Crystal Toolkit is a framework for building web apps for materials science and is currently powering the new Materials Project website.
Home Page: https://docs.crystaltoolkit.org
License: Other
Just mentioning this here in case you were looking for an edge case to include in your testing or something like that.
The website doesn't parse this very long CIF file of this C110 H106 Ge2 Li2 N8 O2 organic molecular crystal (or whatever this is) correctly.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-LYoiKB-_-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-V-DabJ_m-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-pgfKFLoB-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-LYoiKB-_-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
It appears the conversion of objects to scenes is monkey patched into place. There should be a better way to do this.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-ed06eNmj-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-IKrMrdo3-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Component will allow users to:
Input surface energies, crystal shape and miller indices or vasprun.xml file to visualize an interactive Wulff shape
Can upload a vasprun.xml file or accept manual parameters
plotly dash interface will allow:
Specs of each surface when hovering mouse over a specific facet on the Wulff shape, i.e. Wulff area fraction, surface energy, miller index
Morphology evolution, can take in non-stoichiometric or adsorbed/doped surfaces. User can select chemical potentials as constant or variable. Draggable chemical potential bar will allow for user to vary surface energy (and thus visual morphology evolution) as a function of chemical potential.
Question:
For this component, do we want to add the plotly interface for WulffShapes to pymatgen or crystaltoolkit for now?
I checked out the repo, did
conda create -n xtaltoolkit python=3.7
pip install numpy scipy
pip install -r requirements.txt
pip install pythreejs
python app.py
and got the following:
(xtaltoolkit) Donnys-MBP:crystaltoolkit dwinston$ python app.py
/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/core.py:39: UserWarning:
Caching has not been set up, app performance may be degraded.
Traceback (most recent call last):
File "app.py", line 171, in <module>
html.Div([transformation_component.standard_layout]),
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/transformations/core.py", line 216, in standard_layout
self.choices_layout,
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/core.py", line 221, in __getattr__
and item.split("_layout")[0] in self.supported_layouts
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/core.py", line 233, in supported_layouts
return self.all_layouts.keys()
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/transformations/core.py", line 176, in all_layouts
for name, transformation in self.transformations.items()
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/transformations/core.py", line 176, in <listcomp>
for name, transformation in self.transformations.items()
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/core.py", line 221, in __getattr__
and item.split("_layout")[0] in self.supported_layouts
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/core.py", line 233, in supported_layouts
return self.all_layouts.keys()
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/transformations/core.py", line 44, in all_layouts
options = html.Div(self.options_layout, id=self.id("options"))
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/components/transformations/supercell.py", line 37, in options_layout
options = get_matrix_input(self.id(), label="Scaling matrix")
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/helpers/inputs.py", line 93, in get_matrix_input
row.append(matrix_element(f"{i}{j}", value=default[i][j]))
File "/Users/dwinston/repos/crystaltoolkit/crystal_toolkit/helpers/inputs.py", line 85, in matrix_element
value=value,
File "/Users/dwinston/miniconda3/envs/xtaltoolkit/lib/python3.7/site-packages/dash/development/base_component.py", line 323, in wrapper
return func(*args, **kwargs)
File "/Users/dwinston/miniconda3/envs/xtaltoolkit/lib/python3.7/site-packages/dash_core_components/Input.py", line 89, in __init__
super(Input, self).__init__(**args)
File "/Users/dwinston/miniconda3/envs/xtaltoolkit/lib/python3.7/site-packages/dash/development/base_component.py", line 94, in __init__
', '.join(sorted(self._prop_names))
TypeError: Unexpected keyword argument `inputmode`
Allowed arguments: autoComplete, autoFocus, className, debounce, disabled, id, inputMode, list, loading_state, max, maxLength, min, minLength, multiple, n_blur, n_blur_timestamp, n_submit, n_submit_timestamp, name, pattern, placeholder, readOnly, required, selectionDirection, selectionEnd, selectionStart, size, spellCheck, step, style, type, value
(xtaltoolkit) Donnys-MBP:crystaltoolkit dwinston$
Please advise.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-VIYBK6pB-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package robocrys (0.2.6) not found.
at /usr/local/.pyenv/versions/3.9.2/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-6PL0SMs1-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Besides the file upload area, it would be nice if POSCAR and CIF files could be copy-pasted into a text area.
