590300_0 conda-forge
aom 3.8.1 h59595ed_0 conda-forge
app-model 0.2.4 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
autopep8 2.1.1 pypi_0 pypi
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pypi_0 pypi
blosc 1.21.5 h0f2a231_0 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py39h3d6467e_1 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-blosc2 2.13.2 hb4ffafa_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cachey 0.2.1 pyh9f0ad1d_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
charls 2.4.2 h59595ed_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
cmap 0.1.3 pypi_0 pypi
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.1 pyhd8ed1ab_0 conda-forge
cycler 0.12.1 pypi_0 pypi
cytoolz 0.12.3 py39hd1e30aa_0 conda-forge
dask-core 2024.2.0 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.1 py39h3d6467e_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.14 pypi_0 pypi
distributed 2024.2.0 pypi_0 pypi
docstring_parser 0.15 pyhd8ed1ab_0 conda-forge
docutils 0.17.1 py39hf3d152e_4 conda-forge
einops 0.7.0 pypi_0 pypi
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.5.0 hcb278e6_1 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
filelock 3.13.1 pypi_0 pypi
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_1 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.4.0 pyhd8ed1ab_0 conda-forge
fsspec 2024.2.0 pyhca7485f_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
glib 2.78.3 hfc55251_0 conda-forge
glib-tools 2.78.3 hfc55251_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
gst-plugins-base 1.22.9 h8e1006c_0 conda-forge
gstreamer 1.22.9 h98fc4e7_0 conda-forge
h5py 3.10.0 pypi_0 pypi
harfbuzz 8.3.0 h3d44ed6_0 conda-forge
heapdict 1.0.1 py_0 conda-forge
hsluv 5.0.4 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
imagecodecs 2024.1.1 py39hf9b8f0e_0 conda-forge
imageio 2.34.0 pyh4b66e23_0 conda-forge
imageio-ffmpeg 0.4.9 pypi_0 pypi
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.0.1 pyha770c72_0 conda-forge
importlib_metadata 7.0.1 hd8ed1ab_0 conda-forge
importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge
in-n-out 0.1.9 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.2 pyhd33586a_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
ipython-genutils 0.2.0 pypi_0 pypi
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
jsonschema 4.21.1 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.0 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.1 py39hf3d152e_0 conda-forge
jupytext 1.16.2 pypi_0 pypi
jxrlib 1.1 hd590300_3 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py39h7633fee_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lazy_loader 0.3 pyhd8ed1ab_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libavif16 1.0.4 h1dcd450_0 conda-forge
libblas 3.9.0 21_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 21_linux64_openblas conda-forge
libclang 15.0.7 default_hb11cfb5_4 conda-forge
libclang13 15.0.7 default_ha2b6cf4_4 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libdeflate 1.19 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgfortran-ng 13.2.0 h69a702a_5 conda-forge
libgfortran5 13.2.0 ha4646dd_5 conda-forge
libglib 2.78.3 h783c2da_0 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libgpg-error 1.47 h71f35ed_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblapack 3.9.0 21_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.42 h2797004_0 conda-forge
libpq 16.2 h33b98f1_0 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.45.1 h2797004_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libsystemd0 255 h3516f8a_0 conda-forge
libtiff 4.6.0 ha9c0a0a_2 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.6.0 hd429924_1 conda-forge
libxml2 2.12.5 h232c23b_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
libzopfli 1.0.3 h9c3ff4c_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
loguru 0.7.2 pypi_0 pypi
lz4-c 1.9.4 hcb278e6_0 conda-forge
