Merge branch 'bring-in-examples' of github.com:FAIRmat-NFDI/pynxtools…

…-apm into bring-in-examples

.github/workflows/pytest.yml

@@ -33,6 +33,10 @@ jobs:
         run: |
           curl -LsSf https://astral.sh/uv/install.sh | sh
           uv pip install coverage coveralls
+      - name: Install nomad
+        if: "${{ matrix.python_version != '3.8' && matrix.python_version != '3.12'}}"
+        run: |
+          uv pip install nomad-lab@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git          
       - name: Install package
         run: |
           uv pip install ".[dev]"

MANIFEST.in

@@ -0,0 +1,5 @@
+prune *
+exclude *
+recursive-include src/pynxtools_apm *.py
+include pyproject.toml README.md dev-requirements.txt
+recursive-include src/pynxtools_apm/nomad/examples

pyproject.toml

@@ -63,6 +63,9 @@ docs = [
 [project.entry-points."pynxtools.reader"]
 apm = "pynxtools_apm.reader:APMReader"
 
+[project.entry-points.'nomad.plugin']
+apm_example = "pynxtools_mpes.nomad.entrypoints:apm_example"
+
 [tool.setuptools.packages.find]
 where = [
     "src",

src/pynxtools_apm/nomad/entrypoints.py

@@ -0,0 +1,41 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+"""Entry points for XPS examples."""
+
+try:
+    from nomad.config.models.plugins import ExampleUploadEntryPoint
+except ImportError as exc:
+    raise ImportError(
+        "Could not import nomad package. Please install the package 'nomad-lab'."
+    ) from exc
+
+apm_example = ExampleUploadEntryPoint(
+    title="Atom Probe Microscopy",
+    category="FAIRmat examples",
+    description="""
+        This example presents the capabilities of the NOMAD platform to store and standardize atom probe data.
+        It shows the generation of a NeXus file according to the
+        [NXapm](https://fairmat-nfdi.github.io/nexus_definitions/classes/contributed_definitions/NXapm.html#nxapm)
+        application definition and a successive analysis of an example data set.
+        The example contains a small atom probe dataset from an experiment with a LEAP instrument to get you started
+        and keep the size of your NOMAD installation small. Once started, we recommend changing the respective
+        input file in the NOMAD Oasis ELN to run the example with your own datasets.
+    """,
+    path="nomad/examples",
+    local_path="examples/data/uploads/apm.zip",
+)