added ruff, pre-commit as github actions

.github/workflows/lint.yaml

@@ -1,6 +1,10 @@
 name: Lint and Auto-Fix Code
 
-on: [push, pull_request]
+on:
+  push:
+  pull_request:
+    branches:
+      - main
 
 jobs:
   lint_and_fix:
@@ -26,3 +30,17 @@ jobs:
       - name: Run flake8 (lint only)
         run: flake8 .
 
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+
+      - name: Install pre-commit
+        run: pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files
+

.gitignore

@@ -1,3 +1,6 @@
 .idea/
 /.venv
 dist
+pytest_cache
+src/osipi/__pycache__
+tests/__pycache__

.pre-commit-config.yaml

@@ -1,32 +1,23 @@
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.8  # Use the latest version
     hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-      - id: check-yaml
-
+      - id: ruff
+        args: [--fix]  # Optional: to enable lint fixes
+      - id: ruff-format
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 7.0.0
     hooks:
       - id: flake8
-        args: [ '--max-line-length=100' ]
-
-
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-        args: [--line-length=70]
-
-  - repo: https://github.com/PyCQA/docformatter
-    rev: v1.4
+        args:
+          - --exclude=venv,.git,__pycache__,.eggs,.mypy_cache,.pytest_cache
+          - --max-line-length=100
+          - --ignore=E203
+          - --per-file-ignores=__init__.py:F401
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
     hooks:
-      - id: docformatter
-        args: [--in-place, --recursive, --blank, --force-wrap, --wrap-summaries=100,--wrap-descriptions=100]
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
 
-  - repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v1.5.7
-    hooks:
-      - id: autopep8
-        args: [--in-place, --aggressive, --aggressive, --recursive, --max-line-length=100]

docs/examples/aif/plot_aif_parker.py

@@ -6,10 +6,10 @@
 """
 
 import matplotlib.pyplot as plt
+
 # %%
 # Import necessary packages
 import numpy as np
-
 import osipi
 
 # %%

docs/examples/aif/plot_dummy.py

@@ -7,10 +7,10 @@
 """
 
 import matplotlib.pyplot as plt
+
 # %%
 # Import necessary packages
 import numpy as np
-
 import osipi
 
 # %%

docs/examples/tissue/plot_extended_tofts.py

@@ -7,10 +7,10 @@
 """
 
 import matplotlib.pyplot as plt
+
 # %%
 # Import necessary packages
 import numpy as np
-
 import osipi
 
 # %%

docs/examples/tissue/plot_tofts.py

@@ -7,10 +7,10 @@
 """
 
 import matplotlib.pyplot as plt
+
 # %%
 # Import necessary packages
 import numpy as np
-
 import osipi
 
 # %%

docs/source/conf.py

@@ -4,6 +4,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 import os
+
 # -- Project information ---------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 import sys