magicgui 0.8.1 pyhd8ed1ab_0 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py39hd1e30aa_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
matplotlib-scalebar 0.8.1 pypi_0 pypi
mdit-py-plugins 0.4.1 pypi_0 pypi
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
microfilm 0.2.1 pypi_0 pypi
mpg123 1.32.4 h59595ed_0 conda-forge
msgpack-python 1.0.7 py39h7633fee_0 conda-forge
mypy_extensions 1.0.0 pyha770c72_0 conda-forge
mysql-common 8.0.33 hf1915f5_6 conda-forge
mysql-libs 8.0.33 hca2cd23_6 conda-forge
napari 0.4.19 pyh9208f05_0 conda-forge
napari-animation 0.0.8 pypi_0 pypi
napari-annotation-project 0.1.1 pypi_0 pypi
napari-assistant 0.4.7 pypi_0 pypi
napari-console 0.0.9 pyh9208f05_0 conda-forge
napari-convpaint 0.4.0 pypi_0 pypi
napari-guitils 0.1.0 pypi_0 pypi
napari-matplotlib 0.2.1 pypi_0 pypi
napari-nifti 0.0.12 pypi_0 pypi
napari-plugin-engine 0.2.0 pyhd8ed1ab_2 conda-forge
napari-sediment 0.1.dev309+g5655932 pypi_0 pypi
napari-skimage-regionprops 0.10.1 pypi_0 pypi
napari-svg 0.1.10 pyhd8ed1ab_0 conda-forge
napari-time-series-plotter 0.0.6 pypi_0 pypi
napari-time-slicer 0.5.0 pypi_0 pypi
napari-tools-menu 0.1.19 pypi_0 pypi
napari-workflows 0.2.10 pypi_0 pypi
ncurses 6.4 h59595ed_2 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
netcdf4 1.6.5 pypi_0 pypi
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
npe2 0.7.4 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.98 h1d7d5a4_0 conda-forge
numcodecs 0.12.1 py39h3d6467e_0 conda-forge
numpy 1.26.4 py39h474f0d3_0 conda-forge
numpydoc 1.5.0 pyhd8ed1ab_0 conda-forge
nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi
nvidia-cudnn-cu12 8.9.2.26 pypi_0 pypi
nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi
nvidia-curand-cu12 10.3.2.106 pypi_0 pypi
nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi
nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi
nvidia-nccl-cu12 2.19.3 pypi_0 pypi
nvidia-nvjitlink-cu12 12.3.101 pypi_0 pypi
nvidia-nvtx-cu12 12.1.105 pypi_0 pypi
openjpeg 2.5.0 h488ebb8_3 conda-forge
openssl 3.2.1 hd590300_0 conda-forge
packaging 23.2 pyhd8ed1ab_0 conda-forge
pandas 2.2.0 py39hddac248_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
partd 1.4.1 pyhd8ed1ab_0 conda-forge
pcre2 10.42 hcad00b1_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.2.0 py39had0adad_0 conda-forge
pint 0.23 pyhd8ed1ab_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
ply 3.11 py_1 conda-forge
pooch 1.8.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
psutil 5.9.8 py39hd1e30aa_0 conda-forge
psygnal 0.9.5 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio-client 16.1 hb77b528_5 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pyclesperanto-prototype 0.24.4 pypi_0 pypi
pycodestyle 2.11.1 pypi_0 pypi
pyconify 0.1.6 pyhd8ed1ab_0 conda-forge
pydantic 1.10.13 py39hd1e30aa_1 conda-forge
pydantic-compat 0.1.1 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pyopencl 2024.2.2 pypi_0 pypi
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.1 pypi_0 pypi
pyperclip 1.8.2 pypi_0 pypi
pyproject_hooks 1.0.0 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py39h52134e7_5 conda-forge
pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge
pyrsistent 0.20.0 pypi_0 pypi
pyshp 2.3.1 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.18 h0755675_1_cpython conda-forge
python-build 1.0.3 pyhd8ed1ab_0 conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytools 2024.1.3 pypi_0 pypi
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py39h44dd56e_1 conda-forge
pyyaml 6.0.1 py39hd1e30aa_1 conda-forge
pyzmq 25.1.2 py39h8c080ef_0 conda-forge
qt-main 5.15.8 h5810be5_19 conda-forge
qtconsole-base 5.5.1 pyha770c72_0 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
rav1e 0.6.6 he8a937b_2 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.33.0 pyhd8ed1ab_0 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rich 13.7.0 pyhd8ed1ab_0 conda-forge
rpds-py 0.18.0 py39h9fdd4d6_0 conda-forge
