Apm app

.pre-commit-config.yaml

@@ -1,9 +1,9 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.8.3
+    rev: v0.9.3
     hooks:
       # Run the linter.
       - id: ruff
       # Run the formatter.
-      - id: ruff-format
+      - id: ruff-format

.vscode/launch.json

@@ -0,0 +1,31 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "pynx-core debug",
+            "type": "python",
+            "request": "launch",
+            "cwd": "${workspaceFolder}",
+            "program": "../../.py3.11.11/bin/dataconverter",
+            "args": [//workflow files str.str, hits.hits, root.root should be created via touch str.str ...
+                     //fancyfile.mimetype,
+                     "--reader",
+                     "apm",
+                     "--nxdl",
+                     "NXapm",
+                     "--output=out.nxs"]
+        },
+        {
+            "name": "nomad parse",
+            "type": "python",
+            "request": "launch",
+            "cwd": "${workspaceFolder}",
+            "program": "../../.py3.11.11/bin/nomad",
+            "justMyCode": false,
+            "args": ["parse", "--show-archive", "../../pynx-apm/pynxtools_apm/tests/prod/ger_saarbruecken_pauly.073.0.nxs"]
+        },
+    ]
+}

dev-requirements.txt

@@ -2,17 +2,17 @@
 #    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
     # via mkdocs-material
-certifi==2024.8.30
+certifi==2024.12.14
     # 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
@@ -28,15 +28,15 @@ colorama==0.4.6
     #   pytest
 contourpy==1.3.1
     # via matplotlib
-coverage==7.6.9
+coverage==7.6.10
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
 distlib==0.3.9
     # via virtualenv
-filelock==3.16.1
+filelock==3.17.0
     # via virtualenv
-fonttools==4.55.2
+fonttools==4.55.6
     # via matplotlib
 ghp-import==2.1.0
     # via mkdocs
@@ -46,20 +46,20 @@ hjson==3.1.0
     # via
     #   mkdocs-macros-plugin
     #   super-collections
-identify==2.6.3
+identify==2.6.6
     # 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
     # via pytest
-jinja2==3.1.4
+jinja2==3.1.5
     # via
     #   mkdocs
     #   mkdocs-macros-plugin
     #   mkdocs-material
-kiwisolver==1.4.7
+kiwisolver==1.4.8
     # via matplotlib
 lxml==5.3.0
     # via pynxtools (pyproject.toml)
@@ -76,7 +76,7 @@ markupsafe==3.0.2
     # via
     #   jinja2
     #   mkdocs
-matplotlib==3.9.3
+matplotlib==3.10.0
     # via ase
 mergedeep==1.3.4
     # via
@@ -94,13 +94,13 @@ 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==9.5.50
     # via pynxtools (pyproject.toml)
 mkdocs-material-extensions==1.3.1
     # via
     #   pynxtools (pyproject.toml)
     #   mkdocs-material
-mypy==1.13.0
+mypy==1.14.1
     # via pynxtools (pyproject.toml)
 mypy-extensions==1.0.0
     # via mypy
@@ -133,21 +133,21 @@ pathspec==0.12.1
     # via
     #   mkdocs
     #   mkdocs-macros-plugin
-pillow==11.0.0
+pillow==11.1.0
     # via matplotlib
 platformdirs==4.3.6
     # via
     #   mkdocs-get-deps
     #   virtualenv
 pluggy==1.5.0
     # via pytest
-pre-commit==4.0.1
+pre-commit==4.1.0
     # via pynxtools (pyproject.toml)
-pygments==2.18.0
+pygments==2.19.1
     # via mkdocs-material
-pymdown-extensions==10.12
+pymdown-extensions==10.14.1
     # via mkdocs-material
-pyparsing==3.2.0
+pyparsing==3.2.1
     # via matplotlib
 pytest==8.3.4
     # via
@@ -181,43 +181,43 @@ regex==2024.11.6
     # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
-ruff==0.8.2
+ruff==0.9.3
     # via pynxtools (pyproject.toml)
-scipy==1.14.1
+scipy==1.15.1
     # via ase
 six==1.17.0
     # via
     #   anytree
     #   python-dateutil
-structlog==24.4.0
+structlog==25.1.0
     # via pynxtools (pyproject.toml)
 super-collections==0.5.3
     # via mkdocs-macros-plugin
 termcolor==2.5.0
     # via mkdocs-macros-plugin
-tomli==2.2.1 ; python_full_version <= '3.11'
+tomli==2.2.1 ; python_full_version == '3.11'
     # via coverage
-types-pytz==2024.2.0.20241003
+types-pytz==2024.2.0.20241221
     # 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
     # via pynxtools (pyproject.toml)
 typing-extensions==4.12.2
     # via mypy
-tzdata==2024.2
+tzdata==2025.1
     # via pandas
-urllib3==2.2.3
+urllib3==2.3.0
     # via
     #   requests
     #   types-requests
-uv==0.5.7
+uv==0.5.24
     # via pynxtools (pyproject.toml)
-virtualenv==20.28.0
+virtualenv==20.29.1
     # via pre-commit
 watchdog==6.0.0
     # via mkdocs
-xarray==2024.11.0
+xarray==2025.1.1
     # via pynxtools (pyproject.toml)
 zipp==3.21.0
     # via importlib-metadata