docs/source/generated/examples/aif/plot_aif_parker.ipynb

@@ -1,86 +1,113 @@
 {
-  "cells": [
-    {
-      "cell_type": "markdown",
-      "metadata": {},
-      "source": [
-        "\n# The Parker AIF - a play with variables\n\nSimulating a Parker AIF with different settings. \n"
-      ]
-    },
-    {
-      "cell_type": "markdown",
-      "metadata": {},
-      "source": [
-        "Import necessary packages\n\n"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "collapsed": false
-      },
-      "outputs": [],
-      "source": [
-        "import numpy as np\nimport matplotlib.pyplot as plt\nimport osipi"
-      ]
-    },
-    {
-      "cell_type": "markdown",
-      "metadata": {},
-      "source": [
-        "Generate synthetic AIF with default settings and plot the result.\n\n"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "collapsed": false
-      },
-      "outputs": [],
-      "source": [
-        "# Define time points in units of seconds - in this case we use a time resolution of 0.5 sec and a total duration of 6 minutes.\nt = np.arange(0, 6*60, 0.5)\n\n# Create an AIF with default settings\nca = osipi.aif_parker(t)\n\n# Plot the AIF over the full range\nplt.plot(t, ca, 'r-')\nplt.plot(t, 0*t, 'k-')\nplt.xlabel('Time (sec)')\nplt.ylabel('Plasma concentration (mM)')\nplt.show()"
-      ]
-    },
-    {
-      "cell_type": "markdown",
-      "metadata": {},
-      "source": [
-        "The bolus arrival time (BAT) defaults to 0s. What happens if we change it? Let's try, by changing it in steps of 30s:\n\n"
-      ]
-    },
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "collapsed": false
-      },
-      "outputs": [],
-      "source": [
-        "ca = osipi.aif_parker(t, BAT=0)\nplt.plot(t, ca, 'b-', label='BAT = 0s')\nca = osipi.aif_parker(t, BAT=30)\nplt.plot(t, ca, 'r-', label='BAT = 30s')\nca = osipi.aif_parker(t, BAT=60)\nplt.plot(t, ca, 'g-', label='BAT = 60s')\nca = osipi.aif_parker(t, BAT=90)\nplt.plot(t, ca, 'm-', label='BAT = 90s')\nplt.xlabel('Time (sec)')\nplt.ylabel('Plasma concentration (mM)')\nplt.legend()\nplt.show()\n\n# Choose the last image as a thumbnail for the gallery\n# sphinx_gallery_thumbnail_number = -1"
-      ]
-    }
-  ],
-  "metadata": {
-    "kernelspec": {
-      "display_name": "Python 3",
-      "language": "python",
-      "name": "python3"
-    },
-    "language_info": {
-      "codemirror_mode": {
-        "name": "ipython",
-        "version": 3
-      },
-      "file_extension": ".py",
-      "mimetype": "text/x-python",
-      "name": "python",
-      "nbconvert_exporter": "python",
-      "pygments_lexer": "ipython3",
-      "version": "3.9.16"
-    }
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "\n# The Parker AIF - a play with variables\n\nSimulating a Parker AIF with different settings. \n"
+   ]
   },
-  "nbformat": 4,
-  "nbformat_minor": 0
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Import necessary packages\n\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import osipi"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Generate synthetic AIF with default settings and plot the result.\n\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "# Define time points in units of seconds - in this case we use a time resolution of 0.5 sec and a total duration of 6 minutes.\n",
+    "t = np.arange(0, 6 * 60, 0.5)\n",
+    "\n",
+    "# Create an AIF with default settings\n",
+    "ca = osipi.aif_parker(t)\n",
+    "\n",
+    "# Plot the AIF over the full range\n",
+    "plt.plot(t, ca, \"r-\")\n",
+    "plt.plot(t, 0 * t, \"k-\")\n",
+    "plt.xlabel(\"Time (sec)\")\n",
+    "plt.ylabel(\"Plasma concentration (mM)\")\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The bolus arrival time (BAT) defaults to 0s. What happens if we change it? Let's try, by changing it in steps of 30s:\n\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "ca = osipi.aif_parker(t, BAT=0)\n",
+    "plt.plot(t, ca, \"b-\", label=\"BAT = 0s\")\n",
+    "ca = osipi.aif_parker(t, BAT=30)\n",
+    "plt.plot(t, ca, \"r-\", label=\"BAT = 30s\")\n",
+    "ca = osipi.aif_parker(t, BAT=60)\n",
+    "plt.plot(t, ca, \"g-\", label=\"BAT = 60s\")\n",
+    "ca = osipi.aif_parker(t, BAT=90)\n",
+    "plt.plot(t, ca, \"m-\", label=\"BAT = 90s\")\n",
+    "plt.xlabel(\"Time (sec)\")\n",
+    "plt.ylabel(\"Plasma concentration (mM)\")\n",
+    "plt.legend()\n",
+    "plt.show()\n",
+    "\n",
+    "# Choose the last image as a thumbnail for the gallery\n",
+    "# sphinx_gallery_thumbnail_number = -1"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
 }

docs/source/generated/examples/aif/plot_aif_parker.py

@@ -6,10 +6,10 @@
 """
 
 import matplotlib.pyplot as plt
+
 # %%
 # Import necessary packages
 import numpy as np
-
 import osipi
 
 # %%