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Merge branch 'update-deps' into 'master'

Browse source 
upgrade dependencies

See merge request caimira/caimira!483
This commit is contained in:
Luis Aleixo 2024-02-28 14:55:06 +01:00
commit e0c2e959a2
8 changed files with 128 additions and 104 deletions
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3
.gitlab-ci.yml
View file

@ -12,7 +12,6 @@ include:
variables:
project_name: caimira
PY_VERSION: "3.9"
# ###################################################################################################
@ -110,7 +109,7 @@ check_openshift_config_prod:
- /kaniko/executor --context ${CI_PROJECT_DIR}/${DOCKER_CONTEXT_DIRECTORY} --dockerfile ${CI_PROJECT_DIR}/${DOCKERFILE_DIRECTORY}/Dockerfile --destination ${CI_REGISTRY_IMAGE}/${IMAGE_NAME}:${IMAGE_TAG}
# Print the full registry path of the pushed image
- echo "Image pushed successfully to ${CI_REGISTRY_IMAGE}/${IMAGE_NAME}:${IMAGE_TAG}"
auth-service-image_builder:
extends:

4
README.md
View file

@ -156,9 +156,7 @@ pytest ./caimira
### Running the profiler
The profiler is enabled in one of the following cases:
- the calculator app is running in `debug` mode
- the environment variable `CAIMIRA_PROFILER_ENABLED` is set to 1
The profiler is enabled when the environment variable `CAIMIRA_PROFILER_ENABLED` is set to 1.
When visiting http://localhost:8080/profiler, you can start a new session and choose between [PyInstrument](https://github.com/joerick/pyinstrument) or [cProfile](https://docs.python.org/3/library/profile.html#module-cProfile). The app includes two different profilers, mainly because they can give different information.

4
app-config/openshift/deploymentconfig.yaml
View file

@ -284,7 +284,7 @@
key: ARVE_API_KEY
name: arve-api
- name: DATA_SERVICE_ENABLED
value: 'False'
value: 'True'
image: '${PROJECT_NAME}/calculator-app'
ports:
- containerPort: 8080
@ -363,7 +363,7 @@
- name: CAIMIRA_CALCULATOR_PREFIX
value: /calculator-open
- name: DATA_SERVICE_ENABLED
value: 'False'
value: 'True'
image: '${PROJECT_NAME}/calculator-app'
ports:
- containerPort: 8080

4
caimira/apps/calculator/__init__.py
View file

@ -516,8 +516,8 @@ def make_app(
'filename': 'userguide.html.j2'}),
]
profiler = os.environ.get('CAIMIRA_PROFILER_ENABLED', 0)
if debug or profiler:
profiler_enabled = os.environ.get('CAIMIRA_PROFILER_ENABLED', 0)
if profiler_enabled:
urls += [
(get_root_url(CaimiraProfiler.ROOT_URL), ProfilerPage),
(get_root_url(r'{root_url}/(.*)'.format(root_url=CaimiraProfiler.ROOT_URL)), ProfilerReport),

4
caimira/profiler.py
View file

@ -195,6 +195,10 @@ class CaimiraProfiler:
@property
def is_active(self):
"""Return True if a session is active."""
enabled = os.environ.get("CAIMIRA_PROFILER_ENABLED", 0)
if not enabled:
return False
if not os.path.exists(self._cache_filepath):
return False

6
caimira/tests/apps/calculator/test_report_generator.py
View file

@ -1,8 +1,8 @@
import concurrent.futures
from functools import partial
import os
import time
import numpy.testing
import numpy as np
import pytest
@ -16,7 +16,7 @@ def test_generate_report(baseline_form) -> None:
# generate a report for it. Because this is what happens in the caimira
# calculator, we confirm that the generation happens within a reasonable
# time threshold.
time_limit: float = 20.0 # seconds
time_limit: float = float(os.environ.get("CAIMIRA_TESTS_CALCULATOR_TIMEOUT", 10.))
start = time.perf_counter()
@ -25,6 +25,8 @@ def test_generate_report(baseline_form) -> None:
concurrent.futures.ThreadPoolExecutor, 1,
))
end = time.perf_counter()
total = end-start
print(f"Time limit: {time_limit} | Time taken: {end} - {start} = {total} < {time_limit}")
assert report != ""
assert end - start < time_limit

