Update readme

README.md

@@ -30,7 +30,7 @@ a Docker image of this tool to Synapse Docker Registry. This image of this
 example tool can be submitted as-is on [NLPSandbox.io] to benchmark its
 performance -- just don't expect a high performance!
 
-## Contents
+## Table of contents
 
 - [Specification](#Specification)
 - [Requirements](#Requirements)
@@ -46,6 +46,7 @@ performance -- just don't expect a high performance!
   - [Enabling version updates](#Enabling-version-updates)
   - [Generating a new NLP Sandbox tool using
     openapi-generator](#Generating-a-new-NLP-Sandbox-tool-using-openapi-generator)
+  - [Install the development dependencies](#Install-the-development-dependencies)
   - [Keeping your tool up-to-date](#Keeping-your-tool-up-to-date)
   - [Testing](#Testing)
   - [Preventing an NLP Sandbox tool from connecting to remote
@@ -59,27 +60,35 @@ performance -- just don't expect a high performance!
 
 ## Specification
 
+- Tool version: 1.2.1
 - NLP Sandbox schemas version: 1.2.0
-- NLP Sandbox tool version: 1.2.1
 - Docker image: [docker.synapse.org/syn22277123/phi-annotator-example]
 
-
 ## Requirements
 
 - [Docker Engine] >=19.03.0
 
-
 ## Usage
 
 ### Running with Docker
 
-The command below starts this NLP Sandbox PHI annotator locally.
+To download the tool image published and run it.
+
+```console
+docker compose pull
+docker compose up
+```
+
+Alternatively, you can build the image and run it.
 
 ```console
 docker compose up --build
 ```
 
 You can stop the container run with `Ctrl+C`, followed by `docker compose down`.
+Add the option `-d` or `--detach` to start the container in detached mode. If
+`docker compose` in not available on your system, please install [docker
+compose].
 
 ### Running with Python
 
@@ -93,21 +102,16 @@ conda activate phi-annotator
 Install and start this NLP Sandbox PHI annotator.
 
 ```console
-cd server && pip install -r requirements.txt
+cd server
+pip install -r requirements.txt
 python -m openapi_server
 ```
 
 ### Accessing this NLP Sandbox tool User Interface
 
 This NLP Sandbox tool provides a web interface that you can use to annotate
-clinical notes. This web client has been automatically generated by
-[openapi-generator]. To access the UI, open a new tab in your browser and
-navigate to one of the following address depending on whether you are running
-the tool using Docker (production) or Python (development).
-
-- Using Docker: http://localhost/ui
-- Using Python: http://localhost:8080/ui
-
+clinical notes. To access the UI, open your browser and navigate to
+http://localhost:8080/ui.
 
 ## Development
 
@@ -207,6 +211,21 @@ The URL is composed of different elements:
   can be replaced by a specific release version `x.y.z` of the [NLP Sandbox
   schemas].
 
+### Install the development dependencies
+
+Install the Node.js dependencies required to run `npm run <script>`.
+
+```console
+npm ci
+```
+
+Install the Python dependencies required for tasks like linting and testing.
+
+```console
+cd server
+pip install -r dev-requirements.txt -r test-requirements.txt
+```
+
 ### Keeping your tool up-to-date
 
 The NLP Sandbox schemas is updated after receiving contribution from the
@@ -284,7 +303,6 @@ that it works fine while it does not have access to the internet. Note that when
 being evaluated on [NLPSandbox.io], additional measures are put in place to
 prevent tools from connecting to remote servers.
 
-
 ## Versioning
 
 ### GitHub release tags
@@ -354,3 +372,4 @@ Thinking about contributing to this project? Get started by reading our
 [Patient schema]: https://github.com/nlpsandbox/nlpsandbox-schemas/blob/main/openapi/commons/components/schemas/Patient.yaml
 [semantic versioning]: https://semver.org/
 [NLP Sandbox schemas CHANGELOG]: .github/CHANGELOG.md
+[docker compose]: https://docs.docker.com/compose/install/

server/dev-requirements.txt

@@ -0,0 +1 @@
+flake8==4.0.1