Generate initial parser

.cruft.json

@@ -0,0 +1,27 @@
+{
+  "template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin",
+  "commit": "e759475d3f8905df4354ca83d8ce6cd632ffce99",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "full_name": "Jose Pizarro",
+      "email": "[email protected]",
+      "github_username": "FAIRmat-NFDI",
+      "plugin_name": "nomad-parser-vasp",
+      "module_name": "nomad_parser_vasp",
+      "short_description": "A NOMAD parser plugin for VASP input/output files.",
+      "version": "0.1.0",
+      "license": "Apache Software License 2.0",
+      "include_schema_package": true,
+      "include_normalizer": false,
+      "include_parser": true,
+      "include_app": false,
+      "include_example_uploads": false,
+      "_copy_without_render": [
+        "*.html"
+      ],
+      "_template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin"
+    }
+  },
+  "directory": null
+}

.github/workflows/actions.yml

@@ -0,0 +1,71 @@
+name: install-and-test
+on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ["3.9", "3.10", "3.11"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{matrix.python_version}}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{matrix.python_version}}
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        uv pip install -e '.[dev]'
+    - name: mypy
+      run: |
+        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/nomad_parser_vasp/schema_packages src/nomad_parser_vasp/parsers tests
+    - name: Test with pytest
+      run: |
+        python -m pytest -sv tests
+  build-and-install:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+    - name: Build the package
+      run: |
+        pip install uv
+        uv pip install --upgrade pip --system
+        uv pip install build --system
+        python -m build --sdist
+    - name: Install the package
+      run: |
+        uv pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple --system
+  ruff-linting:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+        - uses: chartboost/ruff-action@v1
+          with:
+            args: "check ."
+  ruff-formatting:
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+        - uses: chartboost/ruff-action@v1
+          with:
+            args: "format . --check --verbose"

.github/workflows/coveralls.yml

@@ -0,0 +1,44 @@
+name: Testing with coveralls Report
+on: [push]
+
+# https://docs.github.com/en/actions/using-jobs/assigning-permissions-to-jobs
+# `contents` is for permission to the contents of the repository.
+# `pull-requests` is for permission to pull request
+permissions:
+  contents: write
+  checks: write
+  pull-requests: write
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  coveralls-test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        uv pip install -e '.[dev]'
+        uv pip install coveralls
+    - name: Build coverage file
+      run: |
+        pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=src tests | tee pytest-coverage.txt
+    - name: Pytest coverage comment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: pytest-coverage.txt
+        junitxml-path: pytest.xml
+    - name: Submit to coveralls
+      continue-on-error: true
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        coveralls --service=github

.github/workflows/mkdocs-deploy.yml

@@ -0,0 +1,24 @@
+name: Deploy MkDocs Site
+
+on:
+  push:
+    branches:
+      - main # Triggers deployment on push to the main branch
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Deploy docs
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          CONFIG_FILE: mkdocs.yml
+          REQUIREMENTS: requirements_docs.txt

.github/workflows/publish.yml

@@ -0,0 +1,43 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Build and Publish Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+env:
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+    - name: Install uv
+      run: |
+        curl -LsSf https://astral.sh/uv/install.sh | sh
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        uv pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -0,0 +1,130 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.pyenv
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

.vscode/settings.json

@@ -0,0 +1,21 @@
+{
+  "editor.rulers": [
+    90
+  ],
+  "editor.renderWhitespace": "all",
+  "editor.tabSize": 4,
+  "files.trimTrailingWhitespace": true,
+  "[python]": {
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+      "source.fixAll": "explicit",
+      "source.organizeImports": "explicit"
+    },
+    "editor.defaultFormatter": "charliermarsh.ruff"
+  },
+  "python.testing.pytestArgs": [
+    "tests"
+  ],
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true
+}

LICENSE

@@ -1,3 +1,4 @@
+
                                  Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/
@@ -178,15 +179,15 @@
    APPENDIX: How to apply the Apache License to your work.
 
       To apply the Apache License to your work, attach the following
-      boilerplate notice, with the fields enclosed by brackets "[]"
+      boilerplate notice, with the fields enclosed by brackets "{}"
       replaced with your own identifying information. (Don't include
       the brackets!)  The text should be enclosed in the appropriate
       comment syntax for the file format. We also recommend that a
       file or class name and description of purpose be included on the
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright [yyyy] [name of copyright owner]
+   Copyright {yyyy} {name of copyright owner}
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.