Marohn-Group · peterhys · Apr 7, 2025 · Apr 9, 2025 · Apr 9, 2025 · Apr 14, 2025
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -31,9 +31,9 @@ assignees: ''
 
 <!-- Please complete the following information -->
 
-- **OS:** [e.g., macOS 13.0, Ubuntu 22.04, Windows 11]
+- **OS:** [e.g., macOS 26.0, Ubuntu 22.04, Windows 11]
 - **Python Version:** [e.g., 3.9.7, 3.10.5]
-- **mrfmsim Version:** [e.g., 0.1.0, or commit hash if installed from source]
+- **mrfmsim Version:** [e.g., 0.1.0]
 - **Installation Method:** [e.g., pip, conda, from source]
 
 ## Error Messages/Stack Traces
@@ -54,4 +54,5 @@ Paste error message here
 
 ## Possible Solution
 
-<!-- If you have suggestions on how to fix the bug, please share them here -->
+<!-- If you have suggestions on how to fix the bug,
+please share them here -->
diff --git a/.github/ISSUE_TEMPLATE/documentation.md b/.github/ISSUE_TEMPLATE/documentation.md
@@ -24,6 +24,5 @@ assignees: ''
 
 ## Additional Context
 
-<!-- Add any other context, examples, or screenshots about the documentation issue here -->
-
-
+<!-- Add any other context, examples,
+or screenshots about the documentation issue here -->
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -28,11 +28,10 @@ assignees: ''
 
 ## Additional Context
 
-<!-- Add any other context, screenshots, code examples, or references about the feature request here -->
+<!-- Add any other context, screenshots, code examples,
+or references about the feature request here -->
 
 ## Potential Implementation
 
-<!-- If you have ideas about how this could be implemented, please share them here -->
-
-
-
+<!-- If you have ideas about how this could be implemented,
+please share them here -->
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,3 +1,15 @@
+## Description
+
+<!-- Provide a clear and concise description of your changes -->
+
+## Changes Made
+
+<!-- List the key changes made in this PR -->
+
+- 
+- 
+- 
+
 ## Type of Pull Request
 
 <!-- Check the appropriate box by replacing [ ] with [x] -->
@@ -11,36 +23,24 @@
 - [ ] Test coverage improvement
 - [ ] Other (please describe):
 
-## Description
-
-<!-- Provide a clear and concise description of your changes -->
-
 
 ## Related Issue(s)
 
 <!-- Link to related issue(s) if applicable -->
 <!-- Example: Fixes #123, Closes #456, Related to #789 -->
 
 
-## Changes Made
-
-<!-- List the key changes made in this PR -->
-
-- 
-- 
-- 
-
 ## Breaking Changes
 
 <!-- If this PR introduces breaking changes, describe them here -->
 <!-- Otherwise, write "None" -->
 
 
-## Testing Performed
+## Testing
 
 <!-- Describe the testing you have performed to verify your changes -->
 
-- [ ] All existing tests pass (`tox` or `pytest`)
+- [ ] All existing tests pass (`tox`)
 - [ ] Added new tests for new functionality
 - [ ] Manual testing performed (describe below)
 
@@ -58,31 +58,18 @@
 - [ ] Added usage examples (if applicable)
 - [ ] Documentation builds without errors (`cd docs && make html`)
 
-## Code Quality
+## Checklist
 
 <!-- Check all that apply -->
 
-- [ ] Code follows PEP 8 style guidelines
+- [ ] Code follows PEP 8 style guidelines (use ``Black`` formatter's default settings)
 - [ ] Used meaningful variable and function names
 - [ ] Code is modular and readable
-
-## Checklist
-
-<!-- Check all that apply -->
-
-- [ ] My code follows the project's coding standards
-- [ ] I have performed a self-review of my own code
-- [ ] I have commented my code, particularly in hard-to-understand areas
-- [ ] My changes generate no new warnings or errors
-- [ ] I have checked that this PR focuses on a single feature or bug fix
+- [ ] Commented code, particularly in hard-to-understand areas
+- [ ] Changes generate no new warnings or errors
+- [ ] PR focuses on a single feature or bug fix
 
 ## Additional Notes
 
-<!-- Any additional information that reviewers should know -->
-
-
-## Screenshots (if applicable)
-
-<!-- Add screenshots here if relevant -->
-
-
+<!-- Any additional information that reviewers should know
+Add screenshots here if relevant -->
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -10,13 +10,21 @@ and this project adheres to
 [unreleased]
 ------------
 
-Minor fixes to documentation.
+Added Cylinder Magnet and minor fixes to docstrings and documentation.
 
