Added an optional deps group nomad to assure that an installation of …

…pynxtools-apm does not actively modify the environment with versions of these that nomad needs, otherwise nomad did not start reporting that h5grove was unable to load pydantic_settings

dev-requirements.txt

@@ -4,9 +4,7 @@ anyio==4.8.0
     # via
     #   httpx
     #   jupyter-server
-anytree==2.12.1
-    # via pynxtools
-appnope==0.1.4 ; sys_platform == 'darwin'
+appnope==0.1.4 ; platform_system == 'Darwin'
     # via ipykernel
 argon2-cffi==23.1.0
     # via jupyter-server
@@ -15,9 +13,7 @@ argon2-cffi-bindings==21.2.0
 arrow==1.3.0
     # via isoduration
 ase==3.24.0
-    # via
-    #   ifes-apt-tc-data-modeling
-    #   pynxtools
+    # via ifes-apt-tc-data-modeling
 asttokens==3.0.0
     # via stack-data
 async-lru==2.0.4
@@ -53,13 +49,9 @@ charset-normalizer==3.4.1
     # via requests
 click==8.1.8
     # via
-    #   click-default-group
     #   mkdocs
     #   mkdocs-click
     #   pip-tools
-    #   pynxtools
-click-default-group==1.2.4
-    # via pynxtools
 colorama==0.4.6
     # via
     #   build
@@ -109,7 +101,6 @@ h5py==3.12.1
     #   h5grove
     #   ifes-apt-tc-data-modeling
     #   jupyterlab-h5web
-    #   pynxtools
 hjson==3.1.0
     # via
     #   mkdocs-macros-plugin
@@ -130,8 +121,6 @@ idna==3.10
     #   requests
 ifes-apt-tc-data-modeling==0.2.2
     # via pynxtools-apm (pyproject.toml)
-importlib-metadata==8.6.1
-    # via pynxtools
 iniconfig==2.0.0
     # via pytest
 ipykernel==6.29.5
@@ -226,8 +215,6 @@ jupyterlab-widgets==3.0.13
     # via ipywidgets
 kiwisolver==1.4.8
     # via matplotlib
-lxml==5.3.0
-    # via pynxtools
 markdown==3.7
     # via
     #   markdown-include
@@ -254,7 +241,6 @@ mergedeep==1.3.4
     # via
     #   mkdocs
     #   mkdocs-get-deps
-    #   pynxtools
 mistune==3.1.0
     # via nbconvert
 mkdocs==1.6.1
@@ -323,12 +309,10 @@ numpy==1.26.4
     #   matplotlib
     #   numexpr
     #   pandas
-    #   pynxtools
     #   radioactivedecay
     #   scipy
     #   tables
     #   tifffile
-    #   xarray
 orjson==3.10.15
     # via h5grove
 overrides==7.7.0
@@ -347,15 +331,12 @@ packaging==24.2
     #   pint
     #   pytest
     #   tables
-    #   xarray
 paginate==0.5.7
     # via mkdocs-material
 pandas==2.2.3
     # via
     #   ifes-apt-tc-data-modeling
-    #   pynxtools
     #   radioactivedecay
-    #   xarray
 pandocfilters==1.5.1
     # via nbconvert
 parso==0.8.4
@@ -411,8 +392,6 @@ pygments==2.19.1
     #   nbconvert
 pymdown-extensions==10.14.1
     # via mkdocs-material
-pynxtools @ git+https://github.com/FAIRmat-NFDI/pynxtools@9ca60a34223623eae954b290d0eb1acb9b213cb1#egg=apm_app
-    # via pynxtools-apm (pyproject.toml)
 pyparsing==3.2.1
     # via matplotlib
 pyproject-hooks==1.2.0
@@ -455,7 +434,6 @@ pyyaml==6.0.2
     #   mkdocs-macros-plugin
     #   pre-commit
     #   pymdown-extensions
-    #   pynxtools
     #   pyyaml-env-tag
 pyyaml-env-tag==0.1
     # via mkdocs
@@ -504,7 +482,6 @@ setuptools==75.8.0
     #   pip-tools
 six==1.17.0
     # via
-    #   anytree
     #   python-dateutil
     #   rfc3339-validator
 sniffio==1.3.1
@@ -531,7 +508,7 @@ tifffile==2025.1.10
     # via h5grove
 tinycss2==1.4.0
     # via bleach
-tomli==2.2.1 ; python_full_version <= '3.11'
+tomli==2.2.1 ; python_full_version == '3.11'
     # via coverage
 tornado==6.4.2
     # via
@@ -601,9 +578,5 @@ wheel==0.45.1
     # via pip-tools
 widgetsnbextension==4.0.13
     # via ipywidgets
-xarray==2025.1.1
-    # via pynxtools
 xmltodict==0.14.2
     # via ifes-apt-tc-data-modeling
-zipp==3.21.0
-    # via importlib-metadata

pyproject.toml

@@ -23,7 +23,7 @@ classifiers = [
 ]
 dependencies = [
     "pint==0.17",
-    "pynxtools@git+https://github.com/FAIRmat-NFDI/pynxtools#egg=apm_app",
+    # "pynxtools@git+https://github.com/FAIRmat-NFDI/pynxtools@apm_app",
     "ifes_apt_tc_data_modeling>=0.2.2",
     "numpy<=1.26.4",
 ]
@@ -58,6 +58,11 @@ docs = [
     "mkdocs-click",
     "markdown-include"
 ]
+nomad = [
+    "python-json-logger==2.0.2",
+    "h5grove==1.3.0",
+    "jsonschema==4.17.3"
+]
 
 [project.entry-points."pynxtools.reader"]
 apm = "pynxtools_apm.reader:APMReader"