nomad-north-apmtools 0.1.0__tar.gz

nomad_north_apmtools-0.1.0/.cruft.json

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+{
+  "template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin",
+  "commit": "0dcee23a249225f398052817c6f2ea52c9ddb307",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "full_name": "Markus Kühbach",
+      "email": "markus.kuehbach@physik.hu-berlin.de",
+      "github_username": "FAIRmat-NFDI",
+      "plugin_name": "nomad-north-apmtools",
+      "module_name": "nomad_north_apmtools",
+      "short_description": "NOMAD NORTH plugin for analysis of atom probe data",
+      "version": "0.1.0",
+      "license": "Apache Software License 2.0",
+      "include_schema_package": false,
+      "include_normalizer": false,
+      "include_parser": false,
+      "include_app": false,
+      "include_example_uploads": false,
+      "include_action": false,
+      "include_north_tools": true,
+      "north_tool_name": "apmtools",
+      "_copy_without_render": [
+        "*.html",
+        "*.png"
+      ],
+      "_template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin",
+      "_commit": "0dcee23a249225f398052817c6f2ea52c9ddb307"
+    }
+  },
+  "directory": null
+}

nomad_north_apmtools-0.1.0/.dockerignore

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+# 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

nomad_north_apmtools-0.1.0/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for more information:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+# https://containers.dev/guide/dependabot
+
+version: 2
+updates:
+ - package-ecosystem: "pip"
+   directory: "/"
+   schedule:
+     interval: "monthly"

nomad_north_apmtools-0.1.0/.github/workflows/actions.yml

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+name: install-and-test-workflow
+
+on: [push]
+
+env:
+  UV_VERSION: 0.9
+  PYTHON_VERSION: 3.12
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  install-and-test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+          version: ${{ env.UV_VERSION }}
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+          python-version: ${{ env.PYTHON_VERSION }}
+    - name: Install dependencies
+      run: |
+        uv sync --all-extras
+    - name: Test with pytest
+      run: |
+        uv run --with coverage coverage run -m pytest -sv
+    - name: Submit to coveralls
+      continue-on-error: true
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: |
+        uv run --with coveralls coveralls --service=github
+
+  ruff-linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v3
+      - run: ruff check .
+      # Uncomment the following line to enable format check
+      # - run: ruff format --check .

nomad_north_apmtools-0.1.0/.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
+
+env:
+  REGISTRY: ghcr.io
+  UV_VERSION: 0.9
+  PYTHON_VERSION: 3.12
+  UV_SYSTEM_PYTHON: true
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: ${{ env.UV_VERSION }}
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Build and Deploy
+        run: |
+          uv run --extra dev mkdocs gh-deploy --force --remote-branch gh-pages

nomad_north_apmtools-0.1.0/.github/workflows/publish.yml

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+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+env:
+  PYTHON_VERSION: 3.12
+  IMAGE: "ghcr.io/fairmat-nfdi/nomad-north-apmtools"
+
+jobs:
+  build-docker-image:
+    uses: ./.github/workflows/publish_north.yml
+    secrets: inherit
+
+  build:
+    name: Build Package
+    runs-on: ubuntu-latest
+    needs: build-docker-image
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - name: Install uv and set the Python version to ${{ env.PYTHON_VERSION }}
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Overwrite the image tag
+        run: |
+          IMAGE_TAG=$(grep -oP "${{ env.IMAGE }}:\K[^'\",]+" src/nomad_north_apmtools/north_tools/__init__.py)
+
+          sed -i "s|${{ env.IMAGE }}:${IMAGE_TAG}|${{ env.IMAGE }}:${GITHUB_REF_NAME}|g" \
+          src/nomad_north_apmtools/north_tools/__init__.py
+
+      - name: build package
+        run: |
+          SETUPTOOLS_SCM_PRETEND_VERSION=${GITHUB_REF_NAME#v} uv build
+      - name: Upload dist artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist-artifacts
+          path: dist/
+
+  deploy:
+    name: Upload to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/nomad-north-apmtools
+    permissions:
+      id-token: write
+    steps:
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-artifacts
+          path: dist/
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

nomad_north_apmtools-0.1.0/.github/workflows/publish_north.yml

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+name: Build and publish docker images
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_call:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_TAG: main
+  NORTH_TOOL_DIR: src/nomad_north_apmtools/north_tools/apmtools
+
+permissions:
+  packages: write
+  contents: read
+  attestations: write
+  id-token: write
+
+jobs:
+  build:
+    name: apmtools 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
+      - name: Log in to GitHub Container Registry
+        if: ${{ github.event_name != 'pull_request' }}
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - 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 publish apmtools image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: ${{ env.NORTH_TOOL_DIR }}/Dockerfile
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

nomad_north_apmtools-0.1.0/.gitignore

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+# 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/

nomad_north_apmtools-0.1.0/.vscode/settings.json

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+{
+  "editor.rulers": [
+    88
+  ],
+  "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
+}

nomad_north_apmtools-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+title: 'nomad-north-apmtools: NOMAD NORTH plugin for analysis of atom probe data'
+version: 0.1.0
+message:
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Markus
+    family-names: Kühbach
+    orcid: 'https://orcid.org/0000-0002-7117-5196'
+  - given-names: Ádám
+    family-names: Fekete
+    orcid: 'https://orcid.org/0000-0002-6263-897X'
+  - given-names: Lukas
+    family-names: Pielsticker
+    orcid: 'https://orcid.org/0000-0001-9361-8333'
+  - given-names: Rubel
+    family-names: Mozumder
+    orcid: 'https://orcid.org/0009-0007-5926-6646'
+  - given-names: Sherjeel
+    family-names: Shabih
+    orcid: 'https://orcid.org/0009-0008-6635-4465'
+  - given-names: Sandor
+    family-names: Brockhauser
+    orcid: 'https://orcid.org/0000-0002-9700-4803'
+  - given-names: Heiko B.
+    family-names: Weber
+    orcid: 'https://orcid.org/0000-0002-6403-9022'
+  - given-names: Christoph T.
+    family-names: Koch
+    orcid: 'https://orcid.org/0000-0002-3984-1523'
+  - given-names: Claudia
+    family-names: Draxl
+    orcid: 'https://orcid.org/0000-0003-3523-6657'
+repository-code: https://github.com/FAIRmat-NFDI/nomad-north-apmtools
+keywords:
+  - NeXus
+  - pynxtools-apm
+  - NOMAD
+  - paraprobe-toolbox
+  - APAV
+  - CompositionSpace
+  - APyT
+  - Atom probe microscopy
+abstract:
+  nomad-north-apmtools is a nomad-north-desktop-base NORTH tool plugin for NOMAD (https://nomad-lab.eu/nomad-lab/).
+
+  The work is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 460197019 (FAIRmat)
+  (https://gepris.dfg.de/gepris/projekt/460197019?language=en).
+license: Apache Software License 2.0
+funding:
+  - name: Deutsche Forschungsgemeinschaft
+    award-number: 460197019
+    title: FAIRmat - FAIR Data Infrastructure for Condensed-Matter Physics and the Chemical Physics of Solids
+    award-uri: https://gepris.dfg.de/gepris/projekt/460197019?language=en