Update Repo Structure To Match Pathogen-repo-guide

Mar 13, 2025 by ADMIN 51 views

Improving Repo Structure for Clarity and Consistency

As we continue to develop and maintain our repos, it's essential to ensure that our structure and directories are clear, consistent, and easy to understand. Recently, a user in office hours expressed confusion about the structure of this repo, highlighting the need for improvement. By aligning our repo structure with the Pathogen-Repo-Guide, we can provide a more straightforward explanation and direct users to relevant documentation.

Benefits of a Consistent Repo Structure

A well-organized repo structure offers several benefits, including:

Improved clarity: A clear and consistent structure makes it easier for users to navigate and understand the repo's content.
Enhanced collaboration: A well-organized repo facilitates collaboration among team members, reducing confusion and errors.
Increased efficiency: A consistent structure enables users to quickly find the information they need, saving time and effort.

Current State of the Repo

Our current repo structure is not aligned with the Pathogen-Repo-Guide, which has led to confusion among users. To address this issue, we need to update our repo structure to match the guide.

TODOs

[ ] Update the repo structure to match the Pathogen-Repo-Guide: This involves reorganizing the directories and files to align with the guide.
[ ] Add a top-level nextstrain-pathogen.yaml file: This file will serve as a central configuration file for the repo.
[ ] Move the top-level workflow to a phylogenetic directory: This will help to categorize and organize the workflows within the repo.
[ ] Update the rebuild workflow to use the phylogenetic directory: This will ensure that the rebuild workflow is consistent with the updated repo structure.
[ ] Add the phylogenetic/build-configs/ci directory: This will provide a clear and consistent location for CI build configurations.
[ ] Update the CI workflow to pathogen-repo-ci.yaml@master: This will ensure that the CI workflow is consistent with the updated repo structure.
[ ] Update the RSV pathogen-repo-ci in other repos (Augur, Docker-Base, Conda-Base): This will ensure that the RSV pathogen-repo-ci is consistent across all relevant repos.

Step-by-Step Guide to Updating the Repo Structure

To update the repo structure, follow these steps:

Step 1: Update the Repo Structure

Update the directory structure to match the Pathogen-Repo-Guide.
Create a new nextstrain-pathogen.yaml file at the top level of the repo.
Move the top-level workflow to a phylogenetic directory.

Step 2: Update the Rebuild Workflow

Update the rebuild workflow to use the phylogenetic directory.
Ensure that the rebuild workflow is consistent with the updated repo structure.

Step 3: Add the `phylogenetic/build-configs/ci` Directory

Create a new phylogenetic/build-configs/ci directory.
Move the CI build configurations to this new directory.

Step 4: Update the CI Workflow

Update the CI workflow to use the pathogen-repo-ci.yaml@master file.
Ensure that the CI workflow is consistent with the updated repo structure.

Step 5: Update the RSV Pathogen-Repo-CI in Other Repos

Update the RSV pathogen-repo-ci in other relevant repos (Augur, Docker-Base, Conda-Base).
Ensure that the RSV pathogen-repo-ci is consistent across all relevant repos.

Conclusion

Updating the repo structure to match the Pathogen-Repo-Guide will improve clarity, consistency, and collaboration among team members. By following the step-by-step guide outlined above, we can ensure that our repo structure is well-organized and easy to understand. This will ultimately benefit users and facilitate a more efficient and effective workflow.

Future Work

Regularly review and update the repo structure: To ensure that the repo structure remains consistent and up-to-date.
Provide clear documentation: To help users understand the repo structure and navigate the repo.
Continuously improve collaboration: To foster a culture of collaboration and open communication among team members.

Q: Why is it necessary to update the repo structure?

A: The current repo structure is not aligned with the Pathogen-Repo-Guide, which has led to confusion among users. By updating the repo structure, we can provide a more straightforward explanation and direct users to relevant documentation.

Q: What are the benefits of a consistent repo structure?

A: A well-organized repo structure offers several benefits, including:

Improved clarity: A clear and consistent structure makes it easier for users to navigate and understand the repo's content.
Enhanced collaboration: A well-organized repo facilitates collaboration among team members, reducing confusion and errors.
Increased efficiency: A consistent structure enables users to quickly find the information they need, saving time and effort.

Q: What changes will be made to the repo structure?

A: The following changes will be made to the repo structure:

Add a top-level nextstrain-pathogen.yaml file: This file will serve as a central configuration file for the repo.
Move the top-level workflow to a phylogenetic directory: This will help to categorize and organize the workflows within the repo.
Update the rebuild workflow to use the phylogenetic directory: This will ensure that the rebuild workflow is consistent with the updated repo structure.
Add the phylogenetic/build-configs/ci directory: This will provide a clear and consistent location for CI build configurations.
Update the CI workflow to pathogen-repo-ci.yaml@master: This will ensure that the CI workflow is consistent with the updated repo structure.
Update the RSV pathogen-repo-ci in other repos (Augur, Docker-Base, Conda-Base): This will ensure that the RSV pathogen-repo-ci is consistent across all relevant repos.

Q: How will the update process affect users?

A: The update process will not affect users in a significant way. However, users may notice some changes in the repo structure and workflow. To minimize disruptions, we will:

Provide clear documentation: To help users understand the updated repo structure and navigate the repo.
Offer support: To assist users with any questions or issues related to the updated repo structure.
Regularly review and update the repo structure: To ensure that the repo structure remains consistent and up-to-date.

Q: What is the timeline for the update process?

A: The update process will be completed in several stages, with the following timeline:

Stage 1: Update the repo structure: This will take approximately 2-3 weeks to complete.
Stage 2: Update the rebuild workflow: This will take approximately 1-2 weeks to complete.
Stage 3: Add the phylogenetic/build-configs/ci directory: This will take approximately 1-2 weeks to complete.
Stage 4: Update the CI workflow: This will take approximately 1-2 weeks to complete.
Stage 5: Update the RSV pathogen-repo-ci in other repos: This will take approximately 2-3 weeks to complete.

Q: Who will be responsible for the update process?

A: The following team members will be responsible for the update process:

[Name]: Will lead the update process and ensure that the repo structure is updated correctly.
[Name]: Will assist with updating the rebuild workflow and adding the phylogenetic/build-configs/ci directory.
[Name]: Will assist with updating the CI workflow and RSV pathogen-repo-ci in other repos.

Q: How will the update process be communicated to users?

A: The update process will be communicated to users through:

Email notifications: Users will receive email notifications about the update process and any changes to the repo structure.
Repo updates: The repo will be updated regularly to reflect the changes to the repo structure.
Documentation updates: The documentation will be updated to reflect the changes to the repo structure.

Q: What if I have questions or concerns about the update process?

A: If you have questions or concerns about the update process, please reach out to the team members responsible for the update process. We will be happy to assist you and provide any necessary support.