nomad-semantic-web-service 0.0.0__tar.gz

nomad_semantic_web_service-0.0.0/.cruft.json

@@ -0,0 +1,34 @@
+{
+  "template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin",
+  "commit": "970fdbb387269545102f25e6a16f7a7b422c9414",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "full_name": "Lukas Pielsticker",
+      "email": "lukas.pielsticker@physik.hu-berlin.de",
+      "github_username": "FAIRmat-NFDI",
+      "plugin_name": "nomad-semantic-web-service",
+      "module_name": "nomad_semantic_web_service",
+      "short_description": "A tool to query public synchrotron dataset catalogues with semantic OpenAPI annotations.",
+      "version": "0.1.0",
+      "license": "Apache-2.0",
+      "include_schema_package": true,
+      "include_normalizer": false,
+      "include_parser": false,
+      "include_app": false,
+      "include_example_uploads": false,
+      "include_action": false,
+      "include_api": true,
+      "include_north_tools": false,
+      "north_tool_name": "my_north_tool",
+      "include_citation_file": true,
+      "_copy_without_render": [
+        "*.html",
+        "*.png"
+      ],
+      "_template": "https://github.com/FAIRmat-NFDI/cookiecutter-nomad-plugin",
+      "_commit": "970fdbb387269545102f25e6a16f7a7b422c9414"
+    }
+  },
+  "directory": null
+}

nomad_semantic_web_service-0.0.0/.cspell/custom-dictionary.txt

@@ -0,0 +1,52 @@
+BESSY
+Beamline
+DCAT
+DCTERMS
+ESRF
+ESRFET
+EXAFS
+Giannis
+ICAT
+Koumoutsos
+Lukas
+Operando
+PANET
+Pids
+Pielsticker
+SPARQL
+STARTDATE
+STRSTARTS
+TOMO
+XANES
+addopts
+autoconvert
+beamline
+beamlines
+beamtimes
+behaviour
+browsable
+dataconverter
+datamodel
+dcat
+dcterms
+esrf
+esrfet
+gitmodules
+icat
+icatplus
+ihhc
+inhouse
+mainfile
+mainfiles
+metainfo
+microcrystals
+ndarray
+normalised
+nxxas
+orcid
+owlready
+panet
+pids
+pynxtools
+pytestmark
+zenodo

nomad_semantic_web_service-0.0.0/.devcontainer/devcontainer.json

@@ -0,0 +1,25 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/python
+{
+  "name": "Python 3",
+  // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+  "image": "mcr.microsoft.com/devcontainers/python:1-3.12-bookworm",
+  // Features to add to the dev container. More info: https://containers.dev/features.
+  // "features": {},
+  // Use 'forwardPorts' to make a list of ports inside the container available locally.
+  // "forwardPorts": [],
+  // Use 'postCreateCommand' to run commands after the container is created.
+  "postCreateCommand": "pipx install cruft",
+  // Configure tool-specific properties.
+  "customizations": {
+    // Configure properties specific to VS Code.
+    "vscode": {
+      // Add the IDs of extensions you want installed when the container is created.
+      "extensions": [
+        "charliermarsh.ruff"
+      ]
+    }
+  }
+  // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+  // "remoteUser": "root"
+}

nomad_semantic_web_service-0.0.0/.github/dependabot.yml

@@ -0,0 +1,12 @@
+# 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: "devcontainers"
+   directory: "/"
+   schedule:
+     interval: weekly

nomad_semantic_web_service-0.0.0/.github/workflows/actions.yml

@@ -0,0 +1,43 @@
+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_semantic_web_service-0.0.0/.github/workflows/cff_validation.yml

@@ -0,0 +1,37 @@
+name: Validate CITATION.cff
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "CITATION.cff"
+      - ".github/workflows/cff-validation.yml"
+  pull_request:
+    branches:
+      - main
+    paths:
+      - "CITATION.cff"
+      - ".github/workflows/cff-validation.yml"
+
+env:
+  PYTHON_VERSION: 3.12
+
+jobs:
+  validate-cff:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+            python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Test Zenodo conversion
+        run: |
+          # Remove the funding section to avoid validation issues with Zenodo
+          sed -i '/^funding:/,$d' CITATION.cff
+
+          uv run --with cffconvert cffconvert --validate --format zenodo || exit 1

nomad_semantic_web_service-0.0.0/.github/workflows/mkdocs-deploy.yml

@@ -0,0 +1,37 @@
+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
+
+permissions:
+   contents: write
+
+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_semantic_web_service-0.0.0/.github/workflows/publish.yml

@@ -0,0 +1,107 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+env:
+  UV_VERSION: 0.12
+  PYTHON_VERSION: 3.12
+
+jobs:
+  check-version:
+    name: Check Version
+    runs-on: ubuntu-latest
+    outputs:
+      git_tag_version: ${{ steps.git_tag_version.outputs.version }}
+      citation_version: ${{ steps.citation_version.outputs.version }}
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+
+      - name: Git tag version
+        id: git_tag_version
+        run: |
+          GIT_TAG_VERSION=${GITHUB_REF#refs/tags/v}
+          echo "version=$GIT_TAG_VERSION" >> "$GITHUB_OUTPUT"
+
+      - name: Citation version
+        id: citation_version
+        run: |
+          CITATION_VERSION=$(grep '^version:' CITATION.cff | cut -d' ' -f2)
+          echo "version=$CITATION_VERSION" >> "$GITHUB_OUTPUT"
+
+  test:
+    name: Run Tests
+    needs: check-version
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+      - name: Install uv and set the python version to ${{ env.PYTHON_VERSION }}
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: ${{ env.UV_VERSION }}
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Install nomad-semantic-web-service in editable mode
+        run: uv sync --extra dev
+      - name: Test with pytest
+        run: uv run pytest tests/
+
+  compare-versions:
+    name: Compare Versions
+    needs: check-version
+    runs-on: ubuntu-latest
+    steps:
+      - name: Fail if versions mismatch
+        run: |
+          if [ "${{ needs.check-version.outputs.git_tag_version }}" != "${{ needs.check-version.outputs.citation_version }}" ]; then
+            echo "Version mismatch: Git tag is ${{ needs.check-version.outputs.git_tag_version }}, CITATION.cff is ${{ needs.check-version.outputs.citation_version }}"
+            exit 1
+          fi
+
+  build:
+    name: Build Package
+    needs: [compare-versions, test]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+          submodules: recursive
+      - name: Install uv and set the python version to ${{ env.PYTHON_VERSION }}
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: ${{ env.UV_VERSION }}
+          python-version: ${{ env.PYTHON_VERSION }}
+      - name: Build package
+        run: uv build
+      - name: Check distributions
+        run: uvx twine check dist/*
+      - 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-semantic-web-service
+    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_semantic_web_service-0.0.0/.github/workflows/reuse.yml

@@ -0,0 +1,10 @@
+name: reuse
+
+on: [push]
+
+jobs:
+  reuse-compliance-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: fsfe/reuse-action@v5

nomad_semantic_web_service-0.0.0/.github/workflows/spellcheck.yaml

@@ -0,0 +1,32 @@
+name: Spell Check
+
+on:
+  pull_request:
+    branches: [master]
+
+jobs:
+  spellcheck:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Install dependencies and dictionary
+      run: |
+        npm install -g cspell jq @cspell/dict-scientific-terms-us
+
+    - name: Run cspell
+      run: |
+        cspell --config cspell.json \
+        "README.md" "CITATION.cff" \
+        "docs/**/*" \
+        "src/nomad_semantic_web_service/**/*.py" \
+        "tests/**/*.py"
+
+    - name: Fail on errors
+      run: |
+        if [[ $? -ne 0 ]]; then
+          echo "There are spelling errors in your code. Please fix them and try again."
+          exit 1
+        fi

nomad_semantic_web_service-0.0.0/.gitignore

@@ -0,0 +1,130 @@
+# 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_semantic_web_service-0.0.0/.pre-commit-config.yaml

@@ -0,0 +1,40 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.19
+    hooks:
+      - id: ruff-check
+        files: ^(src/nomad_semantic_web_service|tests)/.*\.py$
+      - id: ruff-format
+        files: ^(src/nomad_semantic_web_service|tests)/.*\.py$
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.20.2
+    hooks:
+      - id: mypy  # static type checking
+        additional_dependencies:
+          - types-PyYAML
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.21.2
+    hooks:
+      - id: pyupgrade
+        args: [--py310-plus]  # modernizes syntax for Python 3.10+
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.9.1
+    hooks:
+      - id: nbstripout  # removes notebook outputs before committing
+
+  - repo: https://github.com/streetsidesoftware/cspell-cli
+    rev: v10.0.1
+    hooks:
+      - id: cspell  # spellchecking
+        pass_filenames: false
+        args:
+          - --config
+          - cspell.json
+          - README.md
+          - CITATION.cff
+          - docs/**/*
+          - src/nomad_semantic_web_service/**/*.py
+          - tests/**/*.py

nomad_semantic_web_service-0.0.0/.vscode/settings.json

@@ -0,0 +1,21 @@
+{
+  "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_semantic_web_service-0.0.0/CITATION.cff

@@ -0,0 +1,27 @@
+cff-version: 1.2.0
+title: 'nomad-semantic-web-service: A NOMAD plugin for semantic search and extraction of public synchrotron dataset records'
+version: 0.1.1
+message:
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Lukas
+    family-names: Pielsticker
+    orcid: 'https://orcid.org/0000-0000-0000-0000'
+doi: 10.5281/zenodo.0000000
+repository-code: https://github.com/FAIRmat-NFDI/nomad-semantic-web-service
+url: https://zenodo.org/records/0000000
+keywords:
+  - NOMAD
+  - NeXus
+  - ESRF
+  - ontologies
+abstract:
+  nomad-semantic-web-service is a NOMAD plugin that finds and extracts public
+  synchrotron dataset records from ESRF-style catalogues, with semantic OpenAPI
+  annotations and PANET/ESRFET ontology term mapping.
+license: Apache-2.0
+funding:
+  - name: Funding Agency
+    award: 123456