Merge pull request #55 from boschresearch/docs-improvements

Docs improvements
boschresearch · Dec 12, 2023 · ab8ae4d · ab8ae4d
2 parents ae9f443 + 8c2af12
commit ab8ae4d
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -27,6 +27,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install -U setuptools setuptools_scm wheel
         pip install -e .[all,docs]
+        pip install -e ./tools/odbclient
         sudo apt-get install pandoc
     - name: Build docs
       run: sphinx-build -b html docs _build/html
diff --git a/INSTALLATION.md b/INSTALLATION.md
@@ -15,16 +15,17 @@ You need a python installation e.g. a virtual environment with `pip` a recent
 (brand new ones might not work) python versions installed. There are several
 ways to achieve that.
 
-#### Using anaconda
+#### Using miniconda or anaconda
 
-Install anaconda or miniconda [http://anaconda.com] on your computer and create
-a virtual environment with the package `pip` installed. See the [conda
+Install [miniconda](https://conda.io/miniconda.html) or
+[anaconda](http://anaconda.com) on your computer and create a virtual
+environment with python installed. See the [conda
 documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
 on how to do that. The newly created environment must be activated.
 
 The following command lines should do it
 ```
-conda create -n pylife-env python=3.9 pip --yes
+conda create -n pylife-env python=3.11 --yes
 conda activate pylife-env
 ```
 
@@ -50,7 +51,6 @@ That installs pyLife with all the dependencies to use pyLife in python
 programs. You might want to install some further packages like `jupyter` in
 order to work with jupyter notebooks.
 
-
 There is no conda package as of now, unfortunately.
 
 
@@ -75,7 +75,7 @@ Create an environment – usually a good idea to use a prefixed environment in
 your pyLife working directory and activate it.
 
 ```
-conda create -p .venv python=3.9 pip --yes
+conda create -p .venv python=3.11 pip --yes
 conda activate ./.venv
 ```
 

diff --git a/docs/3rd-party-licenses.md b/docs/3rd-party-licenses.md
diff --git a/docs/3rd-party-licenses.txt b/docs/3rd-party-licenses.txt
@@ -0,0 +1,5 @@
+3rd Party Licenses
+==================
+
+.. literalinclude:: ../3rd-party-licenses.txt
+    :language: text
diff --git a/docs/conf.py b/docs/conf.py
@@ -28,6 +28,8 @@
     vdisplay = Xvfb()
     vdisplay.start()
 
+os.environ['PYDEVD_DISABLE_FILE_VALIDATION'] = "1"
+
 ipython_dir = os.path.join(__projectdir__, "_build", "ipythondir")
 os.environ['IPYTHONDIR'] = ipython_dir
 
@@ -47,10 +49,14 @@
         ep.preprocess(nb, {'metadata': {'path': os.path.dirname(fn)}})
 
 
+
+
 # Don't try to use C-code for the pytensor stuff when building the docs.
 # Otherwise the demo notebooks fail on readthedocs
 os.environ['PYTHONWARNINGS'] = 'ignore'
 
+os.environ["PYVISTA_JUPYTER_BACKEND"] = 'html'
+
 import asyncio
 
 # See https://bugs.python.org/issue37373 :(
@@ -128,7 +134,11 @@
 templates_path = ["_templates"]
 
 # The suffix of source filenames.
-source_suffix = [".rst", ".md", ".txt", ".ipynb"]
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.txt': 'restructuredtext',
+    '.md': 'markdown',
+}
 
