fixing...

Author: jzstark

chapters/algodiff.md

@@ -1192,7 +1192,7 @@ let f y =
 
 For this functions $f: \mathbf{R}^4 \rightarrow \mathbf{R}^4$, we can then find its Jacobian matrix. Suppose the given point of interest of where all four input variables equals one. Then we can use the `Algodiff.D.jacobian` function in this way.
 
-```text
+```ocaml
 let y = Mat.ones 1 4
 let result = jacobian f y
 
@@ -1208,7 +1208,7 @@ R3  0.53033 0.176777  0  0
 
 Next, we find the eigenvalues of this jacobian matrix with the Linear Algebra module in Owl that we have introduced in previous chapter.
 
-```text
+```ocaml
 let eig = Owl_linalg.D.eigvals j
 
 val eig : Owl_dense_matrix_z.mat =

chapters/convention.md

@@ -46,7 +46,7 @@ For unary operators such as `Arr.sin x`, the situation is rather straightforward
 
 For `Arr.add_ x y`, the question is where to store the final result when both inputs are ndarray. Let's look at the type of `Arr.add_` function.
 
-```text
+```ocaml
 val Arr.add_ : ?out:Arr.arr -> Arr.arr -> Arr.arr -> unit
 ```
 
@@ -275,55 +275,32 @@ As you can see, the operators above do not allow interoperation on different num
 
 Some people just like Pythonic way of working, `Owl.Ext` module is specifically designed for this purpose, to make prototyping faster and easier. Once you open the module, `Ext` immediately provides a set of operators to allow you to interoperate on different number types, as below. It automatically casts types for you if necessary.
 
--------------    -------------     --------------------------
-Operator         Example           Operation
--------------    -------------     --------------------------
-`+`              `x + y`           add
-
-`-`              `x - y`           sub
-
-`*`              `x * y`           mul
-
-`/`              `x / y`           div
-
-`=`              `x = y`           comparison, return bool
-
-`!=`             `x != y`          comparison, return bool
-
-`<>`             `x <> y`          same as `!=`
-
-`>`              `x > y`           comparison, return bool
-
-`<`              `x < y`           comparison, return bool
-
-`>=`             `x >= y`          comparison, return bool
-
-`<=`             `x <= y`          comparison, return bool
-
-`=.`             `x =. y`          element_wise comparison
-
-`!=.`            `x !=. y`         element_wise comparison
+Operator         | Example           | Operation
+-------------    | -------------     | --------------------------
+`+`              | `x + y`           | add
+`-`              | `x - y`           | sub
+`*`              | `x * y`           | mul
+`/`              | `x / y`           | div
+`=`              | `x = y`           | comparison, return bool
+`!=`             | `x != y`          | comparison, return bool
+`<>`             | `x <> y`          | same as `!=`
+`>`              | `x > y`           | comparison, return bool
+`<`              | `x < y`           | comparison, return bool
+`>=`             | `x >= y`          | comparison, return bool
+`<=`             | `x <= y`          | comparison, return bool
+`=.`             | `x =. y`          | element_wise comparison
+`!=.`            | `x !=. y`         | element_wise comparison
+`<>.`            | `x <>. y`         | same as `!=.`
+`>.`             | `x >. y`          | element_wise comparison
+`<.`             | `x <. y`          | element_wise comparison
+`>=.`            | `x >=. y`         | element_wise comparison
+`<=.`            | `x <=. y`         | element_wise comparison
+`%`              | `x % y`           | element_wise mod divide
+`**`             | `x ** y`          | power function
+`*@`             | `x *@ y`          | matrix multiply
+`min2`           | `min2 x y`        | element-wise min
+`max2`           | `max2 x y`        | element-wise max
 
-`<>.`            `x <>. y`         same as `!=.`
-
-`>.`             `x >. y`          element_wise comparison
-
-`<.`             `x <. y`          element_wise comparison
-
-`>=.`            `x >=. y`         element_wise comparison
-
-`<=.`            `x <=. y`         element_wise comparison
-
-`%`              `x % y`           element_wise mod divide
-
-`**`             `x ** y`          power function
-
-`*@`             `x *@ y`          matrix multiply
-
-`min2`           `min2 x y`        element-wise min
-
-`max2`           `max2 x y`        element-wise max
--------------    -------------     --------------------------
 : Operator extensions {#tbl:convention:ext}
 
 You may have noticed, the operators ended with `$` (e.g., `+$`, `-$` ...) disappeared from the table, which is simply because we can add/sub/mul/div a scalar with a matrix directly and we do not need these operators any more. Similar for comparison operators, because we can use the same `>` operator to compare a matrix to another matrix, or compare a matrix to a scalar, we do not need `>$` any longer. Allowing interoperation makes the operator table much shorter.
@@ -346,7 +323,7 @@ Note that `Ext` contains its own `Ext.Dense` module which further contains the f
 
 These modules are simply the wrappers of the original modules in `Owl.Dense` module so they provide most of the APIs already implemented. The extra thing these wrapper modules does is to pack and unpack the raw number types for you automatically. However, you can certainly use the raw data types then use the constructors defined in `Owl_ext_types` to wrap them up by yourself. The constructors are defined as below.
 
-```text
+```ocaml
 
   type ext_typ =
     F   of float
@@ -411,7 +388,7 @@ Before we finish this chapter, I want to point out the caveat. `Ext` tries to mi
 
 In Owl, `Dense` module contains the modules of dense data structures. For example, `Dense.Matrix` supports the operations of dense matrices. Similarly, `Sparse` module contains the modules of sparse data structures.
 
-```text
+```ocaml
 Dense.Ndarray;;   (* dense ndarray *)
 Dense.Matrix;;    (* dense matrix *)
 
@@ -536,7 +513,7 @@ Mat.zeros 5 5;;          (* same as Dense.Matrix.D.zeros 5 5 *)
 
 More examples besides creation functions are as follows.
 
-```text
+```ocaml
 Mat.load "data.mat";;    (* same as Dense.Matrix.D.load "data.mat" *)
 Mat.of_array 5 5 x;;     (* same as Dense.Matrix.D.of_array 5 5 x *)
 Mat.linspace 0. 9. 10;;  (* same as Dense.Matrix.D.linspace 0. 9. 10 *)
@@ -562,7 +539,7 @@ As I mentioned before, there are four basic number types. You can therefore cast
 
 In fact, all these function rely on the following `cast` function.
 
-```text
+```ocaml 
 
   val cast : ('a, 'b) kind -> ('c, 'd) t -> ('a, 'b) t
 

chapters/dataframe.md

@@ -145,7 +145,7 @@ However, if you just want to append one or two rows, the previous method seems a
 There are also functions allow you to retrieve the properties, for example:
 
 
-```text
+```ocaml
 
   val copy : t -> t          (* return the copy of a dataframe. *)
 
@@ -204,7 +204,7 @@ R1 Carol  30
 
 How can we miss the classic iteration functions in the functional programming? Dataframe includes the following methods to traverse the rows in a dataframe. We did not include any method to traverse columns because they can be simply extracted out as series then processed separately.
 
-```text
+```ocaml
 
   val iteri_row : (int -> elt array -> unit) -> t -> unit
 
@@ -229,7 +229,7 @@ Applying these functions to a dataframe is rather straightforward. All the eleme
 One interesting thing worth mentioning here is that there are several functions are associated with extended indexing operators. This allows us to write quite concise code in our application.
 
 
-```text
+```ocaml
 
   val ( .%( ) ) : t -> int * string -> elt
   (* associated with `get_by_name` *)
@@ -352,7 +352,7 @@ R2 Carol  3000.
 CSV (Comma-Separated Values) is a common format to store tabular data. The module provides simple support to process CSV files. The two core functions are as follows.
 
 
-```text
+```ocaml
 
   val of_csv : ?sep:char -> ?head:string array -> ?types:string array -> string -> t
 
@@ -383,7 +383,7 @@ Owl_pretty.pp_dataframe Format.std_formatter df
 
 The result should look like this. We have truncated out some rows to save space here.
 
-```text
+```ocaml
   funding data in csv file
 
        +-----------------+-----------------+-------+---------+-------------+-----+----------+----------+--------------+------------

chapters/introduction.md

@@ -373,7 +373,7 @@ The Second example demonstrates how to plot figures in notebook. Because Owl's P
 
 To load the image into browser, we need to call the `Jupyter_notebook.display_file` function. Then we can see the plot [@fig:introduction:example00] is correctly rendered in the notebook running in your browser. Plotting capability greatly enriches the content of an interactive presentation.
 
-```text
+```ocaml
 Jupyter_notebook.display_file ~base64:true "image/png" "plot_00.png"
 ```
 

