Fix setup and add new schema

.github/workflows/actions.yml

@@ -0,0 +1,74 @@
+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
+
+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 uv
+        uv pip install -e '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple --system
+        uv pip install coveralls --system
+    - name: mypy
+      run: |
+        python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional src/nomad_parser_magres/schema_packages src/nomad_parser_magres/parsers tests
+    - 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
+  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 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/mkdocs-deploy.yml

@@ -4,6 +4,9 @@ on:
   push:
     branches:
       - main # Triggers deployment on push to the main branch
+
+permissions:
+  contents: write
 
 jobs:
   deploy:
@@ -13,16 +16,9 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.x"
-
-      - name: Install Dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install mkdocs mkdocs-material==8.1.1 pymdown-extensions mkdocs-click
-
-      - name: Build and Deploy
-        run: |
-          mkdocs gh-deploy --force --remote-branch gh-pages
+      - 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

@@ -1,84 +1,43 @@
-# Upload python package to pypi server and github release.
-# Reference: https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+# 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
 
-name: Upload Python Package
+# 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
+
 jobs:
-  # publish-to-pypi:
-  #   name: >-
-  #     Publish distribution to PyPI
-  #   runs-on: ubuntu-latest
-  #   environment:
-  #     name: pypi
-  #     url: https://pypi.org/p/nomad-schema-plugin-example
-  #   permissions:
-  #     id-token: write # IMPORTANT: mandatory for trusted publishing
-  #
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - name: Set up Python
-  #       uses: actions/setup-python@v4
-  #       with:
-  #         python-version: "3.9"
-  #     - name: Install pypa/build
-  #       run: >-
-  #         python3 -m
-  #         pip install
-  #         build
-  #         --user
-  #     - name: Build a binary wheel and a source tarball
-  #       run: python3 -m build
-  #     - name: Publish distribution  to PyPI
-  #       uses: pypa/gh-action-pypi-publish@release/v1
+  deploy:
 
-  github-release:
-    name: >-
-      Sign the Python distribution with Sigstore
-      and upload them to GitHub Release
     runs-on: ubuntu-latest
-    permissions:
-      contents: write # IMPORTANT: mandatory for making GitHub Releases
-      id-token: write # IMPORTANT: mandatory for sigstore
 
     steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.9"
-      - name: Install pypa/build
-        run: >-
-          python3 -m
-          pip install
-          build
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: python3 -m build
-      - name: Sign the dists with Sigstore
-        uses: sigstore/gh-action-sigstore-python@v1.2.3
-        with:
-          inputs: >-
-            ./dist/*.tar.gz
-            ./dist/*.whl
-      - name: Create GitHub Release
-        env:
-          GITHUB_TOKEN: ${{ github.token }}
-        run: >-
-          gh release create
-          '${{ github.ref_name }}'
-          --repo '${{ github.repository }}'
-          --notes ""
-      - name: Upload artifact signatures to GitHub Release
-        env:
-          GITHUB_TOKEN: ${{ github.token }}
-        # Upload to GitHub Release using the `gh` CLI.
-        # `dist/` contains the built packages, and the
-        # sigstore-produced signatures and certificates.
-        run: >-
-          gh release upload
-          '${{ github.ref_name }}' dist/**
-          --repo '${{ github.repository }}'
+    - uses: actions/checkout@v3
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        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

@@ -20,12 +20,12 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
 *.egg
 MANIFEST
+_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -46,10 +46,12 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
+coverage.txt
 *.cover
 *.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -72,6 +74,7 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -82,7 +85,9 @@ profile_default/
 ipython_config.py
 
 # pyenv
-.python-version
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -91,7 +96,22 @@ ipython_config.py
 #   install all needed dependencies.
 #Pipfile.lock
 
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
 __pypackages__/
 
 # Celery stuff
@@ -104,12 +124,12 @@ celerybeat.pid
 # Environments
 .env
 .venv
+.pyenv
 env/
 venv/
 ENV/
 env.bak/
 venv.bak/
-.pyenv
 
 # Spyder project settings
 .spyderproject
@@ -129,5 +149,25 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
-# VSCode launch json
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  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
+
+# comments scripts
+comments.py
+todos*
+questions*
+warnings*
+important*