Open RichStone99 opened 1 month ago
labzw
commented
4 weeks ago Having exactly the same error. I feel this might be a bug in morphosamplers. It seems natively Pydantic does not support ndarray.
Solved or bypassed this issue by adding
class Config:
arbitrary_types_allowed = Truein dipole.py path.py sphere.py surface.py files under /YOUR/CONDA/PATH/envs/relion-5.0/lib/python3.10/site-packages/morphosamplers/models
alisterburt
commented
4 weeks ago @RichStone99 @labzw apologies for this - could you please run pip show morphosamplers and pip show pydantic in your RELION 5 conda environment and tell me the output? We recently moved to only supporting pydantic>=2 which may be the root cause of this issue for you
CACNYC
commented
4 weeks ago @alisterburt I have an identical error to @RichStone99 @labzw :
Traceback (most recent call last):
File "
Output of pip show morphosamplers: (relion-5.0) [spuser@spgpu TS01 projecti$ pip show morphosamplers Name: morphosamplers Version: 0.0.15 Summary: A library for sampling image data along morphological objects such as splines and surfaces. Home-page: https: //github.com/kevinyamauchi/morphosamplers Author: Kevin Yamauchi Author-email: kevin.yamauchi@gmail.com License: BSD 3-Clause License Location: /opt/miniconda3/envs/relion-5.0/lib/python3.10/site-packages Requires: einops, numpy, psygnal, pydantic, pydantic-compat, scipy, typing-extensions •Required-by: napari-threedee, relion
Output of pip show pydantic: (relion-5.0) [spuser@spgpu TS_01 projecti$ pip show pydantic -Name: pydantic Version: 1.10.18 Summary: Data validation and settings management using python type hints Home-page: https: //github.com/pydantic/pydantic rAuthor: Samuel Colvin l Author-email: s@muelcolvin.com License: MIT Location: /opt/miniconda3/envs/relion-5.0/lib/python3.10/site-packages Requires: typing-extensions Required-by: app-model, mdocfile, morphosamplers, napari, napari-threedee, npez, pydantic-compat
Ah, then pydantic 1.x is the culprit?
Thanks for your help Alister!
CACNYC
commented
4 weeks ago Hmm, it looks like I have a napari version constraint with napari 0.4.18
[spuser@spgpu TS_01_project]$ pip install --upgrade pydantic Defaulting to user installation because normal site-packages is not writeable Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com Requirement already satisfied: pydantic in /opt/miniconda3/envs/relion-5.0/lib/python3.10/site-packages (1.10.18) Collecting pydantic Downloading pydantic-2.9.2-py3-none-any.whl.metadata (149 kB) Collecting annotated-types>=0.6.0 (from pydantic) Downloading annotated_types-0.7.0-py-none-any. whl.metadata (15 kB) Collecting pydantic-core==2.23.4 (from pydantic) Downloading pydantic_core-2.23.4-cp310-c310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB) Requirement already satisfied: typing-extensions>=4.6.1 in /opt/miniconda3/envs/relion-5.0/Lib/python3.10/site-packages (from pydantic) (4.12.2) Downloading pydantic-2.9.2-py3-none-any.whl (434 kB) DownLoading pydantic_core-2.23,4-cp310-cp310-manyLinux_2_17_x86_64.manylinux2014_x86_64.wh1 (2.1 MB) Downloading annotated_types-0.7.0-py3-none-any.whl (13 kB) Installing collected packages: pydantic-core, annotated-types, pydantic 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. napari 0.4.18 requires pydantic<2,>=1.9.0, but you have pydantic 2.9.2 which is incompatible. Successfully installed annotated-types-0.7.0 pydantic-2.9.2 pydantic-core-2.23.4
In relion5:
Traceback (most recent call last):
File "
bogdantoader
commented
3 weeks ago Hello, downgrading to the following versions in the conda environment should fix the issue:
morphosamplers.version '0.0.13' pydantic.version '1.10.18' napari.version '0.4.18'
CACNYC
commented
3 weeks ago Hello, downgrading to the following versions in the conda environment should fix the issue:
morphosamplers.version '0.0.13' pydantic.version '1.10.18' napari.version '0.4.18'
Thanks Bogdan, I can confirm that rolling back morphosamplers to version 0.0.13, combined with pydantic 1.10.18 and napari 0.4.18, allowed both the Exclude tilt and Pick tomograms job types to run and complete successfully.
labzw
commented
1 week ago Update:
Remove and recreate conda environment with latest environment.yml works!
