Merge pull request #92 from n-takumasa/fix

Fix example and docs
maroba · Dec 30, 2024 · e42d226 · e42d226
2 parents b0258bc + ad3d468
commit e42d226
Show file tree

Hide file tree

Showing 15 changed files with 168 additions and 102 deletions.
diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
@@ -31,7 +31,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install pytest pytest-cov
+          python -m pip install pytest pytest-cov ipykernel nbclient matplotlib
       - name: Install package
         run: pip install -e .
       - name: Show installed packages

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -7,7 +7,7 @@ version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+   configuration: docs/source/conf.py
 
 build:
   os: ubuntu-22.04

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -8,3 +8,6 @@ scipy
 sphinxcontrib.bibtex>=2.0
 sphinx_rtd_theme
 ipython
+ipykernel
+nbsphinx
+nbsphinx-link
diff --git a/docs/conf.py → docs/source/conf.py b/docs/conf.py → docs/source/conf.py
@@ -37,15 +37,18 @@
 # ones.
 extensions = [
     "sphinx.ext.autodoc",
+    "sphinx.ext.doctest",
     "sphinx.ext.intersphinx",
     "IPython.sphinxext.ipython_console_highlighting",
     "IPython.sphinxext.ipython_directive",
     "sphinx.ext.mathjax",
     "nbsphinx",
+    "nbsphinx_link",
 ]
 
 
 nbsphinx_execute = "always"
+nbsphinx_kernel_name = "python3"
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]

diff --git a/docs/source/examples-periodic.ipynb b/docs/source/examples-periodic.ipynb
diff --git a/docs/source/examples-periodic.nblink b/docs/source/examples-periodic.nblink
@@ -0,0 +1,3 @@
+{
+  "path": "../../examples/examples-periodic.ipynb"
+}
diff --git a/docs/source/getstarted.rst b/docs/source/getstarted.rst
@@ -247,7 +247,7 @@ This returns
      ('H', 'C'): {(-3, 0): -1.0, (-2, 0): 4.0, (-1, 0): -5.0, (0, -1): 1.0, (0, 0): 0.0, (0, 1): 1.0},
      ('H', 'H'): {(-3, 0): -1.0, (-2, 0): 4.0, (-1, 0): -5.0, (0, -3): -1.0, (0, -2): 4.0, (0, -1): -5.0, (0, 0): 4.0}}
 
-In the interior of the grid (the :code:`('C', 'C') case), the stencil looks
+In the interior of the grid (the :code:`('C', 'C')` case), the stencil looks
 like this:
 
 .. image:: images/laplace2d.png

diff --git a/docs/index.rst → docs/source/index.rst b/docs/index.rst → docs/source/index.rst
@@ -6,7 +6,7 @@ A Python package for finite difference numerical derivatives
 and partial differential equations in any number of dimensions.
 
 
-.. image:: source/images/findiff_logo.png
+.. image:: images/findiff_logo.png
     :width: 300
     :align: center
 
@@ -33,11 +33,11 @@ Content
 .. toctree::
     :maxdepth: 1
 
-    source/getstarted
-    source/examples
-    source/theory
-    source/citation
-    source/modules
+    getstarted
+    examples
+    theory
+    citation
+    modules
 
 
 Indices and tables

diff --git a/examples/examples-basic.ipynb b/examples/examples-basic.ipynb
@@ -20,18 +20,20 @@
   },
   {
    "cell_type": "code",
+   "execution_count": 14,
    "metadata": {
     "collapsed": false,
     "jupyter": {
-     "is_executing": true
+     "is_executing": true,
+     "outputs_hidden": false
     }
    },
+   "outputs": [],
    "source": [
     "import numpy as np\n",
+    "\n",
     "from findiff import Diff"
-   ],
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
    "cell_type": "markdown",
@@ -42,24 +44,22 @@
     "Suppose we want to differentiate two 1D-arrays `f` and `g`, which are filled with values from a function\n",
     "\n",
     "$$\n",
-    "f(x) = \\sin(x) \\quad \\mbox{and}\\quad g(x) = \\cos(x)\n",
+    "f(x) = \\sin(x) \\quad \\text{and}\\quad g(x) = \\cos(x)\n",
     "$$\n",
     "\n",
     "and we want to take the 2nd derivative. This is easy done analytically:\n",
     "\n",
     "$$\n",
-    "\\frac{d^2f}{dx^2} = -\\sin(x) \\quad \\mbox{and}\\quad \\frac{d^2g}{dx^2} = -\\cos(x)\n",
+    "\\frac{d^2f}{dx^2} = -\\sin(x) \\quad \\text{and}\\quad \\frac{d^2g}{dx^2} = -\\cos(x)\n",
     "$$\n",
     "\n",
     "Let's do this numerically with _findiff_. First we set up the grid and the arrays:"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 15,
+   "metadata": {},
    "outputs": [],
    "source": [
     "x = np.linspace(0, 10, 100)\n",
@@ -77,12 +77,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 16,
+   "metadata": {},
    "outputs": [],
-   "source": "d2_dx2 = Diff(0, dx=dx, acc=2)"
+   "source": [
+    "d2_dx2 = Diff(0, dx, acc=2)"
+   ]
   },
   {
    "cell_type": "markdown",
@@ -95,10 +95,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 17,
+   "metadata": {},
    "outputs": [],
    "source": [
     "result_f = d2_dx2(f)\n",
@@ -123,28 +121,36 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 18,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "{'backward': {'coefficients': array([-1.,  4., -5.,  2.]),\n",
-       "  'offsets': array([-3, -2, -1,  0])},\n",
-       " 'center': {'coefficients': array([ 1., -2.,  1.]),\n",
-       "  'offsets': array([-1,  0,  1])},\n",
+       "{'center': {'coefficients': array([ 1., -2.,  1.]),\n",
+       "  'offsets': array([-1,  0,  1]),\n",
+       "  'accuracy': 2},\n",
        " 'forward': {'coefficients': array([ 2., -5.,  4., -1.]),\n",
-       "  'offsets': array([0, 1, 2, 3])}}"
+       "  'offsets': array([0, 1, 2, 3]),\n",
+       "  'accuracy': 2},\n",
+       " 'backward': {'coefficients': array([-1.,  4., -5.,  2.]),\n",
+       "  'offsets': array([-3, -2, -1,  0]),\n",
+       "  'accuracy': 2}}"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
+    "from findiff import coefficients\n",
+    "\n",
     "coefficients(deriv=2, acc=2)"
    ]
   },
@@ -157,29 +163,35 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 19,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "{'backward': {'coefficients': array([  -0.53253968,    6.42373016,  -35.55158728,  119.41369042,\n",
-       "         -271.26190464,  439.39444427, -521.11333314,  457.02976176,\n",
-       "         -295.51984119,  138.59325394,  -44.43730158,    7.56162698]),\n",
-       "  'offsets': array([-11, -10,  -9,  -8,  -7,  -6,  -5,  -4,  -3,  -2,  -1,   0])},\n",
-       " 'center': {'coefficients': array([ 3.17460317e-04, -4.96031746e-03,  3.96825397e-02, -2.38095238e-01,\n",
+       "{'center': {'coefficients': array([ 3.17460317e-04, -4.96031746e-03,  3.96825397e-02, -2.38095238e-01,\n",
        "          1.66666667e+00, -2.92722222e+00,  1.66666667e+00, -2.38095238e-01,\n",
        "          3.96825397e-02, -4.96031746e-03,  3.17460317e-04]),\n",
-       "  'offsets': array([-5, -4, -3, -2, -1,  0,  1,  2,  3,  4,  5])},\n",
-       " 'forward': {'coefficients': array([   7.56162876,  -44.43731776,  138.59331976, -295.52000468,\n",
-       "          457.03003946, -521.1136706 ,  439.39474213, -271.26209495,\n",
-       "          119.41377646,  -35.55161345,    6.42373497,   -0.53254009]),\n",
-       "  'offsets': array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11])}}"
+       "  'offsets': array([-5, -4, -3, -2, -1,  0,  1,  2,  3,  4,  5]),\n",
+       "  'accuracy': 10},\n",
+       " 'forward': {'coefficients': array([   7.56163106,  -44.43733488,  138.59338192, -295.52014839,\n",
+       "          457.03027109, -521.11394092,  439.39497337, -271.26223908,\n",
+       "          119.41384033,  -35.55163256,    6.42373843,   -0.53254037]),\n",
+       "  'offsets': array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11]),\n",
+       "  'accuracy': 1},\n",
+       " 'backward': {'coefficients': array([  -0.53253968,    6.42373016,  -35.55158728,  119.41369042,\n",
+       "         -271.26190464,  439.39444426, -521.11333313,  457.02976175,\n",
+       "         -295.51984119,  138.59325394,  -44.43730158,    7.56162698]),\n",
+       "  'offsets': array([-11, -10,  -9,  -8,  -7,  -6,  -5,  -4,  -3,  -2,  -1,   0]),\n",
+       "  'accuracy': 7}}"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -199,12 +211,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 20,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
+    "from findiff import FinDiff\n",
+    "\n",
     "d2_dx2 = FinDiff(0, dx, 2, acc=10)\n",
     "result = d2_dx2(f)"
    ]
@@ -229,10 +246,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 21,
+   "metadata": {},
    "outputs": [],
    "source": [
     "x, y, z = [np.linspace(0, 10, 100)]*3\n",
@@ -250,10 +265,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 22,
+   "metadata": {},
    "outputs": [],
    "source": [
     "d_dx = FinDiff(0, dx)\n",
@@ -269,10 +282,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 23,
+   "metadata": {},
    "outputs": [],
    "source": [
     "d3_dx2dy = FinDiff((0, dx, 2), (1, dy))\n",
@@ -304,9 +315,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 24,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -330,12 +344,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 25,
+   "metadata": {},
    "outputs": [],
    "source": [
+    "from findiff import Coefficient\n",
+    "\n",
     "linear_op = Coefficient(X) * FinDiff(0, dx) + Coefficient(Y**2) * FinDiff(1, dy)"
    ]
   },
@@ -348,10 +362,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
-   "metadata": {
-    "collapsed": true
-   },
+   "execution_count": 26,
+   "metadata": {},
    "outputs": [],
    "source": [
     "result = linear_op(f)"
@@ -360,7 +372,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": ".venv",
    "language": "python",
    "name": "python3"
   },
@@ -374,9 +386,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.4"
+   "version": "3.13.1"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }