Jupyterlab openmpp poc (#518) #527
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* feat: install openmpp as jupyterlab service * fix: generate dockerfiles * chore: trigger auto-deploy * fix: copy oms startup script * fix: copy script in correct docker bit * fix: make script executable * fix: update openm version, fix config * fix: sync issue * fix: prepare openmpp config for prod deployment * fix: move config to start-oms script
chuckbelisle
pushed a commit
that referenced
this pull request
Sep 27, 2023
* update base image and fix errors * Update 6_remote-desktop.Dockerfile: remove light-locker The light-locker removal command was failing, as light-locker was not installed... so I removed the removal command but when I launch the container on Kubeflow... the screen is locked. * make generate-dockerfiles * trigger CI/CD * remove light-locker later in build process the screen is still locking. :-/ * remove xfce4-screensaver the screen is still locking. :-/ * test(pspp): French UI Test PSPP from Ubuntu Repo to make sure French UI is shown. Remove installer script and update Dockerfile. * add apt-get update * remove pspp.sh * remove pspp.sh * Update build_push.yaml: actions/setup-python@v4 (#490) update actions/setup-python@v2 to actions/setup-python@v4 * Update build_push.yaml: deprecate set-output (#491) * Update build_push.yaml: deprecate set-output update workflow to use $GITHUB_OUTPUT instead of set-output. See: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/ * Update build_push.yaml: update syntax * Update build_push.yaml: update syntax for interpolation * Update build_push.yaml: change notebook name variable name * update remaining set-output commands * Update Makefile: reset set-output commands for Makefile Github Actions was complaining about set-output in the Makefile but I think we have to leave these lines alone since they are used by Make and not by Github Actions. * Update Makefile (#508) * Update rstudio.desktop: /usr/bin/rstudio The previously set location no longer exists. * Update 6_rstudio.Dockerfile: update Rstudio version I've updated rstudio-server to a (hopefully) compatible version. * make generate-dockerfiles * downgrade: rstudio-desktop to 2023.06.0-421 * update(r-studio-desktop.sh): sha256 * update(Rprofile.site): dev repo * update(Rprofile.site): reset R repo * update(6_rstudio): mkdir -p /etc/rstudio builds were failing because this dir did not exist * update set-output to GITHUB_OUTPUT (#501) * update set-output to GITHUB_OUTPUT * create(6_rstudio-server.Dockerfile) * update(6_rstudio): mkdir -p /etc/rstudio * update(0_cpu, 0_cpu_sas): BASE_VERSION=2023-08-07 * update(6_rstudio): remove tidymodels, causing test to fail * update(test_packages): add tidymodels to exclude list * update(test_packages): add more to exclusion list * update(CUDA): update ubuntu1804 to ubuntu2204 * update(test_packages): tidymodels ==> r-tidymodels * update(test_packages): comment out two jupyterlab extensions * update(jupyterlab): jupyterlab-git==0.42.0 * update(jupyterlab): update packages and vscode * update(jupyterlab): refactor dockerfile - switch from conda to mamba - switch some conda statements to pip * make generate-dockerfiles * downgrade tidymodels to 1.0.0 We'll have to wait until the rstudio image is based on R 4.3 before we can upgrade to tidymodels==1.1.0 * Update Makefile: remove buildkit=0 remove buildkit=0 * update (0_Rocker, r-studio-desktop): 2023.06.2-561 * update rstudio-server: 2023.06.2-561 * update(PR): based on comments * update(jupyterlab): jupyter-dash caused build fail so I tried removing the version pinning, it wasn't breaking before so I'm not sure what changed. * update(rstudio): remove pin on tidymodels since it breaks on the newer versions of R but we don't have a consistent version of R across images so it might be helpful to unpin tidymodels so we can let the system resolve a compatible version. * update(get-nvidia-stuff): 1804 to 2204 * Downgrade remote desktop (#519) * revert(remote-desktop): to previous working state * update(r-studio-desktop): revert installer * update(PR): based on comments * update(jupyterlab): jupyter-dash caused build fail so I tried removing the version pinning, it wasn't breaking before so I'm not sure what changed. * update(rstudio): remove pin on tidymodels since it breaks on the newer versions of R but we don't have a consistent version of R across images so it might be helpful to unpin tidymodels so we can let the system resolve a compatible version. * update(get-nvidia-stuff): 1804 to 2204 * Update Dockerfile --------- Co-authored-by: Bryan Paget <bryan.paget@statcan.gc.ca> * make generate-dockerfiles * update branch (#524) * Update build_push.yaml: actions/setup-python@v4 (#490) update actions/setup-python@v2 to actions/setup-python@v4 * Update build_push.yaml: deprecate set-output (#491) * Update build_push.yaml: deprecate set-output update workflow to use $GITHUB_OUTPUT instead of set-output. See: https://github.blog/changelog/2022-10-11-github-actions-deprecating-save-state-and-set-output-commands/ * Update build_push.yaml: update syntax * Update build_push.yaml: update syntax for interpolation * Update build_push.yaml: change notebook name variable name * update remaining set-output commands * Update Makefile: reset set-output commands for Makefile Github Actions was complaining about set-output in the Makefile but I think we have to leave these lines alone since they are used by Make and not by Github Actions. * Update Makefile (#508) * update set-output to GITHUB_OUTPUT (#501) * update set-output to GITHUB_OUTPUT * feat(workflows): integrate hadolint (dockle failed) (#500) * feat(workflow): leverage hadolint * Remove minio (#522) --------- Co-authored-by: Jose Manuel (Ito) <jose.matsuda@statcan.gc.ca> Co-authored-by: Wendy Gaultier <wvgaultier@gmail.com> * revert(6_jupyterlab): revert digression * make generate-dockerfiles * Update 6_jupyterlab.Dockerfile Fix issue with JupyterLab extensions * Update 6_rstudio.Dockerfile: remove tidymodels Tidymodels is a troublesome package, will leave to the user to install, if needed. * make generate-dockerfiles * update(jupyterlab): 4.0.5 I was getting errors saying xxx extension needs to be included in build. * update(jupyterlab): 4.0.5 I was getting errors saying xxx extension needs to be included in build. * update(jupyterlab): 4.0.5 I was getting errors saying xxx extension needs to be included in build. * update(jupyterlab): fix extensions I reworked the package install script to use fewer RUN blocks. I also discovered jupyter_contrib_nbextensions prefers pip over mamba. Local testing suggests I've stopped the jupyterlab build errors. * update(test_packages): add jupyter ext to exclude list I added pillow and pyyaml to the exclude list since they are not imported by name (e.g. import pil, import yaml). * Make torch available (#520) * update(pytorch): remove virtual env * update(pytorch): remove virtual env * update(cpu, pytorch): mamba install pytorch to base * update(pytorch): adjust torch installation * update(pytorch): add ipykernel and conda env * update(pytorch): remove CUDA The PyTorch install command includes CUDA drivers, so I'll try installing those instead of our custom install script. * update(pytorch): add ipykernel * update(pytorch): add gputil gputil has nvidia-smi * update(tensorflow): add cuda to mamba command I also tweaked the pytorch image to use mamba for the clean command * update(tensorflow): add cuda to mamba command I also tweaked the pytorch image to use mamba for the clean command * update(tensorflow): remove tensorflow-gpu tensorflow works for both gpu and cpu * update(gpu-notebooks): remove conda env tensorflow tests are failing, I think they expect tensorflow to be installed in the base env, which is what I prefer, so I'll move pytorch into the base env as well. * update(cpu, pytorch, tensorflow): consistency * update(test_tensorflow): use tensorflow env * update(test_packages): add gputil to exclude list * update(test_packages): add cudnn, cudatoolkit to exclude list * update(pytorch, tensorflow): ipykernel install * revert(cpu): fix cpu conda env * update(tests): gpu available * update(makefile): restore tensorflow build * update(tests): remove GPU test Github Actions won't have a GPU * update(jupyterlab): jupyter-dash caused build fail so I tried removing the version pinning, it wasn't breaking before so I'm not sure what changed. * update(PR): based on comments * update(rstudio): remove pin on tidymodels since it breaks on the newer versions of R but we don't have a consistent version of R across images so it might be helpful to unpin tidymodels so we can let the system resolve a compatible version. * update(get-nvidia-stuff): 1804 to 2204 * revert(2_tensorflow): prev working configuration * update(0_Rocker): remove whitespace delta * update(2_tensorflow): new line * Update test_tensorflow.py: revert test We are not yet using a Tensorflow conda env. --------- Co-authored-by: Bryan Paget <bryan.paget@statcan.gc.ca> * Update test_packages.py: add missing comma * Jupyterlab openmpp poc (#518) * feat: install openmpp as jupyterlab service * fix: generate dockerfiles * chore: trigger auto-deploy * fix: copy oms startup script * fix: copy script in correct docker bit * fix: make script executable * fix: update openm version, fix config * fix: sync issue * fix: prepare openmpp config for prod deployment * fix: move config to start-oms script * Jupyterlab openmpp poc (#518) (#527) * feat: install openmpp as jupyterlab service * fix: generate dockerfiles * chore: trigger auto-deploy * fix: copy oms startup script * fix: copy script in correct docker bit * fix: make script executable * fix: update openm version, fix config * fix: sync issue * fix: prepare openmpp config for prod deployment * fix: move config to start-oms script Co-authored-by: Pat Ledgerwood <32804494+vexingly@users.noreply.github.com> * Jupyterlab openmpp poc (#518) (#528) * feat: install openmpp as jupyterlab service * fix: generate dockerfiles * chore: trigger auto-deploy * fix: copy oms startup script * fix: copy script in correct docker bit * fix: make script executable * fix: update openm version, fix config * fix: sync issue * fix: prepare openmpp config for prod deployment * fix: move config to start-oms script Co-authored-by: Pat Ledgerwood <32804494+vexingly@users.noreply.github.com> * update(jupyterlab): add --openssl-legacy-provider npm build ompp-ui was failing, adding --openssl-legacy-provider to the build command resolved the issue. * update(jupyterlab): add ARG NODE_OPTIONS npm build ompp-ui was failing, adding --openssl-legacy-provider to the build command resolved the issue locally but breaks on Github Actions, will try ARG NODE_OPTIONS=--openssl-legacy-provider. --------- Co-authored-by: Bryan Paget <bryan.paget@statcan.gc.ca> Co-authored-by: Jose Manuel (Ito) <jose.matsuda@statcan.gc.ca> Co-authored-by: Wendy Gaultier <wvgaultier@gmail.com> Co-authored-by: Pat Ledgerwood <32804494+vexingly@users.noreply.github.com>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
feat: install openmpp as jupyterlab service
fix: generate dockerfiles
chore: trigger auto-deploy
fix: copy oms startup script
fix: copy script in correct docker bit
fix: make script executable
fix: update openm version, fix config
fix: sync issue
fix: prepare openmpp config for prod deployment
fix: move config to start-oms script
Description
What your PR adds/fixes/removes
Tests / Quality Checks
Are there breaking changes?
Ask yourself the next question;
If no, then carry on. If yes, there is a breaking change and we want to maintain the previous image do the following
Automated Testing/build and deployment
auto-deploytag to the PR before pushing in order to build and push the image to ACR so you can test it in cluster as a custom image?JupyterLab extensions
jupyter labextension listfrom inside the notebook)?VS Code tests
Code review
auto-deploytag to your PR before your most recent push to this repo? This causes CI to build the image and push to our ACR, letting reviewers access the built image without having to create it themselvesk8scc01covidacrdev.azurecr.io/jupyterlab-cpu:746d058e2f37e004da5ca483d121bfb9e0545f2b)?