merge master

.github/workflows/python-publish.yml

@@ -32,7 +32,6 @@ jobs:
       - name: Build package
         run: python -m build
       - name: Publish package
-        if: startsWith(github.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
         with:
           user: __token__

.gitignore

@@ -3,7 +3,7 @@
 *.py[cod]
 *.so
 *.cfg
-!.isort.cfg
+!propulate/.isort.cfg
 !setup.cfg
 *.orig
 *.log
@@ -49,11 +49,6 @@ MANIFEST
 # Per-project virtualenvs
 .venv*/
 
-*.pkl
-
+*.pickle
 MNIST
-*cpt.p
-*cpt.p.bkp
-scripts/*.png
-
-voucher_propulate.txt
+*.bkp

CONTRIBUTING.md

@@ -0,0 +1,140 @@
+# Contributing to Propulate
+
+Welcome to ``Propulate``! We're thrilled that you're interested in contributing to our open-source project. 
+By participating, you can help improve the project and make it even better. 
+
+## How to Contribute
+
+1. **Fork the Repository**: Click the "Fork" button at the top right corner of this repository's page to create your own copy.
+
+2. **Clone Your Fork**: Clone your forked repository to your local machine using Git:
+   ```bash
+   git clone https://github.com/Helmholtz-AI-Energy/propulate.git
+   ```
+
+3. **Create a Branch**: Create a new branch for your contribution. Choose a descriptive name:
+   ```bash
+   git checkout -b your-feature-name
+   ```
+
+4. **Make Changes**: Make your desired changes to the codebase. Please stick to the following guidelines: 
+   * `Propulate` uses [*Black*](https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html) code style and so should you if you would like to contribute.
+   * Please use type hints in all function definitions.
+   * Please use American English for all comments and docstrings in the code.
+   * `Propulate` uses Sphinx autoapi to automatically create API reference documentation from docstrings in the code. 
+     Please use the [NumPy Docstring Standard](https://numpydoc.readthedocs.io/en/latest/format.html) for your docstrings:
+
+     ```python
+     """
+     Short Description
+
+     Long Description (if needed)
+
+     Parameters
+     ----------
+     param1 : type
+         Description of param1.
+
+     param2 : type, optional
+         Description of param2. (if it's an optional argument)
+
+     Returns
+     -------
+     return_type
+         Description of the return value.
+
+     Other Parameters
+     ----------------
+     param3 : type
+         Description of param3. (if there are additional parameters)
+
+     Raises
+     ------
+     ExceptionType
+         Description of when and why this exception might be raised.
+
+     See Also
+     --------
+     other_function : Related function or module.
+
+     Examples
+     --------
+        >>> import numpy as np
+        >>> x = np.array([1, 2, 3])
+        >>> y = np.square(x)
+        >>> print(y)
+     array([1, 4, 9])
+
+     Notes
+     -----
+     Additional notes, recommendations, or important information.
+     """
+     ```
+     When applicable, please make references to parent modules and classes using ```:class:`ParentClassName` ```
+as follows:
+
+     ```python
+     """
+     This is the docstring for MyClass.
+
+     Parameters
+     ----------
+     param1 : type
+              Description of param1.
+
+     Attributes
+     ----------
+     attr1 : type
+         Description of attr1.
+
+     See Also
+     --------
+     :class:`ParentClassName` : Reference to the parent class.
+
+     """
+
+     class ParentClassName:
+         """
+         The docstring for the parent class.
+         """
+
+     class MyClass(ParentClassName):
+         """
+         The docstring for MyClass.
+    
+         Parameters
+         ----------
+         param2 : type
+                  Description of param2.
+        
+         Attributes
+         ----------
+         attr2 : type
+                 Description of attr2.
+         """
+     ```
+     In the example above, ``` :class:`ParentClassName` ``` is used to create a reference to the parent class `ParentClassName`. 
+     Sphinx autoapi will automatically generate links to the parent class documentation.
+
+
+5. **Commit Changes**: Commit your changes with a clear and concise commit message:
+   ```bash
+   git commit -m "Add your commit message here"
+   ```
+
+6. **Push Changes**: Push your changes to your fork on GitHub:
+   ```bash
+   git push origin your-feature-name
+   ```
+
+7. **Open a Pull Request**: Go to the [original repository](https://github.com/Helmholtz-AI-Energy/propulate.git) and click the "New Pull Request" button. Follow the guidelines in the template to submit your pull request.
+
+## Code of Conduct
+
+Please note that we have a [Code of Conduct](CODE_OF_CONDUCT.md), and we expect all contributors to follow it. Be kind and respectful to one another.
+
+## Questions or Issues
+
+If you have questions or encounter any issues, please create an issue in the [Issues](https://github.com/Helmholtz-AI-Energy/propulate/issues) section of this repository.
+
+Thank you for your contribution!

README.md

@@ -63,3 +63,6 @@ OpenMPI.
 
 
 
+
+
+

RELEASE.md

@@ -0,0 +1,8 @@
+# Releasing a new version of Propulate
+
+The current workflow for releasing a new version of `Propulate` is as follows:
+1. Make sure the master branch is up-to-date and contains the version of the software that it is to be released.
+2. On the master branch, update the version number in `setup.cfg`. We use semantic versioning.
+3. Rebase release branch onto current master branch.
+4. Make Github release from current master, including corresponding version tag.
+5. Push release branch. This will trigger a Github action publishing the new release on PyPI.

docs/conf.py

@@ -47,8 +47,6 @@
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
-
-
 # -- Options for HTML output -------------------------------------------------
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
@@ -65,7 +63,7 @@
 html_theme_options = {
     "logo_only": True,
     "style_nav_header_background": "#e5eaec",
-    "style_external_links": True
+    "style_external_links": True,
 }
 
 # Add any paths that contain custom static files (such as style sheets) here,

docs/requirements.txt

@@ -1,4 +1,4 @@
-sphinx-autoapi==2.1.0
+sphinx-autoapi==3.0.0
 sphinx-rtd-theme==1.2.0
 sphinxcontrib-napoleon
 sphinxemoji