Merge pull request #279 from materialsproject/test-diffraction

Add `apps/examples/tests/test_diffraction.py` with E2E test for basic diffraction example

Author: janosh

.github/workflows/url-check.yml

@@ -0,0 +1,20 @@
+name: Check URLs
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  lychee-link-check:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@v3
+
+      - name: Check for broken links
+        uses: lycheeverse/lychee-action@v1
+        with:
+          # exclude loopback to skip localhost URLs from checking
+          args: --exclude-loopback './**/*.md' './**/*.rst'

.pre-commit-config.yaml

@@ -5,8 +5,9 @@ default_stages: [commit]
 
 default_install_hook_types: [pre-commit, commit-msg]
 
-# ignore generated doc and dependency lock files
-exclude: ^(docs/.+|.*lock.*|.*\.(svg|js|css))$
+# ignore generated docs and dependency lock files, the directory
+# jupyterlab-extension/ and all SVG, JS and CSS files
+exclude: ^(docs/.+|.*lock.*|jupyterlab-extension/.+|.*\.(svg|js|css))$
 
 repos:
   - repo: https://github.com/PyCQA/isort
@@ -72,3 +73,9 @@ repos:
       - id: nbqa-isort
       - id: nbqa-flake8
         args: [--ignore=E402]
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.0
+    hooks:
+      - id: nbstripout
+        args: [--drop-empty-cells, --keep-output]

README.md

@@ -32,7 +32,7 @@ The [Crystal Toolkit Development Team](https://github.com/materialsproject/cryst
 * [Matt McDermott](https://github.com/mattmcdermott) contributed phase diagram, X-ray Diffraction, X-ray Absorption Spectrum components
 * [Jason Munro](https://github.com/munrojm) contributed band structure component
 * [Stephen Weitzner](https://github.com/sweitzner) contributed POV-Ray integration (in progress)
-* [Richard Tran](https://github.com/richardtran415) for contributing plotly-powered Wulff shapes to pymatgen, which Crystal Toolkit uses
+* [Richard Tran](https://github.com/CifLord) for contributing plotly-powered Wulff shapes to pymatgen, which Crystal Toolkit uses
 * [Guy Moore](https://github.com/guymoore13) for contributing magnetic moment visualization
 
 New contributors are welcome, please see our [Code of Conduct.](code-of-conduct.md) If you are a new contributor please modify this README in your Pull Request to add your name to the list.
@@ -53,7 +53,7 @@ Thank you to all the authors and maintainers of the libraries Crystal Toolkit
 depends upon, and in particular [pymatgen](http://pymatgen.org) for crystallographic
 analysis and [Dash from Plotly](https://plot.ly/products/dash/) for their web app framework.
 
-Thank you to the [NERSC Spin](http://www.nersc.gov/users/data-analytics/spin/) service for
+Thank you to the [NERSC Spin](https://www.nersc.gov/systems/spin) service for
 hosting the app and for their technical support.
 
 Cross-browser Testing Platform and Open Source <3 generously provided by [Sauce Labs](https://saucelabs.com)

crystal_toolkit/apps/examples/bandstructure.py

@@ -5,12 +5,11 @@
 # dos and bs data from local jsons
 from monty.serialization import loadfn
 
-# standard Crystal Toolkit import
 import crystal_toolkit.components as ctc
 from crystal_toolkit.helpers.layouts import H1, Container
 from crystal_toolkit.settings import SETTINGS
 
-# create Dash app as normal, assets folder set for visual styles only
+# assets folder set for visual styles only
 app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
 
 # If callbacks created dynamically they cannot be statically checked at app startup.

crystal_toolkit/apps/examples/basic_hello_structure.py

@@ -6,7 +6,6 @@
 
 import crystal_toolkit.components as ctc
 
-# app = dash.Dash(external_stylesheets=['https://cdnjs.cloudflare.com/ajax/libs/bulma/0.7.2/css/bulma.min.css'])
 app = dash.Dash()
 
 # create our crystal structure using pymatgen

crystal_toolkit/apps/examples/diffraction.py

@@ -4,12 +4,10 @@
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 
-# standard Crystal Toolkit import
 import crystal_toolkit.components as ctc
 from crystal_toolkit.helpers.layouts import H1, H3, Container
 from crystal_toolkit.settings import SETTINGS
 
