FAIRmat-NFDI · mkuehbach · Mar 25, 2025 · Mar 21, 2025 · Mar 21, 2025 · Mar 21, 2025
diff --git a/.github/workflows/nomad-requirements.yml b/.github/workflows/nomad-requirements.yml
@@ -32,7 +32,7 @@ jobs:
       working-directory: ./nomad
       run: |
         echo "" >> test_plugins.txt
-        echo "pynxtools[convert]@git+https://github.com/FAIRmat-NFDI/pynxtools.git@${{ github.head_ref || github.ref_name }}" >> test_plugins.txt
+        echo "pynxtools@git+https://github.com/FAIRmat-NFDI/pynxtools.git@${{ 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:
@@ -48,4 +48,4 @@ jobs:
       run: |
         uv pip install -r requirements-plugins.txt
       env:
-        PYTHONPATH: ""  # Ensure no pre-installed packages interfere with the test
+        PYTHONPATH: ""  # Ensure no pre-installed packages interfere with the test
diff --git a/CITATION.cff b/CITATION.cff
@@ -4,7 +4,7 @@ message:
   If you use this software, please cite it using the
   metadata from this file.
 type: software
-version: 0.10.0
+version: 0.10.1
 authors:
   - given-names: Sherjeel
     family-names: Shabih
@@ -60,7 +60,12 @@ authors:
   - 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'
 doi: 10.5281/zenodo.13862041
 repository-code: 'https://github.com/FAIRmat-NFDI/pynxtools'
 url: https://doi.org/10.5281/zenodo.13862042
@@ -84,4 +89,4 @@ abstract:
   [FAIRmat page](https://www.fairmat-nfdi.eu/fairmat/about-fairmat/consortium-fairmat) for more info.
 
 
-license: Apache-2.0
+license: Apache-2.0
diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -2,17 +2,19 @@
 #    uv pip compile --universal -p 3.11 --extra=dev --extra=docs --output-file=dev-requirements.txt pyproject.toml
 anytree==2.12.1
     # via pynxtools (pyproject.toml)
-ase==3.23.0
+ase==3.24.0
     # via pynxtools (pyproject.toml)
-babel==2.16.0
+babel==2.17.0
     # via mkdocs-material
-certifi==2024.8.30
+backrefs==5.8
+    # via mkdocs-material
+certifi==2025.1.31
     # via requests
 cfgv==3.4.0
     # via pre-commit
-charset-normalizer==3.4.0
+charset-normalizer==3.4.1
     # via requests
-click==8.1.7
+click==8.1.8
     # via
     #   pynxtools (pyproject.toml)
     #   click-default-group
@@ -28,40 +30,40 @@ colorama==0.4.6
     #   pytest
 contourpy==1.3.1
     # via matplotlib
-coverage==7.6.9
+coverage==7.7.1
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
 distlib==0.3.9
     # via virtualenv
-filelock==3.16.1
+filelock==3.18.0
     # via virtualenv
-fonttools==4.55.2
+fonttools==4.56.0
     # via matplotlib
 ghp-import==2.1.0
     # via mkdocs
-h5py==3.12.1
+h5py==3.13.0
     # via pynxtools (pyproject.toml)
 hjson==3.1.0
     # via
     #   mkdocs-macros-plugin
     #   super-collections
-identify==2.6.3
+identify==2.6.9
     # via pre-commit
 idna==3.10
     # via requests
-importlib-metadata==8.5.0
+importlib-metadata==8.6.1
     # via pynxtools (pyproject.toml)
-iniconfig==2.0.0
+iniconfig==2.1.0
     # via pytest
-jinja2==3.1.4
+jinja2==3.1.6
     # via
     #   mkdocs
     #   mkdocs-macros-plugin
     #   mkdocs-material
-kiwisolver==1.4.7
+kiwisolver==1.4.8
     # via matplotlib
-lxml==5.3.0
+lxml==5.3.1
     # via pynxtools (pyproject.toml)
 markdown==3.7
     # via
@@ -76,7 +78,7 @@ markupsafe==3.0.2
     # via
     #   jinja2
     #   mkdocs
-matplotlib==3.9.3
+matplotlib==3.10.1
     # via ase
 mergedeep==1.3.4
     # via
@@ -94,13 +96,13 @@ mkdocs-get-deps==0.2.0
     # via mkdocs
 mkdocs-macros-plugin==1.3.7
