Merge pull request #8 from FAIRmat-NFDI/docs-setup

docs setup + h5md transfer

Author: JFRudzinski

.github/workflows/actions.yml

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+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

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+# /.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 "you@example.com"
+          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

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+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

docs/parsers/fhi-aims/fhi-aims_about.md

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+# FHI-aims

docs/parsers/h5md/h5md_about.md

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+# H5MD-NOMAD: A flexible data-storage schema for uploading molecular simulations to NOMAD
+
+## Overview
+
+Most computational data in NOMAD is harvested with code-specific parsers that recognize the output files from a particular software and retrieve the appropriate (meta)data accordingly.
+However, this approach is not possible for many modern molecular simulation engines that use fully-flexible scriptable input and non-fixed output files.
+["HDF5 for molecular data" (H5MD)](http://h5md.nongnu.org/) is a data schema for storage of molecular simulation data, based on the HDF5 file format.
+This page describes an extension of the H5MD schema, denoted H5MD-NOMAD, which adds specificity to several of the H5MD guidelines while also retaining reasonable flexibility. This enables simulation data stored according to the H5MD-NOMAD schema to be stored in the NOMAD.
+
+**Due to the nature of extending upon the original H5MD schema, portions of this doc page was duplicated, extended, or summarized from the [H5MD webpage](http://h5md.nongnu.org/).**