Bioconductor/GenomeInfoDb

Proposed contribution task for Outreachy applicants: Enable "offline mode" for xenTro10

Closed this issue · 11 comments

hpages commented

This task depends on issue #46 being completed first (i.e. PR accepted and merged, and issue closed). Although it's not a requirement that the 2 tasks be completed by the same applicant, it will be a more interesting learning experience if they are.

See ?getChromInfoFromUCSC in the GenomeInfoDb package for information about the "offline mode". See README.TXT file in the GenomeInfoDb/inst/extdata/assembled_molecules_info/UCSC/ folder for how to enable "offline mode" for a registered UCSC genome.

IMPORTANT NOTES TO OUTREACHY APPLICANTS:

  • Make sure to complete all the Preliminary tasks listed here before you start working on this task. In particular, make sure that you have R 4.2 and that you are set up to use the devel version of Bioconductor (currently 3.16).
  • Only one applicant can work on this task. If you choose to work on this task, please make sure to assign yourself so other applicants know that the task is already being worked on. If later on you change your mind, please unassign yourself. It's ok to change your mind!
  • To work on this task, please fork the GenomeInfoDb repository. Then do your work on that fork.
  • Always test your changes before you commit them to your fork. This consists in installing the modified package, starting R, loading the package, and playing around with the new functionality. This process is called "ad hoc manual testing". Once everything behaves and looks as expected, run R CMD build and R CMD check on the package. Note that R CMD check should always be run on the source tarball produced by R CMD build.
  • R CMD check might produce some NOTEs and even some WARNINGs. These are ok if they existed before your changes. You can check that by taking a look at the daily report produced by our automated builds here: https://bioconductor.org/checkResults/devel/bioc-LATEST/ Make sure to not introduce new NOTEs or WARNINGs!
  • Once your work is ready to be merged, please submit a PR (Pull Request).
  • Remember to record your contribution on Outreachy at https://www.outreachy.org/outreachy-december-2022-internship-round/communities/bioconductor/refactor-the-bsgenomeforge-tools/contributions/.
Simplecodez commented

Please assign me to this task.
Thank you

  • 👍1
Simplecodez commented

Sir, i just created a PR for this task. I will be anticipating your feedback.
Thank you.

hpages commented

Thanks. PR #75 merged.

FYI I will also make these additional changes to the package:

  • Add xenTro10/UCB_Xtro_10.0 to the unit tests.
  • Add your name (first and last names) as a contributor to the package. Hopefully you are you ok with that, but it's totally fine if you are not. Don't hesitate to let me know. Also let me know if you want your middle name to be added too (you can send it to me by email or direct message on Slack).

Next task in your group is this issue. Note that this time the issue belongs to the BSgenome repository. Whenever you are ready, go there and ask to be assigned to the issue.

Simplecodez commented

Thanks. PR #75 merged.

FYI I will also make these additional changes to the package:

  • Add xenTro10/UCB_Xtro_10.0 to the unit tests.
  • Add your name (first and last names) as a contributor to the package. Hopefully you are you ok with that, but it's totally fine if you are not. Don't hesitate to let me know. Also let me know if you want your middle name to be added too (you can send it to me by email or direct message on Slack).

Wow, I am so honoured sir. I am totally fine with my name being added as a contributor. I will send my middle name now sir.
Thank you for all the help you rendered to me.

Next task in your group is this issue. Note that this time the issue belongs to the BSgenome repository. Whenever you are ready, go there and ask to be assigned to the issue.

Simplecodez commented

I have just sent my middle name via email.
Thank you

hpages commented

Thanks, I just added you to the package (see commit 78ae840).

The build results for GenomeInfoDb 1.33.16 will appear here tomorrow (Saturday). If this new version passes BUILD and CHECK, then it will propagate to the Bioconductor public repositories and become available via BiocManager::install().

Simplecodez commented

I have just sent my middle name via email. Thank you

Thanks, I just added you to the package (see commit 78ae840).

Wow, I really honoured sir. Words can not express how I feel now. Thank you so much for all the support you gave me.

The build results for GenomeInfoDb 1.33.16 will appear here tomorrow (Saturday). If this new version passes BUILD and CHECK, then it will propagate to the Bioconductor public repositories and become available via BiocManager::install().

Alright sir. Looking forward to tomorrow.
Thank you

hpages commented

You're welcome! 😃

Simplecodez commented

Thanks, I just added you to the package (see commit 78ae840).

The build results for GenomeInfoDb 1.33.16 will appear here tomorrow (Saturday). If this new version passes BUILD and CHECK, then it will propagate to the Bioconductor public repositories and become available via BiocManager::install().

Wow, I just checked the link again after checking earlier and GenomeInfoDb 1.33.16 is already there. Thank you for everything.

hpages commented

My pleasure 😃 Don't miss the package landing page on our website (look at the Author field): https://bioconductor.org/packages/3.16/GenomeInfoDb 🎉

Simplecodez commented

My pleasure 😃 Don't miss the package landing page on our website (look at the Author field): https://bioconductor.org/packages/3.16/GenomeInfoDb 🎉

Wow, I am super excited and honoured sir. This means a lot to me. I am really blessed to have you as my mentor.
Thank you so much sir.