Merge pull request #4 from nomad-coe/package

Package

.github/workflows/actions.yaml

@@ -12,16 +12,43 @@ jobs:
     - name: Install dependencies
       run: |
         pip install --upgrade pip
-        pip install .[dev,tests]
+        pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
+        : # we need the latest nomad version for testing
+        pip install --ignore-installed nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
+        pip install coverage coveralls
     - name: mypy
       run: |
         python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional runschema tests
     - name: Test with pytest
-      if: success() || failure()
+      continue-on-error: true
       run: |
-        python -m pytest -sv tests
+        python -m coverage run -m pytest -sv tests
+    - 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@v3
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      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:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
       - uses: chartboost/ruff-action@v1
+        with:
+          args: "check"

.github/workflows/mkdocs-deploy.yml

@@ -0,0 +1,28 @@
+name: deploy-mkdocs
+
+on:
+  push:
+    branches:
+      - develop # Triggers deployment on push to the main branch
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - 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

.github/workflows/publish.yml

@@ -0,0 +1,54 @@
+name: upload-package
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  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/[email protected]
+        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 }}'

docs/assets/.gitignore

@@ -0,0 +1 @@
+nomad-oasis*.zip

docs/explanation/explanation.md

@@ -0,0 +1,4 @@
+# Explanation
+
+!!! note "Attention"
+    Please update the document with relevant information specific to your plugin.

docs/how_to/contribute_to_the_documentation.md

@@ -0,0 +1,4 @@
+# Contribute to the documentation
+
+!!! note "Attention"
+    Please update the document with relevant information specific to your plugin.

docs/how_to/contribute_to_this_plugin.md

@@ -0,0 +1,5 @@
+# Contribute to This Plugin
+
+!!! note "Attention"
+    Please update the document with relevant information specific to your plugin.
+

docs/how_to/install_this_plugin.md

@@ -0,0 +1,4 @@
+# Install This Plugin
+
+!!! note "Attention"
+    Please update the document with relevant information specific to your plugin.

docs/how_to/use_this_plugin.md

@@ -0,0 +1,10 @@
+# How to Use This Plugin
+
+This plugin can be used in a NOMAD Oasis instalation..
+
+## Add This Plugin to Your NOMAD instalation
+
+Read the [NOMAD plugin documentation](https://nomad-lab.eu/prod/v1/staging/docs/plugins/plugins.html#add-a-plugin-to-your-nomad) for all details on how to deploy the plugin on your NOMAD instance.
+
+!!! note "Attention"
+    Please update the document with relevant information specific to your plugin.

docs/index.md

@@ -0,0 +1,48 @@
+# Welcome to the `nomad-schema-plugin-run` documentation
+
+This is a collection of schema for the NOMAD root section `run`.
+
+## Introduction
+
+!!! note "Attention"
+    Please update the document with relevant information specific to your plugin.
+
+<div markdown="block" class="home-grid">
+<div markdown="block">
+
+### Tutorial
+
+A series of tutorials will guide you through the main functionality of `nomad-schema-plugin-run`.
+
+- [Tutorial](tutorial/tutorial.md)
+
+</div>
+<div markdown="block">
+
+### How-to guides
+
+How-to guides provide step-by-step instructions for a wide range of tasks, with the overarching topics:
+
+- [Install this plugin](how_to/install_this_plugin.md)
+- [Use this plugin](how_to/use_this_plugin.md)
+- [Contribute to this plugin](how_to/contribute_to_this_plugin.md)
+- [Contribute to the documentation](how_to/contribute_to_the_documentation.md)
+
+</div>
+
+<div markdown="block">
+
+### Explanation
+
+The explanation [section](explanation/explanation.md) provides background knowledge on this plugin.
+
+</div>
+<div markdown="block">
+
+### Reference
+
+The reference [section](reference/references.md) includes all CLI commands and arguments, all configuration options,
+the possible schema annotations and their arguments, and a glossary of used terms.
+
+</div>
+</div>

docs/reference/references.md

@@ -0,0 +1,4 @@
+# References
+
+!!! note "Attention"
+    Please update the document with relevant information specific to your plugin.

