white space formatting

janosh · janosh · commit 57754b855adf · 2022-07-25T19:16:56.000-07:00
diff --git a/.github/workflows/pytest_docs.yml b/.github/workflows/pytest_docs.yml
@@ -50,4 +50,3 @@ jobs:
         PERCY_TOKEN: ${{ secrets.PERCY_TOKEN }}
       run: |
         poetry run pytest --color=yes --webdriver Firefox --headless crystal_toolkit/apps/examples/tests/
-
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -1,6 +1,6 @@
 name: release
 
-on: 
+on:
   workflow_dispatch
 
 jobs:
diff --git a/README.md b/README.md
@@ -41,16 +41,16 @@ New contributors are welcome, please see our [Code of Conduct.](code-of-conduct.
 
 The Crystal Toolkit repo currently contains three major parts:
 
-* An object-orientated Python framework for rendering materials science data based on the schema employed by the Materials Proejct
+* An object-orientated Python framework for rendering materials science data based on the schema employed by the Materials Project
 * A few custom Plotly Dash components (Simple3DSceneComponent, JSONComponent, GraphComponent)
 * Some example apps using these components
 
 It is likely the custom Plotly Dash components might be spun off into a separate repo at some point to reduce the complexity of the Crystal Toolkit repo itself.
 
 ## Acknowledgements
 
-Thank you to all the authors and maintainers of the libraries Crystal Toolkit 
-depends upon, and in particular [pymatgen](http://pymatgen.org) for crystallographic 
+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
diff --git a/code-of-conduct.md b/code-of-conduct.md
@@ -46,4 +46,3 @@ This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 1.3.0, available at https://www.contributor-covenant.org/version/1/3/0/code-of-conduct.html
 
 [homepage]: https://www.contributor-covenant.org
-
diff --git a/crystal_toolkit/apps/assets/crystaltoolkit.css b/crystal_toolkit/apps/assets/crystaltoolkit.css
@@ -1,7 +1,3 @@
-
-
-
 body, html, .body {
   background: #f3f3f3 !important;
 }
-
diff --git a/crystal_toolkit/apps/assets/doi_cache.json b/crystal_toolkit/apps/assets/doi_cache.json
@@ -1 +1 @@
-{"10.26434/chemrxiv.11294480.v1": "D. Waroquiers, J. George, M. Horton, S. Schenk, K. Persson, G.-M. Rignanese, X. Gonze, and G. Hautier, \u201cChemEnv\u202f: A Fast and Robust Coordination Environment Identification Tool,\u201d Dec. 2019.\n", "10.3389/fmats.2017.00034": "N. E. R. Zimmermann, M. K. Horton, A. Jain, and M. Haranczyk, \u201cAssessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization,\u201d Frontiers in Materials, vol. 4, Nov. 2017.\n"}
+{"10.26434/chemrxiv.11294480.v1": "D. Waroquiers, J. George, M. Horton, S. Schenk, K. Persson, G.-M. Rignanese, X. Gonze, and G. Hautier, \u201cChemEnv\u202f: A Fast and Robust Coordination Environment Identification Tool,\u201d Dec. 2019.\n", "10.3389/fmats.2017.00034": "N. E. R. Zimmermann, M. K. Horton, A. Jain, and M. Haranczyk, \u201cAssessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization,\u201d Frontiers in Materials, vol. 4, Nov. 2017.\n"}
diff --git a/crystal_toolkit/apps/assets/task_ids_on_load.json b/crystal_toolkit/apps/assets/task_ids_on_load.json
diff --git a/crystal_toolkit/apps/examples/GaN_bs.json b/crystal_toolkit/apps/examples/GaN_bs.json
diff --git a/crystal_toolkit/apps/examples/GaN_dos.json b/crystal_toolkit/apps/examples/GaN_dos.json
diff --git a/crystal_toolkit/apps/examples/Si_bs.json b/crystal_toolkit/apps/examples/Si_bs.json
diff --git a/crystal_toolkit/apps/examples/Si_dos.json b/crystal_toolkit/apps/examples/Si_dos.json
diff --git a/crystal_toolkit/core/ElementColorSchemes.yaml b/crystal_toolkit/core/ElementColorSchemes.yaml
@@ -222,4 +222,4 @@ Extras:  # for custom element types
   Xbcp: [0, 0, 255]  # bond critical point
   Xrcp: [255, 0, 0]  # ring critical point
   Xccp: [255, 255, 0]  # cage critical point
-  Xncp: [0, 255, 255]  # non-nuclear attractor
+  Xncp: [0, 255, 255]  # non-nuclear attractor
diff --git a/crystal_toolkit/defaults.json b/crystal_toolkit/defaults.json
@@ -18,4 +18,4 @@
             "radius": 0.5
         }
     }
-}
+}
diff --git a/crystal_toolkit/mpid_cache.json b/crystal_toolkit/mpid_cache.json
diff --git a/docs_rst/CNAME b/docs_rst/CNAME
@@ -1 +1 @@
-docs.crystaltoolkit.org
+docs.crystaltoolkit.org
diff --git a/docs_rst/Makefile b/docs_rst/Makefile
@@ -21,4 +21,4 @@ help:
 	@sphinx-apidoc -e -f -o source/ ../crystal_toolkit ../crystal_toolkit/apps
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 	@cp -r "$(BUILDDIR)/html/." ../docs/
-	@cp CNAME ../docs/
+	@cp CNAME ../docs/
diff --git a/docs_rst/_static/css/badge_only.css b/docs_rst/_static/css/badge_only.css
diff --git a/docs_rst/components/dash_components.rst b/docs_rst/components/dash_components.rst
@@ -20,4 +20,4 @@ its functionality.
 
