synced plate_replication, absolute_quant, and matrix_tube development. Added unit test for matrix_tube_pipeline

[RodolfoSalido]

Added a matrix_tube_pipeline notebook. Reworked Dani's unit tests and added some more tests.

[RodolfoSalido]

@cbrenchy

[RodolfoSalido]

Hi Charlie, after talking with Caitriona, I'm actually going to add some extra validation steps and errors to this Pull Request. I should have then done between today and tomorrow.

[charles-cowart]

Hi Charlie, after talking with Caitriona, I'm actually going to add some extra validation steps and errors to this Pull Request. I should have then done between today and tomorrow.

Let me know when you want me to review it again.

[RodolfoSalido]

I think we ready for another round of review. We added more tests and error handling.

[charles-cowart]

I think we ready for another round of review. We added more tests and error handling.

This looks like a mighty amount of changes - some big changes in metapool.py as well as 41 files modified in total. I'll have to review this in the background. I'll get it to you as soon as possible.

[RodolfoSalido]

A lot of the file changes are associated with standardized test data. We homogenized some input file structures so that we could validate importing files to the notebooks.

[charles-cowart]

@RodolfoSalido Hi Rodolfo! Thanks for your patience and doing the PR! It's now merged into Biocore:dev branch. Please don't forget to update the dev branch from your fork to the latest from biocore:dev branch and git pull to your local branch to sync everything back up again.

[RodolfoSalido]

So the PR get’s merged without tracking commits right? So I just need to discard my local commits (which are now merged) and sync with upstream biocore:dev branch ?

On Nov 29, 2023, at 2:12 PM, Charles Cowart @.***> wrote:

@RodolfoSalido https://github.com/RodolfoSalido Hi Rodolfo! Thanks for your patience and doing the PR! It's now merged into Biocore:dev branch. Please don't forget to update the dev branch from your fork to the latest from biocore:dev branch and git pull to your local branch to sync everything back up again.

— Reply to this email directly, view it on GitHub https://github.com/biocore/metagenomics_pooling_notebook/pull/153#issuecomment-1832783333, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEVFI5LYCKRDGL5ZKD2SNLYG6XLTAVCNFSM6AAAAAA7LX4EQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZSG44DGMZTGM. You are receiving this because you were mentioned.

[charles-cowart]

Yeah it's all squash and merge by default now on metapool. No what I would do is go to your fork of metapool on GitHub, switch to dev branch, and it should tell you that your branch is one commit behind biocore:dev. There should be a button to sync. After you've synced your fork, you can update your local dev branch by just using git pull.

[RodolfoSalido]

My fork believes that it’s 16 commits ahead and 1 behind.

The 16 commits are those that recently got merged, and the 1 behind is the PR. I synced my fork by merging the 1 commit I was behind, but now my branch believes it’s 17 commits ahead.

What I suggested was to just discard my 16 commits and sync fork with upstream, but idk if that will resolve this more flawlessly.

I’ll try it…

-Rodolfo

On Nov 29, 2023, at 2:19 PM, Charles Cowart @.***> wrote:

Yeah it's all squash and merge by default now on metapool. No what I would do is go to your fork of metapool on GitHub, switch to dev branch, and it should tell you that your branch is one commit behind biocore:dev. There should be a button to sync. After you've synced your fork, you can update your local dev branch by just using git pull.

— Reply to this email directly, view it on GitHub https://github.com/biocore/metagenomics_pooling_notebook/pull/153#issuecomment-1832791305, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADEVFI52KYZZF56P4RKYGVTYG6YHHAVCNFSM6AAAAAA7LX4EQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMZSG44TCMZQGU. You are receiving this because you were mentioned.

[charles-cowart]

Try the following. This will pull the info from your fork to local, but not overwrite your local branch: git fetch origin This will reset your local dev branch to what's in your fork on GitHub: git reset --hard origin/dev

[RodolfoSalido]

Did what you suggested and my forked:dev branch is synced with biocore:dev, but my GitHub remote still believes it's 17 commits ahead of of biocore:dev.

I don't know if that matters at all though.

[charles-cowart]

We'll take the easy route and just delete your branches and then recreate them.

Go to the pull-down menu where it says 'dev' branch, and select 'View all branches' at the bottom of the menu. You should see a list of all your branches, including dev. At the right of the entry there is a pencil logo to rename the branch and a trashcan to delete it. I would go ahead and delete it. Then you can press the green New Branch button on the upper right and create a new dev branch from your fork based on the main repo's dev branch. Now your fork is updated.

To update your local repo, type 'git -d dev' in your local repo to delete your local dev branch. Then type git pull origin dev to pull down the latest version.

[RodolfoSalido]

Sounds good. Thanks for the input