scikit-image 0.22.0 py39hddac248_2 conda-forge
scikit-learn 1.4.1.post1 pypi_0 pypi
scipy 1.12.0 py39h474f0d3_2 conda-forge
setuptools 69.0.3 pyhd8ed1ab_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_0 conda-forge
simpleitk 2.3.1 pypi_0 pypi
sip 6.7.12 py39h3d6467e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sortedcontainers 2.4.0 pypi_0 pypi
soupsieve 2.5 pypi_0 pypi
spectral 0.23.1 pypi_0 pypi
sphinx 4.5.0 pyh6c4a22f_0 conda-forge
sphinxcontrib-applehelp 1.0.4 pyhd8ed1ab_0 conda-forge
sphinxcontrib-devhelp 1.0.2 py_0 conda-forge
sphinxcontrib-htmlhelp 2.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-qthelp 1.0.3 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
superqt 0.6.1 pyh9208f05_0 conda-forge
svt-av1 1.8.0 h59595ed_0 conda-forge
tblib 3.0.0 pypi_0 pypi
tifffile 2024.2.12 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomli-w 1.0.0 pyhd8ed1ab_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
torch 2.2.0 pypi_0 pypi
torchvision 0.17.0 pypi_0 pypi
tornado 6.3.3 py39hd1e30aa_1 conda-forge
tqdm 4.66.2 pyhd8ed1ab_0 conda-forge
traitlets 5.14.1 pyhd8ed1ab_0 conda-forge
transforms3d 0.4.1 pypi_0 pypi
triton 2.2.0 pypi_0 pypi
typer 0.9.0 pyhd8ed1ab_0 conda-forge
typing-extensions 4.9.0 hd8ed1ab_0 conda-forge
typing_extensions 4.9.0 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
urllib3 2.2.0 pyhd8ed1ab_0 conda-forge
vispy 0.14.1 py39h51dfa90_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pypi_0 pypi
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
wrapt 1.16.0 py39hd1e30aa_0 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.41 hd590300_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.7 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zarr 2.17.0 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 h59595ed_0 conda-forge
zfp 1.0.1 h59595ed_0 conda-forge
zict 3.0.0 pypi_0 pypi
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
It looks like your installation looks for missing packages outside the environment (in ~/.local/lib) and finds the outdated color package there. This is a very strange configuration as the whole point of environments is to not use anything outside them. In any case that should be solved by updating the plugin and its dependencies with pip install git+https://github.com/guiwitz/napari-sediment.git -U
aloboa
commented
5 months ago Unfortunately, I get the same problem after pip install git+https://github.com/guiwitz/napari-sediment.git -U
I have created a new environment and started again:
(base) alobo@pop-os:~$ conda create -n sediment2 python=3.9 napari pyqt -c conda-forge
(base) alobo@pop-os:~$ conda activate sediment2
(sediment2) alobo@pop-os:~$ pip install git+https://github.com/guiwitz/napari-sediment.git
and get:
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
hyperspy 1.6.4 requires numba, which is not installed.
nbconvert 7.6.0 requires beautifulsoup4, which is not installed.
ncvue 4.1.2 requires netcdf4, which is not installed.
ncvue 4.1.2 requires pyshp, which is not installed.
Successfully installed cmap-0.2.1 cycler-0.12.1 distributed-2024.5.2 einops-0.8.0 filelock-3.14.0 h5py-3.11.0 ipython-genutils-0.2.0 matplotlib-scalebar-0.8.1 microfilm-0.2.1 napari-annotation-project-0.1.1 napari-convpaint-0.4.0 napari-guitils-0.1.0 napari-matplotlib-2.0.1 napari-sediment-0.1.dev309+g5655932 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-8.9.2.26 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.20.5 nvidia-nvjitlink-cu12-12.5.40 nvidia-nvtx-cu12-12.1.105 pyparsing-3.1.2 pyrsistent-0.20.0 scikit-learn-1.5.0 sortedcontainers-2.4.0 spectral-0.23.1 tblib-3.0.0 threadpoolctl-3.5.0 torch-2.3.0 torchvision-0.18.0 triton-2.3.0 webencodings-0.5.1 zict-3.0.0I start napari, select napari Sediment and get the same problem:
RuntimeError: Failed to import command at 'napari_sediment.sediment_widget:SedimentWidget': module 'numpy' has no attribute 'complex'.
