Pre-commit hooks and black code formatting

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# Add pre-commit hooks and run black
+98f5c275d4b1cb2d13852ed75c278d9816347355

.github_changelog_generator

@@ -1 +1 @@
-since-tag=1.0.0
+since-tag=1.0.0

.gitignore

@@ -120,5 +120,5 @@ figs/*
 *.sharpy
 
 # Exceptions
-# !tests/coupled/multibody/floating_wind_turbine/oc3_cs_v07.floating.h5 
+# !tests/coupled/multibody/floating_wind_turbine/oc3_cs_v07.floating.h5
 !tests/coupled/multibody/floating_wind_turbine/oc3_cs_v07.floating.h*

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v3.2.0
+  hooks:
+  - id: trailing-whitespace
+  - id: end-of-file-fixer
+  - id: check-yaml
+  - id: check-added-large-files
+- repo: https://github.com/psf/black
+  rev: 22.10.0
+  hooks:
+  - id: black
+  - id: black
+    args: [--line-length=120]
+    types: [python]
+- repo: https://github.com/pycqa/isort
+  rev: 5.10.1
+  hooks:
+  - id: isort
+    types: [python]
+- repo: https://github.com/PyCQA/flake8
+  rev: 5.0.4
+  hooks:
+  - id: flake8
+    args: [--max-line-length=120]
+    types: [python]
+- repo: https://github.com/PyCQA/bandit
+  rev: 1.7.4
+  hooks:
+  - id: bandit
+    args: [-r]
+    types: [python]

.zenodo.json

@@ -1,11 +1,11 @@
 {
-    "license": "other-open", 
-    "title": "SHARPy: A dynamic aeroelastic simulation toolbox for very flexible aircraft and wind turbines", 
-    "upload_type": "software", 
+    "license": "other-open",
+    "title": "SHARPy: A dynamic aeroelastic simulation toolbox for very flexible aircraft and wind turbines",
+    "upload_type": "software",
     "creators": [
         {
-            "orcid": "0000-0002-8133-9481", 
-            "affiliation": "Imperial College London", 
+            "orcid": "0000-0002-8133-9481",
+            "affiliation": "Imperial College London",
             "name": "Alfonso del Carre"
         },
         {
@@ -14,15 +14,15 @@
             "name": "Norberto Goizueta"
         },
         {
-            "orcid": "0000-0003-4840-5392", 
-            "affiliation": "Imperial College London", 
+            "orcid": "0000-0003-4840-5392",
+            "affiliation": "Imperial College London",
             "name": "Arturo Mu\u00f1oz-Sim\u00f3n"
-        }, 
+        },
         {
-            "orcid": "0000-0002-6706-3220", 
+            "orcid": "0000-0002-6706-3220",
             "affiliation": "Imperial College London",
             "name": "Rafael Palacios"
         }
-    ], 
+    ],
     "access_right": "open"
 }

Dockerfile

@@ -41,4 +41,3 @@ RUN cd sharpy_dir && \
     rm -rf build
 
 ENTRYPOINT ["/bin/bash", "--init-file", "/root/bashrc"]
-

README.md

@@ -16,7 +16,7 @@ wings and wind turbines.
 
 ### Contact
 
-For more information on the [research team](http://www.imperial.ac.uk/aeroelastics/people/) developing SHARPy or to get 
+For more information on the [research team](http://www.imperial.ac.uk/aeroelastics/people/) developing SHARPy or to get
 in touch, [visit our homepage](http://www.imperial.ac.uk/aeroelastics).
 
 ## Physical Models
@@ -25,8 +25,8 @@ SHARPy is a modular aeroelastic solver that currently uses two specific models f
 
 For the structural model, SHARPy employs a nonlinear, geometrically-exact displacement and rotation-based composite beam formulation,
 augmented with Lagrange multipliers for additional kinematic constraints.
-This model has the advantage of providing the solution directly in the physical problem's degrees of freedom, making the 
-coupling with the aerodynamic solver simple and not requiring any post-processing. The 1D beam formulation used limits 
+This model has the advantage of providing the solution directly in the physical problem's degrees of freedom, making the
+coupling with the aerodynamic solver simple and not requiring any post-processing. The 1D beam formulation used limits
 the analyses that can be done by SHARPy to slender structures, such as high aspect ratio wings.
 
 The aerodynamic model utilises the Unsteady Vortex Lattice Method (UVLM). The aerodynamic surfaces are modelled as a thin
@@ -70,16 +70,16 @@ The documentation for SHARPy can be found [here](http://ic-sharpy.readthedocs.io
 
 ## Installing SHARPy
 
-For the latest documentation, see the 
+For the latest documentation, see the
 [installation docs](https://ic-sharpy.readthedocs.io/en/latest/content/installation.html).
 
 As of version v1.0.1, SHARPy can also be obtained from Docker Hub to avoid compilation
-and platform-dependant issues. If you are interested, make sure you check 
+and platform-dependant issues. If you are interested, make sure you check
 the [SHARPy Docker distribution docs](https://ic-sharpy.readthedocs.io/en/latest/content/installation.html#using-sharpy-from-a-docker-container).
 
