Tidy README formatting

README.md

@@ -21,12 +21,13 @@ Main features:
 
 creating tables and views
 
-```
+```sh
 $ pip install git+https://github.com/libAtoms/abcd.git
 ```
 
 Example Docker installation on Ubuntu:
-```
+
+```sh
 sudo apt-get update
 sudo apt upgrade
 sudo apt install docker.io
@@ -37,13 +38,13 @@ newgrp docker # or exit and log in
 
 Docker can be tested by running:
 
-```
+```sh
 docker run hello-world
 ```
 
 Example Python setup on Ubuntu (pip must be updated for poetry to be used successfully):
 
-```
+```sh
 sudo apt install software-properties-common
 sudo add-apt-repository ppa:deadsnakes/ppa
 sudo apt install python3.10
@@ -56,7 +57,7 @@ curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10
 
 Building and installing ABCD dependencies via poetry:
 
-```
+```sh
 git clone https://github.com/libAtoms/abcd.git
 curl -sSL https://install.python-poetry.org | python3 -
 export PATH="/home/ubuntu/.local/bin:$PATH"
@@ -69,33 +70,34 @@ poetry build
 
 If you have an already running MongoDB server, or install your own, then you are ready to go. Alternatively,
 
-```
+```sh
 docker run -d --rm --name abcd-mongodb -v <path-on-your-machine-to-store-database>:/data/db -p 27017:27017 mongo
 ```
 
 will download and install a docker and run a database in it.
 
 To connect to a mongodb that is already running, use
-```
+
+```sh
 abcd login mongodb://localhost
 ```
 
 If you are running `abcd` inside a docker, and want to connect to a mongodb outside that docker use something like this (example is for Mac OS):
 
-```
+```sh
 abcd login mongodb://docker.for.mac.localhost
 ```
 
 The above login command will place create an `~/.abcd` file with the following contents:
 
-```
+```sh
 {"url": "mongodb://localhost"}
 ```
 
 ### OpenSearch
 If you have an already running OpenSearch server, or install your own, then you are ready to go. Alternatively,
 
-```
+```sh
 sudo swapoff -a # optional
 sudo sysctl -w vm.swappiness=1 # optional
 sudo sysctl -w fs.file-max=262144 # optional
@@ -105,24 +107,27 @@ docker run -d --rm --name abcd-opensearch -v <path-on-your-machine-to-store-data
 
 will download and install an OpenSearch image and run it. The connection can be tested with:
 
-```
+```sh
 curl -vvv -s --insecure -u admin:admin --fail https://localhost:9200
 ```
 
 To connect to an OpenSearch database that is already running, use
-```
+
+```sh
 abcd login opensearch://username:password@localhost
 ```
 
 ## Remote access
 
 You can set up an `abcd` user on your machine where the database is running, and then access it remotely for discovering data. Make sure you have the `~/.abcd` file created for this user, then put this in the `.ssh/authorized_keys` file (substituting your public key for the last part):
-```
+
+```sh
 command="/path/to/abcd --remote  ${SSH_ORIGINAL_COMMAND}",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty ssh-rsa <public-key> your@email
 ```
 
 Then you'll be able to access the database remotely using, e.g.
-```
+
+```sh
 ssh [email protected] summary
 ```
 
@@ -135,17 +140,17 @@ The database has a simple GUI, coupled with a visualiser. Data for now needs to
 Currently a manual uploaded image is available, that was built on 7/2/2020 by Tamas K. Stenczel.
 To access it:
 1. pull the image
-    ```
+    ```sh
     docker pull stenczelt/projection-abcd:latest
     ```
 
 2. create a docker network, which enables the containers to communicate with each other and the outside world as well 
-    ```
+    ```sh
     docker network create --driver bridge abcd-network
     ```
 
 3. run the mongo (ABCD) and the visualiser as well
-    ```
+    ```sh
     docker run -d --rm --name abcd-mongodb-net -v <path-on-your-machine-to-store-database>:/data/db -p 27017:27017 --network abcd-network mongo
 
     docker run -it --rm --name visualiser-dev -p 9999:9999 --network abcd-network stenczelt/projection-abcd
@@ -156,7 +161,8 @@ To access it:
 This will start the visualiser with ABCD integration! Have fun!
 
 After usage, for cleanup:
-```
+
+```sh
 docker stop visualiser-dev abcd-mongodb-net         # stop the containers
 docker rm visualiser-dev abcd-mongodb-net           # remove them if --rm did not
 docker network rm abcd-network                      # remove the docker network
@@ -166,6 +172,6 @@ docker network rm abcd-network                      # remove the docker network
 
 Unit tests are automatically run on push and creation of pull requests. Unit testing using mock databases can also be run in the command line using:
 
-```
+```sh
 python -m unittest tests
 ```