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

…-mpes into bring-in-examples

.github/workflows/pylint.yml

@@ -21,10 +21,10 @@ jobs:
           uv pip install -r dev-requirements.txt
       - name: ruff check
         run: |
-          ruff check pynxtools_mpes tests
+          ruff check src/pynxtools_mpes tests
       - name: ruff format
         run: |
-          ruff format --check pynxtools_mpes tests
+          ruff format --check src/pynxtools_mpes tests
       - name: mypy
         run: |
-          mypy pynxtools_mpes tests
+          mypy src/pynxtools_mpes tests

MANIFEST.in

@@ -1,4 +1,5 @@
 prune *
 exclude *
-recursive-include pynxtools_mpes *.py
-include pyproject.toml README.md dev-requirements.txt
+recursive-include src/pynxtools_mpes *.py
+include pyproject.toml README.md dev-requirements.txt
+recursive-include src/pynxtools_mpes/nomad/examples

docs/reference/mpes.md

@@ -2,7 +2,7 @@
 
 The reader supports [HDF5](https://www.hdfgroup.org/solutions/hdf5/) files created using the MPES instruments at the Department of Physical Chemistry of the [Fritz Haber Institute of the Max Planck Society (FHI)](https://pc.fhi-berlin.mpg.de).
 
-The reader for can be found [here](https://github.com/FAIRmat-NFDI/pynxtools-mpes/blob/main/pynxtools_mpes/reader.py).
+The reader for can be found [here](https://github.com/FAIRmat-NFDI/pynxtools-mpes/blob/main/src/pynxtools_mpes/reader.py).
 
 Example data for the MPES reader is available [here](https://github.com/FAIRmat-NFDI/pynxtools-mpes/tree/main/tests/data).
 

mkdocs.yaml

@@ -20,7 +20,7 @@ nav:
 plugins:
   - search
   - macros:
-      module_name: pynxtools_mpes/mkdocs
+      module_name: src/pynxtools_mpes/mkdocs
 
 theme:
   name: material

pyproject.toml

@@ -55,13 +55,18 @@ docs = [
 [project.entry-points."pynxtools.reader"]
 mpes = "pynxtools_mpes.reader:MPESReader"
 
-[tool.setuptools]
-packages = ["pynxtools_mpes"]
+[project.entry-points.'nomad.plugin']
+mpes_example = "pynxtools_mpes.nomad.entrypoints:mpes_example"
+
+[tool.setuptools.packages.find]
+where = [
+    "src",
+]
 
 [tool.setuptools_scm]
 
 [tool.ruff]
-include = ["pynxtools_mpes/*.py", "tests/*.py"]
+include = ["src/*.py", "tests/*.py"]
 line-length = 88
 indent-width = 4
 

src/pynxtools_mpes/nomad/entrypoints.py

@@ -0,0 +1,40 @@
+#
+# 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 mpes 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
+
+mpes_example = ExampleUploadEntryPoint(
+    title="Multidimensional photoemission spectroscopy (MPES)",
+    category="FAIRmat examples",
+    description="""
+        This example presents the capabilities of the NOMAD platform to store and standardize multidimensional photoemission spectroscopy (MPES) experimental data. It contains three major examples:
+
+      - Taking a pre-binned file, here stored in a h5 file, and converting it into the standardized MPES NeXus format.
+        There exists a [NeXus application definition for MPES](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes) which details the internal structure of such a file.
+      - Binning of raw data (see [here](https://www.nature.com/articles/s41597-020-00769-8) for additional resources) into a h5 file and consecutively generating a NeXus file from it.
+      - An analysis example using data in the NeXus format and employing the [pyARPES](https://github.com/chstan/arpes) analysis tool to reproduce the main findings of [this paper](https://arxiv.org/pdf/2107.07158.pdf).
+    """,
+    path="nomad/examples",
+    local_path="examples/data/uploads/mpes.zip",
+)

tests/test_nomad_example.py

@@ -0,0 +1,62 @@
+#
+# 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.
+#
+"""Test for NOMAD examples in reader plugins."""
+
+import pytest
+
+try:
+    from nomad.parsing.parser import ArchiveParser
+    from nomad.datamodel import EntryArchive, Context
+except ImportError:
+    pytest.skip(
+        "Skipping NOMAD example tests because nomad is not installed",
+        allow_module_level=True,
+    )
+
+from pynxtools.testing.nomad_example import get_file_parameter, test_nomad_example
+
+
+@pytest.mark.parametrize(
+    "mainfile", get_file_parameter("../src/pynxtools_mpes/nomad/examples")
+)
+def test_nomad_examples(mainfile, no_warn):
+    """Test if NOMAD examples work."""
+    test_nomad_example(mainfile)
+
+
+@pytest.mark.parametrize(
+    "config, expected_local_path",
+    [
+        pytest.param(
+            {
+                "title": "mpes_example",
+                "description": "mpes_example",
+                "category": "test",
+                "path": "nomad/examples",
+            },
+            f"examples/data/uploads/mpes.zip",
+            id="mpes_example",
+        ),
+    ],
+)
+def test_nomad_example_upload_entry_point_valid(config, expected_local_path):
+    test_example_upload_entry_point_valid(
+        plugin_package="pynxtools-mpes",
+        config=config,
+        expected_local_path=expected_local_path,
+    )

tests/test_reader.py

@@ -1,5 +1,22 @@
+#
+# 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.
+#
 """
-Basic example based test for the stm reader
+Basic example based test for the MPES reader
 """
 
 from pathlib import Path