docs/stylesheets/extra.css

@@ -0,0 +1,69 @@
+
+.md-header__button.md-logo :where(img,svg) {
+    width: 100%;
+    height: 30px;
+}
+
+.md-header, .md-header__inner {
+    background-color: #fff;
+    color: #2A4CDF;
+}
+
+.md-header[data-md-state=shadow] {
+    box-shadow: 0px 2px 4px -1px rgb(0 0 0 / 20%), 0px 4px 5px 0px rgb(0 0 0 / 14%), 0px 1px 10px 0px rgb(0 0 0 / 12%);
+    transition: box-shadow 200ms linear;
+}
+
+.md-header__inner {
+    height: 80px;
+}
+
+.md-header__topic {
+    font-size: 24px;
+}
+
+.md-footer {
+    background-color: #2A4CDF;
+}
+
+.md-search__form:hover {
+    background-color: rgba(0,0,0,.13);
+}
+
+.md-typeset h1 {
+    color: black;
+    font-weight: 700;
+}
+
+.youtube {
+    position: relative;
+    width: 100%;
+    height: 0;
+    padding-bottom: 56.25%;
+}
+
+.youtube iframe {
+    position: absolute;
+    top: 0;
+    left: 0;
+    width: 100%;
+    height: 100%;
+}
+
+.home-grid {
+    display: grid;
+    grid-template-columns: 1fr 1fr;
+    grid-column-gap: 24px;
+    row-gap: 24px;
+}
+
+.home-grid div {
+    border-radius: 4px;
+    padding: 24px;
+    background-color: #f3e9d9;
+}
+
+.home-grid h3 {
+    margin-top: 0;
+    font-weight: 700;
+}

docs/theme/partials/header.html

@@ -0,0 +1,86 @@
+{#-
+  This file was automatically generated - do not edit
+-#}
+{% set class = "md-header" %}
+{% if "navigation.tabs.sticky" in features %}
+  {% set class = class ~ " md-header--lifted" %}
+{% endif %}
+<header class="{{ class }}" data-md-component="header">
+  <nav class="md-header__inner md-grid" aria-label="{{ lang.t('header.title') }}">
+    <a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}" title="{{ config.site_name | e }}" class="md-header__button md-logo" aria-label="{{ config.site_name }}" data-md-component="logo">
+      {% include "partials/logo.html" %}
+    </a>
+    <label class="md-header__button md-icon" for="__drawer">
+      {% include ".icons/material/menu" ~ ".svg" %}
+    </label>
+    <div class="md-header__title" data-md-component="header-title">
+      <div class="md-header__ellipsis">
+        <div class="md-header__topic">
+          <span class="md-ellipsis">
+            {{ config.site_name }}
+          </span>
+        </div>
+        <div class="md-header__topic" data-md-component="header-topic">
+          <span class="md-ellipsis">
+            {% if page and page.meta and page.meta.title %}
+              {{ page.meta.title }}
+            {% else %}
+              {{ page.title }}
+            {% endif %}
+          </span>
+        </div>
+      </div>
+    </div>
+    {% if not config.theme.palette is mapping %}
+      <form class="md-header__option" data-md-component="palette">
+        {% for option in config.theme.palette %}
+          {% set primary = option.primary | replace(" ", "-") | lower %}
+          {% set accent  = option.accent  | replace(" ", "-") | lower %}
+          <input class="md-option" data-md-color-media="{{ option.media }}" data-md-color-scheme="{{ option.scheme }}" data-md-color-primary="{{ primary }}" data-md-color-accent="{{ accent }}" {% if option.toggle %} aria-label="{{ option.toggle.name }}" {% else %} aria-hidden="true" {% endif %} type="radio" name="__palette" id="__palette_{{ loop.index }}">
+          {% if option.toggle %}
+            <label class="md-header__button md-icon" title="{{ option.toggle.name }}" for="__palette_{{ loop.index0 or loop.length }}" hidden>
+              {% include ".icons/" ~ option.toggle.icon ~ ".svg" %}
+            </label>
+          {% endif %}
+        {% endfor %}
+      </form>
+    {% endif %}
+    {% if config.extra.alternate %}
+      <div class="md-header__option">
+        <div class="md-select">
+          {% set icon = config.theme.icon.alternate or "material/translate" %}
+          <button class="md-header__button md-icon" aria-label="{{ lang.t('select.language.title') }}">
+            {% include ".icons/" ~ icon ~ ".svg" %}
+          </button>
+          <div class="md-select__inner">
+            <ul class="md-select__list">
+              {% for alt in config.extra.alternate %}
+                <li class="md-select__item">
+                  <a href="{{ alt.link | url }}" hreflang="{{ alt.lang }}" class="md-select__link">
+                    {{ alt.name }}
+                  </a>
+                </li>
+                {% endfor %}
+            </ul>
+          </div>
+        </div>
+      </div>
+    {% endif %}
+    {% if "search" in config["plugins"] %}
+      <label class="md-header__button md-icon" for="__search">
+        {% include ".icons/material/magnify.svg" %}
+      </label>
+      {% include "partials/search.html" %}
+    {% endif %}
+    {% if config.repo_url %}
+      <div class="md-header__source">
+        {% include "partials/source.html" %}
+      </div>
+    {% endif %}
+  </nav>
+  {% if "navigation.tabs.sticky" in features %}
+    {% if "navigation.tabs" in features %}
+      {% include "partials/tabs.html" %}
+    {% endif %}
+  {% endif %}
+</header>

docs/tutorial/tutorial.md

@@ -0,0 +1,4 @@
+# Tutorial
+
+!!! note "Attention"
+    Please update the document with relevant information specific to your plugin.