`np.complex` was a deprecated alias for the builtin `complex`. To avoid this error in existing code, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecationsMy conda list is now:
(sediment2) alobo@pop-os:~$ conda list
# packages in environment at /home/alobo/miniconda3/envs/sediment2:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alabaster 0.7.16 pyhd8ed1ab_0 conda-forge
alsa-lib 1.2.11 hd590300_1 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge
aom 3.9.0 hac33072_0 conda-forge
app-model 0.2.7 pyhd8ed1ab_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
asciitree 0.3.3 py_2 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
blosc 1.21.5 hc2324a3_1 conda-forge
brotli 1.1.0 hd590300_1 conda-forge
brotli-bin 1.1.0 hd590300_1 conda-forge
brotli-python 1.1.0 py39h3d6467e_1 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-blosc2 2.14.4 hb4ffafa_1 conda-forge
ca-certificates 2024.6.2 hbcca054_0 conda-forge
cachey 0.2.1 pyh9f0ad1d_0 conda-forge
cairo 1.18.0 h3faef2a_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
charls 2.4.2 h59595ed_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
cmap 0.2.1 pypi_0 pypi
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
cycler 0.12.1 pypi_0 pypi
cytoolz 0.12.3 py39hd1e30aa_0 conda-forge
dask-core 2024.5.2 pyhd8ed1ab_0 conda-forge
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.1 py39h3d6467e_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
distributed 2024.5.2 pypi_0 pypi
docstring_parser 0.16 pyhd8ed1ab_0 conda-forge
docutils 0.21.2 pyhd8ed1ab_0 conda-forge
einops 0.8.0 pypi_0 pypi
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
expat 2.6.2 h59595ed_0 conda-forge
fasteners 0.17.3 pyhd8ed1ab_0 conda-forge
filelock 3.14.0 pypi_0 pypi
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_2 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
freetype-py 2.4.0 pyhd8ed1ab_0 conda-forge
fsspec 2024.6.0 pyhff2d567_0 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
giflib 5.2.2 hd590300_0 conda-forge
glib 2.80.2 hf974151_0 conda-forge
glib-tools 2.80.2 hb6ce0ca_0 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
gst-plugins-base 1.24.4 h9ad1361_0 conda-forge
gstreamer 1.24.4 haf2f30d_0 conda-forge
h5py 3.11.0 pypi_0 pypi
harfbuzz 8.5.0 hfac3d4d_0 conda-forge
heapdict 1.0.1 py_0 conda-forge
hsluv 5.0.4 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.7 pyhd8ed1ab_0 conda-forge
imagecodecs 2024.6.1 py39hbbab4d9_0 conda-forge
imageio 2.34.1 pyh4b66e23_0 conda-forge
imagesize 1.4.1 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
in-n-out 0.2.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.3 pyhd33586a_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
ipython-genutils 0.2.0 pypi_0 pypi
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py39hf3d152e_0 conda-forge
jxrlib 1.1 hd590300_3 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.5 py39h7633fee_1 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lazy_loader 0.4 pyhd8ed1ab_0 conda-forge
lcms2 2.16 hb7c19ff_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_2 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libavif16 1.0.4 hd2f8ffe_4 conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcap 2.69 h0f662aa_0 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge
libclang13 18.1.6 default_h5d6823c_0 conda-forge
libcups 2.3.3 h4637d8d_4 conda-forge
libdeflate 1.20 hd590300_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libexpat 2.6.2 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc-ng 13.2.0 h77fa898_7 conda-forge
libgcrypt 1.10.3 hd590300_0 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libgfortran-ng 13.2.0 h69a702a_7 conda-forge
libgfortran5 13.2.0 hca663fb_7 conda-forge
libglib 2.80.2 hf974151_0 conda-forge
libgomp 13.2.0 h77fa898_7 conda-forge
libgpg-error 1.49 h4f305b6_0 conda-forge
libhwy 1.1.0 h00ab1b0_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
libjxl 0.10.2 hcae5a98_0 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libllvm15 15.0.7 hb3ce162_4 conda-forge
libllvm18 18.1.6 hb77312f_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 16.3 ha72fbe1_0 conda-forge
