Updates from main

.github/workflows/tests.yaml

@@ -0,0 +1,36 @@
+name: FENIAX tests
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [3.11, 3.12]
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f ./tests/requirements.txt ]; then pip install -r ./tests/requirements.txt; fi
+
+    - name: Run tests
+      run: |
+        pip install .
+        pytest tests

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+# To install the git pre-commit hooks run:
+#   pre-commit install --install-hooks
+# To update the versions:
+#   pre-commit autoupdate
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.4
+  hooks:
+    # Run the linter.
+    - id: ruff
+      args: [--fix, --show-fixes]
+    # Run the formatter.
+    - id: ruff-format
+- repo: https://github.com/tox-dev/pyproject-fmt
+  rev: "1.5.2"
+  hooks:
+    - id: pyproject-fmt
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.5.0
+  hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+      exclude: '.*\.pth$'
+    - id: debug-statements

README.md

@@ -1,10 +1,8 @@
 # Finite Element models 4 Intrinsic Nonlinear Aeroelastics in JAX [FENIAX]
 
-FEM4INAS is an aeroelastic toolbox  written and parallelized in Python, which acts as a post-processor of commercial software such as MSC Nastran. 
+FENIAX is an aeroelastic toolbox  written and parallelized in Python, which acts as a post-processor of commercial software such as MSC Nastran. 
 Arbitrary FE models built for linear aeroelastic analysis are enhanced with geometric nonlinear effects, flight dynamics and linearized state-space solutions about nonlinear equilibrium.
 
-![XRF1](./docs/images/xrf1-model3.jpg)
-
 ## Installation
 
 - Currently the code has been tested and is developed in Linux and MacOS.
@@ -23,7 +21,7 @@ pip install -e .[all]
 Although it is not necessary, If conda is being used as package manager, one can make a specific environment as,
 
 ```
-conda create -n fem4inas python=3.11
+conda create -n feniax python=3.11
 conda activate fem4inas
 ```
 
@@ -35,13 +33,61 @@ pytest tests
 
 - Thus a typical installation would comprise of these 4 steps:
 ```
-conda create -n fem4inas python=3.11
+conda create -n feniax.python=3.11
 conda activate fem4inas
 pip install -e .[all]
 pytest tests
 ```
 
-## Examples
+## Documentation
+Available at https://acea15.github.io/FENIAX/
+## Simulation Examples
+
+The most relevant examples in the code base are shown here, these and more can be found in the folder `/examples`
+They are also part of a large test suite that is integrated into the development using CI/CD.
+
+!!! tip
+    Navigate to the code of the various examples, including the simulation input settings and postprocessing of the simulation --exactly as it was used for the articles backing the software.
+
+
+### Nonlinear structural static results
+!!! success
+    Validated with MSC Nastran nonlinear solution (sol 400)
+
+[Notebook](./docs/documentation/examples/SailPlane/sailplane_nb.md)
+
+### Wing free dynamics
+!!! success
+    Validated with MSC Nastran nonlinear solution (sol 400)
+
+[Notebook](./docs/documentation/examples/wingSP/wingSP_nb.md)
+
+
+![Wing free dynamics](./docs/media/wingSP_optimized.gif)
+
+
+### Free flying structure
+
+[Bio](https://mechanics.stanford.edu/simo)
+
+[Notebook](./docs/documentation/examples/wingSP/wingSP_nb.md)
+
+#### 2D dynamics
+![Free flying structure 2D](./docs/media/SimoFFB2D_optimized.gif)
+#### 3D dynamics
+![Free flying structure 3D](./docs/media/SimoFFB3D_optimized.gif)
+
+### Industrial Aircraft model
+!!! success
+    Linear response validated with MSC Nastran linear aeroelastic solution (sol 146)
+
+#### Gust clamped model
+
+[Notebook](./docs/documentation/examples/XRF1/xrf1_nb.md)
+
+
+![XRF1-gustclamped](./docs/media/xrf1_gust_optimized.gif)
 
-The folder examples contains various instances with models, input files and postprocessing of the results. See each README.org for for more info.
 
+#### Gust trimmed flight
+![XRF1-Trim+gust](./docs/media/xrf1_trimgust_optimized.gif)

docs/documentation/JAX.md

@@ -0,0 +1,3 @@
+# JAX 
+
+![Jax logo](./img/jaxlogo.png)

docs/documentation/LICENSE.md

@@ -0,0 +1 @@
+/home/acea/projects/FENIAX/LICENSE.md

docs/documentation/UML.md

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+# example
+
+```mermaid
+classDiagram
+   class Driver {
+            +pre_simulation()
+            +run_cases()
+    }
+
+     class IntrinsicDriver {
+             #integration: IntrinsicIntegration
+             #simulation: Simulation
+             #opt: Optimisation
+             #systems: [System]
+             -__init__(config: Config)
+             #_set_case()
+             #_set_integration()
+             #_set_simulation()
+             #_set_systems()
+     }
+
+     class  XLoads {
+             +q: [jnp.ndarray]
+             +Rab: [jnp.ndarray]
+             +GAFs: [jnp.ndarray]
+             +followerF()
+             +deadF()
+             +gravityF()
+             +modalAero()
+             }
+
+     class IntrinsicIntegration {
+                     + <math>phi_1, phi_2, psi_1, psi_2</math>
+                     + <math>Gamma_1, Gamma_2 </math>
+                     -__init__(X, Ka, Ma)		
+                     +run()
+                     #compute_modalshapes()
+                     #compute_modalcouplings()
+     }
+
+     class Simulation {
+                     +systems: [System]
+                     #workflow: dict
+                     #opt: Optimisation
+                     +trigger()
+                     #run_systems()
+                     #post_run()
+             }
+     class SerialSimulation {
+     }
+     class ParallelSimulation {
+     }
+     class SingleSimulation {
+     }
+     class CoupledSimulation {
+     }
+
+     class IntrinsicSystem {
+            -dq: callable
+            -solver: callable
+            +sol: obj
+            #set_generator() -> dq
+            #set_solver() -> solver
+
+     }
+     Driver <|-- IntrinsicDriver
+     Simulation <|-- SingleSimulation
+     SingleSimulation -- SerialSimulation 
+     SerialSimulation -- ParallelSimulation
+     ParallelSimulation -- CoupledSimulation					
+
+```

docs/documentation/api/couplings.md

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+::: intrinsic.couplings

docs/documentation/api/inputs.md

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+# Input containers
+
+## Intrinsic modal solution
+
+::: preprocessor.containers.intrinsicmodal

docs/documentation/api/modes.md

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+::: intrinsic.modes

docs/documentation/examples.md

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+# Examples
+

docs/documentation/examples/SailPlane/figs

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+../../../reports/CPC24/figs

docs/documentation/examples/SailPlane/figs_ext

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+../../../reports/CPC24/figs_ext