hub issueshttps://gitlab.pasteur.fr/groups/hub/-/issues2024-01-30T16:10:26+01:00https://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/12Upgrade autoscaller api version2024-01-30T16:10:26+01:00Bryan BRANCOTTEUpgrade autoscaller api versionUsed verison is not compatible anymore with k8s clusters
https://gitlab.pasteur.fr/hub/shiny-k8s-example/-/jobs/342492Used verison is not compatible anymore with k8s clusters
https://gitlab.pasteur.fr/hub/shiny-k8s-example/-/jobs/342492Bryan BRANCOTTEBryan BRANCOTTEhttps://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/11La desactivation de l'autoscalling laisse l'HPA en place2024-01-30T16:15:17+01:00Bryan BRANCOTTELa desactivation de l'autoscalling laisse l'HPA en placePour reproduire, il faut déployer avec l'autoscalling, puis le enabled=false. Les templates alors produit n'ont plus l'HPA, qui reste donc en place et continue de travailler.Pour reproduire, il faut déployer avec l'autoscalling, puis le enabled=false. Les templates alors produit n'ont plus l'HPA, qui reste donc en place et continue de travailler.https://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/10Améliorer la création de l'image Docker2023-09-27T10:20:41+02:00Elodie CHAPEAUBLANCAméliorer la création de l'image DockerEssayer un "try catch" pour l'erreur
Essayer de récupérer les erreurs lors de l'installation des packages R.
Si erreur dans au niveau de l'installation ( ex manque de dépendance ), le job devient "failed"Essayer un "try catch" pour l'erreur
Essayer de récupérer les erreurs lors de l'installation des packages R.
Si erreur dans au niveau de l'installation ( ex manque de dépendance ), le job devient "failed"https://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/9Comment passer une API key à l'image ?2023-09-22T13:43:56+02:00Bryan BRANCOTTEComment passer une API key à l'image ?Il faut documenter comment on passe une API key, un login/password à l'image sans l'écrire en dur dans le code, mais via les settings>CI/CD>Variables.
Il faut aussi pour l'exécution en local faire un fichier .env, le donner à dockercomp...Il faut documenter comment on passe une API key, un login/password à l'image sans l'écrire en dur dans le code, mais via les settings>CI/CD>Variables.
Il faut aussi pour l'exécution en local faire un fichier .env, le donner à dockercompose et le mettre dans le gitignorehttps://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/8enable acces_log2023-07-21T10:42:29+02:00Elodie CHAPEAUBLANCenable acces_log
https://docs.posit.co/shiny-server/#access-logs
An access log can be configured globally using the access_log parameter. This log is not enabled by default. This setting controls the location of the access log as well as the format use...
https://docs.posit.co/shiny-server/#access-logs
An access log can be configured globally using the access_log parameter. This log is not enabled by default. This setting controls the location of the access log as well as the format used. The access log can be useful to audit the security and activity taking place on your Shiny Server installation. These logs can be audited manually or automatically to inspect how often various resources are being accessed, or by whom they are being accessed (using the originating IP address). Currently, one access log is created for the entire Shiny Server process; all Shiny applications share this access log.
A ajouter si nécessaire.https://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/7error install packages docs2023-07-10T17:40:11+02:00Elodie CHAPEAUBLANCerror install packages docs
Erreur lors de la commande `pip install -r requirements.txt`
```
virtualenv .venv -p python3
created virtual environment CPython3.10.6.final.0-64 in 114ms
creator CPython3Posix(dest=/home/echapeau/Projets/19417_kubernetes_shiny/gitla...
