docker dev & test environment

[jorgeboucas]

Docker environment should allow development and testing of py4cytoscape and RCy3. It therefore needs:

• [x] Jupyter notebook: python and R kernels
• [x] R-Studio server
• [x] Cytoscape (image tags matching Cytoscape version)
• [x] Readme: development and automated test
• [x] hub.docker.com/repository/docker/cytoscape/py4cytoscape

[bdemchak]

Jorge ... very nice ... how can we get another tester to verify this?

Also, I'm very happy to have this in py4cytoscape. I'm not sure that an R person would know to look here. Should this be a separate repo, or duplicated in the R repo, or what?? I don't think there's an obvious choice here.

[jorgeboucas]

I am gonna start opening issues from tests performed inside the container, I guess this will force @bdemchak and @kozo2 to give it a try at the docker env.

Regarding the location, I would keep it first for the development of py4cytoscape and testing in parallel of RCy3 functions. Once fully seen as a good resource we can then figure out how to bring the RCy3 people on board with a proper name and hub location.

Meanwhile, could we get a hub.docker.com/repository/docker/cytoscape/py4cytoscape repo?

[kozo2]

@jorgeboucas I would like to move from Docker Hub to GitHub Container Registry. For that, we need to set

Could you give me some time to contact the Cytoscape github organization administrator?

[kozo2]

@jorgeboucas I'm sorry, I changed my mind. As you say, we'd better use Docker Hub. I will ask Cytoscapers to get hub.docker.com/repository/docker/cytoscape/py4cytoscape repo. It seems that we can use Docker Hub without restrictions if it is approved by Docker's open source program. https://www.docker.com/blog/expanded-support-for-open-source-software-projects/

[kozo2]

@jorgeboucas I configured the Docker Hub automated build. But it failed like https://hub.docker.com/repository/registry-1.docker.io/cytoscape/py4cytoscape/builds/6fedbd17-95de-4e4f-87a2-e1314b46ff7f Please let me know if you have any ideas for resolving this error.

[bdemchak]

docker dev & test environment #17

[kozo2]

@jorgeboucas We decided to collect information about Cytoscape's Docker in https://github.com/cytoscape/docker-cytoscape-desktop . Also, we will use https://github.com/jupyter/docker-stacks for the base image of py4cytoscape. (See https://github.com/cytoscape/docker-cytoscape-desktop/tree/master/py4cytoscape .) So I would like to remove your docker folder from the py4cytoscape repository. If you disagree with this policy, please reply here.

[bdemchak]

I have no objection ... sounds smart to me. If you decide to do this, please remember to make your changes on 1.3.0 instead of master. Once you do this, I'll release 1.3.0. Thanks.

[kozo2]

I will wait for a day. And if there's no reply, I will make my changes (on 1.3.0 instead of master).

[kozo2]

@bdemchak @jorgeboucas I deleted the docker directory from 1.3.0 branch. (See https://github.com/cytoscape/py4cytoscape/issues/17#issuecomment-1133143055 for the reason.)