libsndfile 1.2.2 hc60ed4a_1 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.45.3 h2797004_0 conda-forge
libstdcxx-ng 13.2.0 hc0a3c3a_7 conda-forge
libsystemd0 255 h3516f8a_1 conda-forge
libtiff 4.6.0 h1dd3fc0_3 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.7.0 h662e7e4_0 conda-forge
libxml2 2.12.7 hc051c1a_1 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
libzopfli 1.0.3 h9c3ff4c_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
magicgui 0.8.2 pyhd8ed1ab_1 conda-forge
markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.5 py39hd1e30aa_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
matplotlib-scalebar 0.8.1 pypi_0 pypi
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
microfilm 0.2.1 pypi_0 pypi
mpg123 1.32.6 h59595ed_0 conda-forge
msgpack-python 1.0.8 py39h95fdab5_0 conda-forge
mysql-common 8.3.0 hf1915f5_4 conda-forge
mysql-libs 8.3.0 hca2cd23_4 conda-forge
napari 0.4.19.post1 pyh9208f05_0 conda-forge
napari-annotation-project 0.1.1 pypi_0 pypi
napari-console 0.0.9 pyh9208f05_0 conda-forge
napari-convpaint 0.4.0 pypi_0 pypi
napari-guitils 0.1.0 pypi_0 pypi
napari-matplotlib 2.0.1 pypi_0 pypi
napari-plugin-engine 0.2.0 pyhd8ed1ab_2 conda-forge
napari-sediment 0.1.dev309+g5655932 pypi_0 pypi
napari-svg 0.1.10 pyhd8ed1ab_0 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.2.1 pyhd8ed1ab_0 conda-forge
npe2 0.7.5 pyhd8ed1ab_0 conda-forge
nspr 4.35 h27087fc_0 conda-forge
nss 3.100 hca3bf56_0 conda-forge
numcodecs 0.12.1 py39h84cc369_1 conda-forge
numpy 1.26.4 py39h474f0d3_0 conda-forge
numpydoc 1.7.0 pyhd8ed1ab_1 conda-forge
nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi
nvidia-cudnn-cu12 8.9.2.26 pypi_0 pypi
nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi
nvidia-curand-cu12 10.3.2.106 pypi_0 pypi
nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi
nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi
nvidia-nccl-cu12 2.20.5 pypi_0 pypi
nvidia-nvjitlink-cu12 12.5.40 pypi_0 pypi
nvidia-nvtx-cu12 12.1.105 pypi_0 pypi
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.1 h4ab18f5_0 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py39hfc16268_1 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
partd 1.4.2 pyhd8ed1ab_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 10.3.0 py39h90c7501_0 conda-forge
pint 0.23 pyhd8ed1ab_1 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge
ply 3.11 pyhd8ed1ab_2 conda-forge
pooch 1.8.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.46 pyha770c72_0 conda-forge
psutil 5.9.8 py39hd1e30aa_0 conda-forge
psygnal 0.11.1 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pulseaudio-client 17.0 hb77b528_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pyconify 0.1.6 pyhd8ed1ab_0 conda-forge
pydantic 2.7.3 pyhd8ed1ab_0 conda-forge
pydantic-compat 0.1.2 pyhd8ed1ab_0 conda-forge
pydantic-core 2.18.4 py39ha68c5e3_0 conda-forge
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge
pyparsing 3.1.2 pypi_0 pypi
pyproject_hooks 1.1.0 pyhd8ed1ab_0 conda-forge
pyqt 5.15.9 py39h52134e7_5 conda-forge
pyqt5-sip 12.12.2 py39h3d6467e_5 conda-forge
pyrsistent 0.20.0 pypi_0 pypi
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.19 h0755675_0_cpython conda-forge
python-build 1.2.1 pyhd8ed1ab_0 conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.9 4_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pywavelets 1.4.1 py39h44dd56e_1 conda-forge
pyyaml 6.0.1 py39hd1e30aa_1 conda-forge
pyzmq 26.0.3 py39ha1047a2_0 conda-forge
qt-main 5.15.8 hc9dc06e_21 conda-forge
qtconsole-base 5.5.2 pyha770c72_0 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
rav1e 0.6.6 he8a937b_2 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.35.1 pyhd8ed1ab_0 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
rich 13.7.1 pyhd8ed1ab_0 conda-forge
rpds-py 0.18.1 py39ha68c5e3_0 conda-forge
scikit-image 0.22.0 py39hddac248_2 conda-forge
scikit-learn 1.5.0 pypi_0 pypi
scipy 1.13.1 py39haf93ffa_0 conda-forge
setuptools 70.0.0 pyhd8ed1ab_0 conda-forge
shellingham 1.5.4 pyhd8ed1ab_0 conda-forge
sip 6.7.12 py39h3d6467e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.2.0 hdb0a2a9_1 conda-forge
snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge
sortedcontainers 2.4.0 pypi_0 pypi
spectral 0.23.1 pypi_0 pypi
sphinx 7.3.7 pyhd8ed1ab_0 conda-forge
sphinxcontrib-applehelp 1.0.8 pyhd8ed1ab_0 conda-forge
sphinxcontrib-devhelp 1.0.6 pyhd8ed1ab_0 conda-forge
sphinxcontrib-htmlhelp 2.0.5 pyhd8ed1ab_0 conda-forge
sphinxcontrib-jsmath 1.0.1 pyhd8ed1ab_0 conda-forge
sphinxcontrib-qthelp 1.0.7 pyhd8ed1ab_0 conda-forge
sphinxcontrib-serializinghtml 1.1.10 pyhd8ed1ab_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
superqt 0.6.6 pyh9208f05_0 conda-forge
svt-av1 2.1.0 hac33072_0 conda-forge
tabulate 0.9.0 pyhd8ed1ab_1 conda-forge
tblib 3.0.0 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2024.5.22 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pyhd8ed1ab_0 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomli-w 1.0.0 pyhd8ed1ab_0 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
torch 2.3.0 pypi_0 pypi
torchvision 0.18.0 pypi_0 pypi
tornado 6.4 py39hd1e30aa_0 conda-forge
tqdm 4.66.4 pyhd8ed1ab_0 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
triton 2.3.0 pypi_0 pypi
typer 0.12.3 pyhd8ed1ab_0 conda-forge
typer-slim 0.12.3 pyhd8ed1ab_0 conda-forge
typer-slim-standard 0.12.3 hd8ed1ab_0 conda-forge
typing-extensions 4.12.1 hd8ed1ab_0 conda-forge
typing_extensions 4.12.1 pyha770c72_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
vispy 0.14.2 py39h21f1d72_1 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pypi_0 pypi
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
wrapt 1.16.0 py39hd1e30aa_0 conda-forge
xcb-util 0.4.0 hd590300_1 conda-forge
xcb-util-image 0.4.0 h8ee46fc_1 conda-forge
xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge
xcb-util-renderutil 0.3.9 hd590300_1 conda-forge
xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge
xkeyboard-config 2.41 hd590300_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.9 h8ee46fc_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.11 hd590300_0 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zarr 2.18.2 pyhd8ed1ab_0 conda-forge
zeromq 4.3.5 h75354e8_4 conda-forge
zfp 1.0.1 h59595ed_0 conda-forge
zict 3.0.0 pypi_0 pypi
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.3.1 h4ab18f5_1 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forgeI have installed netcdf4, hyperspy, numba, ncvue, pyshp and had a clean installation of
(sediment2) alobo@pop-os:~$ pip install git+https://github.com/guiwitz/napari-sediment.git
but the problem remains the same:
RuntimeError: Failed to import command at 'napari_sediment.sediment_widget:SedimentWidget': module 'numpy' has no attribute 'complex'.
`np.complex` was a deprecated alias for the builtin `complex`. To avoid this error in existing code, use `complex` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.complex128` here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
malloc_consolidate(): unaligned fastbin chunk detected
Convpaint starts up fine.
guiwitz
commented
5 months ago What happens when you do pip install colour-science? Not all packages that are requirements get installed, probably because your conda has a weird setting making it look for packages in other places. Maybe you can also post the result of conda config.
aloboa
commented
5 months ago What happens when you do pip install colour-science ?
(sediment2) alobo@pop-os:~$ pip install colour-science
Requirement already satisfied: colour-science in ./.local/lib/python3.9/site-packages (0.3.16)
Requirement already satisfied: imageio in ./miniconda3/envs/sediment2/lib/python3.9/site-packages (from colour-science) (2.34.1)
Requirement already satisfied: scipy<2.0.0,>=1.1.0 in ./.local/lib/python3.9/site-packages (from colour-science) (1.11.3)
Requirement already satisfied: six in ./miniconda3/envs/sediment2/lib/python3.9/site-packages (from colour-science) (1.16.0)
Requirement already satisfied: numpy<1.28.0,>=1.21.6 in ./miniconda3/envs/sediment2/lib/python3.9/site-packages (from scipy<2.0.0,>=1.1.0->colour-science) (1.26.4)
Requirement already satisfied: pillow>=8.3.2 in ./miniconda3/envs/sediment2/lib/python3.9/site-packages (from imageio->colour-science) (10.3.0)But then same problem at starting napari Sedment
Maybe you can also post the result of conda config.