Hi
following the workshop. Got the error
AttributeError: 'Molecule' object has no attribute 'get_scene' when I try to view(molecule).
Edit: This error shows up for the CO and HCN molecule examples, but not for structure.
Cheers, Hud
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-V-DabJ_m-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-LYoiKB-_-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-fl-ZmZ1E-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-qNqhbW30-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.0/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
A UI component for pymatgen.analysis.phase_diagram.PhaseDiagram
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-uzpZbZFV-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-YnEhdDbL-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-DKTN33od-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
The website doesn't display non-stoichiometric compositions correctly:
I modified the first period following Mn:
- <sub>4</sub><span>.</span><sub>264</sub>
+ <sub>4.264</sub>to render correctly. Originally looked like the not-subscripted dot following Co.
BandStructure and DOS and combined plots
Can we add a visualizer for trajectories in the scene with a widget to play/stop/loop with trajectory images? Since pymatgen has the capabilities to work with trajectories, it will be useful to have it in the crystaltoolkit as well. If possible, we can discuss more about this.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-fl-ZmZ1E-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-6PL0SMs1-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
I don't see any instructions for avoiding a Redis connection error or for installing Redis, e.g. in the Dockerfile. Here's what I do:
docker run -p 127.0.0.1:6379:6379 -d redis
It is important to not just -p 6379:6379 on some networks, because that exposes an insecure Redis instance. For example, I got my MAC address banned on the LBL network for exposing it.
Can we add instructions somewhere?
A UI component for pymatgen.core.spectrum.Spectrum
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-6PL0SMs1-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
A UI component that renders a periodic table similar to pymatgen.util.plotting.periodic_table_heatmap, but also allows interaction by selecting multiple elements.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-fl-ZmZ1E-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
The bot created this issue to inform you that pyup.io has been set up on this repo.
Once you have closed it, the bot will open pull requests for updates as soon as they are available.
Using the GraphComponent.
This can be a component to display a FireWorks Workflow object or a jobflow Flow object, for use in creating dashboards for monitoring jobs.
I'm having some trouble displaying one particular structure (Fe5GeTe2.zip) in Jupyter Lab using crystal toolkit. Normally I can run a cell with just the pymatgen structure object, and crystal toolkit will automatically render the structure below the cell. However, with this specific structure all I receive is a printout of the structure object and the following error:
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
~/miniconda3/envs/scan/lib/python3.8/site-packages/IPython/core/formatters.py in __call__(self, obj, include, exclude)
968
969 if method is not None:
--> 970 return method(include=include, exclude=exclude)
971 return None
972 else:
~/miniconda3/envs/scan/lib/python3.8/site-packages/crystal_toolkit/__init__.py in _repr_mimebundle_(self, include, exclude)
56 if hasattr(self, "get_scene"):
57 return {
---> 58 "application/vnd.mp.ctk+json": self.get_scene().to_json(),
59 "text/plain": help_text_ct + self.__repr__(),
60 }
~/miniconda3/envs/scan/lib/python3.8/site-packages/crystal_toolkit/renderables/structure.py in get_structure_scene(self, origin, legend, draw_image_atoms)
97 )
98
---> 99 site_scene = site.get_scene(legend=legend,)
100 for scene in site_scene.contents:
101 primitives[scene.name] += scene.contents
~/miniconda3/envs/scan/lib/python3.8/site-packages/crystal_toolkit/renderables/site.py in get_site_scene(self, connected_sites, connected_sites_not_drawn, hide_incomplete_edges, incomplete_edge_length_scale, connected_sites_colors, connected_sites_not_drawn_colors, origin, draw_polyhedra, explicitly_calculate_polyhedra_hull, bond_radius, legend)
105 positions=[position],
106 color="#ffffff",
--> 107 radius=self.properties["display_radius"][0],
108 phiStart=phiEnd,
109 phiEnd=np.pi * 2,
KeyError: 'display_radius'
I've tried to trace back the error through the crystal toolkit source code, but unfortunately it's a bit beyond me. The problem appears to be that a site object in crystal toolkit lacks the "display_radius" property, but I'm not sure how this happens. Does it have to do with certain sites having occupancies of less than 1? I can load a different structure in the same notebook and it renders perfectly fine. I'm working with crystal toolkit version 2021.4.2, and JupyterLab version 3.1.0.
