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70fdc70
Added new Julia datascience notebook with some standard datascience-r…
SebastianPrehn Jan 12, 2024
90a3293
Modified architecture.yml file to include the new datascience notebook
SebastianPrehn Jan 12, 2024
e7a49b7
Update kernel for Julia 1.10 pre-optimization
SebastianPrehn Jan 24, 2024
9a07128
Merge branch 'dev' into julia-datascience-notebook
SebastianPrehn Jan 26, 2024
0bf954a
Test for Surrogates package added
SebastianPrehn Jan 26, 2024
2defe65
Add the jupyterlab version tag to the images
rasmunk Feb 8, 2024
205f42a
Adjust the pipelines such that both a latest and jupyterlab tagged ve…
rasmunk Feb 8, 2024
b333966
Add OpenMPI as a compiled installation to the SLURM Notebook
rasmunk Feb 12, 2024
0a6d4c5
Include the OpenMPI library path
rasmunk Feb 12, 2024
f842925
Ensure that the default python3 kernel also has the path to the OpenM…
rasmunk Feb 13, 2024
a6f4faf
Remove redundant permission calls
rasmunk Feb 13, 2024
852e58b
Remove redundant permission calls
rasmunk Feb 13, 2024
cb9bcf4
Remove redundant permission calls
rasmunk Feb 13, 2024
fb5e4aa
Update README.rst
rasmunk Feb 27, 2024
4521e77
Update README.rst
rasmunk Feb 27, 2024
4a23d1c
Bump black from 22.3.0 to 24.3.0
dependabot[bot] Mar 20, 2024
2be7281
Merge pull request #68 from ucphhpc/dependabot/pip/black-24.3.0
rasmunk Mar 21, 2024
4bda1bb
Update requirements-dev.txt
rasmunk Mar 27, 2024
7a33147
Merge branch 'ucphhpc:master' into julia-datascience-notebook
SebastianPrehn Apr 10, 2024
56eef56
Merge dev branch to bump jupyterlab version 4.1.5, OpenMPI to 5.0.2 a…
rasmunk Apr 12, 2024
616be29
Update architecture.yml
rasmunk Apr 14, 2024
9dd9c3f
Update Dockerfile.cuda
rasmunk Jun 6, 2024
5652ec1
Merge branch 'ucphhpc:master' into julia-datascience-notebook
SebastianPrehn Jul 4, 2024
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1,235 changes: 1,048 additions & 187 deletions 1.gocd.yml

Large diffs are not rendered by default.

5 changes: 2 additions & 3 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,7 @@
.PHONY: installcheck uninstallcheck test test-all push push-all

OWNER:=ucphhpc
TAG:=dev
JUPYTERLAB_VERSION:=4.0.12
TAG:=latest
PACKAGE_TIMEOUT:=600
ALL_IMAGES:=base-notebook python-notebook statistics-notebook r-notebook slurm-notebook python-cuda-notebook gpu-notebook datascience-notebook chemistry-notebook fenics-notebook qsharp-notebook hpc-notebook hpc-ocean-notebook hpc-gpu-notebook ocean-notebook geo-notebook bio-notebook bio-bigdata-notebook bio-bsa-notebook sme-notebook jwst-notebook julia-notebook cern-notebook

Expand All @@ -18,7 +17,7 @@ help:
@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'

init:
. $(VENV)/activate; python3 init-notebooks.py --branch dev --tag $(TAG) --jupyterlab-version $(JUPYTERLAB_VERSION)
. $(VENV)/activate; python3 init-notebooks.py --branch master --tag $(TAG)

clean:
rm -fr .env
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14 changes: 8 additions & 6 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,17 @@ Getting Started
Before any of the images can be built, the Dockerfiles for each Notebook has to be generated first.
The reason for this is that by default each notebook defined by a `Jinja2 <https://jinja2docs.readthedocs.io/en/stable/>`__ template.

To ensure that the nessesary libraries are installed to generate the Notebooks, we recommend that you create a virtual environment
This entire process can also be simplified by simply executing ``make`` in the root directory, which will create an initial Python virtual environment and use the current `architecture.yml` file setup to generate the Dockerfiles and the associated GOCD configuration::

make

Alternatively, you can also setup the environment manually with the following steps.

To start with, you should ensure that the nessesary libraries are installed to generate the Notebooks, we recommend that you create a virtual environment
and install the associated requiremnets::

username@hostname:~/jupyter/nbi-jupyter-docker-stacks$ python3 -m virtualenv venv
username@hostname:~/jupyter/nbi-jupyter-docker-stacks$ source venv
username@hostname:~/jupyter/nbi-jupyter-docker-stacks$ source venv/bin/activate
(venv) username@hostname:~/jupyter/nbi-jupyter-docker-stacks$ pip install -r requirements.txt

Afterwards, you should now be able to use the ``init-notebooks.py`` script to generate template and render the Jinja2 template files::
Expand All @@ -44,10 +50,6 @@ pipelines as part of the UCPH CI/CD infrastructure.

The Notebooks and the associated GOCD configuration file are generated based on the definitions specified in the ``architecture.yml`` file.

This entire process can also be simplified by simply executing ``make`` in the root directory, which will create an initial Python virtual environment and use the current `architecture.yml` file setup to generate the Dockerfiles and the associated GOCD configuration::

make

--------
Building
--------
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