 Link to documentation for creating ``Scene`` objects inside Python.
 
-Link to ``Simple3DScene`` Dash component to render resulting ``Scene`` object.
+Link to ``Simple3DScene`` Dash component to render resulting ``Scene`` object.
diff --git a/docs_rst/first_component.rst b/docs_rst/first_component.rst
@@ -48,4 +48,4 @@ The basic steps are to:
 At this point, the component should be working. It needs a simple **example app**
 to be added to ``crystal_toolkit.apps.examples`` and a corresponding **test** that
 the example app runs, and finally a short documentation page in ``docs_rst``. Please
-copy from the existing examples as necessary.
+copy from the existing examples as necessary.
diff --git a/docs_rst/first_web_app.rst b/docs_rst/first_web_app.rst
@@ -124,4 +124,4 @@ Additionally, you should run the app using ``gunicorn`` rather than using ``pyth
 directly so that there are multiple workers available to handle callbacks --
 this will result in a huge performance improvement.
 
-All of the recommendations in the main `Dash documentation <https://dash.plot.ly>`_ also apply.
+All of the recommendations in the main `Dash documentation <https://dash.plot.ly>`_ also apply.
diff --git a/docs_rst/helpers.rst b/docs_rst/helpers.rst
@@ -28,4 +28,4 @@ Three-dimensional scenes created using the
 `Scene <source/crystal_toolkit.core.scene>`_ class can be rendered
 by the ``Simple3DScene`` Dash component, but also other tools including
 pythreejs (for Jupypter integration), POV-Ray (for high-quality rendering) and
-asymptote (for LaTeX integration).
+asymptote (for LaTeX integration).
diff --git a/docs_rst/index.rst b/docs_rst/index.rst
@@ -11,4 +11,4 @@
    jupyter
    API Docs<source/crystal_toolkit>
 
-.. include:: introduction.rst
+.. include:: introduction.rst
diff --git a/docs_rst/jupyter.rst b/docs_rst/jupyter.rst
@@ -12,14 +12,14 @@ Installation
 There are two steps to using Crystal Toolkit inside Jupyter:
 
 1. Make sure Jupyter Lab is installed and run using ``jupyter lab``, version 3.x.
-   Crystal Toolkit is not supported in the older Jupyter notebooks or older versions 
+   Crystal Toolkit is not supported in the older Jupyter notebooks or older versions
    of Jupyter Lab.
 
