No inner sections (#525)

* use pynxtools.nomad.schema.Root * not using inner sections * fix for doc links if name contains _ * fix format * linting * fixing tests * fixing mime-type for WSL * fix for handling raw files in subdirectories * use references in steps, and results in NexusMeasurement * make nexus attributes searchable by importing them to NOMAD as Quantities * temporary fix for boolean array as signals or axes - show first element as the field value * handling arrays of strings * handling attribute if it is an array of numbers * fix for handling bool (arrays) coming from hdf5 * add array size and ndim as attributes (#537) * field statistics are now searchable quantities themselves * NexusBaseSection for registering NeXUs Group instance names as searchable quantity <name> * fix for registering stats * searcable __name for variadic quantities * bringing statistic definitions to a common place * Update src/pynxtools/nomad/parser.py Co-authored-by: Lukas Pielsticker <[email protected]> * Update src/pynxtools/nomad/schema.py Co-authored-by: Lukas Pielsticker <[email protected]> * use mapping instead of if/elif-s * manage std instead of var * fix for ganareting __name/stat quantities * fix for handling attributes * ruffing * ruffing * linting * fix for tests * adjust to nomad's python requirement --------- Co-authored-by: GinzburgLev <[email protected]> Co-authored-by: Laurenz Rettig <[email protected]> Co-authored-by: Lukas Pielsticker <[email protected]>
FAIRmat-NFDI · Feb 14, 2025 · e985c92 · e985c92
1 parent d3b15e2
commit e985c92
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Showing 7 changed files with 329 additions and 185 deletions.
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -34,7 +34,7 @@ jobs:
           curl -LsSf https://astral.sh/uv/install.sh | sh
           uv pip install coverage coveralls
       - name: Install nomad
-        if: "${{ matrix.python_version != '3.8'}}"
+        if: "${{ matrix.python_version != '3.8' && matrix.python_version != '3.9'}}"
         run: |
           uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
       - name: Install pynx

diff --git a/dev-requirements.txt b/dev-requirements.txt
@@ -181,7 +181,7 @@ regex==2024.11.6
     # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
-ruff==0.9.3
+ruff==0.9.6
     # via pynxtools (pyproject.toml)
 scipy==1.14.1
     # via ase

diff --git a/src/pynxtools/nomad/entrypoints.py b/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",