 Changed
 ^^^^^^^
 
 - Change the CERMITD experiment graph to avoid output duplication.
+- Change the API to use the latest version of the mmodel package (0.9.0).
+- Modify the Nan treatment of ``polarization.rel_dpol_sat_td`` (#4)
+- Reformat the docstrings and documentations
 
+Added
+^^^^^ 
+
+- Add ``CylinderMagnetApprox`` class to approximate the magnetic field of a cylinder magnet (#4)
+- Add pull request and issue templates.
 
 [0.3.0] - 2025-02-25
 ----------------------

diff --git a/README.rst b/README.rst
@@ -65,6 +65,11 @@ To test in different environments::
     tox
 
 
+Contributing
+^^^^^^^^^^^^
+
+We welcome contributions! Please see our `Contributing Guide <docs/contribute.rst>`_ for details on how to follow our development guidelines and submit pull requests.
+
 .. rubric:: References
 
 .. [#Sidles1995jan] Sidles, J. A.; Garbini, J. J.; Bruland, K. J.; Rugar, D.; 

diff --git a/docs/basic/geometry.rst b/docs/basic/geometry.rst
@@ -1,9 +1,9 @@
 Experiment geometry
 =============================
 
-For experiments in the *mrfmsim*, two experimental geometry
+For experiments in the *mrfmsim*, two experimental geometries
 are used: "hangdown" and SPAM (springiness preservation by aligning magnetization).
-The two geometry are shown in the figure below.
+The two geometries are shown in the figure below.
 
 .. image:: ../_static/mrfm-setups.pdf
     :width: 800px

diff --git a/docs/basic/inheritance.rst b/docs/basic/inheritance.rst
@@ -67,5 +67,5 @@ ExperimentGroup
 ----------------
 
 The ``mrfmsim.group.ExperimentGroup`` class adds additional properties
-``epxeriments`` and ``epxeriment_defaults`` alongside the parent class's
+``experiments`` and ``experiment_defaults`` alongside the parent class's
 ``models`` and ``model_defaults`` properties. 
diff --git a/docs/basic/plugin.rst b/docs/basic/plugin.rst
@@ -5,13 +5,13 @@ Ancillary features are added to the mrfmsim ecosystem through plugin packages.
 The separation of the core functionality and the plugins allows for an easy maintenance
 of the mrfmsim package. The core functionalities do not depend on the plugins.
 
-mrfmsim-ymal: YAML configuration plugin
+mrfmsim-yaml: YAML configuration plugin
 ---------------------------------------
 
 mrfmsim classes can be fully defined using YAML configuration files. The plugin
 creates a ``MrfmSimLoader`` and a ``MrfmSimDumper`` that can be used to load and
 dump the mrfmsim classes to and from YAML files. For detailed usage of the package
-see the `mrfmsim-ymal <https://github.com/Marohn-Group/mrfmsim-yaml>`_.
+see the `mrfmsim-yaml <https://github.com/Marohn-Group/mrfmsim-yaml>`_.
 
 To define an experiment or experiment group with YAML files, the available tags are:
 "!func", "!import", "!nodes", "!Graph", "!Experiment", and "!ExperimentGroup".

