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No inner sections #525

Merged
merged 33 commits into from
Feb 14, 2025
Merged

No inner sections #525

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36a121e
use pynxtools.nomad.schema.Root
sanbrock Jan 10, 2025
c1bc7d5
not using inner sections
sanbrock Jan 17, 2025
fc5b95b
fix for doc links if name contains _
sanbrock Jan 21, 2025
bfce048
fix format
sanbrock Jan 21, 2025
274e0d6
linting
sanbrock Jan 21, 2025
27fa71c
fixing tests
sanbrock Jan 21, 2025
8fb4953
fixing mime-type for WSL
sanbrock Jan 24, 2025
bd22578
fix for handling raw files in subdirectories
sanbrock Jan 24, 2025
8f1a0b4
use references in steps, and results in NexusMeasurement
sanbrock Jan 29, 2025
de2e94a
make nexus attributes searchable by importing them to NOMAD as Quanti…
sanbrock Jan 30, 2025
9c4a361
temporary fix for boolean array as signals or axes - show first eleme…
GinzburgLev Feb 4, 2025
2c4e3f6
handling arrays of strings
sanbrock Feb 4, 2025
4aabf3b
handling attribute if it is an array of numbers
sanbrock Feb 4, 2025
2d7106b
fix for handling bool (arrays) coming from hdf5
sanbrock Feb 4, 2025
dfffd21
add array size and ndim as attributes (#537)
rettigl Feb 5, 2025
e2371c4
field statistics are now searchable quantities themselves
sanbrock Feb 6, 2025
3508079
NexusBaseSection for registering NeXUs Group instance names as search…
sanbrock Feb 6, 2025
ebafcf7
fix for registering stats
sanbrock Feb 7, 2025
27421b6
searcable __name for variadic quantities
sanbrock Feb 12, 2025
cb4fa29
bringing statistic definitions to a common place
sanbrock Feb 13, 2025
f6548e9
Update src/pynxtools/nomad/parser.py
sanbrock Feb 13, 2025
1231d17
Update src/pynxtools/nomad/schema.py
sanbrock Feb 13, 2025
5259fd2
use mapping instead of if/elif-s
sanbrock Feb 13, 2025
3f3d09d
manage std instead of var
sanbrock Feb 13, 2025
81218f8
fix for ganareting __name/stat quantities
sanbrock Feb 14, 2025
1d6c2cc
fix for handling attributes
sanbrock Feb 14, 2025
04bd30a
ruffing
sanbrock Feb 14, 2025
ed34b3d
ruffing
sanbrock Feb 14, 2025
6073eff
linting
sanbrock Feb 14, 2025
8879fd9
fix for tests
sanbrock Feb 14, 2025
946dff6
Merge branch 'master' into no_inner_sections
sanbrock Feb 14, 2025
0ff536f
adjust to nomad's python requirement
sanbrock Feb 14, 2025
cb93adf
Merge remote-tracking branch 'refs/remotes/origin/no_inner_sections' …
sanbrock Feb 14, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/pytest.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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'}}"
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I think at some point we should just drop support for python<3.10, like NOMAD did. I can do this in a separate PR.

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
Expand Down
2 changes: 1 addition & 1 deletion dev-requirements.txt
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Expand Up @@ -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
Expand Down
24 changes: 17 additions & 7 deletions src/pynxtools/nomad/entrypoints.py
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Expand Up @@ -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 (
Expand All @@ -76,7 +76,7 @@ def load(self):
SearchQuantities,
)

schema = "pynxtools.nomad.schema.NeXus"
schema = "pynxtools.nomad.schema.Root"

nexus_app = AppEntryPoint(
name="NexusApp",
Expand Down Expand Up @@ -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,
),
],
Expand Down Expand Up @@ -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}
},
Expand All @@ -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",
Expand Down
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