materialsproject/crystaltoolkit

Crystal Toolkit is a framework for building web apps for materials science and is currently powering the new Materials Project website.

Crystal Toolkit

Citations

You can read more about Crystal Toolkit in our preprint, available here.

A citation.cff file is available or a BibTeX citation is as follows:

@article{horton2023crystal,
  title={Crystal Toolkit: A Web App Framework to Improve Usability and Accessibility of Materials Science Research Algorithms},
  author={Horton, Matthew and Shen, Jimmy-Xuan and Burns, Jordan and Cohen, Orion and Chabbey, Fran{\c{c}}ois and Ganose, Alex M and Guha, Rishabh and Huck, Patrick and Li, Hamming Howard and McDermott, Matthew and others},
  journal={arXiv preprint arXiv:2302.06147},
  year={2023}
}

If you use Crystal Toolkit, either for your own web apps, or by incorporating images generated by Crystal Toolkit in your work, please make sure to cite it appropriately! Citations are a good way to recognize the contributions of the Crystal Toolkit developers, and allow us to see how it has been used by the community.

Interested in contributing?

A current list of new contributor issues can be seen here. If you would like a new-contributor issue assigned, get in touch with project maintainers!

Status

Installation

pip install crystal-toolkit

Documentation

Documentation can be found at docs.crystaltoolkit.org.

Example Apps

Description
bandstructure.py Demonstrates capabilities of the BandstructureAndDosComponent component
basic_hello_structure.py Uses StructureMoleculeComponent to show a simple pymatgen structure
basic_hello_structure_interactive.py Adds a button to the basic_hello_structure.py to toggle between two structures interactively
basic_hello_world.py Bare-bones example showing how to render the text "Hello scientist!" in Dash app
diffraction.py Demonstrates capabilities of the XRayDiffractionComponent component
diffraction_dynamic.py Adds a button to diffraction.py to load a new structure on the fly
diffraction_empty.py Shows XRayDiffractionComponent can be mounted without a passing structure
kwarg_inputs.py Shows off boolean input (aka toggle), matrix input and slider input components
phase_diagram.py Combines MPRester.get_entries_in_chemsys() and the PhaseDiagram component to plot the Li-O-Co convex hull
pourbaix.py Combines MPRester.get_pourbaix_entries() and the PourbaixDiagramComponent to plot the Fe-CO Pourbaix diagram
structure.py Show cases multiple layout options for the StructureMoleculeComponent
structure_magnetic.py Plots a structure with magnetic moments
matbench_dielectric_structure_on_hover.py Creates a scatter plot hooked up to a StructureMoleculeComponent and DataTable that show the structure and highlight the table row corresponding to the hovered scatter point.
matbench_dielectric_datatable_xrd.py Renders a DataTable hooked up to a StructureMoleculeComponent and XRayDiffractionComponent so that hovering a table row will show the corresponding structure and its XRD pattern.
transformations.py Combines StructureMoleculeComponent and AllTransformationsComponent to apply interactive structure transformations
transformations_minimal.py Shows how to restrict the types of allowed transformations
write_structure_screenshot_to_file.py Shows to save interactive structure views as image files

Team and Contribution Policy

The Crystal Toolkit Development Team includes:

• Matthew Horton, lead
• François Chabbey for React components
• Jimmy Shen contributed pythreejs support, surface plotting, initial arrows/axes support, and various bug fixes
• Joey Montoya contributed Pourbaix component
• Shyam Dwaraknath for planned contributions for ellipsoid support and architectural design
• Donny Winston, assisted by Tyler Huntington, for helping embed Crystal Toolkit in a Django app
• Matt McDermott contributed phase diagram, X-ray Diffraction, X-ray Absorption Spectrum components
• Jason Munro contributed band structure component
• Janosh Riebesell contributed Phonon band structure component, 3 example apps, tests
• Stephen Weitzner contributed POV-Ray integration (in progress)
• Richard Tran for contributing plotly-powered Wulff shapes to pymatgen, which Crystal Toolkit uses
• Guy Moore for contributing magnetic moment visualization
• Steve Zeltmann for contributing electron diffraction
• Patrick Huck, releases, operations, bugfixes and POC for MP / MPContribs

New contributors are welcome, please see our Code of Conduct. If you are a new contributor please modify this README in your Pull Request to add your name to the list.

Future of This Repository

The Crystal Toolkit repository is home of an object-oriented Python framework for rendering materials science data based on the schema employed by the Materials Project.

The custom Plotly Dash components that power Crystal Toolkit are now maintained in a separate repository for ease of development, as well as the custom React components. These components were formerly included in the Crystal Toolkit repo, and are still considered part of Crystal Toolkit in spirit.

There are some important issues still to be resolved, as well as general improvements to documentation and test suite planned. Some currently-private code is also planned to be re-incorporated into the public Crystal Toolkit repo.

Acknowledgements

Thank you to all the authors and maintainers of the libraries Crystal Toolkit depends upon, and in particular pymatgen for crystallographic analysis and Dash from Plotly for their web app framework.

Thank you to the NERSC Spin service for hosting the app and for their technical support.

Contact

Please contact @mkhorton with any queries or add an issue on the GitHub Issues page.

crystaltoolkit's Issues

Dependabot can't resolve your Python dependency files

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│     ):

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Error - Not importing view

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

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│     ):

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Long CIF edge case

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.

cryst_misparsed.cif.zip

Dependabot can't resolve your Python dependency files

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│     ):

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Axes toggle on Visualisation doesn't appear to work.

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

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.

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Dependabot can't resolve your Python dependency files

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│     ):

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Issues displaying a crystal structure - related to site occupancies?

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!

Add text area for pasting CIF/POSCAR content

Besides the file upload area, it would be nice if POSCAR and CIF files could be copy-pasted into a text area.

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Dependabot can't resolve your Python dependency files

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│     ):

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`PeriodicTable` component

A UI component that renders a periodic table similar to pymatgen.util.plotting.periodic_table_heatmap, but also allows interaction by selecting multiple elements.

AttributeError: 'Molecule' object has no attribute 'get_scene'

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

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.

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Dependabot can't resolve your Python dependency files

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.

View the update logs.

Dependabot can't resolve your Python dependency files

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│     ):

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Failed start docker container No module named 'maggma'

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

species_and_occu -> site.species ?

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

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.

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Dependabot can't resolve your Python dependency files

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│     ):

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Dependabot can't resolve your Python dependency files

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│     ):

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Electronic structure components

BandStructure and DOS and combined plots

Update "LocalEnv" view to be more human-understandable

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.

Wulff shape and morphology evolution component

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?

Shareable links for custom structure

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.

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Cannot display 3D model

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

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.

View the update logs.

FireWorks `Workflow` or jobflow `Flow` component

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.

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Dependabot can't resolve your Python dependency files

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.

View the update logs.

PhaseDiagramComponent

A UI component for pymatgen.analysis.phase_diagram.PhaseDiagram

redis.exceptions.ConnectionError

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?

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Misformatted decimals on non-stoichiometric compositions

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.

cryst.cif.txt

Dependabot can't resolve your Python dependency files

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.

View the update logs.

`Trajectory` component

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

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.

View the update logs.

Cannot start dev server

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

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.

View the update logs.

`Renderable` class as alternative to monkey patching

It appears the conversion of objects to scenes is monkey patched into place. There should be a better way to do this.

SpectrumComponent

A UI component for pymatgen.core.spectrum.Spectrum

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Initial Update

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.

Dependabot can't resolve your Python dependency files

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.

View the update logs.

Dependabot can't resolve your Python dependency files

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.

View the update logs.