Update dependencies: pytest

.gitlab-ci.yml

@@ -193,7 +193,7 @@ generate pytest timings:
     - <<: [*non-docs-changes, *manual-allow_failure]
 
 python tests:
-  parallel: 3
+  parallel: 4
   extends: .base_test
   script:
     - python -m pytest --cov=nomad --cov-report term --cov-config=.coveragerc -sv tests --splits $CI_NODE_TOTAL --group=$CI_NODE_INDEX

Dockerfile

@@ -138,7 +138,6 @@ COPY .coveragerc \
      MANIFEST.in \
      mkdocs.yml \
      pyproject.toml \
-     pytest.ini \
      README.md \
      README.parsers.md \
      requirements.txt \

pyproject.toml

@@ -96,7 +96,7 @@ dev = [
     'pytest-split',
     'pytest-timeout',
     'pytest-xdist',
-    'pytest>=5.3,<8',
+    'pytest',
     'python-gitlab',
     'ruff',
     'setuptools>=70', # py3.12 doesn't bundle in setuptools, but this is required by mongomock lib
@@ -179,12 +179,16 @@ plugins = ["pydantic.mypy"]
 extra-index-url = [
     "https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple",
 ]
-constraint-dependencies = [# can be removed once pynxtools removes kikuchipy restriction
-    "hyperspy>=1.7.6",
-    "pillow<10.1",
-]
 override-dependencies = [
     'elasticsearch-dsl<8',
     'python-magic',
     'unidecode',
 ]
+
+[tool.pytest.ini_options]
+asyncio_default_fixture_loop_scope = "function"
+testpaths = ["tests"]
+filterwarnings = [
+    "ignore::DeprecationWarning",
+    "ignore::SyntaxWarning",
+]
\ No newline at end of file

pytest.ini

-[pytest]
-testpaths =
-    tests
-filterwarnings =
-    ignore::DeprecationWarning
\ No newline at end of file