 2. Ensure Crystal Toolkit is installed as normal, ``pip install crystal-toolkit --upgrade``
 
-3. Restart Jupyter Lab completely. You be asked to perform a "build," click OK and it's normal 
+3. Restart Jupyter Lab completely. You be asked to perform a "build," click OK and it's normal
    for this to take a minute. After this it's ready to use!
-   
+
 The extension may still work on Jupyter Lab 2.x by additionally running:
 
    ``jupyter labextension install crystaltoolkit-extension``
diff --git a/docs_rst/mp_app.rst b/docs_rst/mp_app.rst
@@ -1,3 +1,3 @@
 =======================
 A Materials Project App
-=======================
+=======================
diff --git a/docs_rst/troubleshooting.rst b/docs_rst/troubleshooting.rst
@@ -2,4 +2,4 @@
 Troubleshooting
 ===============
 
-This page is intended to help developers of Crystal Toolkit.
+This page is intended to help developers of Crystal Toolkit.
diff --git a/tests/asy_test/single/Makefile b/tests/asy_test/single/Makefile
@@ -1,4 +1,4 @@
-all: interact 
+all: interact
 
 interact:
 	asy  -V GaN.asy
diff --git a/tests/test_pythreejs/pythreejs_test.ipynb b/tests/test_pythreejs/pythreejs_test.ipynb
@@ -17,7 +17,9 @@
    "outputs": [],
    "source": [
     "from pymatgen.io.vasp import Chgcar\n",
+    "\n",
     "from crystal_toolkit.helpers.pythreejs_renderer import view\n",
+    "\n",
     "chgcar = Chgcar.from_file(\"../test_files/chgcar.vasp\")"
    ]
   },

-Original file line number
+Diff line change
@@ @@ -1,6 +1,6 @@ @@
 name: release
 -on:
 +on:
   workflow_dispatch
 jobs:
Original file line number	Diff line number	Diff line change
`@@ -46,4 +46,3 @@ This Code of Conduct is adapted from the [Contributor Covenant][homepage],`
`46`	`46`	`version 1.3.0, available at https://www.contributor-covenant.org/version/1/3/0/code-of-conduct.html`
`47`	`47`
`48`	`48`	`[homepage]: https://www.contributor-covenant.org`
`49`		`-`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,3 @@`
`1`		`-`
`2`		`-`
`3`		`-`
`4`	`1`	`body, html, .body {`
`5`	`2`	`background: #f3f3f3 !important;`
`6`	`3`	`}`
`7`		`-`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		-{"10.26434/chemrxiv.11294480.v1": "D. Waroquiers, J. George, M. Horton, S. Schenk, K. Persson, G.-M. Rignanese, X. Gonze, and G. Hautier, \u201cChemEnv\u202f: A Fast and Robust Coordination Environment Identification Tool,\u201d Dec. 2019.\n", "10.3389/fmats.2017.00034": "N. E. R. Zimmermann, M. K. Horton, A. Jain, and M. Haranczyk, \u201cAssessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization,\u201d Frontiers in Materials, vol. 4, Nov. 2017.\n"}
	`1`	+{"10.26434/chemrxiv.11294480.v1": "D. Waroquiers, J. George, M. Horton, S. Schenk, K. Persson, G.-M. Rignanese, X. Gonze, and G. Hautier, \u201cChemEnv\u202f: A Fast and Robust Coordination Environment Identification Tool,\u201d Dec. 2019.\n", "10.3389/fmats.2017.00034": "N. E. R. Zimmermann, M. K. Horton, A. Jain, and M. Haranczyk, \u201cAssessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization,\u201d Frontiers in Materials, vol. 4, Nov. 2017.\n"}