Feature/adding examples of DeepONets

.github/workflows/update_docs.yml

@@ -0,0 +1,42 @@
+name: Automate Documentation Build #name of action
+
+on: #trigger event
+  push:
+    branches:
+      - master #execute on a push to master branch
+
+permissions:
+  contents: write #grant access to write to master branch
+
+jobs: #define set of jobs. Here there is only one job, each job is instantiated on a Github-hosted runner
+  docs: #name of the job
+    runs-on: ubuntu-latest #runner runs on latest version of Ubuntu
+    steps: #this job is associated with a series of steps
+
+      # step 1: syntax for telling GHA to use this repository's code as "root" directory. Rest of GHA is able to have access
+      - uses: actions/checkout@v3
+      # step 2: #syntax for telling GHA to set-up Python on this runner associated for this whole job
+      - uses: actions/setup-python@v3
+
+      # Step 3: define a step that install dependencies (Sphinx etc) for this runner
+      - name: Install dependencies #name of this step
+        run: | #indicate that following script is meant to be multi-line
+          pip install sphinx sphinx_rtd_theme myst_parser 
+
+      # Step 4: Build docs using sphinx. TZ=UTC needed to circumvent a nuance of running Sphinx on GHA runner
+      - name: Sphinx build
+        run: |
+          TZ=UTC sphinx-build docs html
+
+      # Step 5: Deploy the newly built docs to gh-pages branch
+      - name: Deploy to GitHub Pages
+        #uses a github action "extension" called actions-gh-pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: github.ref == 'refs/heads/master' #ensure that we are on the master branch
+
+        #following is syntax for using actions-gh-pages action
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: html/ #docs to publish to html directory
+          force_orphan: true #common command associated with deploying a GitHub Page

.gitignore

@@ -166,4 +166,6 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+#.idea/
+
+building_parameters/

CONTRIBUTING.md

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+
+## Community Development Guidelines
+
+We welcome contributions and feedback from the open-source community!
+
+### Discussions
+
+[Discussions](https://github.com/pnnl/neuromancer/discussions) should be the first line of contact for new users to provide direct feedback on the library.
+Post your [Ideas](https://github.com/pnnl/neuromancer/discussions/categories/ideas) for new features or examples, 
+showcase your work using neuromancer in [Show and tell](https://github.com/pnnl/neuromancer/discussions/categories/show-and-tell),
+or get support for usage in [Q&As](https://github.com/pnnl/neuromancer/discussions/categories/q-a),
+please post them in one of our  categories.
+
+
+### Contributing examples
+If you have an example of using NeuroMANCER to solve an interesting problem, or of using 
+NeuroMANCER in a unique way please share them in [Show and tell](https://github.com/pnnl/neuromancer/discussions/categories/show-and-tell)
+discussions.
+The best examples might be incorporated into our current library of examples. 
+To submit an example, create a folder for your example/s in the example folder if there isn't 
+currently an applicable folder and place either your executable python file or notebook file there. 
+Push your code back to Github and then submit a pull request. Please make sure to note in a comment at 
+the top of your code if there are additional dependencies to run your example and how to install 
+those dependencies. 
+
+### Contributing code
+
+We welcome contributions to NeuroMANCER. Please accompany contributions with some lightweight unit tests
+via pytest (see test/ folder for some examples of easy to compose unit tests using pytest). 
+In addition to unit tests
+a script utilizing introduced new classes or modules should be placed in the examples folder. 
+To contribute a new well-developed feature please submit a pull request (PR). 
+Before creating a PR, we encourage developers to discuss and document the intended feature
+in [Ideas](https://github.com/pnnl/neuromancer/discussions/categories/ideas) discussion category.
+
+### Reporting issues or bugs
+If you find a bug in the code or want to request a new well-developed feature, please open an [issue](https://github.com/pnnl/neuromancer/issues).
+
+
+## NeuroMANCER development plan
+Here are some upcoming features we plan to develop. Please let us know if you would like to get involved and 
+contribute so we may be able to coordinate on development. If there is a feature that you think would
+be highly valuable but not included below, please open an issue and let us know your thoughts. 
+
++ Control and modelling for networked systems
++ Support for stochastic differential equations (SDEs)
++ Easy to implement modeling and control with uncertainty quantification
++ Proximal operators for dealing with equality and inequality constraints
++ Interface with CVXPYlayers
++ Online learning examples
++ Benchmark examples of DPC compared to deep RL
++ Conda and pip package distribution
++ More versatile and simplified time series dataloading
++ Discovery of governing equations from learned RHS via NODEs and SINDy
++ More domain science examples