Fix broken links to source code (#30)

Author: elegios

docs/how-to-guides/contributing.md

@@ -34,7 +34,7 @@ For convenience, `make lint` will run `dune build @fmt` and `make fix` will run
 ## Git Blame
 
 Since automatic code formatting commits will obscure `git blame` we maintain a
-file  [.git-blame-ignore-revs](.git-blame-ignore-revs) that will contain the
+file  [.git-blame-ignore-revs](https://github.com/miking-lang/miking/blob/develop/.git-blame-ignore-revs) that will contain the
 commit hashes of code formatting commits. We can then run `git blame`, ignoring
 these commits as:
 

docs/reference/externals.md

@@ -14,15 +14,15 @@ in an early stage of development. The example below only covers the case where
 OCaml is the target language.
 
 You can find an example of externals definitions in
-[stdlib/ext/math-ext.mc](stdlib/ext/math-ext.mc) and
-[stdlib/ext/math-ext.ext-ocaml.mc](stdlib/ext/math-ext.ext-ocaml.mc).
+[stdlib/ext/math-ext.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ext/math-ext.mc) and
+[stdlib/ext/math-ext.ext-ocaml.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ext/math-ext.ext-ocaml.mc).
 
 For the sake of this example, lets say we want to define the exponential
 function and that miking targeting OCaml should use `Float.exp` from OCaml's
 standard library for its implementation.
 
-We first define the external in a file under [stdlib/ext](stdlib/ext), let's
-say [stdlib/ext/math-ext.mc](stdlib/ext/math-ext.mc), as
+We first define the external in a file under [stdlib/ext](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ext), let's
+say [stdlib/ext/math-ext.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ext/math-ext.mc), as
 
 ```mc
 external externalExp : Float -> Float
@@ -49,7 +49,7 @@ partially applied.
 As a temporary solution, the next step is to supply a list of implementation for
 our external in the language we target for compilation (in this case OCaml). We
 do this by creating a file
-[stdlib/ext/math-ext.ext-ocaml.mc](stdlib/ext/math-ext.ext-ocaml.mc)
+[stdlib/ext/math-ext.ext-ocaml.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ext/math-ext.ext-ocaml.mc)
 and in it we define a map from external
 identifiers to a list of implementations as follows:
 
@@ -75,7 +75,7 @@ let mathExtMap =
 This map associates the `externalExp` external to a list of expressions in the
 target language, which here only has one element, namely the function
 `Float.exp` from OCaml's standard library. The field `ty` encode the OCaml type
-of this value (see [stdlib/ocaml/ast.mc](stdlib/ocaml/ast.mc)), which is needed
+of this value (see [stdlib/ocaml/ast.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ocaml/ast.mc)), which is needed
 to convert values between miking and OCaml. In the case where you have multiple
 implementations, the compiler will try to pick the implementation which gives
 the least amount of overhead when converting to and from OCaml values. The
@@ -85,11 +85,11 @@ none are needed since it is part of the standard library. If let's say we wanted
 to use `Float.exp` from a library `foo`, then we should instead have the field
 `libraries = ["foo"]`. Finally, we need to add `mathExtMap` to
 `globalExternalImplsMap` in
-[stdlib/ocaml/external-includes.mc](stdlib/ocaml/external-includes.mc).
+[stdlib/ocaml/external-includes.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ocaml/external-includes.mc).
 
 ### Conversion between values
 Conversion between Miking values and OCaml values is defined in
-[stdlib/ocaml/external.mc](stdlib/ocaml/external.mc). Since externals are in an
+[stdlib/ocaml/external.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ocaml/external.mc). Since externals are in an
 early stage of development these conversions are not complete and subject to
 change.
 
@@ -139,16 +139,16 @@ type MyType
 ```
 then no conversion is performed to and from this type.
 
-Please consult [stdlib/ext/ext-test.mc](stdlib/ext/ext-test.mc) and
-[stdlib/ext/ext-test.ext-ocaml.mc](stdlib/ext/ext-test.ext-ocaml.mc), for more
+Please consult [stdlib/ext/ext-test.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ext/ext-test.mc) and
+[stdlib/ext/ext-test.ext-ocaml.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ext/ext-test.ext-ocaml.mc), for more
 examples.
 
