Merge branch 'master' into generalised-zhang-li

.github/environment.yml

@@ -4,7 +4,6 @@ channels:
   - conda-forge
 
 dependencies:
-  - python==3.8
   - pip
   - oommf
   - pip:

.github/workflows/workflow.yml

@@ -17,18 +17,20 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-13, windows-latest]
+        python-version: ["3.8", "3.10"]
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
     - name: Initialisation
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Set up conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
+        python-version: ${{ matrix.python-version }}
         auto-update-conda: true
         activate-environment: conda-environment
         environment-file: .github/environment.yml

.pre-commit-config.yaml

@@ -1,37 +1,23 @@
-default_language_version:
-  python: python3.8
+exclude: 'dev'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-merge-conflict  # checks for files that contain merge conflict strings
   - id: check-toml  # checks toml files for parseable syntax
   - id: debug-statements  # checks for debugger imports and py37+ `breakpoint()` calls in python source
-#  - id: trailing-whitespace   # needs more checks
-#    args: [--markdown-linebreak-ext=md]
-#    exclude: 'oommfc/tests/test_sample/.*'
 
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
   hooks:
-  - id: isort
-
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.6.3
-  hooks:
-  - id: nbqa-isort  # isort inside Jupyter notebooks
-
-- repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
-  hooks:
-  - id: flake8
-    additional_dependencies: [flake8-rst-docstrings]  #, flake8-docstrings]
-
-- repo: https://github.com/psf/black
-  rev: 23.1.0
-  hooks:
-  - id: black-jupyter
+    # Run the linter.
+    - id: ruff
+      types_or: [python, pyi, jupyter]
+      args: [--fix, --exit-non-zero-on-fix]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [python, pyi, jupyter]
 
 # - repo: https://github.com/codespell-project/codespell
 #   rev: v2.1.0

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2022, Marijan Beg and Hans Fangohr
+Copyright 2023, Marijan Beg and Hans Fangohr
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

README.md

@@ -14,7 +14,6 @@
 | Description | Badge |
 | --- | --- |
 | Tests | [![Build status](https://github.com/ubermag/oommfc/workflows/workflow/badge.svg)](https://github.com/ubermag/oommfc/actions?query=workflow%3Aworkflow) |
-|       | [![conda](https://github.com/ubermag/oommfc/workflows/conda/badge.svg)](https://github.com/ubermag/oommfc/actions?query=workflow%3Aconda) |
 | Linting | [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/ubermag/oommfc/master.svg)](https://results.pre-commit.ci/latest/github/ubermag/oommfc/master) |
 |         | [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) |
 | Releases | [![PyPI version](https://badge.fury.io/py/oommfc.svg)](https://badge.fury.io/py/oommfc) |
@@ -79,7 +78,7 @@ Licensed under the BSD 3-Clause "New" or "Revised" License. For details, please
 
 2. M. Beg, R. A. Pepper, and H. Fangohr. User interfaces for computational science: A domain specific language for OOMMF embedded in Python. [*AIP Advances* **7**, 56025](http://aip.scitation.org/doi/10.1063/1.4977225) (2017).
 
-3. Marijan Beg, Martin Lang, Ryan A. Pepper, Thomas Kluyver, Samuel Holt, Swapneel Amit Pathak, and Hans Fangohr. oommfc: OOMMF calculator. DOI: [10.5281/zenodo.3539461](http://doi.org/10.5281/zenodo.3539461) (2022).
+3. Marijan Beg, Martin Lang, Ryan A. Pepper, Thomas Kluyver, Samuel Holt, Swapneel Amit Pathak, and Hans Fangohr. oommfc: OOMMF calculator. DOI: [10.5281/zenodo.3539461](http://doi.org/10.5281/zenodo.3539461) (2023).
 
 ## Acknowledgements
 

binder/environment.yml

@@ -5,4 +5,4 @@ channels:
 