 ## Contributing and Bug reports
 
-If you think you can add a useful feature to SHARPy, want to write documentation or you encounter a bug, by all means, 
+If you think you can add a useful feature to SHARPy, want to write documentation or you encounter a bug, by all means,
 check out the [collaboration guide](https://ic-sharpy.readthedocs.io/en/latest/content/contributing.html).
 
 ## Citing SHARPy

docs/JOSS/paper.bib

@@ -379,10 +379,10 @@ @article{Murua2012-2
 pages = {1575-1585},
 year = {2012},
 doi = {10.2514/1.J051543},
-URL = { 
+URL = {
         https://doi.org/10.2514/1.J051543
 },
-eprint = { 
+eprint = {
         https://doi.org/10.2514/1.J051543
 }
 }
@@ -397,13 +397,13 @@ @article{Simpson2013-2
 year = {2013},
 doi = {10.2514/1.J052136},
 
-URL = { 
+URL = {
         https://doi.org/10.2514/1.J052136
-    
+
 },
-eprint = { 
+eprint = {
         https://doi.org/10.2514/1.J052136
-    
+
 }
 }
 

docs/source/_static/sharpy_guide/sharpy_intro.html

@@ -8451,15 +8451,15 @@
 }
 /* Flexible box model classes */
 /* Taken from Alex Russell http://infrequently.org/2009/08/css-3-progress/ */
-/* This file is a compatability layer.  It allows the usage of flexible box 
+/* This file is a compatability layer.  It allows the usage of flexible box
 model layouts accross multiple browsers, including older browsers.  The newest,
 universal implementation of the flexible box model is used when available (see
-`Modern browsers` comments below).  Browsers that are known to implement this 
+`Modern browsers` comments below).  Browsers that are known to implement this
 new spec completely include:
 
     Firefox 28.0+
     Chrome 29.0+
-    Internet Explorer 11+ 
+    Internet Explorer 11+
     Opera 17.0+
 
 Browsers not listed, including Safari, are supported via the styling under the
@@ -11233,7 +11233,7 @@
   background: #f7f7f7;
   border-top: 1px solid #cfcfcf;
   border-bottom: 1px solid #cfcfcf;
-  /* This injects handle bars (a short, wide = symbol) for 
+  /* This injects handle bars (a short, wide = symbol) for
         the resize handle. */
 }
 div#pager .ui-resizable-handle::after {
@@ -11676,7 +11676,7 @@
 .highlight .il { color: #666666 } /* Literal.Number.Integer.Long */
     </style>
 <style type="text/css">
-    
+
 /* Temporary definitions which will become obsolete with Notebook release 5.0 */
 .ansi-black-fg { color: #3E424D; }
 .ansi-black-bg { background-color: #3E424D; }
@@ -11730,14 +11730,14 @@
   div.cell {
     display: block;
     page-break-inside: avoid;
-  } 
-  div.output_wrapper { 
+  }
+  div.output_wrapper {
     display: block;
-    page-break-inside: avoid; 
+    page-break-inside: avoid;
   }
-  div.output { 
+  div.output {
     display: block;
-    page-break-inside: avoid; 
+    page-break-inside: avoid;
   }
 }
 </style>
@@ -12404,7 +12404,7 @@ <h2 id="Structural-data">Structural data<a class="anchor-link" href="#Structural
 <div class="text_cell_render border-box-sizing rendered_html">
 <ul>
 <li><code>frame_fo_reference_delta [num_elem, num_node_elem, 3]</code> contains the  $\Delta$ vector in body-attached ($A$) frame of reference. As a rule of thumb:
-$$\Delta = \left\{ 
+$$\Delta = \left\{
 \begin{matrix}
 [-1, 0, 0], \quad \text{if right wing} \\
 [1, 0, 0], \quad \text{if left wing} \\
@@ -12588,7 +12588,7 @@ <h3 id="StaticUvlm">StaticUvlm<a class="anchor-link" href="#StaticUvlm">&#182;</
 </li>
 <li><p><code>n_rollup</code> how many steps are carried out to convect the wake with full free-wake. This usually should be <code>0</code>, but if you want a pretty picture, you can use <code>n_rollup = int(mstar*1.5)</code>.</p>
 </li>
-<li><p><code>rollup_dt</code> if <code>n_rollup &gt; 0</code>, set <code>rollup_dt</code> to 
+<li><p><code>rollup_dt</code> if <code>n_rollup &gt; 0</code>, set <code>rollup_dt</code> to
 $$
 \Delta t_{\mathrm{rollup}} = \frac{c/M}{u_\infty}
 $$</p>
@@ -12928,7 +12928,7 @@ <h1 id="Other-useful-software">Other useful software<a class="anchor-link" href=
   </div>
 </body>
 
- 
+
 
 
 </html>