So after I rebuild the latest version and roll back morphosamplers to 0.0.13, I am getting this error now.......
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/exclude_tilt_images/__init__.py", line 1, in <module>
from ._cli import cli
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/exclude_tilt_images/_cli.py", line 8, in <module>
from .relion_tilt_image_excluder import RelionTiltImageExcluderWidget
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/exclude_tilt_images/relion_tilt_image_excluder.py", line 5, in <module>
from .._qt.tilt_image_excluder import TiltImageExcluderWidget
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/tilt_image_excluder.py", line 8, in <module>
from .components.tilt_image_selection_widget import TiltImageSelectionWidget
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tilt_image_selection_widget.py", line 12, in <module>
class TiltImageSelectionWidget(QWidget):
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tilt_image_selection_widget.py", line 17, in TiltImageSelectionWidget
viewer: napari.Viewer,
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/_lazy.py", line 45, in __getattr__
submod = import_module(
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/viewer.py", line 8, in <module>
from napari.components.viewer_model import ViewerModel
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/components/__init__.py", line 19, in <module>
from napari.components.layerlist import LayerList
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/components/layerlist.py", line 9, in <module>
from napari.layers import Layer
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/layers/__init__.py", line 12, in <module>
from napari.layers.points import Points
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/layers/points/__init__.py", line 1, in <module>
from napari.layers.points import _points_key_bindings
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/layers/points/_points_key_bindings.py", line 4, in <module>
from napari.layers.points.points import Points
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/layers/points/points.py", line 38, in <module>
from napari.layers.utils.text_manager import TextManager
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/layers/utils/text_manager.py", line 29, in <module>
class TextManager(EventedModel):
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/layers/utils/text_manager.py", line 83, in TextManager
string: StringEncoding = ConstantStringEncoding(constant='')
File "/usr/bin/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/evented_model.py", line 242, in __init__
super().__init__(**kwargs)
File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__
pydantic.error_wrappers.ValidationError: 1 validation error for ConstantStringEncoding
constant
Unable to avoid copy while creating an array as requested.
If using `np.array(obj, copy=False)` replace it with `np.asarray(obj)` to allow a copy when needed (no behavior change in NumPy 1.x).
For more details, see https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword. (type=value_error)
Installed current relion 5 on centOS 9. Am trying the subtomogram averaging tutorial with the HIV VLP data set. Worked well up to "Reconstruct tomograms". Tomograms have been generated and look fine. But when trying to launch "Pick tomograms", napari didn't open and got the following error message. How can we fix it? Seems to relate to pydantic and/or tomography_python_programs. Btw, napari ran well during, for example, the "Exclude tilt-images" step and inspection of generated tomo in the "Reconstruct tomograms" step. IMOD was used in "Reconstruct tomograms".
Traceback (most recent call last): File "", line 1, in
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/pick/init.py", line 1, in
from .particles import pick_particles
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/pick/particles.py", line 7, in
from napari_threedee.annotators import PointAnnotator
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/napari_threedee/init.py", line 1, in
from . import data_models
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/napari_threedee/data_models/init.py", line 1, in
from .points import N3dPoints
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/napari_threedee/data_models/points.py", line 8, in
from napari_threedee.annotators.base import N3dDataModel
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/napari_threedee/annotators/init.py", line 5, in
from .surfaces import SurfaceAnnotator
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/napari_threedee/annotators/surfaces/init.py", line 1, in
from .annotator import SurfaceAnnotator
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/napari_threedee/annotators/surfaces/annotator.py", line 12, in
from morphosamplers.surface_spline import GriddedSplineSurface
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/morphosamplers/init.py", line 12, in
from morphosamplers.models import Path, Sphere, Surface, Dipole
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/morphosamplers/models/init.py", line 1, in
from .path import Path
File "/home/tangl/sw/miniforge3/envs/relion-5.0/lib/python3.10/site-packages/morphosamplers/models/path.py", line 7, in
class Path(MorphoModel):
File "pydantic/main.py", line 197, in pydantic.main.ModelMetaclass.new
File "pydantic/fields.py", line 504, in pydantic.fields.ModelField.infer
File "pydantic/fields.py", line 434, in pydantic.fields.ModelField.init
File "pydantic/fields.py", line 555, in pydantic.fields.ModelField.prepare
File "pydantic/fields.py", line 829, in pydantic.fields.ModelField.populate_validators
File "pydantic/validators.py", line 765, in find_validators
RuntimeError: no validator found for <class 'numpy.ndarray'>, see
arbitrary_types_allowedin Config