Update Reader according to the App Def modification.

.gitignore

@@ -25,6 +25,8 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+*debug.py
+
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

.vscode/settings.json

@@ -9,8 +9,8 @@
     "python": true,
     "json": true
   },
-  "github.copilot.chat.temporalContext.enabled": true,
   "editor.defaultFormatter": "charliermarsh.ruff",
   "notebook.formatOnSave.enabled": false,
-  "CRS.OnSaveAlFileAction": "Reorganize"
+  "CRS.OnSaveAlFileAction": "Reorganize",
+  "github.copilot.chat.editor.temporalContext.enabled": true
 }

dev-requirements.txt

@@ -1,198 +1,233 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile -p 3.11 --output-file=dev-requirements.txt --extra=dev pyproject.toml
+#    uv pip compile -p 3.11 --output-file=dev-requirements.txt --all-extras pyproject.toml
 anytree==2.12.1
     # via pynxtools
 ase==3.23.0
     # via pynxtools
-asttokens==2.4.1
-    # via stack-data
+babel==2.17.0
+    # via mkdocs-material
+backrefs==5.8
+    # via mkdocs-material
+beautifulsoup4==4.13.3
+    # via mkdocs-mermaid2-plugin
 build==1.0.3
     # via pip-tools
+certifi==2025.1.31
+    # via requests
+charset-normalizer==3.4.1
+    # via requests
 click==8.1.7
     # via
     #   click-default-group
+    #   mkdocs
     #   pip-tools
     #   pynxtools
 click-default-group==1.2.4
     # via pynxtools
+colorama==0.4.6
+    # via mkdocs-material
 contourpy==1.2.1
     # via matplotlib
 cycler==0.12.1
     # via matplotlib
-decorator==5.1.1
-    # via ipython
-executing==2.1.0
-    # via stack-data
+editorconfig==0.17.0
+    # via jsbeautifier
 findiff==0.10.0
     # via pynxtools-spm (pyproject.toml)
-flexcache==0.3
-    # via pint
-flexparser==0.4
-    # via pint
 fonttools==4.51.0
     # via matplotlib
+ghp-import==2.1.0
+    # via mkdocs
 h5py==3.12.1
     # via pynxtools
-imageio==2.36.0
-    # via scikit-image
+hjson==3.1.0
+    # via
+    #   mkdocs-macros-plugin
+    #   super-collections
+idna==3.10
+    # via requests
 importlib-metadata==8.5.0
     # via pynxtools
 iniconfig==2.0.0
     # via pytest
-ipython==8.29.0
-    # via pyspm
-jedi==0.19.2
-    # via ipython
-joblib==1.4.2
-    # via scikit-learn
+jinja2==3.1.6
+    # via
+    #   mkdocs
+    #   mkdocs-macros-plugin
+    #   mkdocs-material
+    #   mkdocstrings
+jsbeautifier==1.15.4
+    # via mkdocs-mermaid2-plugin
 kiwisolver==1.4.5
     # via matplotlib
-lazy-loader==0.4
-    # via scikit-image
 lxml==5.3.0
     # via pynxtools
-matplotlib==3.8.4
+markdown==3.7
     # via
-    #   ase
-    #   pyspm
-    #   seaborn
-matplotlib-inline==0.1.7
-    # via ipython
+    #   mkdocs
+    #   mkdocs-autorefs
+    #   mkdocs-material
+    #   mkdocstrings
+    #   pymdown-extensions
+markupsafe==3.0.2
+    # via
+    #   jinja2
+    #   mkdocs
+    #   mkdocs-autorefs
+    #   mkdocstrings
+matplotlib==3.8.4
+    # via ase
 mergedeep==1.3.4
-    # via pynxtools
+    # via
+    #   mkdocs
+    #   mkdocs-get-deps
+    #   pynxtools
+mkdocs==1.6.1
+    # via
+    #   pynxtools-spm (pyproject.toml)
+    #   mkdocs-autorefs
+    #   mkdocs-macros-plugin
+    #   mkdocs-material
+    #   mkdocs-mermaid2-plugin
+    #   mkdocstrings
+mkdocs-autorefs==1.4.1
+    # via mkdocstrings
+mkdocs-get-deps==0.2.0
+    # via mkdocs
+mkdocs-macros-plugin==1.3.7
+    # via pynxtools-spm (pyproject.toml)
+mkdocs-material==9.6.9
+    # via pynxtools-spm (pyproject.toml)
+mkdocs-material-extensions==1.3.1
+    # via mkdocs-material
+mkdocs-mermaid2-plugin==1.2.1
+    # via pynxtools-spm (pyproject.toml)
+mkdocstrings==0.29.0
+    # via pynxtools-spm (pyproject.toml)
 mpmath==1.3.0
     # via sympy
 mypy==1.8.0
     # via pynxtools-spm (pyproject.toml)
 mypy-extensions==1.0.0