requirements-dev.txt

@@ -5,7 +5,7 @@ aiosmtpd==1.4.6           # via nomad-lab (pyproject.toml)
 alembic==1.15.1           # via jupyterhub, -r requirements.txt
 amqp==5.3.1               # via kombu, -r requirements.txt
 annotated-types==0.7.0    # via pydantic, -r requirements.txt
-anyio==4.8.0              # via httpx, starlette, watchfiles, -r requirements.txt
+anyio==4.9.0              # via httpx, starlette, watchfiles, -r requirements.txt
 arrow==1.3.0              # via isoduration, -r requirements.txt
 ase==3.22.1               # via matid, -r requirements.txt, nomad-lab (pyproject.toml)
 asttokens==2.4.1          # via devtools
@@ -30,7 +30,7 @@ click-plugins==1.1.1      # via celery, -r requirements.txt
 click-repl==0.3.0         # via celery, -r requirements.txt
 colorama==0.4.6           # via click, mkdocs, mkdocs-material, pytest, tqdm, uvicorn, -r requirements.txt
 contourpy==1.3.1          # via matplotlib, -r requirements.txt
-coverage==7.6.12          # via pytest-cov
+coverage==7.7.0           # via pytest-cov
 cryptography==44.0.2      # via certipy, jwcrypto, pyjwt, rfc3161ng, -r requirements.txt
 cycler==0.12.1            # via matplotlib, -r requirements.txt
 deprecation==2.1.0        # via python-keycloak, -r requirements.txt
@@ -93,7 +93,7 @@ mkdocs-get-deps==0.2.0    # via mkdocs
 mkdocs-git-revision-date-localized-plugin==1.4.5  # via nomad-lab (pyproject.toml)
 mkdocs-glightbox==0.4.0   # via nomad-lab (pyproject.toml)
 mkdocs-macros-plugin==1.3.7  # via nomad-lab (pyproject.toml)
-mkdocs-material==9.6.8    # via nomad-lab (pyproject.toml)
+mkdocs-material==9.6.9    # via nomad-lab (pyproject.toml)
 mkdocs-material-extensions==1.3.1  # via mkdocs-material, nomad-lab (pyproject.toml)
 mkdocs-redirects==1.2.2   # via nomad-lab (pyproject.toml)
 mongoengine==0.29.1       # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -108,7 +108,7 @@ networkx==3.4.2           # via matid, pymatgen, -r requirements.txt
 numpy==1.26.4             # via ase, contourpy, h5grove, h5py, matid, matplotlib, monty, pandas, pymatgen, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
 oauthenticator==17.3.0    # via -r requirements.txt, nomad-lab (pyproject.toml)
 oauthlib==3.2.2           # via jupyterhub, -r requirements.txt
-optimade==1.2.1           # via -r requirements.txt, nomad-lab (pyproject.toml)
+optimade==1.2.2           # via -r requirements.txt, nomad-lab (pyproject.toml)
 orjson==3.10.15           # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
 packaging==24.2           # via deprecation, gunicorn, jupyter-events, jupyterhub, matplotlib, mkdocs, mkdocs-macros-plugin, mongomock, pint, plotly, pytest, xarray, -r requirements.txt
 paginate==0.5.7           # via mkdocs-material
@@ -116,7 +116,7 @@ palettable==3.3.3         # via pymatgen, -r requirements.txt
 pamela==1.2.0 ; sys_platform != 'win32'  # via jupyterhub, -r requirements.txt
 pandas==2.2.3             # via pymatgen, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
 pathspec==0.12.1          # via mkdocs, mkdocs-macros-plugin
-pillow==10.0.1            # via matplotlib, -c (workspace), -r requirements.txt
+pillow==11.1.0            # via matplotlib, -r requirements.txt
 pint==0.17                # via -r requirements.txt, nomad-lab (pyproject.toml)
 platformdirs==4.3.6       # via mkdocs-get-deps
 plotly==5.24.1            # via pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
@@ -138,10 +138,10 @@ pyinstrument==5.0.1       # via -r requirements.txt, nomad-lab (pyproject.toml)
 pyjwt==2.10.1             # via oauthenticator, -r requirements.txt, nomad-lab (pyproject.toml)
 pymatgen==2024.5.1        # via -r requirements.txt, nomad-lab (pyproject.toml)
 pymdown-extensions==10.14.3  # via mkdocs-material
-pymongo==4.11.2           # via mongoengine, optimade, -r requirements.txt
+pymongo==4.11.3           # via mongoengine, optimade, -r requirements.txt
 pyparsing==3.2.1          # via matplotlib, rdflib, -r requirements.txt
-pytest==7.4.4             # via pytest-asyncio, pytest-cov, pytest-split, pytest-timeout, pytest-xdist, nomad-lab (pyproject.toml)
-pytest-asyncio==0.23.8    # via nomad-lab (pyproject.toml)
+pytest==8.3.5             # via pytest-asyncio, pytest-cov, pytest-split, pytest-timeout, pytest-xdist, nomad-lab (pyproject.toml)
+pytest-asyncio==0.25.3    # via nomad-lab (pyproject.toml)
 pytest-cov==6.0.0         # via nomad-lab (pyproject.toml)
 pytest-split==0.10.0      # via nomad-lab (pyproject.toml)
 pytest-timeout==2.3.1     # via nomad-lab (pyproject.toml)
@@ -156,7 +156,7 @@ python-magic==0.4.27      # via --override (workspace), -r requirements.txt, nom
 python-magic-bin==0.4.14 ; sys_platform == 'win32'  # via -r requirements.txt, nomad-lab (pyproject.toml)
 python-multipart==0.0.20  # via -r requirements.txt, nomad-lab (pyproject.toml)
 pytz==2025.1              # via mkdocs-git-revision-date-localized-plugin, mongomock, pandas, -r requirements.txt, nomad-lab (pyproject.toml)
-pywin32==309 ; sys_platform == 'win32'  # via docker, -r requirements.txt
+pywin32==310 ; sys_platform == 'win32'  # via docker, -r requirements.txt
 pyyaml==6.0.2             # via jupyter-events, mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, pybtex, pymdown-extensions, pyyaml-env-tag, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml)
 pyyaml-env-tag==0.1       # via mkdocs
 rdflib==5.0.0             # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -173,7 +173,7 @@ ruff==0.11.0              # via nomad-lab (pyproject.toml)
 scikit-learn==1.6.1       # via matid, -r requirements.txt
 scipy==1.15.2             # via ase, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
 sentinels==1.0.0          # via mongomock, -r requirements.txt
-setuptools==76.0.0        # via nomad-lab (pyproject.toml)
+setuptools==76.1.0        # via nomad-lab (pyproject.toml)
 six==1.17.0               # via asttokens, elasticsearch-dsl, pybtex, python-dateutil, rdflib, rfc3339-validator, -r requirements.txt
 smmap==5.0.2              # via gitdb
 sniffio==1.3.1            # via anyio, httpx, -r requirements.txt

requirements-plugins.txt

@@ -3,7 +3,7 @@
 aiofiles==24.1.0          # via python-keycloak, -c requirements-dev.txt
 aniso8601==10.0.0         # via nomad-lab
 annotated-types==0.7.0    # via pydantic, -c requirements-dev.txt
-anyio==4.8.0              # via httpx, -c requirements-dev.txt
+anyio==4.9.0              # via httpx, -c requirements-dev.txt
 ase==3.22.1               # via asr, matid, nomad-lab, -c requirements-dev.txt
 asr==0.4.1                # via nomad-parser-plugins-workflow
 async-property==0.2.2     # via python-keycloak, -c requirements-dev.txt
@@ -85,7 +85,7 @@ panedr==0.8.0             # via nomad-lab, nomad-parser-plugins-atomistic
 parmed==4.3.0             # via nomad-lab
 pathsimanalysis==1.2.0    # via mdanalysis
 phonopy==2.11.0           # via asr, nomad-parser-plugins-workflow
-pillow==10.0.1            # via matplotlib, -c requirements-dev.txt, -c (workspace)
+pillow==11.1.0            # via matplotlib, -c requirements-dev.txt
 pint==0.17                # via nomad-lab, -c requirements-dev.txt
 plotly==5.24.1            # via asr, nomad-lab, pymatgen, -c requirements-dev.txt
 py-spy==0.4.0             # via nomad-lab, -c requirements-dev.txt

