Implement github links

Author: jakubbober

fdm-devito-notebooks/01_vib/vib_undamped.ipynb

@@ -667,7 +667,7 @@
     "with the aid of a calculator\n",
     "and make a function for comparing these results with those from the `solver`\n",
     "function. The `test_three_steps` function in\n",
-    "the file [`vib_undamped.py`](${src_vib}/vib_undamped.py)\n",
+    "the file [`vib_undamped.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped.py)\n",
     "shows the details of how we use the hand calculations to test the code:"
    ]
   },
@@ -908,15 +908,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The complete code appears in the file [`vib_undamped.py`](src-vib/vib_undamped.py).\n",
+    "The complete code appears in the file [`vib_undamped.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped.py).\n",
     "\n",
     "\n",
     "### Visualizing convergence rates with slope markers\n",
     "\n",
     "Tony S. Yu has written a script [`plotslopes.py`](http://goo.gl/A4Utm7)\n",
     "that is very useful to indicate the slope of a graph, especially\n",
     "a graph like $\\ln E = r\\ln \\Delta t + \\ln C$ arising from the model\n",
-    "$E=C\\Delta t^r$. A copy of the script resides in the [`src-vib`](src-vib)\n",
+    "$E=C\\Delta t^r$. A copy of the script resides in the [`src-vib`](https://github.com/devitocodes/devito_book/tree/master/fdm-devito-notebooks/01_vib/src-vib)\n",
     "directory. Let us use it to compare the original method for $u'' + \\omega^2u =0$\n",
     "with the same method applied to the equation with a modified\n",
     "$\\omega$. We make log-log plots of the error versus $\\Delta t$.\n",
@@ -1951,7 +1951,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The code segments are found in the file [`vib_empirical_analysis.py`](src-vib/vib_empirical_analysis.py).\n",
+    "The code segments are found in the file [`vib_empirical_analysis.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_empirical_analysis.py).\n",
     "\n",
     "Since `a[i]` and `p[i]` correspond to\n",
     "the $i$-th amplitude estimate and the $i$-th period estimate, respectively,\n",
@@ -2367,7 +2367,7 @@
     "[Figure](#vib:ode1:tildeomega:plot) plots the discrete frequency\n",
     "([18](#vib:ode1:tildeomega)) and its approximation\n",
     "([19](#vib:ode1:tildeomega:series)) for $\\omega =1$ (based on the\n",
-    "program [`vib_plot_freq.py`](src-vib/vib_plot_freq.py)).\n",
+    "program [`vib_plot_freq.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_plot_freq.py)).\n",
     "Although $\\tilde\\omega$ is a function of $\\Delta t$ in\n",
     "([19](#vib:ode1:tildeomega:series)), it is misleading to think of\n",
     "$\\Delta t$ as the important discretization parameter. mathcal{I}_t is the\n",
@@ -3549,7 +3549,7 @@
    "metadata": {},
    "source": [
     "There is quite some more code dealing with plots also, and we refer\n",
-    "to the source file [`vib_undamped_odespy.py`](src-vib/vib_undamped_odespy.py)\n",
+    "to the source file [`vib_undamped_odespy.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped_odespy.py)\n",
     "for details. Observe that keyword arguments in `f(u,t,w=1)` can\n",
     "be supplied through a solver parameter `f_kwargs` (dictionary of\n",
     "additional keyword arguments to `f`).\n",
@@ -4338,7 +4338,7 @@
     "verification.  The value of `e_E_norm` is also useful for comparing\n",
     "schemes through their ability to preserve energy. Below is a table\n",
     "demonstrating the relative error in total energy for various schemes\n",
-    "(computed by the [`vib_undamped_odespy.py`](src-vib/vib_undamped_odespy.py) program). The test problem is\n",
+    "(computed by the [`vib_undamped_odespy.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped_odespy.py) program). The test problem is\n",
     "$u^{\\prime\\prime} + 4\\pi^2 u =0$ with $u(0)=1$ and $u'(0)=0$, so the\n",
     "period is 1 and $E(t)\\approx 4.93$. We clearly see that the\n",
     "Crank-Nicolson and the Runge-Kutta schemes are superior to the Forward\n",
@@ -4802,7 +4802,7 @@
     "\n",
     "### Solver function\n",
     "\n",
-    "The function below, found in [`vib_undamped_EulerCromer.py`](src-vib/vib_undamped_EulerCromer.py), implements the Euler-Cromer scheme\n",
+    "The function below, found in [`vib_undamped_EulerCromer.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped_EulerCromer.py), implements the Euler-Cromer scheme\n",
     "([54](#vib:model2x2:EulerCromer:veq1b))-([55](#vib:model2x2:EulerCromer:ueq1b)):"
    ]
   },
@@ -4914,7 +4914,7 @@
     "To verify the implementation of the Euler-Cromer method we can adjust\n",
     "`v[1]` so that the computer-generated values can be compared with the\n",
     "formula ([20](#vib:ode1:un:exact)) from in the section [Exact discrete solution](#vib:ode1:analysis:sol). This adjustment is done in an alternative\n",
-    "solver function, `solver_ic_fix` in [`vib_undamped_EulerCromer.py`](src-vib/vib_undamped_EulerCromer.py). Since we now\n",
+    "solver function, `solver_ic_fix` in [`vib_undamped_EulerCromer.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped_EulerCromer.py). Since we now\n",
     "have an exact solution of the discrete equations available, we can\n",
     "write a test function `test_solver` for checking the equality of\n",
     "computed values with the formula ([20](#vib:ode1:un:exact)):"
@@ -4958,9 +4958,9 @@
     "### Convergence rates\n",
     "\n",
     "We may use the `convergence_rates` function in the file\n",
-    "[`vib_undamped.py`](src-vib/vib_undamped.py) to investigate the convergence rate of the\n",
+    "[`vib_undamped.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped.py) to investigate the convergence rate of the\n",
     "Euler-Cromer method, see the `convergence_rate` function in the file\n",
-    "[`vib_undamped_EulerCromer.py`](src-vib/vib_undamped_EulerCromer.py).  Since we could eliminate $v$ to get a\n",
+    "[`vib_undamped_EulerCromer.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped_EulerCromer.py).  Since we could eliminate $v$ to get a\n",
     "scheme for $u$ that is equivalent to the finite difference method for\n",
     "the second-order equation in $u$, we would expect the convergence\n",
     "rates to be the same, i.e., $r = 2$. However,\n",
@@ -5585,7 +5585,7 @@
     "`vib_undamped.py` (which solves $u''+\\omega^2u=0$ directly).  The\n",
     "values should coincide to machine precision since the two numerical\n",
     "methods are mathematically equivalent.  We refer to the file\n",
-    "[`vib_undamped_staggered.py`](src-vib/vib_undamped_staggered.py)\n",
+    "[`vib_undamped_staggered.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib_undamped_staggered.py)\n",
     "for the details of a unit test (`test_staggered`) that checks this property.\n",
     "\n",
     "# Exercises and Problems\n",
@@ -8410,7 +8410,7 @@
     "## Problem 15: Minimize memory usage of a general vibration solver\n",
     "<div id=\"vib:exer:memsave\"></div>\n",
     "\n",
-    "The program [`vib.py`](${src_vib}/vib.py) stores the complete\n",
+    "The program [`vib.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/01_vib/src-vib/vib.py) stores the complete\n",
     "solution $u^0,u^1,\\ldots,u^{N_t}$ in memory, which is convenient for\n",
     "later plotting.  Make a memory minimizing version of this program\n",
     "where only the last three $u^{n+1}$, $u^n$, and $u^{n-1}$ values are\n",
@@ -9049,7 +9049,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,