chapters/linalg.md

@@ -118,7 +118,7 @@ let x = Mat.sequential 4 6;;
 
 You should be able to see the following output in your `utop`.
 
-```text
+```ocaml
 
      C0 C1 C2 C3 C4 C5
   R0  1  2  3  4  5  6

chapters/ndarray.md

@@ -201,7 +201,7 @@ The `map` function can be very useful in implementing vectorised math functions.
 
 If you need indices in the transformation function, you can use the `mapi` function which accepts the 1-d index of the element being accessed.
 
-```text
+```ocaml
 
   val mapi : (int -> 'a -> 'a) -> ('a, 'b) t -> ('a, 'b) t
 
@@ -212,7 +212,7 @@ If you need indices in the transformation function, you can use the `mapi` funct
 
 The `fold` function is often referred to as "reduction" in other programming languages. It has a named parameter called `axis`, with which you can specify along what axis you want to fold a given ndarray.
 
-```text
+```ocaml
 
   val fold : ?axis:int -> ('a -> 'a -> 'a) -> 'a -> ('a, 'b) t -> ('a, 'b) t
 
@@ -231,7 +231,7 @@ The functions `sum`, `sum'`, `prod`, `prod'`, `min`, `min'`, `mean`, and `mean'`
 
 Similarly, if you need indices in folding function, you can use `foldi` which passes in 1-d indices.
 
-```text
+```ocaml
 
   val foldi : ?axis:int -> (int -> 'a -> 'a -> 'a) -> 'a -> ('a, 'b) t -> ('a, 'b) t
 
@@ -243,7 +243,7 @@ Similarly, if you need indices in folding function, you can use `foldi` which pa
 To some extent, the `scan` function is like the combination of `map` and `fold`. It accumulates the value along the specified axis but it does not change the shape of the input. Think about how we generate a cumulative distribution function (CDF) from a probability density/mass function (PDF/PMF).
 The type signature of `scan` looks like this in Ndarray.
 
-```text
+```ocaml
 
   val scan : ?axis:int -> ('a -> 'a -> 'a) -> ('a, 'b) t -> ('a, 'b) t
 
@@ -263,7 +263,7 @@ Again, you can use the `scani` to obtain the indices in the passed in cumulative
 
 The comparison functions themselves can be divided into several groups. The first group compares two ndarrays then returns a boolean value.
 
-```text
+```ocaml
 
   val equal : ('a, 'b) t -> ('a, 'b) t -> bool
 
@@ -278,7 +278,7 @@ The comparison functions themselves can be divided into several groups. The firs
 
 The second group compares two ndarrays but returns an 0-1 ndarray of the same shape. The elements where the predicate is satisfied have value 1 otherwise 0.
 
-```text
+```ocaml
 
   val elt_equal : ('a, 'b) t -> ('a, 'b) t -> ('a, 'b) t
 
@@ -294,7 +294,7 @@ The second group compares two ndarrays but returns an 0-1 ndarray of the same sh
 
 The third group is similar to the first one but compares an ndarray with a scalar value, the return is a Boolean value.
 