 ### Sundials
 A more involved example on the use of externals is an interface to the
 [Sundials](https://computing.llnl.gov/projects/sundials) numerical DAE solver.
 You find the implementation in
-[stdlib/sundials/sundials.mc](stdlib/sundials/sundials.mc) and
-[stdlib/sundials/sundials.ext-ocaml.mc](stdlib/sundials/sundials.ext-ocaml.mc).
+[stdlib/sundials/sundials.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/sundials/sundials.mc) and
+[stdlib/sundials/sundials.ext-ocaml.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/sundials/sundials.ext-ocaml.mc).
 Note that these externals depends on the library `sundialsml`.
 
 
@@ -198,8 +198,8 @@ To install for the current user, run `make install` as usual.
 ### Ipopt
 Another example use of externals is an interface to the constrained Non-Linear
 Program solver [Ipopt](https://coin-or.github.io/Ipopt/). This interface is
-defined in [stdlib/ipopt/ipopt.mc](stdlib/ipopt/ipopt.mc) and
-[stdlib/ipopt/ipopt.ext-ocaml.mc](stdlib/ipopt/ipopt.ext-ocaml.mc). This library
+defined in [stdlib/ipopt/ipopt.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ipopt/ipopt.mc) and
+[stdlib/ipopt/ipopt.ext-ocaml.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/ipopt/ipopt.ext-ocaml.mc). This library
 depends on both the OCaml library [ipoptml](https://github.com/br4sco/ipoptml)
 and the ipopt c library.
 

docs/reference/parallel-programming.md

@@ -10,15 +10,15 @@ atomic operations and threads running on multiple cores.
 The parallel programming primitives consist of atomic references and functions
 for creating and synchronizing threads. In addition to the examples below, more
 documentation can be found in the standard library at
-[stdlib/multicore](stdlib/multicore/).
+[stdlib/multicore](https://github.com/miking-lang/miking/blob/develop/src/stdlib/multicore/).
 
 ## Atomic References
 
 Atomic references are similar to ordinary references, except that operations
 performed on them are *atomic*, which means that no other execution thread can
 interfere with the result. In other words, they are safe to use in
 multi-threaded execution. Atomic references are provided in
-[multicore/atomic.mc](stdlib/multicore/atomic.mc).
+[multicore/atomic.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/multicore/atomic.mc).
 
 `atomicMake` creates a new atomic reference and gives it an initial value. The
 value of the atomic reference can be read by `atomicGet`:
@@ -65,7 +65,7 @@ utest atomicFetchAndAdd a (subi 0 45) with 3 in
 ## Multi-Threaded Execution
 
 Functions for handling threads are provided in
-[multicore/threads.mc](stdlib/multicore/threads.mc).
+[multicore/threads.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/multicore/threads.mc).
 The following example program spawns 10 threads that compete for printing their
 IDs:
 
@@ -110,8 +110,8 @@ different runs.
 
 Externals for thread synchronization in the form of mutual exclusion locks and
 condition variables are defined in
-[multicore/mutex.mc](stdlib/multicore/mutex.mc) and
-[multicore/cond.mc](stdlib/multicore/cond.mc), respectively.
+[multicore/mutex.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/multicore/mutex.mc) and
+[multicore/cond.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/multicore/cond.mc), respectively.
 
 ## Probability distributions
-Externals for probability distributions are defined in `stdlib/ext/dist-ext.mc`. To use these, you must install the `opam` package `owl` (i.e., `opam install owl`)
+Externals for probability distributions are defined in `https://github.com/miking-lang/miking/blob/develop/src/stdlib/ext/dist-ext.mc`. To use these, you must install the `opam` package `owl` (i.e., `opam install owl`)

docs/tutorials/mexpr-tutorial.md

@@ -509,7 +509,7 @@ utest tensorGetExn t0 [] with 'b' in
 ()
 ```
 
-The file [tensor.mc](stdlib/tensor.mc) contains a wide variety of useful tensor
+The file [tensor.mc](https://github.com/miking-lang/miking/blob/develop/src/stdlib/tensor.mc) contains a wide variety of useful tensor
 functions. We can import it into a program using the `include`
 keyword (more on this [later](#MLang)). We can construct a rank 1
 tensor (i.e. vector) as

docusaurus.config.js

@@ -14,10 +14,8 @@ const config = {
   organizationName: 'miking-lang',
   trailingSlash: false,
   deploymentBranch: 'gh-pages',
-  // TODO We should eventually fix broken links and throw if any are found
-  // onBrokenLinks: 'throw',
-  onBrokenLinks: 'warn',
-  onBrokenMarkdownLinks: 'warn',
+  onBrokenLinks: 'throw',
+  onBrokenMarkdownLinks: 'throw',
   favicon: 'img/favicon.ico',
 
   presets: [

src/pages/miking-dppl-readme.md

@@ -277,7 +277,7 @@ For this to be used, the `SMC` macro call in main must be
 changed to: `SMC(sampleMean);`
 
 This example can be found in
-[`rootppl/models/simple-examples/coin_flip_mean.cu`](rootppl/models/simple-examples/coin_flip_mean.cu)
+[`rootppl/models/simple-examples/coin_flip_mean.cu`](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/simple-examples/coin_flip_mean.cu)
 and, being in the `rootppl` directory, compiled with:
 ```
 rppl models/simple-examples/coin_flip_mean.cu
@@ -301,7 +301,7 @@ no statements that alter the weights of the particles.
 Below follows some examples, these are all models that are defined within one single block.
 