Erreur lors de la commande `pip install -r requirements.txt`
```
virtualenv .venv -p python3
created virtual environment CPython3.10.6.final.0-64 in 114ms
creator CPython3Posix(dest=/home/echapeau/Projets/19417_kubernetes_shiny/gitlab/shiny-k8s-docs/.venv, clear=False, no_vcs_ignore=False, global=False)
seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/echapeau/.local/share/virtualenv)
added seed packages: pip==22.0.2, setuptools==59.6.0, wheel==0.37.1
activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator
source .venv/bin/activate
pip install -r requirements.txt
Collecting sphinx
Using cached sphinx-7.0.1-py3-none-any.whl (3.0 MB)
Collecting sphinx_rtd_theme
Downloading sphinx_rtd_theme-1.2.2-py2.py3-none-any.whl (2.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 50.8 MB/s eta 0:00:00
Collecting pygraphviz
Downloading pygraphviz-1.11.zip (120 kB)
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Preparing metadata (setup.py) ... done
Collecting sphinx-autobuild
Downloading sphinx_autobuild-2021.3.14-py3-none-any.whl (9.9 kB)
Collecting packaging>=21.0
Using cached packaging-23.1-py3-none-any.whl (48 kB)
Collecting requests>=2.25.0
Using cached requests-2.31.0-py3-none-any.whl (62 kB)
Collecting sphinxcontrib-jsmath
Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting snowballstemmer>=2.0
Using cached snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB)
Collecting docutils<0.21,>=0.18.1
Using cached docutils-0.20.1-py3-none-any.whl (572 kB)
Collecting imagesize>=1.3
Using cached imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB)
Collecting sphinxcontrib-devhelp
Using cached sphinxcontrib_devhelp-1.0.2-py2.py3-none-any.whl (84 kB)
Collecting sphinxcontrib-htmlhelp>=2.0.0
Using cached sphinxcontrib_htmlhelp-2.0.1-py3-none-any.whl (99 kB)
Collecting Jinja2>=3.0
Using cached Jinja2-3.1.2-py3-none-any.whl (133 kB)
Collecting sphinxcontrib-qthelp
Using cached sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Collecting Pygments>=2.13
Using cached Pygments-2.15.1-py3-none-any.whl (1.1 MB)
Collecting babel>=2.9
Using cached Babel-2.12.1-py3-none-any.whl (10.1 MB)
Collecting sphinxcontrib-applehelp
Using cached sphinxcontrib_applehelp-1.0.4-py3-none-any.whl (120 kB)
Collecting sphinxcontrib-serializinghtml>=1.1.5
Using cached sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB)
Collecting alabaster<0.8,>=0.7
Using cached alabaster-0.7.13-py3-none-any.whl (13 kB)
Collecting sphinx
Using cached sphinx-6.2.1-py3-none-any.whl (3.0 MB)
Collecting docutils<0.21,>=0.18.1
Using cached docutils-0.18.1-py2.py3-none-any.whl (570 kB)
Collecting sphinxcontrib-jquery<5,>=4
Using cached sphinxcontrib_jquery-4.1-py2.py3-none-any.whl (121 kB)
Collecting livereload
Downloading livereload-2.6.3-py2.py3-none-any.whl (24 kB)
Collecting colorama
Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)
Collecting MarkupSafe>=2.0
Downloading MarkupSafe-2.1.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
Collecting urllib3<3,>=1.21.1
Downloading urllib3-2.0.3-py3-none-any.whl (123 kB)
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Collecting charset-normalizer<4,>=2
Downloading charset_normalizer-3.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (201 kB)
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Collecting idna<4,>=2.5
Using cached idna-3.4-py3-none-any.whl (61 kB)
Collecting certifi>=2017.4.17
Using cached certifi-2023.5.7-py3-none-any.whl (156 kB)
Collecting tornado
Downloading tornado-6.3.2-cp38-abi3-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (426 kB)
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Collecting six
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: pygraphviz
Building wheel for pygraphviz (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [55 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.10
creating build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/__init__.py -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/testing.py -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/scraper.py -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/agraph.py -> build/lib.linux-x86_64-3.10/pygraphviz
creating build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_scraper.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_close.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_repr_mimebundle.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
running egg_info
writing pygraphviz.egg-info/PKG-INFO
writing dependency_links to pygraphviz.egg-info/dependency_links.txt
writing top-level names to pygraphviz.egg-info/top_level.txt
reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.png' under directory 'doc'
warning: no files found matching '*.txt' under directory 'doc'
warning: no files found matching '*.css' under directory 'doc'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.svn' found anywhere in distribution
no previously-included directories found matching 'doc/build'
adding license file 'LICENSE'
writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
copying pygraphviz/graphviz.i -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.linux-x86_64-3.10/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.linux-x86_64-3.10
creating build/temp.linux-x86_64-3.10/pygraphviz
x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/home/echapeau/Projets/19417_kubernetes_shiny/gitlab/shiny-k8s-docs/.venv/include -I/usr/include/python3.10 -c pygraphviz/graphviz_wrap.c -o build/temp.linux-x86_64-3.10/pygraphviz/graphviz_wrap.o
pygraphviz/graphviz_wrap.c:3020:10: fatal error: graphviz/cgraph.h: Aucun fichier ou dossier de ce type
3020 | #include "graphviz/cgraph.h"
| ^~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pygraphviz
Running setup.py clean for pygraphviz
Failed to build pygraphviz
Installing collected packages: snowballstemmer, urllib3, tornado, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, six, pygraphviz, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, colorama, charset-normalizer, certifi, babel, alabaster, requests, livereload, Jinja2, sphinx, sphinxcontrib-jquery, sphinx-autobuild, sphinx_rtd_theme
Running setup.py install for pygraphviz ... error
error: subprocess-exited-with-error
× Running setup.py install for pygraphviz did not run successfully.
│ exit code: 1
╰─> [57 lines of output]
running install
/home/echapeau/Projets/19417_kubernetes_shiny/gitlab/shiny-k8s-docs/.venv/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.10
creating build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/__init__.py -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/testing.py -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/scraper.py -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/graphviz.py -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/agraph.py -> build/lib.linux-x86_64-3.10/pygraphviz
creating build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/__init__.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_node_attributes.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_html.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_string.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_scraper.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_edge_attributes.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_unicode.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_graph.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_close.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_readwrite.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_attribute_defaults.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_drawing.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_subgraph.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_clear.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_layout.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
copying pygraphviz/tests/test_repr_mimebundle.py -> build/lib.linux-x86_64-3.10/pygraphviz/tests
running egg_info
writing pygraphviz.egg-info/PKG-INFO
writing dependency_links to pygraphviz.egg-info/dependency_links.txt
writing top-level names to pygraphviz.egg-info/top_level.txt
reading manifest file 'pygraphviz.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.png' under directory 'doc'
warning: no files found matching '*.txt' under directory 'doc'
warning: no files found matching '*.css' under directory 'doc'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.svn' found anywhere in distribution
no previously-included directories found matching 'doc/build'
adding license file 'LICENSE'
writing manifest file 'pygraphviz.egg-info/SOURCES.txt'
copying pygraphviz/graphviz.i -> build/lib.linux-x86_64-3.10/pygraphviz
copying pygraphviz/graphviz_wrap.c -> build/lib.linux-x86_64-3.10/pygraphviz
running build_ext
building 'pygraphviz._graphviz' extension
creating build/temp.linux-x86_64-3.10
creating build/temp.linux-x86_64-3.10/pygraphviz
x86_64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DSWIG_PYTHON_STRICT_BYTE_CHAR -I/home/echapeau/Projets/19417_kubernetes_shiny/gitlab/shiny-k8s-docs/.venv/include -I/usr/include/python3.10 -c pygraphviz/graphviz_wrap.c -o build/temp.linux-x86_64-3.10/pygraphviz/graphviz_wrap.o
pygraphviz/graphviz_wrap.c:3020:10: fatal error: graphviz/cgraph.h: Aucun fichier ou dossier de ce type
3020 | #include "graphviz/cgraph.h"
| ^~~~~~~~~~~~~~~~~~~
compilation terminated.
error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
```https://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/6trigger_job failled2023-07-07T14:19:41+02:00Elodie CHAPEAUBLANCtrigger_job failledVoir pipeline : https://gitlab.pasteur.fr/hub/rshiny-k8s/-/pipelines/106631
avec erreur dans le trigger_job suite à la dernière modification.
--> Les droits du projet gitlab "rshiny-k8s-example" ?Voir pipeline : https://gitlab.pasteur.fr/hub/rshiny-k8s/-/pipelines/106631
avec erreur dans le trigger_job suite à la dernière modification.
--> Les droits du projet gitlab "rshiny-k8s-example" ?Bryan BRANCOTTEBryan BRANCOTTEhttps://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/5Modify docker version2023-07-21T10:42:50+02:00Elodie CHAPEAUBLANCModify docker versionModifier "registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:latest" pour utiliser une autre version de dockerModifier "registry-gitlab.pasteur.fr/dsi-tools/docker-images/docker:latest" pour utiliser une autre version de dockerhttps://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/4add version python2023-07-07T09:56:03+02:00Elodie CHAPEAUBLANCadd version pythonajouter la possibilité de changer facilement la version de python que l'on souhaite utiliser.
Faire les tests dans la branche "add-python" avant de merge dans main.ajouter la possibilité de changer facilement la version de python que l'on souhaite utiliser.
Faire les tests dans la branche "add-python" avant de merge dans main.Bryan BRANCOTTEBryan BRANCOTTEhttps://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/3documentation2023-09-22T13:35:45+02:00Elodie CHAPEAUBLANCdocumentationRédiger la doc sur la branche orpheline dédié.
Chaque partie sera dans un fichier dédiée.
La doc doit prendre en compte les différents profils d'utilisateur : Développeur ++ et User shiny
Elle doit intégrée la partie R shiny et Python...Rédiger la doc sur la branche orpheline dédié.
Chaque partie sera dans un fichier dédiée.
La doc doit prendre en compte les différents profils d'utilisateur : Développeur ++ et User shiny
Elle doit intégrée la partie R shiny et Python shiny.https://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/2start doc on dockerfile and helm2023-07-19T15:46:20+02:00Bryan BRANCOTTEstart doc on dockerfile and helmFaire un fichier par idée
* do_helm, comment générer les fichiers yaml pour pouvoir voir le tempalte produit (helm tempalte)
* recette helm
* Dockerfile, le from harborFaire un fichier par idée
* do_helm, comment générer les fichiers yaml pour pouvoir voir le tempalte produit (helm tempalte)
* recette helm
* Dockerfile, le from harborBryan BRANCOTTEBryan BRANCOTTEhttps://gitlab.pasteur.fr/hub/shiny-k8s/-/issues/1Passer l'image sur harbor2023-06-30T14:09:16+02:00Bryan BRANCOTTEPasser l'image sur harbor- [ ] Demande d'ajout de l'image ubuntu:focal sur harbor
- [ ] Modification du dokerfile en conséquence ( ajout de harbor.pasteur.fr/library/ubuntu )- [ ] Demande d'ajout de l'image ubuntu:focal sur harbor
- [ ] Modification du dokerfile en conséquence ( ajout de harbor.pasteur.fr/library/ubuntu )