 # The encoding of source files.
 # source_encoding = 'utf-8-sig'

diff --git a/docs/demos/data b/docs/demos/data
diff --git a/docs/demos/import_mesh_ansys.nblink b/docs/demos/import_mesh_ansys.nblink
@@ -1,3 +1,4 @@
 {
-    "path": "../../demos/import_mesh_ansys.ipynb"
+    "path": "../../demos/import_mesh_ansys.ipynb",
+    "extra-media": ["../../demos/data"]
 }
diff --git a/docs/demos/import_mesh_vmap.nblink b/docs/demos/import_mesh_vmap.nblink
@@ -1,3 +1,4 @@
 {
-    "path": "../../demos/import_mesh_vmap.ipynb"
+    "path": "../../demos/import_mesh_vmap.ipynb",
+    "extra-media": ["../../demos/data/"]
 }
diff --git a/docs/demos/stress_strength.nblink b/docs/demos/stress_strength.nblink
diff --git a/docs/tutorials.rst b/docs/tutorials.rst
@@ -14,8 +14,8 @@ computer, you can use `MyBinder
 .. toctree::
    :maxdepth: 1
 
-   demos/woehler_curve.nblink
-   demos/load_collective.nblink
-   demos/stress_strength.nblink
-   demos/fkm_nonlinear.nblink
-   demos/fkm_nonlinear_full.nblink
+   tutorials/woehler_curve.nblink
+   tutorials/load_collective.nblink
+   tutorials/stress-strength.rst
+   tutorials/fkm_nonlinear.nblink
+   tutorials/fkm_nonlinear_full.nblink
diff --git a/docs/tutorials/fkm_nonlinear.nblink b/docs/tutorials/fkm_nonlinear.nblink
@@ -0,0 +1,3 @@
+{
+    "path": "../../demos/fkm_nonlinear/fkm_nonlinear.ipynb"
+}
diff --git a/docs/demos/fkm_nonlinear_mesh.nblink → docs/tutorials/fkm_nonlinear_full.nblink b/docs/demos/fkm_nonlinear_mesh.nblink → docs/tutorials/fkm_nonlinear_full.nblink
diff --git a/docs/demos/load_collective.nblink → docs/tutorials/load_collective.nblink b/docs/demos/load_collective.nblink → docs/tutorials/load_collective.nblink
diff --git a/docs/demos/woehler_curve.nblink → docs/tutorials/woehler_curve.nblink b/docs/demos/woehler_curve.nblink → docs/tutorials/woehler_curve.nblink
diff --git a/setup.cfg b/setup.cfg
@@ -99,11 +99,11 @@ analysis =
 
 tsfresh =
     tsfresh
-    numpy>=1.23
 
 pymc =
    pymc
    bambi
+   numpy<1.26  # https://github.com/pymc-devs/pymc/issues/7043#issuecomment-1837141888
 
 all = %(tsfresh)s %(pymc)s
 

diff --git a/src/pylife/materiallaws/rambgood.py b/src/pylife/materiallaws/rambgood.py
@@ -26,13 +26,12 @@ class RambergOsgood:
 
     Parameters
     ----------
-
     E : float
         Young's Modulus
     K : float
-        The strength coefficient, usually named `K'` or ``K_prime`̀  in FKM nonlinear related formulas.
+        The strength coefficient, usually named ``K'`` or ``K_prime`` in FKM nonlinear related formulas.
     n : float
-        The strain hardening coefficient, usually named `n'` or ``n_prime`̀  in FKM nonlinear related formulas.
+        The strain hardening coefficient, usually named ``n'`` or ``n_prime`` in FKM nonlinear related formulas.
 
     Notes
     -----
@@ -156,7 +155,7 @@ def dresiduum(stress):
         abs_stress = optimize.newton(
             func=residuum,
             x0=stress0,
-            fprime=dresiduum, 
+            fprime=dresiduum,
             rtol=rtol, tol=tol
         )
         return abs_stress * sign_strain

diff --git a/src/pylife/mesh/__init__.py b/src/pylife/mesh/__init__.py
@@ -18,14 +18,17 @@
 __maintainer__ = __author__
 
 from .meshsignal import PlainMesh, Mesh
-from .gradient import Gradient
+from .gradient import Gradient, Gradient3D
 from .hotspot import HotSpot
 from .meshmapping import Meshmapper
+from .surface import Surface3D
 
 __all__ = [
     'PlainMesh',
     'Mesh',
     'Gradient',
+    'Gradient3D',
     'HotSpot',
-    'Meshmapper'
+    'Meshmapper',
+    'Surface3D'
 ]