Initial changes

.github/workflows/actions.yaml

@@ -23,9 +23,6 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: |
         coveralls --service=github
-    - name: Test with nomad
-      run: |
-        python -m nomad.cli parse tests/data/test.example-format.txt
   build-and-install:
     runs-on: ubuntu-latest
     steps:
@@ -42,23 +39,18 @@ jobs:
     - name: Install the package
       run: |
         pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
-    - name: Test with nomad
-      run: |
-        python -m nomad.cli parse tests/data/test.example-format.txt
+  ruff-formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: "format ."
   ruff-linting:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: chartboost/ruff-action@v1
         with:
-          args: "check ."
-          version: 0.1.8
-  # to enable auto-formatting check, uncomment the following lines below
-  # ruff-formatting:
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v3
-  #     - uses: chartboost/ruff-action@v1
-  #       with:
-  #         args: "format . --check"
-  #         version: 0.1.8
+          args: "format . --check"
+          version: 0.2.0

.gitignore

@@ -128,3 +128,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# VSCode launch json
+.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
+}

README.md

@@ -1,88 +1,103 @@
-# NOMAD's parser example plugin
+![](https://github.com/nomad-coe/nomad-parser-magres/actions/workflows/actions.yml/badge.svg)
+![](https://coveralls.io/repos/github/nomad-coe/nomad-parser-magres/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/)  
 
-## Getting started
-
-### Fork the project
-
-Go to the github project page https://github.com/nomad-coe/nomad-parser-plugin-example, hit
-fork (and leave a star, thanks!). Maybe you want to rename the project while forking!
-
-### Clone your fork
+# NOMAD's parser for magres
 
-Follow the github instructions. The URL and directory depends on your user name or organization and the
-project name you choose. But, it should look somewhat like this:
+This is a parser plugin for the [magres file format](https://www.ccpnc.ac.uk/output/magres) developed in the CCP-NC for Nuclear Magnetic Resonance (NMR) data.
 
-```
-git clone git@github.com:markus1978/my-nomad-schema.git
-cd my-nomad-schema
-```
+## Getting started
 
 ### Install the dependencies
 
-You should create a virtual environment. You will need the `nomad-lab` package (and `pytest`).
-You need at least Python 3.9.
+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-parser-magres.git
+cd nomad-parser-magres
+python3.9 -m venv .pyenv
+```
 
+Install the `nomad-lab` package:
 ```sh
-python3 -m venv .pyenv
-source .pyenv/bin/activate
 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 (e.g. via `--index-url`). Follow the instructions
-in `requirements.txt`.
+> **Note**: Until we have an official PyPI NOMAD release with the plugin functionality, make
+sure to include NOMAD's internal package registry (via `--index-url` in the above command).
+
 
 ### Run the tests
 
-Make sure the current directory is in your path:
+You can run the unit testing using the `pytest` package:
 
 ```sh
-export PYTHONPATH=.
+python -m pytest -sv
 ```
 
-You can run automated tests with `pytest`:
-
+We recommend to install the `coverage` and `coveralls` packages for a more comprehensive output of the testing:
 ```sh
-pytest -svx tests
+pip install coverage coveralls
+python -m coverage run -m pytest -sv
 ```
 
-### Run linting
+## 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
-ruff check .
+pip install -e .[dev] --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
 ```
 
-### Run auto-formatting
 
-This is entirely optional. To add this as a check in github actions pipeline, uncomment the `ruff-formatting` step in `./github/workflows/actions.yaml`.
+### Setting up the 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 local NOMAD installation.
 
-```sh
-ruff format .
-```
+To deploy the plugin in your local NOMAD installation, follow the next steps:
 
-You can parse an example archive that uses the schema with `nomad`
-(installed via `nomad-lab` Python package):
+1. Add the configurations related to NOMAD. This is already implemented through the plugin definition file ```src/nomad_parser_magres/nomad_plugin.yaml```:
 
-```sh
-nomad parse tests/data/test.example-format.txt --show-archive
-```
+    ```yaml
+    plugin_type: parser
+    name: parsers/magres
+    description: |
+      This plugin is used to parsed magres files into the NOMAD schema.
+    ```
+    and the ```nomad.yaml``` configuration file:
 
-## Developing your schema
+    ```yaml
+    plugins:
+      include:
+        - 'parsers/magres'
+      options:
+        parsers/magres:
+          python_package: nomad_parser_magres
+    ```
+3. Add to your local NOMAD installation the same lines of your plugin ```nomad.yaml``` file.
+4. Add to your local NOMAD installation environment the `PYTHONPATH` to your plugin. This can be done either by running the following command every time you start a new terminal for running the appworker, or by adding it to your virtual environment in the `<path-to-local-nomad-installation>/.pyenv/bin/activate` file:
 
-You can now start to develop you schema. Here are a few things that you might want to change:
+    ```sh
+    export PYTHONPATH="$PYTHONPATH:<path-to-nomad-parser-magres-cloned-repo>/src"
+    ```
 
-- The metadata in `nomad_plugin.yaml`.
-- The name of the Python package `nomadparserexample`. If you want to define multiple plugins, you can nest packages.
-- The name of the example parser `ExampleParser` and the schema definitions it might define.
-- When you change module and class names, make sure to update the `nomad_plugin.yaml` accordingly.
+If you are working in this repository, you just need to activate the environment to start working using the ```nomad-parser.magres``` package locally in your own Python scripts.
+
+### Run linting and auto-formatting
+Ruff auto-formatting is also a part of the GitHub workflow actions. Make sure that before you make a Pull Request to add your contributions to this repo, the following commands run in your local without any errors otherwise the workflow action will fail.
+```sh
+ruff check .
+```
+```sh
+ruff format . --check
+```
+
+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.
 
 
+<!--
 ## Build the python package
 
-The `pyproject.toml` file contains everything that is necessary to turn the project
-into a pip installable python package. Run the python build tool to create a package distribution:
+The `pyproject.toml` file contains everything that is necessary to turn the project into a pip installable python package. Run the python build tool to create a package distribution:
 
 ```
 pip install build
@@ -95,11 +110,5 @@ You can install the package with pip:
 pip install dist/nomad-schema-plugin-example-1.0.tar.gz
 ```
 
-Read more about python packages, `pyproject.toml`, and how to upload packages to PyPI
-on the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/).
-
-
-## Next steps
-
-To learn more about plugins, how to add them to an Oasis, how to publish them, read our
-documentation on plugins: https://nomad-lab.eu/docs/plugins/plugins.html.
+Read more about python packages, `pyproject.toml`, and how to upload packages to PyPI on the [PyPI documentation](https://packaging.python.org/en/latest/tutorials/packaging-projects/).
+-->

nomad.yaml

@@ -6,7 +6,7 @@ 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: 'parsers/example'
+  include: 'parsers/magres'
   options:
-    parsers/example:
-      python_package: nomadparserexample
+    parsers/magres:
+      python_package: nomad_parser_magres