     # via pynxtools (pyproject.toml)
-mkdocs-material==9.5.48
+mkdocs-material==9.6.9
     # via pynxtools (pyproject.toml)
 mkdocs-material-extensions==1.3.1
     # via
     #   pynxtools (pyproject.toml)
     #   mkdocs-material
-mypy==1.13.0
+mypy==1.15.0
     # via pynxtools (pyproject.toml)
 mypy-extensions==1.0.0
     # via mypy
@@ -121,6 +123,7 @@ packaging==24.2
     #   matplotlib
     #   mkdocs
     #   mkdocs-macros-plugin
+    #   pint
     #   pytest
     #   xarray
 paginate==0.5.7
@@ -133,23 +136,25 @@ pathspec==0.12.1
     # via
     #   mkdocs
     #   mkdocs-macros-plugin
-pillow==11.0.0
+pillow==11.1.0
     # via matplotlib
-platformdirs==4.3.6
+pint==0.17
+    # via pynxtools (pyproject.toml)
+platformdirs==4.3.7
     # via
     #   mkdocs-get-deps
     #   virtualenv
 pluggy==1.5.0
     # via pytest
-pre-commit==4.0.1
+pre-commit==4.2.0
     # via pynxtools (pyproject.toml)
-pygments==2.18.0
+pygments==2.19.1
     # via mkdocs-material
-pymdown-extensions==10.12
+pymdown-extensions==10.14.3
     # via mkdocs-material
-pyparsing==3.2.0
+pyparsing==3.2.3
     # via matplotlib
-pytest==8.3.4
+pytest==8.3.5
     # via
     #   pynxtools (pyproject.toml)
     #   pytest-cov
@@ -164,7 +169,7 @@ python-dateutil==2.9.0.post0
     #   matplotlib
     #   mkdocs-macros-plugin
     #   pandas
-pytz==2024.2
+pytz==2025.2
     # via pandas
 pyyaml==6.0.2
     # via
@@ -177,19 +182,17 @@ pyyaml==6.0.2
     #   pyyaml-env-tag
 pyyaml-env-tag==0.1
     # via mkdocs
-regex==2024.11.6
-    # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
-ruff==0.9.6
+ruff==0.11.2
     # via pynxtools (pyproject.toml)
-scipy==1.14.1
+scipy==1.15.2
     # via ase
 six==1.17.0
     # via
     #   anytree
     #   python-dateutil
-structlog==24.4.0
+structlog==25.2.0
     # via pynxtools (pyproject.toml)
 super-collections==0.5.3
     # via mkdocs-macros-plugin
@@ -199,27 +202,27 @@ tomli==2.2.1 ; python_full_version <= '3.11'
     # via coverage
 toposort==1.10
     # via pynxtools (pyproject.toml)
-types-pytz==2024.2.0.20241003
+types-pytz==2025.1.0.20250318
     # via pynxtools (pyproject.toml)
-types-pyyaml==6.0.12.20240917
+types-pyyaml==6.0.12.20241230
     # via pynxtools (pyproject.toml)
-types-requests==2.32.0.20241016
+types-requests==2.32.0.20250306
     # via pynxtools (pyproject.toml)
 typing-extensions==4.12.2
     # via mypy
-tzdata==2024.2
+tzdata==2025.2
     # via pandas
-urllib3==2.2.3
+urllib3==2.3.0
     # via
     #   requests
     #   types-requests
-uv==0.5.7
+uv==0.6.9
     # via pynxtools (pyproject.toml)
-virtualenv==20.28.0
+virtualenv==20.29.3
     # via pre-commit
 watchdog==6.0.0
     # via mkdocs
-xarray==2024.11.0
+xarray==2025.3.0
     # via pynxtools (pyproject.toml)
 zipp==3.21.0
     # via importlib-metadata
diff --git a/pyproject.toml b/pyproject.toml
@@ -66,32 +66,32 @@ dev = [
     "pre-commit",
 ]
 convert = [
-    "pynxtools[apm,ellips,em,igor,mpes,raman,stm,xps,xrd]",
+    "pynxtools[apm,ellips,em,igor,mpes,raman,spm,xps,xrd]",
 ]
 
 apm = [
-    "pynxtools-apm>=0.2.2",
+    "pynxtools-apm>=0.2.3",
 ]
 ellips = [
-    "pynxtools-ellips>=0.0.7",
+    "pynxtools-ellips>=0.0.8",
 ]
 em = [
-    "pynxtools-em>=0.3.1",
+    "pynxtools-em>=0.3.2",
 ]
 igor = [
-    "pynxtools-igor>=0.1.0",
+    "pynxtools-igor>=0.1.1",
 ]
 mpes = [
-    "pynxtools-mpes>=0.2.1",
+    "pynxtools-mpes>=0.2.2",
 ]
 raman = [
-    "pynxtools-raman>=0.0.5",
+    "pynxtools-raman>=0.0.9",
 ]