(sediment2) alobo@pop-os:~$ conda config --show
add_anaconda_token: True
add_pip_as_python_dependency: True
aggressive_update_packages:
- ca-certificates
- certifi
- openssl
allow_conda_downgrades: False
allow_cycles: True
allow_non_channel_urls: False
allow_softlinks: False
allowlist_channels: []
always_copy: False
always_softlink: False
always_yes: None
anaconda_upload: None
auto_activate_base: True
auto_stack: 0
auto_update_conda: True
bld_path:
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: flexible
channel_settings: []
channels:
- defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
conda_build: {}
create_default_packages: []
croot: /home/alobo/miniconda3/conda-bld
custom_channels:
pkgs/main: https://repo.anaconda.com
pkgs/r: https://repo.anaconda.com
pkgs/pro: https://repo.anaconda.com
custom_multichannels:
defaults:
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/r
local:
debug: False
default_channels:
- https://repo.anaconda.com/pkgs/main
- https://repo.anaconda.com/pkgs/r
default_python: 3.9
default_threads: None
deps_modifier: not_set
dev: False
disallowed_packages: []
download_only: False
dry_run: False
enable_private_envs: False
env_prompt: ({default_env})
envs_dirs:
- /home/alobo/miniconda3/envs
- /home/alobo/.conda/envs
error_upload_url: https://conda.io/conda-post/unexpected-error
execute_threads: 1
experimental: []
extra_safety_checks: False
fetch_threads: 5
force: False
force_32bit: False
force_reinstall: False
force_remove: False
ignore_pinned: False
json: False
local_repodata_ttl: 1
migrated_channel_aliases: []
migrated_custom_channels: {}
no_lock: False
no_plugins: False
non_admin_enabled: True
notify_outdated_conda: True
number_channel_notices: 5
offline: False
override_channels_enabled: True
path_conflict: clobber
pinned_packages: []
pip_interop_enabled: False
pkgs_dirs:
- /home/alobo/miniconda3/pkgs
- /home/alobo/.conda/pkgs
proxy_servers: {}
quiet: False
register_envs: True
remote_backoff_factor: 1
remote_connect_timeout_secs: 9.15
remote_max_retries: 3
remote_read_timeout_secs: 60.0
repodata_fns:
- current_repodata.json
- repodata.json
repodata_threads: None
report_errors: None
restore_free_channel: False
rollback_enabled: True
root_prefix: /home/alobo/miniconda3
safety_checks: warn
sat_solver: pycosat
separate_format_cache: False
shortcuts: True
show_channel_urls: None
signing_metadata_url_base: None
solver: libmamba
solver_ignore_timestamps: False
ssl_verify: True
subdir: linux-64
subdirs:
- linux-64
- noarch
target_prefix_override:
trace: False
track_features: []
unsatisfiable_hints: True
unsatisfiable_hints_check_depth: 2
update_modifier: update_specs
use_index_cache: False
use_local: False
use_only_tar_bz2: False
verbosity: 0
verify_threads: 1
(sediment2) alobo@pop-os:~$ Seems solved afer:
(sediment2) alobo@pop-os:~$ pip install colour-science -U
Requirement already satisfied: colour-science in ./.local/lib/python3.9/site-packages (0.3.16)
Collecting colour-science
Downloading colour_science-0.4.4-py3-none-any.whl.metadata (53 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.5/53.5 kB 1.2 MB/s eta 0:00:00
Requirement already satisfied: imageio<3,>=2 in ./miniconda3/envs/sediment2/lib/python3.9/site-packages (from colour-science) (2.34.1)
Requirement already satisfied: numpy<2,>=1.22 in ./miniconda3/envs/sediment2/lib/python3.9/site-packages (from colour-science) (1.26.4)
Requirement already satisfied: scipy<2,>=1.8 in ./.local/lib/python3.9/site-packages (from colour-science) (1.11.3)
Requirement already satisfied: typing-extensions<5,>=4 in ./miniconda3/envs/sediment2/lib/python3.9/site-packages (from colour-science) (4.12.1)
Requirement already satisfied: pillow>=8.3.2 in ./miniconda3/envs/sediment2/lib/python3.9/site-packages (from imageio<3,>=2->colour-science) (10.3.0)
Downloading colour_science-0.4.4-py3-none-any.whl (2.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.3/2.3 MB 17.7 MB/s eta 0:00:00
Installing collected packages: colour-science
Attempting uninstall: colour-science
Found existing installation: colour-science 0.3.16
Uninstalling colour-science-0.3.16:
Successfully uninstalled colour-science-0.3.16
Successfully installed colour-science-0.4.4Clearly pip looks in other places than the environment for packages and I don’t know why. In any case you can also try to use the --ignore-installed option with pip install to force pip to reinstall packages.
Having installed on linux Debian-based 22-04
Once I run napari and select in Plugins/napari Sediment/Sediment The GUI is not displayed and this is what I get in the console: