Feat/coupling expansion

.github/workflows/main.yml

@@ -2,14 +2,13 @@
 name: Python Package Publication
 
 on:
+  pull_request:
+    types: [closed]
+    branches: [master]
   workflow_dispatch:
     inputs:
       release-version:
         required: true
-      dry-run: 
-        required: true
-        default: true
-        type: boolean
       linux:
         type: boolean
         required: true
@@ -37,7 +36,7 @@ jobs:
         with:
           python-versions: 'cp38-cp38 cp39-cp39 cp310-cp310 cp311-cp311'
       - name: upload wheel
-        if:  ${{ !inputs.dry-run }} 
+        if: github.event.pull_request.merged == true || github.event_name == 'workflow_dispatch'
         run: |
           python -m pip install --upgrade pip 
           python -m pip install wheel setuptools twine
@@ -68,13 +67,13 @@ jobs:
           python -m pip install wheel setuptools twine
           python setup.py bdist_wheel
       - name: upload wheel
-        if:  ${{ !inputs.dry-run }} 
+        if: github.event.pull_request.merged == true || github.event_name == 'workflow_dispatch'
         run: |
           twine upload dist/*
         continue-on-error: false
 
   release-build:
-    if:  ${{ !inputs.dry-run }} 
+    if: github.event.pull_request.merged == true || github.event_name == 'workflow_dispatch'
     needs: [ linux-build, other-os-build ]
     runs-on: ubuntu-latest
     steps:

.pre-commit-config.yaml

@@ -2,17 +2,19 @@
 # See https://pre-commit.com/hooks.html for more hooks
 
 exclude: "^\
-  (third-party/.*)|\
+  (third_party/kissfft)|\
   (build/.*)|\
   (.github/.*)|\
   (.vscode/.*)|\
   (^tests)|\
-  (docs/api/.*)
+  (docs/api/.*)|\
+  (core/compute.hpp)|\
+  (defaults.cfg)
   "
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.1.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files # prevents giant files from being committed.
       - id: check-case-conflict # checks for files that would conflict in case-insensitive filesystems.
@@ -26,30 +28,38 @@ repos:
       - id: trailing-whitespace # trims trailing whitespace.
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.5.1
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         files: \.(html|json|markdown|md|yaml|yml)$
         exclude: (^docs/api/.*)
 
-  - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.4
     hooks:
-      - id: isort
-        name: isort (python)
-
-  - repo: https://github.com/pre-commit/mirrors-yapf
-    rev: v0.32.0
-    hooks:
-      - id: yapf
-        files: "^cmtj"
-        args: [--in-place, --recursive]
+      # Run the linter.
+      - id: ruff
+        files: ^cmtj
+        args: ["--fix"]
+        types_or: [python, pyi]
+      # Run the formatter.
+      - id: ruff-format
+        files: ^cmtj
+        types_or: [python, pyi]
 
   - repo: https://github.com/pocc/pre-commit-hooks
     rev: v1.3.5
     hooks:
       - id: cppcheck
-      # - id: clang-format
-      # - id: oclint
-      # - id: uncrustify
-      - id: include-what-you-use
+        args: ["--check-level=exhaustive"]
+        files: ^(cmtj|core)/.*\.(cpp|hpp)$
+        exclude: ^third_party/ | ^core/compute.hpp
+      - id: clang-format
+        args: [-i]
+        files: ^(cmtj|core)/.*\.(cpp|hpp)$
+        exclude: ^third_party/ | ^core/compute.hpp
+      - id: clang-tidy
+        args: [-checks=*]
+        files: ^(cmtj|core)/.*\.(cpp|hpp)$
+        exclude: ^third_party/ | ^core/compute.hpp

CHANGELOG.md

@@ -1,13 +1,24 @@
 # Changelog
 
-# 1.5.0 (WIP)
+# 1.6.0
+
+- Extended the `Stack` models allowing for non-symmetric coupling between devices.
+  `Stack` current drivers can now be of any type and are adequately scaled.
+- Custom definition of the `ScalarDriver` is now possible and documented.
+- Fixed a bug in the `Stack` class which inverted the connection order of in-series connections.
+- Exposed IDMI interaction to Layer and Junction classes.
+- Added `getLayer` method to the `Junction` class and `getJunction` method to the `Stack` class that return a reference to the object.
+- Fixed and expanded the `reservoir` module. Now, `GroupInteraction` can use any dipole interaction function, with 3 provided as default: `computeDipoleInteraction`, `computeDipoleInteractionNoumra` and `nullDipoleInteraction` (0 dipole tensor).
+
+# 1.5.0-1.5.4
 