-# create Dash app as normal
 app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
 
 

crystal_toolkit/apps/examples/diffraction_dynamic.py

@@ -5,12 +5,10 @@
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 
-# standard Crystal Toolkit import
 import crystal_toolkit.components as ctc
 from crystal_toolkit.helpers.layouts import H1, Button, Container
 from crystal_toolkit.settings import SETTINGS
 
-# create Dash app as normal
 app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
 
 xrd_component = ctc.XRayDiffractionComponent(id="xrd-diffraction")

crystal_toolkit/apps/examples/diffraction_empty.py

@@ -4,12 +4,10 @@
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.structure import Structure
 
-# standard Crystal Toolkit import
 import crystal_toolkit.components as ctc
 from crystal_toolkit.helpers.layouts import H1, Container
 from crystal_toolkit.settings import SETTINGS
 
-# create Dash app as normal
 app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
 
 structure = Structure(Lattice.cubic(4.2), ["Na", "K"], [[0, 0, 0], [0.5, 0.5, 0.5]])

crystal_toolkit/apps/examples/phase_diagram.py

@@ -3,10 +3,8 @@
 from pymatgen.analysis.phase_diagram import PhaseDiagram
 from pymatgen.ext.matproj import MPRester
 
-# standard Crystal Toolkit import
 import crystal_toolkit.components as ctc
 
-# create Dash app as normal
 app = dash.Dash()
 
 # If callbacks created dynamically they cannot be statically checked at app startup.
@@ -20,10 +18,10 @@
 
 # first, retrieve entries from Materials Project
 with MPRester() as mpr:
-    # li_entries = mpr.get_entries_in_chemsys(["Li"])
-    # li_o_entries = mpr.get_entries_in_chemsys(["Li", "O"])
-    li_co_o_entries = mpr.get_entries_in_chemsys(["Li", "O", "Co"])
-    # li_co_o_fe_entries = mpr.get_entries_in_chemsys(["Li", "O", "Co", "Fe"])
+    # li_entries = mpr.get_entries_in_chemsys("Li")
+    # li_o_entries = mpr.get_entries_in_chemsys("Li-O")
+    li_co_o_entries = mpr.get_entries_in_chemsys("Li-O-Co")
+    # li_co_o_fe_entries = mpr.get_entries_in_chemsys("Li-O-Co-Fe")
 
 # and then create the phase diagrams
 # li_phase_diagram = PhaseDiagram(li_entries)
@@ -39,7 +37,6 @@
 li_co_o_phase_diagram_component = ctc.PhaseDiagramComponent(li_co_o_phase_diagram)
 # li_co_o_fe_phase_diagram_component = ctc.PhaseDiagramComponent(li_co_o_fe_phase_diagram)
 
-print(li_co_o_entries)
 
 # example layout to demonstrate capabilities of component
 my_layout = html.Div(

crystal_toolkit/apps/examples/pourbaix.py

@@ -2,11 +2,10 @@
 from dash import html
 from pymatgen.ext.matproj import MPRester
 
-# standard Crystal Toolkit import
 import crystal_toolkit.components as ctc
+from crystal_toolkit.settings import SETTINGS
 
-# create Dash app as normal
-app = dash.Dash()
+app = dash.Dash(assets_folder=SETTINGS.ASSETS_PATH)
 
 # If callbacks created dynamically they cannot be statically checked at app startup.
 # For this simple example this is not a problem, but if creating a complicated,
@@ -27,12 +26,13 @@
         html.Button("Get Pourbaix Diagram", id="get-pourbaix"),
         pourbaix_component.layout(),
         html.Div(id="pourbaix-output"),
-    ]
+    ],
+    style=dict(maxWidth="90vw", margin="2em auto"),
 )
 
 ctc.register_crystal_toolkit(app=app, layout=my_layout)
 
-# allow app to be run using "python structure.py"
+# allow app to be run using "python pourbaix.py"
 # in production, deploy behind gunicorn or similar
 # see Dash documentation for more information
 if __name__ == "__main__":