Fix README (#95)

* Improved README explanations

README.md

@@ -1,15 +1,13 @@
 [![NOMAD](https://img.shields.io/badge/Open%20NOMAD-lightgray?logo=data:image/svg+xml;base64,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)](https://nomad-lab.eu/prod/v1/staging/gui/)
-![](https://github.com/nomad-coe/nomad-simulations/actions/workflows/actions.yml/badge.svg)
 ![](https://coveralls.io/repos/github/nomad-coe/nomad-simulations/badge.svg?branch=develop)
-<!-- Add when the repo is published in pypi
 ![](https://img.shields.io/pypi/pyversions/nomad-simulations)
-![](https://img.shields.io/pypi/l/nomad-simulations)
 ![](https://img.shields.io/pypi/v/nomad-simulations)
--->
 
-# `nomad-simulations` schema plugin
 
-This is a plugin for [NOMAD](https://nomad-lab.eu) which contains the base sections schema definitions for materials science simulations.
+
+# `nomad-simulations`
+
+This is a plugin for [NOMAD](https://nomad-lab.eu) which contains the base sections definitions for materials science simulations. This schema can be used at any prefered level by the user, it can be modified and extended, and we welcome external collaborators.
 
 
 ## Getting started
@@ -19,10 +17,10 @@ This is a plugin for [NOMAD](https://nomad-lab.eu) which contains the base secti
 pip install nomad-simulations --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
 ```
 
+
 ## Development
 
 If you want to develop locally this package, clone the project and in the workspace folder, create a virtual environment (note this project uses Python 3.9):
-
 ```sh
 git clone https://github.com/nomad-coe/nomad-simulations.git
 cd nomad-simulations
@@ -41,62 +39,53 @@ pip install uv
 ```
 
 Install the `nomad-lab` package:
-
 ```sh
 uv pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
 ```
 
 **Note!**
-Until we have an official pypi NOMAD release with the plugins functionality. Make
+Until we have an official pypi NOMAD release with the plugins functionality make
 sure to include NOMAD's internal package registry (via `--index-url` in the above command).
 
-The plugin is still under development. If you would like to contribute, install the package in editable mode (with the added `-e` flag) with the development dependencies:
-
+The plugin is still under development. If you would like to contribute, install the package in editable mode (with the added `-e` flag):
 ```sh
 uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
 ```
 
-### Run the tests
 
-You can run local tests using the `pytest` package:
+### Run the tests
 
+You can run locally the tests:
 ```sh
 python -m pytest -sv tests
 ```
 
 where the `-s` and `-v` options toggle the output verbosity.
 
-Our CI/CD pipeline produces a more comprehensive test report using `coverage` and `coveralls` packages. We suggest you to generate your own coverage reports locally by doing:
-
+Our CI/CD pipeline produces a more comprehensive test report using the `pytest-cov` package. You can generate a local coverage report:
 ```sh
 uv pip install pytest-cov
 python -m pytest --cov=src tests
 ```
 
-You can also run the script to generate a local file `coverage.txt` with the same information by doing:
+You can also run the script to generate a local file `coverage.txt` with the same information:
 ```sh
 ./scripts/generate_coverage_txt.sh
 ```
 
-### Setting up plugin on your local installation
-
-Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html) for all details on how to deploy the plugin on your NOMAD instance.
 
 ### Run linting and auto-formatting
 
+We use [Ruff](https://docs.astral.sh/ruff/) for linting and formatting the code. Ruff auto-formatting is also a part of the GitHub workflow actions. You can run locally:
 ```sh
 ruff check .
 ruff format . --check
 ```
 
-Ruff auto-formatting is also a part of the GitHub workflow actions. Make sure that before you make a Pull Request, `ruff format . --check` runs in your local without any errors otherwise the workflow action will fail.
 
 ### Debugging
 
-For interactive debugging of the tests, use `pytest` with the `--pdb` flag.
-We recommend using an IDE for debugging, e.g., _VSCode_.
-If using VSCode, you can add the following snippet to your `.vscode/launch.json`:
-
+For interactive debugging of the tests, use `pytest` with the `--pdb` flag. We recommend using an IDE for debugging, e.g., _VSCode_. If that is the case, add the following snippet to your `.vscode/launch.json`:
 ```json
 {
   "configurations": [
@@ -113,23 +102,21 @@ If using VSCode, you can add the following snippet to your `.vscode/launch.json`
         "args": [
             "-sv",
             "--pdb",
-            "<path to plugin tests>",
+            "<path-to-plugin-tests>",
         ]
     }
   ]
 }
 ```
 
-where `${workspaceFolder}` refers to the NOMAD root.
-
-The settings configuration file `.vscode/settings.json` performs automatically applies the linting upon saving the file progress.
+where `<path-to-plugin-tests>` must be changed to the local path to the test module to be debugged.
 
-### Documentation on Github pages
+The settings configuration file `.vscode/settings.json` automatically applies the linting and formatting upon saving the modified file.
 
-To deploy documentation on Github pages, make sure to [enable GitHub pages via the repo settings](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site#publishing-from-a-branch).
 
-To view the documentation locally, install the documentation related packages using:
+### Documentation on Github pages
 
+To view the documentation locally, install the related packages using:
 ```sh
 uv pip install -r requirements_docs.txt
 ```
@@ -139,6 +126,45 @@ Run the documentation server:
 mkdocs serve
 ```
 
+
+## Adding this plugin to NOMAD
+
+Currently, NOMAD has two distinct flavors that are relevant depending on your role as an user:
+1. [A NOMAD Oasis](#adding-this-plugin-in-your-nomad-oasis): any user with a NOMAD Oasis instance.
+2. [Local NOMAD installation and the source code of NOMAD](#adding-this-plugin-in-your-local-nomad-installation-and-the-source-code-of-nomad): internal developers.
+
+### Adding this plugin in your NOMAD Oasis
+
+Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/howto/oasis/plugins_install.html) for all details on how to deploy the plugin on your NOMAD instance.
+
+### Adding this plugin in your local NOMAD installation and the source code of NOMAD
+
+Modify the script under `/nomad/scripts/install_default_plugins.sh` and add the path to this repository pointing to the `@develop` branch:
+```sh
+<other-content-in-install_default_plugins.sh...>
+pip install git+https://github.com/nomad-coe/nomad-simulations.git@develop
+```
+
+Then, go to your NOMAD folder, activate your NOMAD virtual environment and run:
+```sh
+deactivate
+cd <route-to-NOMAD-folder>/nomad
+source .pyenv/bin/activate
+./scripts/setup_dev_env.sh
+```
+
+Alternatively and only valid for your local NOMAD installation, you can modify `nomad.yaml` to include this plugin:
+```yaml
+plugins:
+  entry_points:
+    include:
+      - ["nomad_simulations.schema_packages:nomad_simulations_plugin"]
+```
+
+**Note!**
+Once you modify your `nomad.yaml` file adding `include`, all the default plugins will be disconnected, so you will need to include them as well.
+
+
 ## Main contributors
 | Name | E-mail     | Topics | Github profiles |
 |------|------------|--------|-----------------|