Skip to content

Conversation

@kabilar
Copy link
Collaborator

@kabilar kabilar commented Apr 3, 2023

  • Add Dev Containers
    • Tutorial Dev Container runs the tutorial jupyter notebook locally or on GitHub Codespaces.
    • Local Test Dev Container runs the pytests locally whereby workflow-optogenetics and element-optogenetics are located in the same parent directory.
  • Add Element activation commands in workflow_optogenetics
  • Add standard repo files: readme, changelog, issue_templates, .github/workflows, etc.
  • Add pytests
  • Note, element-optogenetics==0.1.1 is not released to PyPI due to a .github/workflow dependency on this workflow, so you will need to install from source if running the changes in this pull request.

@kabilar kabilar changed the title Add all workflow files Add all workflow files for first release Apr 20, 2023
@kabilar kabilar requested a review from kushalbakshi May 5, 2023 04:45
@kabilar kabilar marked this pull request as ready for review May 5, 2023 04:45
Copy link
Collaborator

@kushalbakshi kushalbakshi left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

A small suggestion for the notebook, if we want to read from dj_local_conf, we should add the following code before importing datajoint and the workflow:

import os

if os.path.basename(os.getcwd()) == "notebooks":
    os.chdir("..")

@kabilar
Copy link
Collaborator Author

kabilar commented May 5, 2023

A small suggestion for the notebook, if we want to read from dj_local_conf, we should add the following code before importing datajoint and the workflow:

import os

if os.path.basename(os.getcwd()) == "notebooks":
    os.chdir("..")

Thanks @kushalbakshi. Since we are migrating to using Dev Containers and in order to keep the tutorials as streamlined as possible, how about we do the following?

  1. Keep the current configuration with the DataJoint environment variables.
  2. Update the User Guide with instructions on how to use the dj_local_conf.

@kushalbakshi
Copy link
Collaborator

Thanks @kushalbakshi. Since we are migrating to using Dev Containers and in order to keep the tutorials as streamlined as possible, how about we do the following?

1. Keep the current configuration with the [DataJoint environment variables](https://github.com/kabilar/workflow-optogenetics/blob/8dbee85916e4ff92c8aba0d37416eeae0a0d4b04/.devcontainer/Dockerfile#L36-L40C27).

2. Update the [User Guide](https://datajoint.com/docs/elements/user-guide/) with instructions on how to use the `dj_local_conf`.

Yes, that's a good idea. Thank you!

@kushalbakshi kushalbakshi merged commit d4bbf35 into datajoint:main May 8, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants