Moved modules to src/nomad_simulations

Fix config files with the new path

Added Dockerfile, MANIFEST.in, setup.py

Added .vscode with settings

.gitignore

@@ -158,3 +158,6 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# VSCode settings
+.vscode/launch.json

.vscode/settings.json

@@ -0,0 +1,24 @@
+{
+  "python.defaultInterpreterPath": ".pyenv/bin/python",
+  "python.terminal.activateEnvInCurrentTerminal": true,
+  "editor.rulers": [90],
+  "editor.renderWhitespace": "all",
+  "editor.tabSize": 4,
+  "[javascript]": {
+    "editor.tabSize": 2
+  },
+  "files.trimTrailingWhitespace": true,
+  "files.watcherExclude": {
+    "${workspaceFolder}/.pyenv/**": true
+  },
+  "files.exclude": {
+    "\"**/*.pyc\": {\"when\": \"$(basename).py\"}": true,
+    "**/__pycache__": true,
+    "**/node_modules": true
+  },
+  "python.testing.pytestPath": "pytest",
+  "python.testing.pytestArgs": ["tests"],
+  "python.testing.unittestEnabled": false,
+  "editor.defaultFormatter": "charliermarsh.ruff",
+  "editor.formatOnSave": true
+}

Dockerfile

@@ -0,0 +1,15 @@
+FROM gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair:latest
+
+RUN pip install build
+
+COPY \
+    src/nomad_simulations \
+    tests \
+    README.md \
+    LICENSE \
+    pyproject.toml \
+    .
+
+RUN python -m build --sdist
+
+RUN pip install dist/nomad-simulations-*.tar.gz

MANIFEST.in

@@ -0,0 +1 @@
+recursive-include * nomad_plugin.yaml

README.md

@@ -1,5 +1,96 @@
+![](https://github.com/nomad-coe/nomad-schema-plugin-simulation-data/actions/workflows/actions.yml/badge.svg)
+![](https://coveralls.io/repos/github/nomad-coe/nomad-schema-plugin-simulation-data/badge.svg?branch=main)
+[![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/)
+
 # NOMAD's Simulations Schema Plugin
+This is a plugin for [NOMAD](https://nomad-lab.eu) which contains the base sections schema definitions for materials science simulations..
+
+
+<!-- MOVE THIS TO THE DOCUMENTATION PAGE OF THIS PLUGIN --->
+
+## Getting started
+
+
+### Install the dependencies
+
+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-schema-plugin-simulation-data.git
+cd nomad-schema-plugin-simulation-data
+python3.9 -m venv .pyenv
+. .pyenv/bin/activate
+```
+
+Install the `nomad-lab` package:
+```sh
+pip install --upgrade pip
+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
+sure to include NOMAD's internal package registry (via `--index-url` in the above command).
+
+
+### Run the tests
+
+You can the unit testing using the `pytest` package:
+
+```sh
+python -m pytest -sv
+```
+
+We recommend to install the `coverage` and `coveralls` packages for a more comprehensive output of the testing:
+```sh
+pip install coverage coveralls
+python -m coverage run -m pytest -sv
+```
+
+## Development
+
+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:
+
+```sh
+pip install -e .[dev] --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+```
+
+
+### 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.
+
+You need to modify the ```src/nomad_simulations/nomad_plugin.yaml``` to define the plugin adding the following content:
+```yaml
+plugin_type: schema
+name: schemas/nomad_simulations
+description: |
+  This is a collection of NOMAD schemas for simulation data.
+```
+
+and define the ```nomad.yaml``` configuration file of your NOMAD instance in the root folder with the following content:
+```yaml
+plugins:
+  include: 'schema/nomad_simulations'
+  options:
+    schema/nomad_simulations:
+      python_package: nomad_simulations
+```
+
+You also need to add the package folder to the `PYTHONPATH` of the Python environment of your local NOMAD installation. This can be done by specifying the relative path to this repository. Either run the following command every time you start a new terminal for running the appworker, or add it to your virtual environment in `<path-to-local-nomad-installation>/.pyenv/bin/activate` file:
+```sh
+export PYTHONPATH="$PYTHONPATH:<path-to-nomad-simulations-cloned-repo>"
+```
+
+If you are working in this repository, you just need to activate the environment to start working using the ```nomad-nomad_simulations``` package.
+
+### Run linting and auto-formatting
+
+```sh
+ruff check .
+```
+```sh
+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.
 
-This is a plugin for [NOMAD](https://nomad-lab.eu/nomad-lab/) which contains the base sections schema definitions for materials science simulations.
+Alternatively, if you are using VSCode as your IDE, we added the settings configuration file, `.vscode/settings.json`, such that it performs `ruff format` whenever you save progress in a file.
 
-<!--Add Getting started section to install the plugin independently of NOMAD for local and Oasis usage (see e.g. https://github.com/FAIRmat-NFDI/nomad-measurements?tab=readme-ov-file)-->

nomad.yaml

@@ -0,0 +1,12 @@
+normalize:
+  normalizers:
+    include:
+      - MetainfoNormalizer
+plugins:
+  # We only include our schema here. Without the explicit include, all plugins will be
+  # loaded. Many build in plugins require more dependencies. Install nomad-lab[parsing]
+  # to make all default plugins work.
+  include: 'schema/nomad_simulations'
+  options:
+    schema/nomad_simulations:
+      python_package: nomad_simulations

setup.py

@@ -0,0 +1,4 @@
+from setuptools import setup
+
+if __name__ == '__main__':
+    setup()

src/nomad_simulations/nomad_plugin.yaml

@@ -0,0 +1,4 @@
+plugin_type: schema
+name: schemas/nomad_simulations
+description: |
+  This is a collection of NOMAD schemas for simulation data.