diff --git a/README.rst b/README.rst
index 15141988ea9509866e516f574d506b39d4e9063c..ef6bddf099a6700d3c47adc58cd9254db2f74c6c 100644
--- a/README.rst
+++ b/README.rst
@@ -16,7 +16,7 @@ Rapid Peptides Generator (RPG) is a software dedicated to predict proteases-indu
     :alt: Coverage Report
 
 .. image:: https://readthedocs.org/projects/rapid-peptide-generator/badge/?version=latest
-    :target: http://rapid-peptide-generator.readthedocs.io/en/latest/?badge=latest
+    :target: https://rapid-peptide-generator.readthedocs.io/en/latest/?badge=latest
     :alt: Documentation Status
 
 :note: RPG is tested with Gitlab Ci for the following Python version: 3.6 to 3.9
@@ -44,7 +44,7 @@ Installation
 
 In order to install RPG, you can use **pip**:
 
-.. code-block:: none
+.. code-block:: shell
 
     pip3 install rpg
 
@@ -56,6 +56,6 @@ Usage
 
 From the command line:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg --help
diff --git a/docs/userguide.rst b/docs/userguide.rst
index 6462801f507c9b648837d84be3d5a39634e14c44..52556ecdbad87df044d2e73e7bed86c75461600d 100644
--- a/docs/userguide.rst
+++ b/docs/userguide.rst
@@ -8,13 +8,13 @@ Overview
 
 You can run **Rapide Peptides Generator** using the standalone version called:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg
 
 You can obtain help by using:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg --help
 
@@ -27,13 +27,13 @@ From pip
 
 The suggested way of installing the latest **RPG** version is through **pip**:
 
-.. code-block:: none
+.. code-block:: shell
 
     pip3 install rpg
 
 Then you can use:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg --help
 
@@ -42,7 +42,7 @@ From source code
 
 **RPG** is coded in Python. To manually install it from source, get the source and install **RPG** using:
 
-.. code-block:: none
+.. code-block:: shell
 
     git clone https://gitlab.pasteur.fr/nmaillet/rpg/
     cd rpg
@@ -69,7 +69,7 @@ To:
 
 Then, from the main **RPG** directory, use:
 
-.. code-block:: none
+.. code-block:: shell
 
     python3 rpg/RapidPeptidesGenerator.py -\\-help
 
@@ -86,7 +86,7 @@ Getting help
 
 To access build-in help, use:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -\\-help
 
@@ -95,7 +95,7 @@ Listing enzymes
 
 To list all available enzymes, use:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -l
 
@@ -111,7 +111,7 @@ Sequential digestion of one sequence
 
 To perform sequential digestion of the sequence "QWSDORESDF" with enzymes 2 and 5 and store results in `output_file.fasta`, use:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -s QWSDORESDF -o output_file.fasta -e 2 5
 
@@ -122,7 +122,7 @@ Sequential digestion of a (multi)fasta file
 
 To perform sequential digestion of `input_file.fasta` with enzymes 2 and 5 and store results in `output_file.fasta`, use:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -i input_file.fasta -o output_file.fasta -e 2 5
 
@@ -131,7 +131,7 @@ Concurrent digestion of a (multi)fasta file
 
 To perform concurrent digestion of `input_file.fasta` with enzymes 2 and 5 and store results in `output_file.fasta`, use:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -i input_file.fasta -o output_file.fasta -e 2 5 -d c
 
@@ -140,7 +140,7 @@ Adding a new enzyme
 
 To extend the list of the available enzymes and add a new one, use:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -a
 
@@ -198,7 +198,7 @@ In concurrent mode, all enzymes are present at the same time during digestion an
 
 Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after P. The second is called 'afterK' (id 29) and cleaves after K if there is no P just before. Digesting 'PKPKPKPK' using those two enzymes in sequential mode gives the following result (see :ref:`formats` for more information):
 
-.. code-block:: none
+.. code-block:: shell
 
     $ rpg -s PKPKPKPK -e 28 29
     >Input_0_afterP_1_1_115.13198_5.54
@@ -218,7 +218,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after
 
 Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the following result:
 
-.. code-block:: none
+.. code-block:: shell
 
     $ rpg -s PKPKPKPK -e 28 29 -d c
     >Input_0_afterP-afterK_1_1_115.13198_5.54
@@ -252,7 +252,7 @@ Sometimes an enzyme does not cleave at a given position even if requirements are
 