fdm-devito-notebooks/02_wave/wave1D_prog.ipynb

@@ -308,7 +308,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "When this function resides in the file [`wave1D_u0.py`](src-wave/wave1D/wave1D_u0.py), one can run\n",
+    "When this function resides in the file [`wave1D_u0.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/02_wave/src-wave/wave1D/wave1D_u0.py), one can run\n",
     "pytest to check that all test functions with names `test_*()`\n",
     "in this file work:"
    ]
@@ -718,7 +718,7 @@
     "`n` can be divided by 13 without a remainder. That is, the `if` test\n",
     "is true when `n` equals $0, 13, 26, 39, ..., 780, 801$. The associated\n",
     "code is included in the `plot_u` function, inside the `viz` function,\n",
-    "in the file [`wave1D_u0.py`](src-wave/wave1D/wave1D_u0.py).\n",
+    "in the file [`wave1D_u0.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/02_wave/src-wave/wave1D/wave1D_u0.py).\n",
     "\n",
     "## Running a case\n",
     "<div id=\"wave:pde1:guitar:data\"></div>\n",
@@ -806,7 +806,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The associated program has the name [`wave1D_u0.py`](src-wave/wave1D/wave1D_u0.py). Run\n",
+    "The associated program has the name [`wave1D_u0.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/02_wave/src-wave/wave1D/wave1D_u0.py). Run\n",
     "the program and watch the [movie of the vibrating string](mov-wave/guitar_C0.8/movie.html).\n",
     "The string should ideally consist of straight segments, but these are\n",
     "somewhat wavy due to numerical approximation. Run the case with the\n",
@@ -2586,9 +2586,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}

fdm-devito-notebooks/03_diffu/diffu_rw.ipynb

@@ -825,7 +825,7 @@
     "run, and it can be very difficult to spot bugs through averaged statistical\n",
     "quantities.\n",
     "\n",
-    "A full test suite for this notebook, along with the rest of the functions for random walks, can be found in [`random_walk.py`](src-diffu/random_walk.py).\n",
+    "A full test suite for this notebook, along with the rest of the functions for random walks, can be found in [`random_walk.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/03_diffu/src-diffu/random_walk.py).\n",
     "\n",
     "## Demonstration of multiple walks\n",
     "\n",
@@ -1315,7 +1315,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.8.2"
   }
  },
  "nbformat": 4,

fdm-devito-notebooks/04_advec/advec.ipynb

@@ -670,7 +670,7 @@
    "source": [
     "A special scheme is needed to compute $u^1$, but we leave that problem for\n",
     "now. Anyway, this special scheme can be found in \n",
-    "[`advec1D.py`](src-advec/advec1D.py).\n",
+    "[`advec1D.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/04_advec/src-advec/advec1D.py).\n",
     "\n",
     "### Implementation\n",
     "\n",
@@ -1405,7 +1405,7 @@
    "metadata": {},
    "source": [
     "The complete code is found in the file\n",
-    "[`advec1D.py`](src-advec/advec1D.py).\n",
+    "[`advec1D.py`](https://github.com/devitocodes/devito_book/blob/master/fdm-devito-notebooks/04_advec/src-advec/advec1D.py).\n",
     "\n",
     "## A Crank-Nicolson discretization in time and centered differences in space\n",
     "<div id=\"advec:1D:CN\"></div>\n",