-stm = [
-    "pynxtools-spm>=0.0.0",
+spm = [
+    "pynxtools-spm>=0.0.8",
 ]
 xps = [
-    "pynxtools-xps>=0.4.8",
+    "pynxtools-xps>=0.5.0",
 ]
 xrd = [
     "pynxtools-xrd>=0.0.3",

diff --git a/src/pynxtools/definitions b/src/pynxtools/definitions
diff --git a/src/pynxtools/nexus-version.txt b/src/pynxtools/nexus-version.txt
@@ -1 +1 @@
-v2024.02-1913-ga85e10cd
+v2024.02-1920-gecbe9b27
diff --git a/src/pynxtools/nomad/parser.py b/src/pynxtools/nomad/parser.py
@@ -289,7 +289,7 @@ def _populate_data(
                         ]
                         field = field_stats[0]
                         if not np.isfinite(field):
-                            self._logger.warning(
+                            self._logger.info(
                                 "set NaN for field of an array",
                                 target_name=field_name + "[" + data_instance_name + "]",
                             )
@@ -298,7 +298,7 @@ def _populate_data(
                         return
                 else:
                     if field.size == 1 and not np.isfinite(field):
-                        self._logger.warning(
+                        self._logger.info(
                             "set NaN for field of a scalar",
                             target_name=field_name + "[" + data_instance_name + "]",
                         )
+28 −13		contributed_definitions/NXafm.nxdl.xml
+79 −4		contributed_definitions/NXapm.nxdl.xml
+3 −3		contributed_definitions/NXapm_compositionspace_results.nxdl.xml
+39 −27		contributed_definitions/NXbias_spectroscopy.nxdl.xml
+0 −93		contributed_definitions/NXbias_sweep.nxdl.xml
+1 −1		contributed_definitions/NXelectronanalyzer.nxdl.xml
+95 −19		contributed_definitions/NXem.nxdl.xml
+1 −1		contributed_definitions/NXem_calorimetry.nxdl.xml
+11 −1		contributed_definitions/NXlockin.nxdl.xml
+1 −1		contributed_definitions/NXmicrostructure_imm_results.nxdl.xml
+1 −1		contributed_definitions/NXmicrostructure_kanapy_results.nxdl.xml
+46 −11		contributed_definitions/NXpositioner_spm.nxdl.xml
+35 −12		contributed_definitions/NXrcs.nxdl.xml
+21 −4		contributed_definitions/NXscan_control.nxdl.xml
+4 −4		contributed_definitions/NXsensor_scan.nxdl.xml
+37 −55		contributed_definitions/NXspm.nxdl.xml
+18 −103		contributed_definitions/NXstm.nxdl.xml
+27 −60		contributed_definitions/NXsts.nxdl.xml
+54 −28		contributed_definitions/nyaml/NXafm.yaml
+124 −10		contributed_definitions/nyaml/NXapm.yaml
+7 −7		contributed_definitions/nyaml/NXapm_compositionspace_results.yaml
+79 −64		contributed_definitions/nyaml/NXbias_spectroscopy.yaml
+0 −150		contributed_definitions/nyaml/NXbias_sweep.yaml
+3 −3		contributed_definitions/nyaml/NXelectronanalyzer.yaml
+156 −39		contributed_definitions/nyaml/NXem.yaml
+3 −3		contributed_definitions/nyaml/NXem_calorimetry.yaml
+21 −3		contributed_definitions/nyaml/NXlockin.yaml
+3 −3		contributed_definitions/nyaml/NXmicrostructure_imm_results.yaml
+3 −3		contributed_definitions/nyaml/NXmicrostructure_kanapy_results.yaml
+90 −22		contributed_definitions/nyaml/NXpositioner_spm.yaml
+55 −13		contributed_definitions/nyaml/NXrcs.yaml
+40 −12		contributed_definitions/nyaml/NXscan_control.yaml
+9 −5		contributed_definitions/nyaml/NXsensor_scan.yaml
+69 −96		contributed_definitions/nyaml/NXspm.yaml
+37 −202		contributed_definitions/nyaml/NXstm.yaml
+55 −125		contributed_definitions/nyaml/NXsts.yaml
+0 −4		manual/source/classes/contributed_definitions/spm-structure.rst