Minor readme fixes.

readme.md

@@ -20,19 +20,19 @@ is supposed to do: help us do science, so now we are mostly doing that.
 ## Installation
 
 You can install the latest stable version of `pubs` through Pypi, with:
-  ```
+  ```shell
   pip install pubs
   ```
 
 Alternatively, you can:
 
   - install the latest development version with pip:
-    ```
+    ```shell
     pip install --upgrade git+https://github.com/pubs/pubs
     ```
 
   - clone the repository and install it manually:
-    ```
+    ```shell
     git clone https://github.com/pubs/pubs
     cd pubs
     python setup.py install [--user]
@@ -44,32 +44,32 @@ Arch Linux users can also use the [pubs-git](https://aur.archlinux.org/packages/
 ## Getting started
 
 Create your library (by default, goes to `~/.pubs/`).
-  ```
+  ```shell
   pubs init
   ```
 
 Import existing data from bibtex (pubs will try to automatically copy documents defined as 'file' in bibtex):
-  ```
+  ```shell
   pubs import path/to/collection.bib
   ```
 
 or for a .bib file containing a single reference:
-  ```
+  ```shell
   pubs add reference.bib -d article.pdf
   ```
 
 pubs can also automatically retrieve the bibtex from a doi:
-  ```
+  ```shell
   pubs add -D 10.1007/s00422-012-0514-6 -d article.pdf
   ```
 
 or an ISBN (dashes are ignored):
-  ```
+  ```shell
   pubs add -I 978-0822324669 -d article.pdf
   ```
 
 or an arXiv id (automatically downloading arXiv article is in the works):
-  ```
+  ```shell
   pubs add -X math/9501234 -d article.pdf
   ```
 
@@ -79,7 +79,7 @@ or an arXiv id (automatically downloading arXiv article is in the works):
 If you use latex, you can automatize references, by running `pubs export > references.bib` each time you update your library, which also fits well as a `makefile` rule.
 
 This ensures that your reference file is always up-to-date; you can cite a paper in your manuscript a soon as you add it in pubs. This means that if you have, for instance, a DOI on a webpage, you only need to do:
-  ```
+  ```shell
   pubs add -D 10.1007/s00422-012-0514-6
   ```
 
@@ -89,12 +89,12 @@ and then add `\cite{Loeb_2012}` in your manuscript. After exporting the bibliogr
 ## Document management
 
 You can attach a document to a reference:
-  ```
+  ```shell
   pubs doc add Loeb2012_downloaded.pdf Loeb_2012
   ```
 
 And open your documents automatically from the command line:
-  ```
+  ```shell
   pubs doc open Loeb_2012
   pubs doc open --with lp Loeb_2012  # Opens the document with `lp` to actually print it.
   ```
@@ -114,18 +114,18 @@ You can then also conveniently interact with the git repository by using `pubs g
 ## Multiple pubs Repositories
 
 You may want to have different pubs repositories, for different projects. To create an alternate repository:
-  ```
+  ```shell
   pubs --config /path/to/config init --pubsdir /path/to/desired_repository_directory
   ```
 The configuration file and repository will be automatically created.
 
 Then you can add papers to the new repository:
-  ```
+  ```shell
   pubs --config /path/to/config add -D 10.1007/s00422-012-0514-6
   ```
 
 A useful thing might be to define an alias in your shell:
-  ```
+  ```shell
   alias pubs2="pubs --config /path/to/config"
   ```
 and then use `pubs2` as you would use `pubs` directly.  Note that you cannot use the alias plugin below to do this.
@@ -141,8 +141,8 @@ You can add custom commands to pubs by defining aliases in your configuration fi
   count = !pubs list -k "$@" | wc -l
   ```
 
-The first command defines a new subcommand: `pubs open --with evince` will be executed when `pubs evince` is typed.
+The first configuration line defines a new subcommand: `pubs open --with evince` will be executed when `pubs evince` is typed.
-The second starts with a bang: `!`, and is treated as a shell command. If other arguments are provided they are passed to the shell command as in a script. In the example above the `count` alias can take arguments that are be passed to the `pubs list -k` command, hence enabling filters like `pubs count year:2012`.
+The second starts with a bang: `!`, which means that it is treated as a shell command. If other arguments are provided they are passed to the shell command as in a script. In the example above the `count` alias can take arguments that are passed over to the `pubs list -k` command, hence enabling filters like `pubs count year:2012`.
 
 
 ## Autocompletion