 For example, using:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -s QWSDORESDF -e 1 2 3 -m 1.4 2.6
 
@@ -292,7 +292,7 @@ The isoelectric point is computed by solving Henderson–Hasselbalch equation us
 
 The default output is in multi-fasta format. The header then summarizes all this information. For example, on the following multi-fasta result:
 
-.. code-block:: none
+.. code-block:: shell
 
     >Input_0_Asp-N_3_3_419.43738_5.54
     QWS
@@ -321,7 +321,7 @@ Verbosity can be increased or decreased. The output file is not affected by **-v
 
 With default verbosity level (no **-v** nor **-q** option), the output is:
 
-.. code-block:: none
+.. code-block:: shell
 
     $ rpg -s QWSDORESDF -e 1
     >Input_0_Asp-N_3_3_419.43738_5.54
@@ -333,7 +333,7 @@ With default verbosity level (no **-v** nor **-q** option), the output is:
 
 Increasing verbosity by one, *i.e.* using **-v**, adds information about used options. For example:
 
-.. code-block:: none
+.. code-block:: shell
 
     $ rpg -s QWSDORESDF -e 1 -v
     Warning: File 'peptides.fasta' already exit!
@@ -353,7 +353,7 @@ Increasing verbosity by one, *i.e.* using **-v**, adds information about used op
 
 Increasing verbosity by two, *i.e.* using **-vv**, also adds statistics about each of the digested proteins. For example:
 
-.. code-block:: none
+.. code-block:: shell
 
     $ rpg -s QWSDORESDF -e 1 -vv
     Warning: File 'peptides.fasta' already exit!
@@ -382,7 +382,7 @@ Increasing verbosity by two, *i.e.* using **-vv**, also adds statistics about ea
 
 Decreasing verbosity, *i.e.* using **-q** option, removes all information but errors. For example:
 
-.. code-block:: none
+.. code-block:: shell
 
     $ rpg -s QWSDORESDF -e 1 -q 
     Warning: File 'peptides.fasta' already exit!
@@ -399,13 +399,13 @@ Option **-a, -\\-addenzyme** allows the user to define new enzymes. An enzyme co
 
 In the following, nomenclature of `Schechter and Berger <https://www.ncbi.nlm.nih.gov/pubmed/6035483>`_ is used. Amino acids before the cleavage site are designated as `P1`, `P2`, `P3`, etc in the N-terminal direction, and as `P1'`, `P2'`, `P3'`, etc in the C-terminal direction. For example, with cleavage site represented as '|':
 
-.. code-block:: none
+.. code-block:: shell
 
     ...P3-P2-P1-|-P1'-P2'-P3'...
 
 In **RPG**, this nomenclature is represented as:
 
-.. code-block:: none
+.. code-block:: shell
 
     ...(P3)(P2)(P1)(,)(P1')(P2')(P3')...
 
@@ -417,25 +417,25 @@ A rule specifies which amino acid is targeted by the enzyme, the cleavage positi
 
 For example, to define a cleavage occurring **before** A, one must input:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A)
 
 To define a cleavage occurring **after** B, one must input:
 
-.. code-block:: none
+.. code-block:: shell
 
     (B,)
 
 The surrounding context is specified by adding other amino acids, before or after the targeted one. For example, to define a cleavage occurring **before** A, position `P1'`, preceded by B in position `P1`, C in position `P3` and followed by D in position `P2'`, one must input:
 
-.. code-block:: none
+.. code-block:: shell
 
     (C)()(B)(,A)(D)
 
 Note that this enzyme will only cleave if it finds the motif C*BAD, where * could be **any** amino acid. It will **not** cleave BAD, nor C*BA, BA, etc. For example, creating and using enzyme `rpg_example_userguide` (enzyme id 43):
 
-.. code-block:: none
+.. code-block:: shell
 
     $ rpg -a    
     Name of the new enzyme?
@@ -462,7 +462,7 @@ Note that this enzyme will only cleave if it finds the motif C*BAD, where * coul
 
 In order for this enzyme to also cleave before AD (before A in `P1'` followed by D in `P2'` ), on top of the previous rule, one has to define one more rule in **RPG**:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A)(D)
     (C)()(B)(,A)(D)
@@ -470,7 +470,7 @@ In order for this enzyme to also cleave before AD (before A in `P1'` followed by
 It is important to note that for each enzyme, it is enough that one of the rule is broken for the cleavage to not occur. In this example, the defined enzyme will **not** cleave BAD, as it is specified that it will cleave before A preceded by B in `P1` **if there is C in `P3`**. Identically, it will **not** cleave C*BA*, as D is required in `P2'` for both rules.
 
