Some fixes in spm

.cruft.json

@@ -0,0 +1,29 @@
+{
+  "template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
+  "commit": "519f503945368a21d0c44125c0f34cf0d5f46e10",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "reader_name": "spm",
+      "supported_nxdl": "NXspm",
+      "short_description": "NeXus data converter from SPM (Scanning Probe Microscopy).",
+      "technique": "SPM,STS,STM,AFM",
+      "reader_class": "SPMReader",
+      "author_name": "The NOMAD authors",
+      "author_email": "fairmat@physik.hu-berlin.de",
+      "license": "Apache Software License 2.0",
+      "zenodo_record": "17390485",
+      "vscode_settings": false,
+      "include_nomad_app": true,
+      "include_nomad_example_upload": true,
+      "__package_name": "pynxtools-spm",
+      "__module_name": "pynxtools_spm",
+      "__nomad_example": "spm_example_upload_entry_point",
+      "__nomad_app": "",
+      "_copy_without_render": ["*.html"],
+      "_template": "git@github.com:FAIRmat-NFDI/pynxtools-plugin-template.git",
+      "_commit": "519f503945368a21d0c44125c0f34cf0d5f46e10"
+    }
+  },
+  "directory": null
+}

.cspell/custom-dictionary.txt

@@ -1,41 +1,106 @@
-# Custom Dictionary Words
+actv
+Alingment
+Alphabat
+arange
+AXISNAME
+backw
+bais
 Brockhauser
+bruker
+Bruker
+Calib
+caplog
+chann
+channs
+chnl
 Cojal
+cryo
+curnt
+dataconverter
+datamodel
+Demod
 Dobener
 Draxl
-Finishup
+filt
+findiff
+fliplr
+flipud
 Florian
 Forschungsgemeinschaft
+forw
+genfromtxt
 Ginzburg
+González
+gradient
+griddata
+grps
 Haraszti
 Heiko
+imshow
+Incorrect
+infinitiy
+input
+inted
+iupac
+José
+keywith
+Kpage
 Kühbach
+levelname
+localzone
+lockin
+Lockin
 Lukas
+mainfile
 Markus
+metadata
 Mformatter
+miscellaneous
 Mozumder
-NFDI
-Nanonis
-PAMY
-Pielsticker
-Piezo
-Sandor
-Setpoint
-Shabih
-Sherjeel
-Tamás
-Yichen
-dataconverter
-filt
-lockin
+MPES
+multilines
 nanonis
+Nanonis
+NANONIS
 nanonispy
+nbins
+nbsp
+nchanns
+ndarray
+ndir
+nested
+NFDI
+nxdata
 nxdl
+nxdls
 nxformatted
 nxscan
 orcid
+organized
+PAMY
+Pielsticker
 piezo
+Piezo
 plottable
 pynxtools
+regrex
+rhksm
+Sandor
+scandata
+Scanfield
+SCANIT
+sctype
+Setpoint
+Shabih
+Sherjeel
+specdata
+spect
 spym
 subpackages
+Subpackages
+Tamás
+topo
+ureg
+valinit
+valtext
+Yichen

.github/workflows/compatibility_with_pynxtools_release.yml

@@ -0,0 +1,45 @@
+name: Compatibility with pynxtools
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+env:
+  python-version: 3.12
+
+jobs:
+  pynx_compatibility:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        pynxtools-version: ["latest"]
+
+    steps:
+      - uses: actions/checkout@v4
+        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:
+          python-version: ${{ env.python-version }}
+      - name: Install pynxtools-spm
+        run: |
+          uv pip install ".[dev]"
+          uv pip install coverage coveralls
+      - name: Install nomad
+        run: |
+          uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
+      - name: Install pynxtools release version ${{ matrix.pynxtools-version }}
+        run: |
+          if [ "${{ matrix.pynxtools-version }}" == "latest" ]; then
+            uv pip install pynxtools
+          else
+           uv pip install pynxtools==${{ matrix.pynxtools-version }}
+          fi
+      - name: Run tests
+        run: |
+          pytest tests/.

.github/workflows/cruft_update.yml

@@ -0,0 +1,81 @@
+name: Update repository with Cruft
+
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  schedule:
+    - cron: "0 4 * * 1" # Every Monday at 4am
+  workflow_dispatch: # manually
+
+env:
+  python-version: 3.12
+
+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
+
+      - name: Install uv and set the python version to  ${{ env.python-version }}
+        uses: astral-sh/setup-uv@v5
+        with:
+          python-version: ${{ env.python-version }}
+
+      - name: Install Cruft
+        run: uv pip install cruft
+
+      - name: Check if update is available
+        continue-on-error: false
+        id: check
+        run: |
+          CHANGES=0
+          if [ -f .cruft.json ]; then
+            if ! cruft check; then
+              CHANGES=1
+            fi
+          else
+            echo "No .cruft.json file"
+          fi
+
+          echo "has_changes=$CHANGES" >> "$GITHUB_OUTPUT"
+
+      - name: Run update if available
+        if: steps.check.outputs.has_changes == '1'
+        run: |
+          git config --global user.email "github-actions[bot]@users.noreply.github.com"
+          git config --global user.name "GitHub"
+
+          cruft update --skip-apply-ask --refresh-private-variables
+          # git restore --staged .
+
+      - 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 }}
+          delete-branch: true
+          branch-suffix: timestamp
+          title: ${{ matrix.title }}
+          body: |
+            This is an autogenerated PR. ${{ matrix.body }}
+
+            [Cruft](https://cruft.github.io/cruft/) has detected updates from the Cookiecutter repository.

.github/workflows/build_docs.yml → .github/workflows/mkdocs-deploy.yml

@@ -9,7 +9,7 @@ env:
   python-version: 3.12
 
 permissions:
-  contents: write
+   contents: write
 jobs:
   deploy:
     runs-on: ubuntu-latest
@@ -22,7 +22,7 @@ jobs:
         run: |
           git config user.name github-actions[bot]
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
-
+     
       - name: Install uv and set the python version to ${{ env.python-version }}
         uses: astral-sh/setup-uv@v5
         with:
@@ -42,4 +42,4 @@ jobs:
 
       - name: Build and Deploy
         run: |
-          mkdocs gh-deploy --force --remote-branch gh-pages
+          mkdocs gh-deploy --force --remote-branch gh-pages

.github/workflows/nomad-requirements.yml

@@ -0,0 +1,50 @@
+name: NOMAD dependencies compatibility
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+    # Run workflow only when there are changes in pyproject.toml or dev-requirements.txt
+    # paths:
+    #   - 'pyproject.toml'
+    #   - 'dev-requirements.txt'
+
+env:
+  python-version: 3.12
+
+jobs:
+  validate_dependencies:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout pynxtools-spm
+      uses: actions/checkout@v4
+
+    - name: Checkout NOMAD from GitLab
+      run: |
+        git clone --depth 1 --branch develop --recurse-submodules https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git nomad
+        git submodule update --init --recursive --depth 1
+    - name: Add pynxtools-spm dependency in NOMAD test_plugins.txt
+      working-directory: ./nomad
+      run: |
+        echo "" >> test_plugins.txt
+        echo "pynxtools-spm@git+https://github.com/FAIRmat-NFDI/pynxtools-spm.git@${{ github.head_ref || github.ref_name }}" >> test_plugins.txt
+    - 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: 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 --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
+      run: |
+        uv pip install -r requirements-plugins.txt -c requirements-dev.txt --prerelease=allow
+      env:
+        PYTHONPATH: ""  # Ensure no pre-installed packages interfere with the test