diff --git a/docs/contribute.rst b/docs/contribute.rst
@@ -0,0 +1,158 @@
+Contribute
+========================
+
+We welcome contributions to mrfmsim! This guide will help you get started.
+
+Getting Started
+---------------
+
+1. **Fork the Repository**
+
+   Fork the mrfmsim repository on GitHub and clone your fork locally:
+
+   .. code-block:: bash
+
+      git clone https://github.com/Marohn-Group/mrfmsim.git
+      cd mrfmsim
+
+
+2. **Create a Branch**
+
+   Create a new branch for your feature or bug fix:
+
+   .. code-block:: bash
+
+      git checkout -b feature/your-branch-name
+
+Development Guidelines
+----------------------
+
+Code Style
+~~~~~~~~~~
+
+- Follow PEP 8 style guidelines for Python code (use ``Black`` formatter's default settings)
+- Use meaningful variable and function names
+- Keep functions focused and modular
+- Add type hints where appropriate
+
+Documentation
+~~~~~~~~~~~~~
+
+- Write clear docstrings for all public classes, methods, and functions
+- Use reStructuredText (reST) format for docstrings
+- Refer to the `Sphinx docstring guide <https://sphinx-rtd-tutorial.readthedocs.io/en/latest/docstrings.html>`__ for detailed formatting information
+- Include:
+
+  - Brief description of what the function/class does
+  - Parameter descriptions with types and units in **Sphinx** docstring format
+  - Return value description
+  - Usage examples where helpful
+  - Mathematical formulas using Sphinx math directive when relevant
+
+Example docstring format:
+
+.. code-block:: python
+
+   def example_method(x, y, z):
+       r"""Calculate some property.
+
+       Brief description of what this method does and any important
+       details about the calculation or algorithm.
+
+       :param float x: :math:`x` coordinate [nm]
+       :param float y: :math:`y` coordinate [nm]
+       :param float z: :math:`z` coordinate [nm]
+       :return: calculated value
+       :rtype: float
+       """
+       pass
+
+
+Building Documentation
+----------------------
+
+To build the documentation locally:
+
+.. code-block:: bash
+
+   cd docs
+   make html
+
+The built documentation will be in ``docs/_build/html/``.
+
+Testing
+~~~~~~~
+
+- Write tests for all new features and bug fixes
+- Tests should be fast and independent from one another
+- Ensure all tests pass before submitting a pull request
+- Aim for good test coverage of your code
+
+Install test dependencies:
+
+.. code-block:: bash
+
+   pip install ".[test]"
+
+Run tests with tox:
+
+.. code-block:: bash
+
+   tox
+
+This will run tests across multiple Python environments and check code coverage.
+
+
+Submitting a Pull Request
+--------------------------
+
+**Important**: Each pull request should focus on a single feature or bug fix. This makes the code easier to review, test, and maintain.
+
+1. **Push to Your Fork**
+
+   .. code-block:: bash
+
+      git push origin feature/your-feature-name
+
+2. **Create Pull Request**
+
+   - Go to the mrfmsim repository on GitHub
+   - Click "New Pull Request"
+   - Select your fork and the ``develop`` branch as the base branch
+   - Fill out the pull request template with:
+
+     - Type of pull request (bug fix, feature, documentation, etc.)
+     - Description of changes
+     - Related issue numbers (if applicable)
+     - Any breaking changes
+     - Testing performed
+
+3. **Review Process**
+
+   - Maintainers will review your pull request
+   - Address any feedback or requested changes
+   - Once approved, your changes will be merged
+
+
+Reporting Issues
+----------------
+
+When reporting issues, please include:
+
+- A clear description of the problem
+- Steps to reproduce the issue
+- Expected vs. actual behavior
+- Your environment (Python version, OS, etc.)
+- Any relevant error messages or stack traces
+
+Questions?
+----------
+
+If you have questions about contributing, feel free to:
+
+- Open an issue on GitHub
+- Check existing documentation
+- Reach out to the maintainers
+
+Thank you for contributing to mrfmsim!
+
diff --git a/docs/experiment/CermitSat.rst b/docs/experiment/CermitSat.rst
@@ -101,7 +101,7 @@ in the Table below.
 ======================================== =================================================
 
 Variables appearing in eqs. :eq:`eq:x`, :eq:`eq:x-vars`, and subsequent equations. 
-he magnetic field :math:`B_0` is applied along the :math:`z` axis,
+The magnetic field :math:`B_0` is applied along the :math:`z` axis,
 and the equilibrium magnetization :math:`M_0` also lies along the :math:`z` axis.
 
 Steady-state solution

diff --git a/docs/experiment/CermitSingleSpin.rst b/docs/experiment/CermitSingleSpin.rst
@@ -5,7 +5,7 @@ Overview
 --------
 
 The experiments calculate the effective force on a cantilever from a single electron spin located directly below a magnet-tipped cantilever in the "hangdown" and SPAM geometries. 
-There are two experiments in the group: cantilever spin constant shift calculated using the Trapezoid rule ("CermitSingleSpinApprox"), and cantilever spring constant shift calculated directly using elliptic integrals ("CermitSingleSpin"). 
+There are two experiments in the group: cantilever spring constant shift calculated using the Trapezoid rule ("CermitSingleSpinApprox"), and cantilever spring constant shift calculated directly using elliptic integrals ("CermitSingleSpin"). 
 The exact solution only works for spin directly under a **spherical** magnet. The experiments are adopted from Section 3.5 of Eric Moore's dissertation. [#Moore2011Sep]_
 
 

diff --git a/docs/experiment/CermitTD.rst b/docs/experiment/CermitTD.rst
@@ -26,7 +26,7 @@ At low-:math:`B_1` region, we can determine numerically the final magnetization
 .. math::
     :label: eq:Mz(tau0)
 
-    M_z^\mathrm{finial} 
+    M_z^\mathrm{final} 
     \approx e^{-R(\tau_i, \tau_f)} M_z^\mathrm{initial}