pyproject.toml

@@ -63,6 +63,11 @@ dev = [
     "uv",
     "pre-commit",
 ]
+nomad = [
+    "urllib3<=1.26.20",
+    "filelock==3.3.1"
+]
+
 convert = [
     "pynxtools[apm,ellips,em,igor,mpes,raman,stm,xps,xrd]",
 ]

src/pynxtools/dataconverter/helpers.py

@@ -80,13 +80,11 @@ def _log(self, path: str, log_type: ValidationProblem, value: Optional[Any], *ar
 
         if log_type == ValidationProblem.UnitWithoutDocumentation:
             logger.warning(
-                f"The unit, {path} = {value}, "
-                "is being written but has no documentation"
+                f"The unit, {path} = {value}, is being written but has no documentation"
             )
         elif log_type == ValidationProblem.InvalidEnum:
             logger.warning(
-                f"The value at {path} should be on of the "
-                f"following strings: {value}"
+                f"The value at {path} should be on of the following strings: {value}"
             )
         elif log_type == ValidationProblem.MissingRequiredGroup:
             logger.warning(f"The required group, {path}, hasn't been supplied.")
@@ -344,7 +342,7 @@ def get_all_defined_required_children_for_elem(xml_element):
                     list_of_children_to_add.add(f"{name_to_add}/@units")
             elif tag == "group":
                 nxdlpath = (
-                    f'{xml_element.get("nxdlpath")}/{get_nxdl_name_from_elem(child)}'
+                    f"{xml_element.get('nxdlpath')}/{get_nxdl_name_from_elem(child)}"
                 )
                 nxdlbase = xml_element.get("nxdlbase")
                 nx_name = nxdlbase[nxdlbase.rfind("/") + 1 : nxdlbase.rfind(".nxdl")]

src/pynxtools/dataconverter/readers/example/reader.py

@@ -106,22 +106,16 @@ def read(
 
         # virtual datasets slicing
         my_path = str(f"{os.path.dirname(__file__)}/../../../data/")
-        template[("/ENTRY[entry]" "/test_virtual" "_dataset/sliced" "_dataset")] = {
-            "link": (
-                f"{my_path}/xarray_saved_small_" "calibration.h5:/binned/BinnedData"
-            ),
+        template[("/ENTRY[entry]/test_virtual_dataset/sliced_dataset")] = {
+            "link": (f"{my_path}/xarray_saved_small_calibration.h5:/binned/BinnedData"),
             "shape": np.index_exp[:, 1, :, :],
         }
-        template[("/ENTRY[entry]" "/test_virtual" "_dataset/slic" "ed_dataset2")] = {
-            "link": (
-                f"{my_path}/xarray_saved_small" "_calibration.h5:/binned/BinnedData"
-            ),
+        template[("/ENTRY[entry]/test_virtual_dataset/sliced_dataset2")] = {
+            "link": (f"{my_path}/xarray_saved_small_calibration.h5:/binned/BinnedData"),
             "shape": np.index_exp[:, :, :, 1],
         }
-        template[("/ENTRY[entry]" "/test_virtual" "_dataset/slic" "ed_dataset3")] = {
-            "link": (
-                f"{my_path}/xarray_saved_small" "_calibration.h5:/binned/BinnedData"
-            ),
+        template[("/ENTRY[entry]/test_virtual_dataset/sliced_dataset3")] = {
+            "link": (f"{my_path}/xarray_saved_small_calibration.h5:/binned/BinnedData"),
             "shape": np.index_exp[:, :, :, 2:4],
         }
 

