Bring in NOMAD examples (#27)

* Nexus eln examples

* Updates north + pynxtools apm test branch

* Implementing fixes for EM and APM examples in NOMAD

* Pluginise pynxtools

* initial commit for nomad entrypoints

* typo fix in MANIFEST.in

* bring in additional changes from SprintNomadBaseSectionEmApmFixes branch

* add integration tests for nomad example entrypoints

* linting of entrypoints

* missing closing bracket

* return archive dict in testing function

* fix pyproject.toml

* use relative path in tests

* bump ruff to >v0.6

* update dev-requirements and pre-commit

* platform-independent dev-requirements

* update dev-requirements

* use resource in ExampleUploadEntryPoint

* linting

* ruff 0.8 formatting

* bump ruff

* update nomad exmaple tests

* move some test functionality to pynxtools

* update MANIFEST

* simplify nomad import test in test_nomad_examples

* CI: install nomad with infrastructure extra and test also with python 3.12

* fix typo in CI/CD

* update pynxtools dependency

* update pynxtools in dev-requirements

---------

Co-authored-by: Sherjeel Shabih <sshabih@physik.hu-berlin.de>
Co-authored-by: Florian Dobener <florian.dobener@physik.hu-berlin.de>
Co-authored-by: Sandor Brockhauser <sandor.brockhauser@physik.hu-berlin.de>
Co-authored-by: Markus Kuehbach <kuehbach@fhi-berlin.mpg.de>
Co-authored-by: mkuehbach <markus.kuehbach@physik.hu-berlin.de>

.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'}}"
+        run: |
+          uv pip install nomad-lab[infrastructure]@git+https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR.git
       - name: Install package
         run: |
           uv pip install ".[dev]"

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.5.5
+    rev: v0.8.0
     hooks:
       # Run the linter.
       - id: ruff

MANIFEST.in

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