 ##### Coin Flip Posterior
-Full example: [`rootppl/models/simple-examples/coin_flip.cu`](rootppl/models/simple-examples/coin_flip.cu)
+Full example: [`rootppl/models/simple-examples/coin_flip.cu`](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/simple-examples/coin_flip.cu)
 
 In this model, a bias for a coin is sampled from the prior beta distribution. Then we observe that the coin flip is true. This model thus infers the
 posterior distribution of the bias, conditioned on the observation.
@@ -316,7 +316,7 @@ BBLOCK(coinFlip, {
 ```
 
 ##### Gaussian Mixture Model
-Full example: [`rootppl/models/simple-examples/mixture.cu`](rootppl/models/simple-examples/mixture.cu)
+Full example: [`rootppl/models/simple-examples/mixture.cu`](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/simple-examples/mixture.cu)
 
 This model demonstrates an example of *stochastic branching*, meaning that different code is executed depending on the outcome of the sample.
 ```CUDA
@@ -333,7 +333,7 @@ BBLOCK(mixture, {
 ```
 
 ##### Geometric Distribution (Recursive)
-Full example: [`rootppl/models/simple-examples/geometric_recursive.cu`](rootppl/models/simple-examples/geometric_recursive.cu)
+Full example: [`rootppl/models/simple-examples/geometric_recursive.cu`](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/simple-examples/geometric_recursive.cu)
 
 This model combines stochastic branching with recursion. Basic blocks do not fully support recursion themselves, as they take no custom arguments or return values. Instead, a helper function is used to express the recursive model:
 
@@ -357,7 +357,7 @@ Note that the helper function takes its return value and parameters comma-separa
 
 While recursive functions is supported by CUDA, iterative solutions are encouraged. Below is the same model, implemented with a loop instead.
 ##### Geometric Distribution (Iterative)
-Full example: [`rootppl/models/simple-examples/geometric_iterative.cu`](rootppl/models/simple-examples/geometric_iterative.cu)
+Full example: [`rootppl/models/simple-examples/geometric_iterative.cu`](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/simple-examples/geometric_iterative.cu)
 ```CUDA
 BBLOCK(geometric, {
     int numFlips = 1;
@@ -370,8 +370,8 @@ BBLOCK(geometric, {
 
 #### Phylogenetic Models
 
-More sophisticated models can be found in the [phylogenetics directory](rootppl/models/phylogenetics). These probabilistic
-models to inference on observed phylogenetic trees. These observed trees can be found in [phylogenetics/tree-utils/trees.cuh](rootppl/models/phylogenetics/tree-utils/trees.cuh).
+More sophisticated models can be found in the [phylogenetics directory](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/phylogenetics). These probabilistic
+models to inference on observed phylogenetic trees. These observed trees can be found in [phylogenetics/tree-utils/trees.cuh](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/phylogenetics/tree-utils/trees.cuh).
 The correct phylogenetic models contain a link in the top of the file to the WebPPL source code used as reference when implementing them.
 These models contain a number of new things, e.g.:
 - Multiple basic blocks
@@ -381,8 +381,8 @@ These models contain a number of new things, e.g.:
 - Resampling throughout the traversal of the observed tree
 
 ##### Constant-rate birth-death
-In [phylogenetics/crbd](rootppl/models/phylogenetics/crbd), the constant-rate birth-death models can be found.
-The most interesting file here is [crbd.cu](rootppl/models/phylogenetics/crbd/crbd.cu) as it is a correct model
+In [phylogenetics/crbd](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/phylogenetics/crbd), the constant-rate birth-death models can be found.
+The most interesting file here is [crbd.cu](https://github.com/miking-lang/miking-dppl/blob/master/rootppl/models/phylogenetics/crbd/crbd.cu) as it is a correct model
 used by evolutionary biologists. This model uses a pre-processed DFS traversal path over the observed tree, rather than using a call stack.
 
 ##### Further phylogenetic models