src/pynxtools/dataconverter/readers/json_map/reader.py

@@ -56,7 +56,7 @@ def get_val_nested_keystring_from_dict(keystring, data):
         return data[current_key].values
     if isinstance(data[current_key], xarray.core.dataset.Dataset):
         raise NotImplementedError(
-            "Xarray datasets are not supported. " "You can only use xarray dataarrays."
+            "Xarray datasets are not supported. You can only use xarray dataarrays."
         )
 
     return data[current_key]

src/pynxtools/nexus/nexus.py

@@ -439,7 +439,7 @@ def process_node(hdf_node, hdf_path, parser, logger, doc=True):
             if len(hdf_node.shape) <= 1
             else str(decode_if_string(hdf_node[0])).split("\n")
         )
-        logger.debug(f'value: {val[0]} {"..." if len(val) > 1 else ""}')
+        logger.debug(f"value: {val[0]} {'...' if len(val) > 1 else ''}")
     else:
         logger.debug(
             f"===== GROUP (/{hdf_path} "
@@ -460,7 +460,7 @@ def process_node(hdf_node, hdf_path, parser, logger, doc=True):
     for key, value in hdf_node.attrs.items():
         logger.debug(f"===== ATTRS (/{hdf_path}@{key})")
         val = str(decode_if_string(value)).split("\n")
-        logger.debug(f'value: {val[0]} {"..." if len(val) > 1 else ""}')
+        logger.debug(f"value: {val[0]} {'...' if len(val) > 1 else ''}")
         (req_str, nxdef, nxdl_path) = get_nxdl_doc(hdf_info, logger, doc, attr=key)
         if (
             parser is not None

src/pynxtools/nomad/entrypoints.py

@@ -63,7 +63,7 @@ def load(self):
     name="pynxtools parser",
     description="A parser for nexus files.",
     mainfile_name_re=r".*\.nxs",
-    mainfile_mime_re="application/x-hdf5",
+    mainfile_mime_re="application/x-hdf*",
 )
 
 from nomad.config.models.ui import (
@@ -76,7 +76,7 @@ def load(self):
     SearchQuantities,
 )
 
-schema = "pynxtools.nomad.schema.NeXus"
+schema = "pynxtools.nomad.schema.Root"
 
 nexus_app = AppEntryPoint(
     name="NexusApp",
@@ -105,17 +105,17 @@ def load(self):
             Column(quantity=f"entry_type", selected=True),
             Column(
                 title="definition",
-                quantity=f"data.*.ENTRY[*].definition__field#{schema}",
+                quantity=f"data.ENTRY[*].definition__field#{schema}",
                 selected=True,
             ),
             Column(
                 title="start_time",
-                quantity=f"data.*.ENTRY[*].start_time__field#{schema}",
+                quantity=f"data.ENTRY[*].start_time__field#{schema}",
                 selected=True,
             ),
             Column(
                 title="title",
-                quantity=f"data.*.ENTRY[*].title__field#{schema}",
+                quantity=f"data.ENTRY[*].title__field#{schema}",
                 selected=True,
             ),
         ],
@@ -161,8 +161,8 @@ def load(self):
                     "autorange": True,
                     "nbins": 30,
                     "scale": "linear",
-                    "quantity": f"data.Root.datetime#{schema}",
-                    "title": "Procesing Time",
+                    "quantity": f"data.ENTRY.start_time__field#{schema}",
+                    "title": "Start Time",
                     "layout": {
                         "lg": {"minH": 3, "minW": 3, "h": 4, "w": 12, "y": 0, "x": 0}
                     },
@@ -177,6 +177,16 @@ def load(self):
                         "lg": {"minH": 3, "minW": 3, "h": 8, "w": 4, "y": 0, "x": 12}
                     },
                 },
+                {
+                    "type": "terms",
+                    "show_input": False,
+                    "scale": "linear",
+                    "quantity": f"data.ENTRY.definition__field#{schema}",
+                    "title": "Definition",
+                    "layout": {
+                        "lg": {"minH": 3, "minW": 3, "h": 8, "w": 4, "y": 0, "x": 16}
+                    },
+                },
                 {
                     "type": "periodic_table",
                     "scale": "linear",