     # via mypy
-networkx==3.4.2
-    # via scikit-image
 numpy==1.26.4
     # via
     #   ase
     #   contourpy
     #   findiff
     #   h5py
-    #   imageio
     #   matplotlib
     #   pandas
     #   pynxtools
-    #   pyspm
-    #   scikit-image
-    #   scikit-learn
     #   scipy
-    #   seaborn
-    #   tifffile
     #   xarray
 packaging==24.0
     # via
     #   build
-    #   lazy-loader
     #   matplotlib
+    #   mkdocs
+    #   mkdocs-macros-plugin
+    #   pint
     #   pytest
-    #   scikit-image
     #   xarray
+paginate==0.5.7
+    # via mkdocs-material
 pandas==2.2.2
     # via
     #   pynxtools
-    #   seaborn
     #   xarray
-parso==0.8.4
-    # via jedi
-pexpect==4.9.0
-    # via ipython
+pathspec==0.12.1
+    # via
+    #   mkdocs
+    #   mkdocs-macros-plugin
 pillow==10.3.0
+    # via matplotlib
+pint==0.17
     # via
-    #   imageio
-    #   matplotlib
-    #   scikit-image
-pint==0.24.4
-    # via pynxtools-spm (pyproject.toml)
+    #   pynxtools-spm (pyproject.toml)
+    #   pynxtools
 pip==24.3.1
     # via pip-tools
 pip-tools==7.4.0
     # via pynxtools-spm (pyproject.toml)
 platformdirs==4.3.6
-    # via pint
+    # via mkdocs-get-deps
 pluggy==1.4.0
     # via pytest
-prompt-toolkit==3.0.48
-    # via ipython
-psutil==5.9.8
-    # via pyspm
-ptyprocess==0.7.0
-    # via pexpect
-pure-eval==0.2.3
-    # via stack-data
 pygments==2.18.0
-    # via ipython
-pynxtools==0.9.2
+    # via mkdocs-material
+pymdown-extensions==10.14.3
+    # via
+    #   mkdocs-material
+    #   mkdocs-mermaid2-plugin
+    #   mkdocstrings
+pynxtools @ git+https://github.com/FAIRmat-NFDI/pynxtools.git@7fec6369917248838823efdede31cfdb4aaa5871#egg=pynxtools
     # via pynxtools-spm (pyproject.toml)
 pyparsing==3.1.2
     # via matplotlib
 pyproject-hooks==1.0.0
     # via
     #   build
     #   pip-tools
-pyspm==0.6.2
-    # via pynxtools-spm (pyproject.toml)
 pytest==8.0.2
     # via pynxtools-spm (pyproject.toml)
 python-dateutil==2.9.0.post0
     # via
+    #   ghp-import
     #   matplotlib
+    #   mkdocs-macros-plugin
     #   pandas
 pytz==2024.1
     # via pandas
 pyyaml==6.0.2
-    # via pynxtools
-ruff==0.8.2
+    # via
+    #   mkdocs
+    #   mkdocs-get-deps
+    #   mkdocs-macros-plugin
+    #   pymdown-extensions
+    #   pynxtools
+    #   pyyaml-env-tag
+pyyaml-env-tag==0.1
+    # via mkdocs
+requests==2.32.3
+    # via
+    #   mkdocs-material
+    #   mkdocs-mermaid2-plugin
+ruff==0.11.2
     # via pynxtools-spm (pyproject.toml)
-scikit-image==0.24.0
-    # via pyspm
-scikit-learn==1.5.2
-    # via pyspm
 scipy==1.12.0
     # via
     #   ase
     #   findiff
-    #   scikit-image
-    #   scikit-learn
-seaborn==0.13.2
-    # via pyspm
 setuptools==75.6.0
-    # via pip-tools
+    # via
+    #   mkdocs-mermaid2-plugin
+    #   pip-tools
 six==1.16.0
     # via
     #   anytree
-    #   asttokens
+    #   jsbeautifier
     #   python-dateutil
-stack-data==0.6.3
-    # via ipython
+soupsieve==2.6
+    # via beautifulsoup4
+super-collections==0.5.3
+    # via mkdocs-macros-plugin
 sympy==1.12
     # via findiff
-threadpoolctl==3.5.0
-    # via scikit-learn
-tifffile==2024.9.20
-    # via scikit-image
-tqdm==4.67.0
-    # via pyspm
-traitlets==5.14.3
-    # via
-    #   ipython
-    #   matplotlib-inline
+termcolor==2.5.0
+    # via mkdocs-macros-plugin
+toposort==1.10
+    # via pynxtools
 typing-extensions==4.11.0
     # via
-    #   flexcache
-    #   flexparser
-    #   ipython
+    #   beautifulsoup4
     #   mypy
-    #   pint
 tzdata==2024.1
     # via pandas
-wcwidth==0.2.13
-    # via prompt-toolkit
+urllib3==2.3.0
+    # via requests
+watchdog==6.0.0
+    # via mkdocs
 wheel==0.42.0
     # via pip-tools
 xarray==2024.11.0