Apply north

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
-  "commit": "519f503945368a21d0c44125c0f34cf0d5f46e10",
+  "commit": "616d3dc6584cb0f19e85310a083c7a87857c6b8d",
   "checkout": null,
   "context": {
     "cookiecutter": {
@@ -11,18 +11,25 @@
       "reader_class": "SPMReader",
       "author_name": "The NOMAD authors",
       "author_email": "fairmat@physik.hu-berlin.de",
+      "github_username": "",
+      "organization_name": "fairmat-nfdi",
       "license": "Apache Software License 2.0",
       "zenodo_record": "17390485",
-      "vscode_settings": false,
+      "vscode_settings": true,
       "include_nomad_app": true,
       "include_nomad_example_upload": true,
+      "include_north_tools": true,
+      "north_tool_name": "spm",
       "__package_name": "pynxtools-spm",
       "__module_name": "pynxtools_spm",
       "__nomad_example": "spm_example_upload_entry_point",
-      "__nomad_app": "",
-      "_copy_without_render": ["*.html"],
+      "__nomad_app": "spm_app_entry_point",
+      "__north_tool_EP_name": "north_tool",
+      "_copy_without_render": [
+        "*.html"
+      ],
       "_template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
-      "_commit": "519f503945368a21d0c44125c0f34cf0d5f46e10"
+      "_commit": "616d3dc6584cb0f19e85310a083c7a87857c6b8d"
     }
   },
   "directory": null

.cspell/custom-dictionary.txt

@@ -104,3 +104,7 @@ ureg
 valinit
 valtext
 Yichen
+FAIRmat
+fairmat
+jovyan
+ipynb

.dockerignore

@@ -0,0 +1,94 @@
+# Git
+.gitignore
+.gitattributes
+
+# Python
+__pycache__
+*.py[cod]
+*$py.class
+*.so
+.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
+.pytest_cache/
+
+# Virtual Environments
+.venv
+venv/
+ENV/
+env/
+.venv/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+.project
+.pydevproject
+.settings/
+*.sublime-project
+*.sublime-workspace
+
+# CI/CD
+.github/
+.gitlab-ci.yml
+.travis.yml
+.circleci/
+
+# Testing
+.coverage
+.coverage.*
+htmlcov/
+.tox/
+.hypothesis/
+pytest.ini
+.pytest_cache/
+
+# Documentation
+docs/_build/
+site/
+.mkdocs.yml
+mkdocs.yml
+
+# Docker
+Dockerfile*
+.dockerignore
+docker/
+
+# Node (if used)
+node_modules/
+npm-debug.log
+package-lock.json
+
+# Misc
+*.md
+LICENSE
+MANIFEST.in
+*.tar.gz
+*.zip
+.tmp/
+.cache/
+
+# IDE configuration files
+.editorconfig
+.env
+.env.local

.github/workflows/cruft_update.yml

@@ -15,20 +15,7 @@ env:
 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@v4
 
@@ -52,7 +39,6 @@ jobs:
           else
             echo "No .cruft.json file"
           fi
-
           echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
 
       - name: Run update if available
@@ -62,20 +48,29 @@ jobs:
           git config --global user.name "GitHub"
 
           cruft update --skip-apply-ask --refresh-private-variables
-          # git restore --staged .
+
+          # --------------------------------------------------------
+          # HARD BLOCK: never allow workflow updates from Cruft
+          # --------------------------------------------------------
+          git restore --staged .github/workflows || true
+          git restore .github/workflows || true
 
       - 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 }}
+          add-paths: .
+          commit-message: "chore: accept new Cruft update"
+          branch: cruft/update
           delete-branch: true
           branch-suffix: timestamp
-          title: ${{ matrix.title }}
+          title: New updates detected with Cruft
           body: |
-            This is an autogenerated PR. ${{ matrix.body }}
+            This is an autogenerated PR.
+
+            [Cruft](https://cruft.github.io/cruft/)  has detected updates from the
+            Cookiecutter repository.
 
-            [Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.
+            Changes to `.github/workflows` are intentionally excluded
+            from automated updates and must be applied manually.

.github/workflows/nomad-requirements.yml

@@ -39,8 +39,8 @@ jobs:
     - name: Generate (dev-)requirements.txt from modified pyproject.toml
       working-directory: ./nomad
       run: |
-        uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt pyproject.toml
-        uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml
+        uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=infrastructure --output-file=requirements.txt pyproject.toml
+        uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=dev --extra=infrastructure --output-file=requirements-dev.txt requirements.txt pyproject.toml
         uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --output-file=requirements-plugins.txt --unsafe-package nomad-lab -c requirements-dev.txt test_plugins.txt
     - name: Install NOMAD dependencies with pynxtools from current branch
       working-directory: ./nomad

.github/workflows/publish-north.yaml

@@ -0,0 +1,125 @@
+name: Build and publish docker images
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*.*.*"
+  pull_request:
+    branches:
+      - main
+
+env:
+  REGISTRY: ghcr.io
+  UV_VERSION: 0.9
+  PYTHON_VERSION: 3.12
+  JUPYTER_VERSION: 2025-12-31
+  NORTH_TOOL_DIR: src/pynxtools_spm/nomad/north_tools/spm
+  TEST_DATA_DIR: tests/data/north_tools/spm
+  TEST_NOTEBOOKS: CommandLine.ipynb
+
+permissions:
+  packages: write
+  contents: read
+  attestations: write
+  id-token: write
+
+jobs:
+  build:
+    name: Build Jupyter Image
+    runs-on: ubuntu-latest
+    outputs:
+      tags: ${{ steps.meta.outputs.tags }} # list
+      labels: ${{ steps.meta.outputs.labels }} # list
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref || github.ref_name }}
+          fetch-depth: 0
+          show-progress: true
+          submodules: true
+
+      # Replace driver `Docker' by `Docker-container` to support cache export/import
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ github.repository }}
+          # set latest tag for main branch and tags
+          # https://github.com/docker/metadata-action?tab=readme-ov-file#image-name-and-tag-sanitization
+          tags: |
+            type=ref,event=tag
+            type=ref,event=pr,prefix=pr-
+            type=raw,value=main,enable=${{ github.ref == format('refs/heads/{0}', 'main') }}
+          flavor: |
+            latest=auto
+
+      # https://docs.docker.com/build/ci/github-actions/share-image-jobs/
+      # https://github.com/docker/build-push-action
+      - name: Build and export to Jupyter image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ${{ env.NORTH_TOOL_DIR }}/Dockerfile
+          build-args: |
+            UV_VERSION=${{ env.UV_VERSION }}
+            JUPYTER_TAG=${{ env.JUPYTER_VERSION }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          push: false
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          outputs: type=docker,dest=${{ runner.temp }}/jupyter.tar.gz
+      - name: Upload artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: jupyter-image
+          path: ${{ runner.temp }}/jupyter.tar.gz
+  test_and_push_image:
+    name: Test Jupyter Image
+    needs: build
+    runs-on: ubuntu-latest
+    # https://docs.docker.com/build/ci/github-actions/share-image-jobs/
+    steps:
+      - name: Setup Repository
+        uses: actions/checkout@v4
+      - name: Download artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: jupyter-image
+          path: ${{ runner.temp }}
+          pattern: "!*.dockerbuild" # warning at https://github.com/docker/build-push-action?tab=readme-ov-file
+
+      - name: Load and test in Jupyter container
+        run: |
+          docker load -i ${{ runner.temp }}/jupyter.tar.gz
+
+          RAW_TAGS="${{ needs.build.outputs.tags }}"
+          echo "Raw tags: $RAW_TAGS"
+          FIRST_TAG=$(echo "$RAW_TAGS" | tr -s '[:space:]' '\n' | grep -v '^$' | head -n 1)
+          echo "Using tag: $FIRST_TAG"
+
+          for nb in ${{ env.TEST_NOTEBOOKS }}; do
+            echo "Running notebook: $nb"
+            docker run \
+              --mount type=bind,src=./${{ env.TEST_DATA_DIR }},dst="/home/jovyan/north_test" \
+              --rm "$FIRST_TAG" \
+              /bin/bash -c "jupyter execute \$HOME/north_test/$nb"
+          done
+
+      - uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Push Jupyter Image
+        run: |
+          RAW_TAGS="${{ needs.build.outputs.tags }}"
+          for TAG in $RAW_TAGS; do
+            echo "Pushing tag: $TAG"
+            docker push "$TAG"
+          done

.pre-commit-config.yaml

@@ -6,4 +6,28 @@ repos:
       # Run the linter.
       - id: ruff
       # Run the formatter.
-      - id: ruff-format
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.7.1
+    hooks:
+      - id: mypy # static type checking
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.37.3
+    hooks:
+      - id: pyupgrade
+        args: [--py36-plus] # modernizes syntax for Python 3.6+
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.0
+    hooks:
+      - id: nbstripout # removes notebook outputs before committing
+
+  - repo: https://github.com/streetsidesoftware/cspell-cli
+    rev: v6.31.1
+    hooks:
+      - id: cspell # spellchecking
+        pass_filenames: false
+        args:
+          - --config

README.md

@@ -12,7 +12,7 @@
 
 .
 
-This `pynxtools` plugin was generated with [`cookiecutter`](https://github.com/cookiecutter/cookiecutter) using the [`pynxtools-plugin-template`](https://github.com/FAIRmat-NFDI/`pynxtools-plugin-template) template.
+This `pynxtools` plugin was generated with [`cookiecutter`](https://github.com/cookiecutter/cookiecutter) using the [`pynxtools-plugin-template`](https://github.com/FAIRmat-NFDI/pynxtools-plugin-template) template.
 
 ## Installation