Set up template

.cruft.json

@@ -0,0 +1,27 @@
+{
+  "template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin",
+  "commit": "e759475d3f8905df4354ca83d8ce6cd632ffce99",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "full_name": "Nathan Daelman",
+      "email": "[email protected]",
+      "github_username": "FAIRmat-NFDI",
+      "plugin_name": "nomad-parser-plugin-boss",
+      "module_name": "nomad_parser_plugin_boss",
+      "short_description": "Plugin for parsing and displaying BOSS PES arftifacts",
+      "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": true,
+      "_copy_without_render": [
+        "*.html"
+      ],
+      "_template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin"
+    }
+  },
+  "directory": null
+}

.github/workflows/actions.yml

@@ -0,0 +1,56 @@
+name: install-and-test-workflow
+on: [push]
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+        pip install coverage coveralls
+    - name: Test with pytest
+      run: |
+        python -m coverage run -m pytest -sv
+    - name: Submit to coveralls
+      continue-on-error: true
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        coveralls --service=github
+  build-and-install:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.9
+    - name: Build the package
+      run: |
+        pip install --upgrade pip
+        pip install build
+        python -m build --sdist
+    - name: Install the package
+      run: |
+        pip install dist/*.tar.gz --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+  ruff-linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1
+        with:
+          args: "check ."
+  # to enable auto-formatting check, uncomment the following lines below
+  # ruff-formatting:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: chartboost/ruff-action@v1
+  #       with:
+  #         args: "format . --check"

.github/workflows/cruft-update.yml

@@ -0,0 +1,75 @@
+# /.github/workflows/cruft-update.yml
+name: Update repository with Cruft
+permissions:
+  contents: write
+  pull-requests: write
+on:
+  schedule:
+    - cron: "0 14 * * 1" # Every Monday at 2pm (UTC time)
+  workflow_dispatch:
+jobs:
+  update:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - add-paths: .
+            body: Use this to merge the changes to this repository.
+            branch: cruft/update
+            commit-message: "chore: accept new Cruft update"
+            title: New updates detected with Cruft
+          - add-paths: .cruft.json
+            body: Use this to reject the changes in this repository.
+            branch: cruft/reject
+            commit-message: "chore: reject new Cruft update"
+            title: Reject new updates detected with Cruft
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+
+      - name: Install Cruft
+        run: pip3 install cruft
+
+      - name: Check if update is available
+        continue-on-error: false
+        id: check
+        run: |
+          CHANGES=0
+          if [ -f .cruft.json ]; then
+            if ! cruft check; then
+              CHANGES=1
+            fi
+          else
+            echo "No .cruft.json file"
+          fi
+
+          echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
+
+      - name: Run update if available
+        if: steps.check.outputs.has_changes == '1'
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "GitHub"
+
+          cruft update --skip-apply-ask --refresh-private-variables
+          git restore --staged .
+
+      - name: Create pull request
+        if: steps.check.outputs.has_changes == '1'
+        uses: peter-evans/create-pull-request@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          add-paths: ${{ matrix.add-paths }}
+          commit-message: ${{ matrix.commit-message }}
+          branch: ${{ matrix.branch }}
+          delete-branch: true
+          branch-suffix: timestamp
+          title: ${{ matrix.title }}
+          body: |
+            This is an autogenerated PR. ${{ matrix.body }}
+
+            [Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.

.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

.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.

MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include * nomad_plugin.yaml
+graft src/nomad_parser_plugin_boss/example_uploads