 - Dipole interaction added to the `SB Model`
 - Kasdin 1/f noise generator added to the `noise` module and to the solvers
-- reworking the solvers for better performance and stability
-- added a simple noise model to the `utils` class. It exists outside standard simulation procedures.
-- added LLGB bindings and code. The solver is still WIP and doesn't integrate with more advanced features yet.
-- added aliases for `ScalarDriver` -- for example, instead of calling `ScalarDriver.getConstantDriver`, you can now call `constantDriver` directly to create a constant driver.
+- Reworking the solvers for better performance and stability
+- Added a simple noise model to the `utils` class. It exists outside standard simulation procedures.
+- Added LLGB bindings and code. The solver is still WIP and doesn't integrate with more advanced features yet.
+- Added aliases for `ScalarDriver` -- for example, instead of calling `ScalarDriver.getConstantDriver`, you can now call `constantDriver` directly to create a constant driver.
+- Improve stub detection across editors and IDEs
 
 # 1.4.1
 
@@ -40,12 +51,12 @@
 - Adding DW dynamics 1D model with dynamic drivers. (Numba optimised)
 - Adding SB model for energy-based FMR computation. Gradient computed using Adam optimiser.
 - Moving resistance functions from `utils` to `resistance`
-- Introducting docs updates for tutorial notebook (dark/light toggle works now).
+- Introducing docs updates for tutorial notebook (dark/light toggle works now).
 - Reservoir computing is now exposed in Python in the `reservoir` computing module.
 
 ## 1.2.0
 
-- Oersted field computation helper class in [cmtj/models/oersted.py](cmtj/models/oersted.py). Basic functionality is there, but needs to be futher tested and documented. Next release potentially will move the computation to C++ for speed.
+- Oersted field computation helper class in [cmtj/models/oersted.py](cmtj/models/oersted.py). Basic functionality is there, but needs to be further tested and documented. Next release potentially will move the computation to C++ for speed.
 - Added Heun (2nd order) solver and made it default for thermal computation. This is a more stable solver than the Euler solver, but is slower. The Euler solver is still available as an option.
 - Stack class now supports arbitrary layer ids to be coupled.
 - Extended the plotting capabilities of the Stack class. Now supports plotting of the magnetic field and the current density.

README.md

@@ -14,6 +14,7 @@
 - [CMTJ](#cmtj)
   - [Table of contents](#table-of-contents)
   - [Short description](#short-description)
+    - [What can you simulate?](#what-can-you-simulate)
   - [Web GUI](#web-gui)
   - [Quickstart](#quickstart)
     - [Installation :rocket:](#installation-rocket)
@@ -34,6 +35,37 @@ The `cmtj` name may be misleading -- the MTJ (Magnetic Tunnel Junctions) are not
 The library allows for macromagnetic simulation of various multilayer spintronic structures. The package uses C++ implementation of (s)LLGS (stochastic Landau-Lifschitz-Gilbert-Slonczewski) equation with various field contributions included for instance: anisotropy, interlayer exchange coupling, demagnetisation, dipole fields etc.
 It is also possible to connect devices in parallel or in series to have electrically coupled arrays.
 
+### What can you simulate?
+
+Below is a brief list of examples (it's not exhaustive! Check the docs for more).
+
+**Magnetic devices:**
+
+- Magnetic Tunnel Junctions
+  - Voltage-Driven Magnetic Tunnel Junctions
+  - Spin-Torque Oscillators
+  - VCMA sensors and devices
+  - Magnetic Tunnel Junction Arrays
+- SOT devices
+  - Current-Driven SOT
+- Advanced device coupling
+- Reservoirs (dipole coupling)
+- Electrically coupled MTJs
+- Base equations
+  - Landau-Lifshitz-Gilbert-Slonczewski equation
+  - Stochastic Landau-Lifshitz-Gilbert-Slonczewski equation
+  - Landau-Lifshitz-Gilbert-Bloch equation
+- Domain wall motion
+
+**Experimental methods:**
+
+Some of the experimental methods available:
+
+- PIMM
+- Spin-Diode
+- CIMS
+- R(H), M(H)
+
 ## Web GUI
 
 Check out the [streamlit hosted demo here](http://cmtj-simulations.streamlit.app/). You can simulate PIMM spectra and Spin-Diode spectra there. Let us know if you have any issues with the demo.
@@ -144,13 +176,16 @@ pre-commit run -a (or --files core/* cmtj/*)
 
 ## Documentation builds
 
-There are couple of stages to building the documentation
+**Note**
+For stub generation add `__init__.py` to the `cmtj` directory.
+
+There are a couple of stages to building the documentation
 
 1. Build Doxygen documentation
    ```
    doxygen Doxyfile
    ```
-   This is mostly for the C++ documentation. Furture changes may couple C++ and Python docs.
+   This is mostly for the C++ documentation. Future changes may couple C++ and Python docs.
 2. Build stubs
    The stubgen is `pybind11-stubgen` or `mypy stubgen` with the latter being preferred now.
    Before running the stubgen, make sure to install the package with:
@@ -168,8 +203,7 @@ There are couple of stages to building the documentation
    ```
    More info here: https://mypy.readthedocs.io/en/stable/stubgen.html.
 3. Parse stubs to Markdown.
-   This stage is done by running:
-   `python3 docs/docgen.py `
+   This stage is done by running: `python3 docs/docgen.py `
    The deployment of the documentation is done via:
    ```bash
    mkdocs gh-deploy