requirements.txt

@@ -4,7 +4,7 @@ aiofiles==24.1.0          # via python-keycloak
 alembic==1.15.1           # via jupyterhub
 amqp==5.3.1               # via kombu
 annotated-types==0.7.0    # via pydantic
-anyio==4.8.0              # via httpx, starlette, watchfiles
+anyio==4.9.0              # via httpx, starlette, watchfiles
 arrow==1.3.0              # via isoduration
 ase==3.22.1               # via matid, nomad-lab (pyproject.toml)
 async-property==0.2.2     # via python-keycloak
@@ -80,13 +80,13 @@ networkx==3.4.2           # via matid, pymatgen
 numpy==1.26.4             # via ase, contourpy, h5grove, h5py, matid, matplotlib, monty, pandas, pymatgen, scikit-learn, scipy, spglib, tifffile, xarray, nomad-lab (pyproject.toml)
 oauthenticator==17.3.0    # via nomad-lab (pyproject.toml)
 oauthlib==3.2.2           # via jupyterhub
-optimade==1.2.1           # via nomad-lab (pyproject.toml)
+optimade==1.2.2           # via nomad-lab (pyproject.toml)
 orjson==3.10.15           # via h5grove, nomad-lab (pyproject.toml)
 packaging==24.2           # via deprecation, gunicorn, jupyter-events, jupyterhub, matplotlib, mongomock, pint, plotly, xarray
 palettable==3.3.3         # via pymatgen
 pamela==1.2.0 ; sys_platform != 'win32'  # via jupyterhub
 pandas==2.2.3             # via pymatgen, xarray, nomad-lab (pyproject.toml)
-pillow==10.0.1            # via matplotlib, -c (workspace)
+pillow==11.1.0            # via matplotlib
 pint==0.17                # via nomad-lab (pyproject.toml)
 plotly==5.24.1            # via pymatgen, nomad-lab (pyproject.toml)
 ply==3.11                 # via jsonpath-ng
@@ -104,7 +104,7 @@ pydantic-settings==2.8.1  # via h5grove, optimade
 pyinstrument==5.0.1       # via nomad-lab (pyproject.toml)
 pyjwt==2.10.1             # via oauthenticator, nomad-lab (pyproject.toml)
 pymatgen==2024.5.1        # via nomad-lab (pyproject.toml)
-pymongo==4.11.2           # via mongoengine, optimade
+pymongo==4.11.3           # via mongoengine, optimade
 pyparsing==3.2.1          # via matplotlib, rdflib
 python-dateutil==2.9.0.post0  # via arrow, celery, elasticsearch-dsl, jupyterhub, matplotlib, pandas, rfc3161ng
 python-dotenv==1.0.1      # via pydantic-settings, uvicorn
@@ -115,7 +115,7 @@ python-magic==0.4.27      # via --override (workspace), nomad-lab (pyproject.tom
 python-magic-bin==0.4.14 ; sys_platform == 'win32'  # via nomad-lab (pyproject.toml)
 python-multipart==0.0.20  # via nomad-lab (pyproject.toml)
 pytz==2025.1              # via mongomock, pandas, nomad-lab (pyproject.toml)
-pywin32==309 ; sys_platform == 'win32'  # via docker
+pywin32==310 ; sys_platform == 'win32'  # via docker
 pyyaml==6.0.2             # via jupyter-events, pybtex, uvicorn, nomad-lab (pyproject.toml)
 rdflib==5.0.0             # via nomad-lab (pyproject.toml)
 referencing==0.36.2       # via jsonschema, jsonschema-specifications, jupyter-events

tests/app/v1/conftest.py

@@ -19,6 +19,6 @@
 import pytest
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope='module')
 def client(api_v1):
     return api_v1

tests/conftest.py

@@ -220,7 +220,7 @@ def reset_config():
     utils.set_console_log_level(test_log_level)
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope='module')
 def api_v1(monkeysession, user_molds):
     """
     This fixture provides an HTTP client with Python requests interface that accesses
@@ -262,7 +262,7 @@ def api_v1(monkeysession, user_molds):
     return test_client
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope='module')
 def client_with_api_v1(api_v1, monkeysession):
     def call_requests(method, path, *args, **kwargs):
         return getattr(api_v1, method)(path, *args, **kwargs)

tests/test_client.py

@@ -69,7 +69,7 @@ def many_uploads(non_empty_uploaded: tuple[str, str], user1: User, proc_infra):
             pass
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope='module')
 def async_api_v1(monkeysession):
     """
     This fixture provides an HTTP client with AsyncClient that accesses