 dependencies:
   - python==3.10
-  - oommfc
+  - ubermag

docs/controlling-default-runner.ipynb

@@ -3,7 +3,13 @@
   {
    "cell_type": "markdown",
    "id": "84445477",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
    "source": [
     "# Controlling the default runner\n",
     "In this tutorial we show how to globally controll the default runner. First we import `oommfc`."
@@ -86,7 +92,7 @@
     {
      "data": {
       "text/plain": [
-       "ExeOOMMFRunner(/opt/miniconda3/envs/ubermagdev/bin/oommf)"
+       "ExeOOMMFRunner(/home/mlang/miniconda3/envs/ubermagdev310/bin/oommf)"
       ]
      },
      "execution_count": 3,
@@ -117,7 +123,7 @@
     {
      "data": {
       "text/plain": [
-       "OOMMF runner: ExeOOMMFRunner(/opt/miniconda3/envs/ubermagdev/bin/oommf)\n",
+       "OOMMF runner: ExeOOMMFRunner(/home/mlang/miniconda3/envs/ubermagdev310/bin/oommf)\n",
        "runner is cached: True"
       ]
      },
@@ -256,7 +262,7 @@
     {
      "data": {
       "text/plain": [
-       "OOMMF runner: ExeOOMMFRunner(/opt/miniconda3/envs/ubermagdev/bin/oommf)\n",
+       "OOMMF runner: ExeOOMMFRunner(/home/mlang/miniconda3/envs/ubermagdev310/bin/oommf)\n",
        "runner is cached: True"
       ]
      },
@@ -299,14 +305,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Running OOMMF (TclOOMMFRunner) [2022/02/16 11:29]... (0.0 s)\n",
-      "OOMMF error:\n",
-      "\tcommand: tclsh /path/to/oommf_tcl boxsi +fg macrospin.mif -exitondone 1\n",
-      "\tstdout: \n",
-      "\tstderr: couldn't read file \"/path/to/oommf_tcl\": no such file or directory\n",
-      "\n",
-      "\n",
-      "\n",
+      "Running OOMMF (TclOOMMFRunner)[2023/10/18 12:33]... (0.0 s)\n",
       "Cannot find OOMMF.\n"
      ]
     },
@@ -317,8 +316,8 @@
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mValueError\u001b[0m                                Traceback (most recent call last)",
-      "Input \u001b[0;32mIn [10]\u001b[0m, in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0m oommfc\u001b[38;5;241m.\u001b[39mrunner\u001b[38;5;241m.\u001b[39mrunner \u001b[38;5;241m=\u001b[39m oommfc\u001b[38;5;241m.\u001b[39moommf\u001b[38;5;241m.\u001b[39mTclOOMMFRunner(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m/path/to/oommf_tcl\u001b[39m\u001b[38;5;124m'\u001b[39m)\n",
-      "File \u001b[0;32m~/PhD/repos/ubermag-devtools/repos/oommfc/oommfc/oommf/oommf.py:432\u001b[0m, in \u001b[0;36mRunner.runner\u001b[0;34m(self, runner)\u001b[0m\n\u001b[1;32m    429\u001b[0m \u001b[38;5;129m@runner\u001b[39m\u001b[38;5;241m.\u001b[39msetter\n\u001b[1;32m    430\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mrunner\u001b[39m(\u001b[38;5;28mself\u001b[39m, runner):\n\u001b[1;32m    431\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m runner\u001b[38;5;241m.\u001b[39mstatus \u001b[38;5;241m!=\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[0;32m--> 432\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrunner\u001b[38;5;132;01m=}\u001b[39;00m\u001b[38;5;124m cannot be used.\u001b[39m\u001b[38;5;124m'\u001b[39m)\n\u001b[1;32m    433\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_runner \u001b[38;5;241m=\u001b[39m runner\n",
+      "Cell \u001b[0;32mIn[10], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43moommfc\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrunner\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrunner\u001b[49m \u001b[38;5;241m=\u001b[39m oommfc\u001b[38;5;241m.\u001b[39moommf\u001b[38;5;241m.\u001b[39mTclOOMMFRunner(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m/path/to/oommf_tcl\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
+      "File \u001b[0;32m~/repos/ubermag-devtools/repos/oommfc/oommfc/oommf/oommf.py:441\u001b[0m, in \u001b[0;36mRunner.runner\u001b[0;34m(self, runner)\u001b[0m\n\u001b[1;32m    438\u001b[0m \u001b[38;5;129m@runner\u001b[39m\u001b[38;5;241m.\u001b[39msetter\n\u001b[1;32m    439\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mrunner\u001b[39m(\u001b[38;5;28mself\u001b[39m, runner):\n\u001b[1;32m    440\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m runner\u001b[38;5;241m.\u001b[39mstatus \u001b[38;5;241m!=\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[0;32m--> 441\u001b[0m         \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mrunner\u001b[38;5;132;01m=}\u001b[39;00m\u001b[38;5;124m cannot be used.\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m    442\u001b[0m     \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_runner \u001b[38;5;241m=\u001b[39m runner\n",
       "\u001b[0;31mValueError\u001b[0m: runner=TclOOMMFRunner(/path/to/oommf_tcl) cannot be used."
      ]
     }
@@ -344,7 +343,7 @@
     {
      "data": {
       "text/plain": [
-       "OOMMF runner: ExeOOMMFRunner(/opt/miniconda3/envs/ubermagdev/bin/oommf)\n",
+       "OOMMF runner: ExeOOMMFRunner(/home/mlang/miniconda3/envs/ubermagdev310/bin/oommf)\n",
        "runner is cached: True"
       ]
      },
@@ -388,12 +387,18 @@
    "cell_type": "code",
    "execution_count": 13,
    "id": "8c577eb3",
-   "metadata": {},
+   "metadata": {
+    "editable": true,
+    "slideshow": {
+     "slide_type": ""
+    },
+    "tags": []
+   },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "OOMMF runner: ExeOOMMFRunner(/opt/miniconda3/envs/ubermagdev/bin/oommf)\n",
+       "OOMMF runner: ExeOOMMFRunner(/home/mlang/miniconda3/envs/ubermagdev310/bin/oommf)\n",
        "runner is cached: True"
       ]
      },
@@ -423,7 +428,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.10.12"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {