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RubelMozumderRubelMozumder
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Follow pynxtools-plugin-template (#63)
* Follow file structre from pynxtools-plugin-template and bring non-tracked file. * Update Readme file. * Fix spellchecker and linting. * comments out test_nomad_apps.py * Fix zenodo doi in READNME.md file according to the cruft. * Change from PR review.
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‎.cruft.json‎

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{
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"template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
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"commit": "519f503945368a21d0c44125c0f34cf0d5f46e10",
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"checkout": null,
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"context": {
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"cookiecutter": {
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"reader_name": "spm",
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"supported_nxdl": "NXspm",
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"short_description": "NeXus data converter from SPM (Scanning Probe Microscopy).",
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"technique": "SPM,STS,STM,AFM",
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"reader_class": "SPMReader",
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"author_name": "The NOMAD authors",
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"author_email": "fairmat@physik.hu-berlin.de",
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"license": "Apache Software License 2.0",
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"zenodo_record": "17390485",
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"vscode_settings": false,
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"include_nomad_app": true,
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"include_nomad_example_upload": true,
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"__package_name": "pynxtools-spm",
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"__module_name": "pynxtools_spm",
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"__nomad_example": "spm_example_upload_entry_point",
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"__nomad_app": "",
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"_copy_without_render": ["*.html"],
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"_template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
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"_commit": "519f503945368a21d0c44125c0f34cf0d5f46e10"
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}
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},
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"directory": null
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}

‎.cspell/custom-dictionary.txt‎

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# Custom Dictionary Words
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actv
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Alingment
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Alphabat
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arange
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AXISNAME
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backw
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bais
28
Brockhauser
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bruker
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Bruker
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Calib
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caplog
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chann
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channs
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chnl
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Cojal
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cryo
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curnt
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dataconverter
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datamodel
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Demod
422
Dobener
523
Draxl
6-
Finishup
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filt
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findiff
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fliplr
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flipud
728
Florian
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Forschungsgemeinschaft
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forw
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genfromtxt
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Ginzburg
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González
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gradient
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griddata
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grps
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Haraszti
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Heiko
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imshow
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Incorrect
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infinitiy
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input
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inted
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iupac
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José
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keywith
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Kpage
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Kühbach
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levelname
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localzone
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lockin
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Lockin
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Lukas
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mainfile
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Markus
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metadata
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Mformatter
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miscellaneous
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Mozumder
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NFDI
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Nanonis
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PAMY
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Pielsticker
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Piezo
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Sandor
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Setpoint
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Shabih
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Sherjeel
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Tamás
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Yichen
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dataconverter
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filt
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lockin
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MPES
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multilines
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nanonis
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Nanonis
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NANONIS
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nanonispy
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nbins
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nbsp
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nchanns
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ndarray
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ndir
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nested
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NFDI
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nxdata
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nxdl
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nxdls
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nxformatted
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nxscan
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orcid
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organized
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PAMY
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Pielsticker
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piezo
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Piezo
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plottable
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pynxtools
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regrex
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rhksm
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Sandor
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scandata
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Scanfield
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SCANIT
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sctype
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Setpoint
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Shabih
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Sherjeel
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specdata
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spect
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spym
4199
subpackages
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Subpackages
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Tamás
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topo
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ureg
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valinit
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valtext
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Yichen

‎.github/workflows/compatibility_with_pynxtools_release.yml‎

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name: Compatibility with pynxtools
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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env:
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python-version: 3.12
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jobs:
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pynx_compatibility:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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pynxtools-version: ["latest"]
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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submodules: recursive
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- name: Install uv and set the python version to ${{ env.python-version }}
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uses: astral-sh/setup-uv@v5
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with:
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python-version: ${{ env.python-version }}
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- name: Install pynxtools-spm
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run: |
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uv pip install ".[dev]"
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uv pip install coverage coveralls
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- name: Install nomad
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run: |
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uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
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- name: Install pynxtools release version ${{ matrix.pynxtools-version }}
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run: |
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if [ "${{ matrix.pynxtools-version }}" == "latest" ]; then
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uv pip install pynxtools
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else
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uv pip install pynxtools==${{ matrix.pynxtools-version }}
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fi
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- name: Run tests
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run: |
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pytest tests/.

‎.github/workflows/cruft_update.yml‎

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name: Update repository with Cruft
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permissions:
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contents: write
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pull-requests: write
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on:
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schedule:
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- cron: "0 4 * * 1" # Every Monday at 4am
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workflow_dispatch: # manually
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env:
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python-version: 3.12
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jobs:
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update:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: true
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matrix:
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include:
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- add-paths: .
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body: Use this to merge the changes to this repository.
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branch: cruft/update
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commit-message: "chore: accept new Cruft update"
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title: New updates detected with Cruft
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- add-paths: .cruft.json
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body: Use this to reject the changes in this repository.
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branch: cruft/reject
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commit-message: "chore: reject new Cruft update"
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title: Reject new updates detected with Cruft
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steps:
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- uses: actions/checkout@v4
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- name: Install uv and set the python version to ${{ env.python-version }}
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uses: astral-sh/setup-uv@v5
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with:
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python-version: ${{ env.python-version }}
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- name: Install Cruft
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run: uv pip install cruft
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- name: Check if update is available
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continue-on-error: false
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id: check
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run: |
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CHANGES=0
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if [ -f .cruft.json ]; then
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if ! cruft check; then
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CHANGES=1
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fi
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else
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echo "No .cruft.json file"
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fi
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echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
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- name: Run update if available
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if: steps.check.outputs.has_changes == '1'
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run: |
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git config --global user.email "github-actions[bot]@users.noreply.github.com"
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git config --global user.name "GitHub"
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cruft update --skip-apply-ask --refresh-private-variables
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# git restore --staged .
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- name: Create pull request
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if: steps.check.outputs.has_changes == '1'
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uses: peter-evans/create-pull-request@v4
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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add-paths: ${{ matrix.add-paths }}
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commit-message: ${{ matrix.commit-message }}
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branch: ${{ matrix.branch }}
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delete-branch: true
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branch-suffix: timestamp
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title: ${{ matrix.title }}
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body: |
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This is an autogenerated PR. ${{ matrix.body }}
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[Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.

.github/workflows/build_docs.yml renamed to .github/workflows/mkdocs-deploy.yml

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python-version: 3.12
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permissions:
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contents: write
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contents: write
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jobs:
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deploy:
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runs-on: ubuntu-latest
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run: |
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git config user.name github-actions[bot]
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git config user.email 41898282+github-actions[bot]@users.noreply.github.com
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- name: Install uv and set the python version to ${{ env.python-version }}
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uses: astral-sh/setup-uv@v5
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with:
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- name: Build and Deploy
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run: |
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mkdocs gh-deploy --force --remote-branch gh-pages
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mkdocs gh-deploy --force --remote-branch gh-pages

‎.github/workflows/nomad-requirements.yml‎

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name: NOMAD dependencies compatibility
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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# Run workflow only when there are changes in pyproject.toml or dev-requirements.txt
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# paths:
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# - 'pyproject.toml'
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# - 'dev-requirements.txt'
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env:
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python-version: 3.12
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jobs:
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validate_dependencies:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout pynxtools-spm
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uses: actions/checkout@v4
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- name: Checkout NOMAD from GitLab
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run: |
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git clone --depth 1 --branch develop --recurse-submodules https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git nomad
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git submodule update --init --recursive --depth 1
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- name: Add pynxtools-spm dependency in NOMAD test_plugins.txt
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working-directory: ./nomad
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run: |
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echo "" >> test_plugins.txt
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echo "pynxtools-spm@git+https://github.com/FAIRmat-NFDI/pynxtools-spm.git@${{ github.head_ref || github.ref_name }}" >> test_plugins.txt
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- name: Install uv and set the python version to ${{ env.python-version }}
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uses: astral-sh/setup-uv@v5
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with:
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python-version: ${{ env.python-version }}
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- name: Generate (dev-)requirements.txt from modified pyproject.toml
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working-directory: ./nomad
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run: |
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uv pip compile --universal -p ${{ env.python-version }} --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt pyproject.toml
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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
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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
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- name: Install NOMAD dependencies with pynxtools from current branch
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working-directory: ./nomad
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run: |
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uv pip install -r requirements-plugins.txt -c requirements-dev.txt --prerelease=allow
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env:
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PYTHONPATH: "" # Ensure no pre-installed packages interfere with the test

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