9
caimira/tests/apps/calculator/test_webapp.py
View file

@ -1,13 +1,13 @@
import os
from pathlib import Path
import pytest
import tornado.testing
from retry import retry
import caimira.apps.calculator
from caimira.apps.calculator.report_generator import generate_permalink
_TIMEOUT = 20.
_TIMEOUT = float(os.environ.get("CAIMIRA_TESTS_CALCULATOR_TIMEOUT", 10.))
@pytest.fixture
@ -34,7 +34,6 @@ async def test_404(http_server_client):
assert resp.code == 404
@retry(tries=10)
class TestBasicApp(tornado.testing.AsyncHTTPTestCase):
def get_app(self):
return caimira.apps.calculator.make_app()
@ -63,7 +62,6 @@ class TestBasicApp(tornado.testing.AsyncHTTPTestCase):
assert 'expected number of new cases is' in response.body.decode()
@retry(tries=10)
class TestCernApp(tornado.testing.AsyncHTTPTestCase):
def get_app(self):
cern_theme = Path(caimira.apps.calculator.__file__).parent.parent / 'themes' / 'cern'
@ -76,7 +74,6 @@ class TestCernApp(tornado.testing.AsyncHTTPTestCase):
assert 'expected number of new cases is' in response.body.decode()
retry(tries=10)
class TestOpenApp(tornado.testing.AsyncHTTPTestCase):
def get_app(self):
return caimira.apps.calculator.make_app(calculator_prefix="/mycalc")
@ -149,7 +146,7 @@ class TestCERNGenericPage(tornado.testing.AsyncHTTPTestCase):
]
return tornado.web.Application(pages, **app.settings)
@tornado.testing.gen_test(timeout=_TIMEOUT)
def test_user_guide(self):
response = yield self.http_client.fetch(self.get_url('/calculator/user-guide'))