-```text
+```ocaml
 
   val equal_scalar : ('a, 'b) t -> 'a -> bool
 
@@ -310,7 +310,7 @@ The third group is similar to the first one but compares an ndarray with a scala
 
 The fourth group is similar to the second one but compares an ndarray with a scalar value, and the returned value is a 0-1 ndarray.
 
-```text
+```ocaml
 
   val elt_equal_scalar : ('a, 'b) t -> 'a -> ('a, 'b) t
 
@@ -358,7 +358,7 @@ Conceptually, Owl can implement all these functions using the aforementioned `ma
 
 Like native OCaml array, Owl also provides `iter` and `iteri` functions with which you can iterate over all the elements in an ndarray.
 
-```text
+```ocaml
 
   val iteri :(int -> 'a -> unit) -> ('a, 'b) t -> unit
 
@@ -369,7 +369,7 @@ Like native OCaml array, Owl also provides `iter` and `iteri` functions with whi
 One common use case is iterating all the elements and checking if one (or several) predicate is satisfied.
 There is a special set of iteration functions to help you finish this task.
 
-```text
+```ocaml
 
   val is_zero : ('a, 'b) t -> bool
 
@@ -387,7 +387,7 @@ There is a special set of iteration functions to help you finish this task.
 
 The predicates can be very complicated sometimes. In that case you can use the following three functions to pass in arbitrarily complicated functions to check them.
 
-```text
+```ocaml
 
   val exists : ('a -> bool) -> ('a, 'b) t -> bool
 
@@ -399,7 +399,7 @@ The predicates can be very complicated sometimes. In that case you can use the f
 
 All aforementioned functions only tell us whether the predicates are met or not. They cannot tell which elements satisfy the predicate. The following `filter` function can return the 1-d indices of those elements satisfying the predicates.
 
-```text
+```ocaml
 
   val filteri : (int -> 'a -> bool) -> ('a, 'b) t -> int array
 
@@ -409,7 +409,7 @@ All aforementioned functions only tell us whether the predicates are met or not.
 
 We have mentioned that 1-d indices are passed in. The reason is passing in 1-d indices is way faster than passing in n-d indices. However, if you do need n-dimensional indices, you can use the following two functions to convert between 1-d and 2-d indices, both are defined in the `Owl.Utils` module.
 
-```text
+```ocaml
 
   val ind : ('a, 'b) t -> int -> int array
   (* 1-d to n-d index conversion *)
@@ -473,7 +473,7 @@ R5  8  9 10 11
 
 You can also expand the dimensionality of an ndarray, or squeeze out those dimensions having only one element, or even padding elements to an existing ndarray.
 
-```text
+```ocaml
 
   val expand : ('a, 'b) t -> int -> ('a, 'b) t
 
@@ -488,7 +488,7 @@ The `concatenate` allows us to concatenate an array of ndarrays along the specif
 For matrices, there are two operators associated with concatenation: `@||` for concatenating horizontally (i.e. along axis 1); `@=` for concatenating vertically (i.e. along axis 0).
 The `split` is simply the inverse operation of concatenation.
 
-```text
+```ocaml
 
   val concatenate : ?axis:int -> ('a, 'b) t array -> ('a, 'b) t
 
@@ -498,15 +498,15 @@ The `split` is simply the inverse operation of concatenation.
 
 You can also sort an ndarray but note that modification will happen in place.
 
-```text
+```ocaml
 
   val sort : ('a, 'b) t -> unit
 
 ```
 
 Converting between ndarrays and OCaml native arrays can be efficiently done with these conversion functions:
 
-```text
+```ocaml
 
   val of_array : ('a, 'b) kind -> 'a array -> int array -> ('a, 'b) t
 
@@ -521,7 +521,7 @@ Again, there also exist the `to_arrays` and `of_arrays` two functions for the sp
 
 Serialisation and de-serialisation are simply done with the `save` and `load` functions.
 
-```text
+```ocaml
 
   val save : out:string -> ('a, 'b) t -> unit