Even though other structures were rendering fine, I decided to update crystal toolkit to see if that solved the problem. I updated to version 2021.4.29 fine, but when I went to run jupyter labextension install crystaltoolkit-extension, I got the following error:
An error occured.
ValueError: The extension "crystaltoolkit-extension" does not yet support the current version of JupyterLab.
Conflicting Dependencies:
JupyterLab Extension Package
>=3.1.0-alpha.4 <3.2.0 >=2.0.0 <3.0.0 @jupyterlab/rendermime-interfaces
See the log file for details: /tmp/jupyterlab-debug-dad5s_b7.log
Any advice would be appreciated!
When I use Crystal Toolkit in jupyter lab 3.x, there is no error message, but the 3D results cannot be displayed
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-w3lZGCI7-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Failed start docker container with error:
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import File "<frozen importlib._bootstrap>", line 983, in _find_and_load File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 677, in _load_unlocked File "<frozen importlib._bootstrap_external>", line 728, in exec_module File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed File "/home/app/crystal_toolkit/apps/main.py", line 17, in <module> import crystal_toolkit.components as ctc File "/home/app/crystal_toolkit/components/__init__.py", line 24, in <module> from crystal_toolkit.components.bs import ( File "/home/app/crystal_toolkit/components/bs.py", line 11, in <module> from maggma.stores import GridFSStore, JSONStore, MongoStore ModuleNotFoundError: No module named 'maggma'
I tried to build a container from your repository and use the ready container materialsproject/crystal_toolkit
I tried this command in jupyter notebook
from crystal_toolkit import view
ImportError: cannot import name 'view' from 'crystal_toolkit' (/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/crystal_toolkit/init.py)
I have installed Python 3.8.4 and crystal-toolkit 2020.6.4 installed using pip
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-LYoiKB-_-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-V-DabJ_m-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
I would assume the axes toggle is supposed to turn off the axes indicator in the bottom corner but this doesn't appear to be the case.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-nrtMNdc3-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.0/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-HBYx58RQ-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
I get a slew of deprecation warnings from pymatgen for the structure module:
../crystal_toolkit/components/structure.py:1304: DeprecationWarning:
species_and_occu is deprecated
Use site.species instead. This will be deprecated with effect from pymatgen 2020.
I don't know enough about this to start a PR.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-6yV1CVSM-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
It would be great if non-MP structures could be shared with others. I.e. rather than sending others a POSCAR/CIF/JSON file and asking them to upload it themselves, it would be easier to send a link that shows the loaded structure directly.
Unlike the "ChemEnv" view which has been polished, the "LocalEnv" view currently just outputs a string version of the corresponding dictionary. This needs to be formatted in a similar way to the "ChemEnv" view.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-6PL0SMs1-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
Dependabot can't resolve your Python dependency files.
As a result, Dependabot couldn't update your dependencies.
The error Dependabot encountered was:
Creating virtualenv crystal-toolkit-x6hvkueY-py3.9 in /home/dependabot/.cache/pypoetry/virtualenvs
Updating dependencies
Resolving dependencies...
PackageNotFound
Package ifermi (0.1.2) not found.
at /usr/local/.pyenv/versions/3.9.1/lib/python3.9/site-packages/poetry/repositories/pool.py:144 in package
140│ self._packages.append(package)
141│
142│ return package
143│
→ 144│ raise PackageNotFound("Package {} ({}) not found.".format(name, version))
145│
146│ def find_packages(
147│ self, dependency,
148│ ):
If you think the above is an error on Dependabot's side please don't hesitate to get in touch - we'll do whatever we can to fix it.
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