198
requirements.txt
View file

@ -3,109 +3,133 @@
# pip list --format freeze | grep -vi caimira | grep -v pip | grep -v setuptools >> requirements.txt
.[app]
anyio==3.6.2
appnope==0.1.3
argon2-cffi==21.3.0
anyio==4.2.0
appnope==0.1.4
argon2-cffi==23.1.0
argon2-cffi-bindings==21.2.0
asttokens==2.2.1
attrs==22.2.0
Babel==2.11.0
backcall==0.2.0
beautifulsoup4==4.11.2
bleach==6.0.0
certifi==2022.12.7
cffi==1.15.1
charset-normalizer==3.0.1
cloudpickle==2.2.1
comm==0.1.2
contourpy==1.0.7
cycler==0.11.0
debugpy==1.6.6
arrow==1.3.0
asttokens==2.4.1
async-lru==2.0.4
attrs==23.2.0
Babel==2.14.0
beautifulsoup4==4.12.3
bleach==6.1.0
certifi==2024.2.2
cffi==1.16.0
charset-normalizer==3.3.2
cloudpickle==3.0.0
comm==0.2.1
contourpy==1.2.0
cycler==0.12.1
debugpy==1.8.1
decorator==5.1.1
defusedxml==0.7.1
entrypoints==0.4
executing==1.2.0
fastjsonschema==2.16.2
fonttools==4.38.0
exceptiongroup==1.2.0
executing==2.0.1
fastjsonschema==2.19.1
fonttools==4.49.0
fqdn==1.5.1
h11==0.14.0
h3==3.7.6
idna==3.4
importlib-metadata==6.0.0
importlib-resources==5.12.0
ipykernel==6.22.0
httpcore==1.0.3
httpx==0.26.0
idna==3.6
importlib-metadata==7.0.1
importlib-resources==6.1.1
ipykernel==6.29.2
ipympl==0.9.3
ipython==8.10.0
ipython==8.18.1
ipython-genutils==0.2.0
ipywidgets==7.7.3
jedi==0.18.2
Jinja2==3.0.3
joblib==1.2.0
json5==0.9.11
jsonschema==4.17.3
jupyter-client==6.1.12
jupyter-core==5.3.0
jupyter-server==1.23.6
jupyterlab-pygments==0.2.2
jupyterlab-server==2.20.0
jupyterlab-widgets==1.1.3
kiwisolver==1.4.4
loky==3.3.0
MarkupSafe==2.1.2
matplotlib==3.7.0
ipywidgets==7.8.1
isoduration==20.11.0
jedi==0.19.1
Jinja2==3.1.3
joblib==1.3.2
json5==0.9.14
jsonpointer==2.4
jsonschema==4.21.1
jsonschema-specifications==2023.12.1
jupyter_client==8.6.0
jupyter_core==5.7.1
jupyter-events==0.9.0
jupyter-lsp==2.2.2
jupyter_server==2.12.5
jupyter_server_terminals==0.5.2
jupyterlab==4.1.1
jupyterlab_pygments==0.3.0
jupyterlab_server==2.25.3
jupyterlab-widgets==1.1.7
kiwisolver==1.4.5
loky==3.4.1
MarkupSafe==2.1.5
matplotlib==3.8.3
matplotlib-inline==0.1.6
memoization==0.4.0
mistune==0.8.4
nbclassic==0.5.3
nbclient==0.5.13
nbconvert==6.5.4
nbformat==5.8.0
nest-asyncio==1.5.6
notebook==6.5.3
notebook-shim==0.2.2
numpy==1.24.2
packaging==23.0
pandas==1.5.3
pandocfilters==1.5.0
mistune==3.0.2
nbclient==0.7.4
nbconvert==7.16.0
nbformat==5.9.2
nest-asyncio==1.6.0
notebook==7.1.0
notebook_shim==0.2.4
numpy==1.26.4
overrides==7.7.0
packaging==23.2
pandas==2.2.0
pandocfilters==1.5.1
parso==0.8.3
pexpect==4.8.0
pickleshare==0.7.5
Pillow==9.4.0
platformdirs==3.0.0
prometheus-client==0.16.0
prompt-toolkit==3.0.37
psutil==5.9.4
pexpect==4.9.0
pillow==10.2.0
platformdirs==4.2.0
prometheus_client==0.20.0
prompt-toolkit==3.0.43
psutil==5.9.8
ptyprocess==0.7.0
pure-eval==0.2.2
py==1.11.0
pycparser==2.21
Pygments==2.14.0
pyparsing==3.0.9
pyrsistent==0.19.3
Pygments==2.17.2
pyinstrument==4.6.2
PyJWT==2.8.0
pyparsing==3.1.1
python-dateutil==2.8.2
pytz==2022.7.1
pyzmq==25.0.0
requests==2.28.2
python-json-logger==2.0.7
pytz==2024.1
PyYAML==6.0.1
pyzmq==25.1.2
referencing==0.33.0
requests==2.31.0
retry==0.9.2
ruptures==1.1.8
scikit-learn==1.2.1
scipy==1.10.1
Send2Trash==1.8.0
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
rpds-py==0.18.0
ruptures==1.1.9
scikit-learn==1.4.1.post1
scipy==1.12.0
Send2Trash==1.8.2
six==1.16.0
sniffio==1.3.0
soupsieve==2.4
stack-data==0.6.2
terminado==0.17.1
threadpoolctl==3.1.0
timezonefinder==6.1.9
soupsieve==2.5
stack-data==0.6.3
terminado==0.18.0
threadpoolctl==3.3.0
timezonefinder==6.4.1
tinycss2==1.2.1
tornado==6.2
traitlets==5.9.0
types-retry==0.9.9.2
urllib3==1.26.14
voila==0.2.16
wcwidth==0.2.6
tomli==2.0.1
tornado==6.4
traitlets==5.14.1
types-python-dateutil==2.8.19.20240106
types-retry==0.9.9.4
typing_extensions==4.9.0
tzdata==2024.1
uri-template==1.3.0
urllib3==2.2.0
voila==0.5.5
wcwidth==0.2.13
webcolors==1.13
webencodings==0.5.1
websocket-client==1.5.1
websockets==10.4
wheel==0.36.2
widgetsnbextension==3.6.2
zipp==3.14.0
websocket-client==1.7.0
websockets==12.0
wheel==0.41.3
widgetsnbextension==3.6.6
zipp==3.17.0