Merge branch 'main' into capytaine_v2_min_mesh

sandialabs · Oct 27, 2023 · abc6540 · abc6540
2 parents f55d3c3 + 8d383e3
commit abc6540
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diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -76,20 +76,9 @@ The documentation uses the Jupyter notebook tutorials in the `examples` director
 When building the documentation locally you will need to have installed [pandoc](https://pandoc.org/installing.html) and [gifsicle](https://github.com/kohler/gifsicle).
 We recommend installing pandoc using its Anaconda distribution: `conda install -c conda-forge pandoc`.
 
-**NOTE:** it may be expedient at times to:
+**NOTE:** it may be expedient at times to avoid running the tutorial notebooks. To do so, add [`nbsphinx_execute = 'never'`](https://nbsphinx.readthedocs.io/en/0.9.3/configuration.html#nbsphinx_execute) to `docs/source/conf.py`. Make sure not to commit these changes!
 
- 1. **Avoid running the tutorial notebooks:** Add [`nbsphinx_execute = 'never'`](https://nbsphinx.readthedocs.io/en/0.9.3/configuration.html#nbsphinx_execute) to `docs/source/conf.py`
- 2. **Disable the link check operation:** Comment out the `linkcheck` call in `docs/build_docs.py`
-
-```python
-if __name__ == '__main__':
-    source.make_theory_animations
-    # linkcheck()
-    html()
-    cleanup()
-```
-
-Make sure not to commit these changes!
+If you add or change any hyperlinks in the documentation, we recommend checking the "Build documentation" warnings in the GitHub Actions CI workflow to make sure the links will not cause an issue. The CI will not fail due to broken links, only issue a warning (see [issue #286](https://github.com/sandialabs/WecOptTool/issues/286)).
 
 ### Editing the tutorials
 The tutorials are used as part of the Documentation.

diff --git a/docs/build_docs.py b/docs/build_docs.py
@@ -18,7 +18,7 @@ def linkcheck():
                  linkcheck_dir,
                  doctree_dir,
                  'linkcheck',
-                 warningiserror=True)
+                 warningiserror=False)
     app.build()
 
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -57,26 +57,6 @@ def setup(app):
                      'app.add_directive',
                      'app.add_role',]
 
-linkcheck_ignore = [
-    'https://github.com/HIPS/autograd/blob/master/docs/tutorial.md#',
-    'https://doi.org/10.2172/1330189',
-    'https://sandialabs.github.io/WecOptTool/*',
-    'https://doi.org/10.1080/17445302.2015.1089052',
-    'https://digitalops.sandia.gov/*',
-]
-
-linkcheck_request_headers = {
-    'https://doi.org/10.1109/TSTE.2014.2371536': {
-        'User-Agent': 'my-app/0.0.1'
-    },
-    'https://doi.org/10.1109/9.467672': {
-        'User-Agent': 'my-app/0.0.1'
-    },
-    'https://doi.org/10.1109/TSTE.2023.3272868': {
-        'User-Agent': 'my-app/0.0.1'
-    },
-}
-
 # -- References (BibTex) -----------------------------------------------------
 bibtex_bibfiles = ['wecopttool_refs.bib']
 bibtex_encoding = 'utf-8-sig'

diff --git a/examples/data/bem.nc b/examples/data/bem.nc
diff --git a/examples/tutorial_1_WaveBot.ipynb b/examples/tutorial_1_WaveBot.ipynb
@@ -97,25 +97,6 @@
     "ndof = fb.nb_dofs"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Next we will add the mass and hydrostatic stiffness properties. \n",
-    "If these values are known they can be added directly.\n",
-    "Here we will use the fact that the WaveBot is free floating and assume constant density to calculate these properties, which Capytaine can natively perform with the `FloatingBody` created above. For convenience, this functionality has been wrapped in `wecopttool.hydrostatics`."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "stiffness = wot.hydrostatics.stiffness_matrix(fb).values\n",
-    "mass = wot.hydrostatics.inertia_matrix(fb).values"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -260,8 +241,6 @@
    "source": [
     "wec = wot.WEC.from_bem(\n",
     "    bem_data,\n",
-    "    inertia_matrix=mass,\n",
-    "    hydrostatic_stiffness=stiffness,\n",
     "    constraints=constraints,\n",
     "    friction=None,\n",
     "    f_add=f_add,\n",
@@ -536,8 +515,6 @@
     "# Update WEC\n",
     "\n",
     "wec_2 = wot.WEC.from_bem(bem_data,\n",
-    "                         inertia_matrix=mass,\n",
-    "                         hydrostatic_stiffness=stiffness,\n",
     "                         constraints=constraints_2,\n",
     "                         friction=None,\n",
     "                         f_add=f_add_2\n",
@@ -582,8 +559,6 @@
    "source": [
     "wec_2_nocon = wot.WEC.from_bem(\n",
     "    bem_data,\n",
-    "    inertia_matrix=mass,\n",
-    "    hydrostatic_stiffness=stiffness,\n",
     "    constraints=None,\n",
     "    friction=None,\n",
     "    f_add=f_add_2)\n",
@@ -736,10 +711,6 @@
     "    nfreq = 50\n",
     "    bem_data = wot.run_bem(fb, freq)\n",
     "\n",
-    "    # Mass & hydrostatic stiffness\n",
-    "    stiffness_3 = wot.hydrostatics.stiffness_matrix(fb).values\n",
-    "    mass_3 = wot.hydrostatics.inertia_matrix(fb).values\n",
-    "\n",
     "    # Impedance definition\n",
     "    omega = bem_data.omega.values\n",
     "    gear_ratio = 12.0\n",
@@ -788,8 +759,6 @@
     "\n",
     "    # Create WEC\n",
     "    wec = wot.WEC.from_bem(bem_data,\n",
-    "            inertia_matrix=mass_3,\n",
-    "            hydrostatic_stiffness=stiffness_3,\n",
     "            constraints=constraints,\n",
     "            friction=None, \n",
     "            f_add=f_add,\n",
@@ -898,7 +867,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.10.9"
   },
   "vscode": {
    "interpreter": {