 
-.. code-block:: none
+.. code-block:: shell
 
     $rpg -a
     Name of the new enzyme?
@@ -506,14 +506,14 @@ It is important to note that for each enzyme, it is enough that one of the rule
 
 The order of inputted rules is not relevant. In other words, this enzyme:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A)(D)
     (C)()(B)(,A)(D)
 
 and this second one:
 
-.. code-block:: none
+.. code-block:: shell
 
     (C)()(B)(,A)(D)
     (,A)(D)
@@ -522,7 +522,7 @@ are identical.
 
 It is possible to define none-related cleavage rules for the same enzyme, for example:
 
-.. code-block:: none
+.. code-block:: shell
 
     (G,)(G)
     (P)(W,)(E)(T)
@@ -531,13 +531,13 @@ This enzyme will cleave after G (position `P1`) followed by G in `P1'` and also
 
 Note that each rule must concern only **one** cleavage site. It is not possible to input rule like:
 
-.. code-block:: none
+.. code-block:: shell
 
     (A,)(B,)
 
 This would define an enzyme cleaving after A in `P1` followed by B in `P1'` but also cleaving after B in `P1` preceded by A in `P2`. The proper way to input this is by using two separate rules:
 
-.. code-block:: none
+.. code-block:: shell
 
     (A,)(B)
     (A)(B,)
@@ -552,19 +552,19 @@ An exception specifies when a cleavage should **not** occur. **Exceptions must a
 
 For example, to define a cleavage occurring **before** A (`P1'` ), one must input:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A)
 
 Exceptions can then be inputted. For example, to define "a cleavage occurs before A, except when P is in `P2'` ", the following exception needs to be added:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A)(P)
 
 This enzyme will always cleave before A when not followed by P:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -a
     Name of the new enzyme?
@@ -594,13 +594,13 @@ This enzyme will always cleave before A when not followed by P:
 
 It is possible to input complex exceptions. For the previous enzyme, we can add the following exception:
 
-.. code-block:: none
+.. code-block:: shell
 
     (G)(T)()(,A)()(F)
 
 This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` ) or preceded by G in `P3`, T in `P2`, by any amino acid in `P1` and `P2'`, and F in `P3'` **at the same time**:
 
-.. code-block:: none
+.. code-block:: shell
 
     rpg -a             
     Name of the new enzyme?
@@ -648,13 +648,13 @@ This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` )
 
 It is important to understand that an exception should always be linked to a rule. If one inputs this rule:
 
-.. code-block:: none
+.. code-block:: shell
 
     (A,)
 
 followed by this exception:
 
-.. code-block:: none
+.. code-block:: shell
 
     (B,)(C)
 
@@ -671,26 +671,26 @@ To make enzyme creation easier to use, two tricks are available.
 
 The first one simplifies the definition of enzymes cleaving **before** and **after** a given amino acid. Defining an enzyme cleaving, for example, before **and** after A, can be done with two rules:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A)
     (A,)
 
 or simply using:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A,)
 
 The second trick is the use of the keyword `or`. This allows multiple possibilities for on position. For example:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A or B)
 
 is equivalent to:
 
-.. code-block:: none
+.. code-block:: shell
 
     (,A)
     (,B)
@@ -701,7 +701,7 @@ Those two tricks help on complex enzymes. For example, :ref:`peps13` preferentia
 
 It can be defined either by:
 
-.. code-block:: none
+.. code-block:: shell
 
     cleaving rules:
 
@@ -737,7 +737,7 @@ It can be defined either by:
 
 or, in a condensed way:
 
-.. code-block:: none
+.. code-block:: shell
 
     cleaving rule:
 
diff --git a/setup.py b/setup.py
index 07f4d833416f8a912132969ae570ac6a69586170..5cf63e4edc4fa867554e55bd892a8c4daaad02e9 100644
--- a/setup.py
+++ b/setup.py
@@ -140,7 +140,7 @@ setup(
     #
     # For an analysis of "install_requires" vs pip's requirements files see:
     # https://packaging.python.org/en/latest/requirements.html
-    install_requires=[''],  # Optional
+    #install_requires=[''],  # Optional
 
     # List additional groups of dependencies here (e.g. development
     # dependencies). Users will be able to install these using the "extras"