From c07c575730cb0d15872c660787245724e475d8da Mon Sep 17 00:00:00 2001
From: Theodore Chang <theodore.chang@physik.hu-berlin.de>
Date: Wed, 19 Mar 2025 14:28:51 +0000
Subject: [PATCH] Update dependencies: pytest
---
.gitlab-ci.yml | 2 +-
Dockerfile | 1 -
pyproject.toml | 14 +++++++++-----
pytest.ini | 5 -----
requirements-dev.txt | 20 ++++++++++----------
requirements-plugins.txt | 4 ++--
requirements.txt | 10 +++++-----
tests/app/v1/conftest.py | 2 +-
tests/conftest.py | 4 ++--
tests/test_client.py | 2 +-
10 files changed, 31 insertions(+), 33 deletions(-)
delete mode 100644 pytest.ini
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5fdf953a3b..7110cc6567 100644
--- a/.gitlab-ci.yml
+++ b/.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
diff --git a/Dockerfile b/Dockerfile
index 8b6add58be..4cdea3916d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -138,7 +138,6 @@ COPY .coveragerc \
MANIFEST.in \
mkdocs.yml \
pyproject.toml \
- pytest.ini \
README.md \
README.parsers.md \
requirements.txt \
diff --git a/pyproject.toml b/pyproject.toml
index 127747787c..aab752e1c9 100644
--- a/pyproject.toml
+++ b/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
diff --git a/pytest.ini b/pytest.ini
deleted file mode 100644
index c0a535889d..0000000000
--- a/pytest.ini
+++ /dev/null
@@ -1,5 +0,0 @@
-[pytest]
-testpaths =
- tests
-filterwarnings =
- ignore::DeprecationWarning
\ No newline at end of file
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 7118a0dfec..5dc8cabb70 100644
--- a/requirements-dev.txt
+++ b/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
diff --git a/requirements-plugins.txt b/requirements-plugins.txt
index 600a2dc394..63224413e5 100644
--- a/requirements-plugins.txt
+++ b/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
diff --git a/requirements.txt b/requirements.txt
index 33eacb4090..e4eed40e73 100644
--- a/requirements.txt
+++ b/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
diff --git a/tests/app/v1/conftest.py b/tests/app/v1/conftest.py
index d4a1e15fc4..fdbeafb6ae 100644
--- a/tests/app/v1/conftest.py
+++ b/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
diff --git a/tests/conftest.py b/tests/conftest.py
index a72d3e2687..9b3d5985c3 100644
--- a/tests/conftest.py
+++ b/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)
diff --git a/tests/test_client.py b/tests/test_client.py
index 35211bf701..7cc68cf1c3 100644
--- a/tests/test_client.py
+++ b/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
--
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