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Reproducibility docs: final.final merge into main #620

Merged
merged 244 commits into from
Jul 18, 2024
Merged

Reproducibility docs: final.final merge into main #620

merged 244 commits into from
Jul 18, 2024

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sjspielman
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@sjspielman sjspielman commented Jul 17, 2024 •
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I think this one actually closes #605

In my fork, I synced a couple remaining ewings diffs to match their main version, so this PR is from my fork's reproducibility-docs into main. There are no more ewings diffs!

Let me know if we prefer that I first file sjspielman/reproducibility-docs -> AlexsLemonade/reproducibility-docs to make sure this repo's branch is its final version, before this PR heading into main. I didn't think it mattered too much to do that, but I definitely can!

sjspielman and others added 30 commits June 5, 2024 12:20
@sjspielman
add section on result script
268213a
@sjspielman
link to data access doc
cf9c0ff
@sjspielman
workflows should run on the repro branch
b18d4cf
@sjspielman
Nextflow to dict
098fbdb
@sjspielman
spelling
7fac86e
@sjspielman
Move over the tools docs
d743e5d
@sjspielman
Delete current tools focs from software-platforms
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@sjspielman
rename
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@sjspielman
Update relative links
615c17f
@sjspielman
bullet spacing
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@sjspielman
typo
d80b085
@sjspielman
initialize the repro docs directory
2ab0350
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Add index file for managing software directory
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@sjspielman
Add renv docs
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@sjspielman
Add conda docs
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@sjspielman
add reporting dependencies doc
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@sjspielman
fix one relative link
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rellink fixes
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@sjspielman
Merge pull request AlexsLemonade#505 from sjspielman/sjspielman/489-m…
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…ove-tools

Port project tools into getting started
@sjspielman
workflows should run on the repro branch
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@sjspielman @jaclyn-taroni
Apply suggestions from code review
795d32a 
Co-authored-by: Jaclyn Taroni <[email protected]>
@sjspielman
Merge pull request AlexsLemonade#510 from sjspielman/sjspielman/repro…
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…-ghas

GHAs should run on reproducibility branch
@sjspielman
Merge branch 'reproducibility-docs' into sjspielman/software-renv
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Merge branch 'reproducibility-docs' into sjspielman/software-conda
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Merge branch 'reproducibility-docs' into sjspielman/reporting-software
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merge upstream and fix workflow conflicts
2d568c3
@sjspielman @jaclyn-taroni
Apply suggestions from code review
dd8dbfc 
Co-authored-by: Jaclyn Taroni <[email protected]>
@sjspielman
fix typos
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Merge pull request AlexsLemonade#506 from sjspielman/sjspielman/softw…
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…are-renv

(1/5) Rearrange software docs: Using renv
@sjspielman
Merge pull request AlexsLemonade#507 from sjspielman/sjspielman/softw…
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…are-conda

(2/5) Rearrange software docs: Using conda
sjspielman and others added 13 commits July 12, 2024 11:47
@sjspielman
update tools language
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@sjspielman @jashapiro
Apply suggestions from code review
50cffa9 
Co-authored-by: Joshua Shapiro <[email protected]>
@sjspielman
Merge pull request AlexsLemonade#600 from sjspielman/sjspielman/509-u…
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…pdate-project-tools

Update project-tools language
@sjspielman
Merge branch 'reproducibility-docs' into sjspielman/521-repro-index
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@sjspielman
figure with bigger font
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thinner lines
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Merge pull request AlexsLemonade#599 from sjspielman/sjspielman/521-r…
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…epro-index

Add reproducibility index file
@sjspielman
remove branch from GHAs
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@sjspielman
Merge pull request AlexsLemonade#616 from sjspielman/sjspielman/remov…
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…e-repro-from-gha

Remove reproducibility-docs branch from GHAs
@sjspielman
merge main, fix conflicts
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@sjspielman
Merge pull request AlexsLemonade#618 from sjspielman/reproducibility-…
229d19e 
…docs

Merge main into reproducibility docs
@sjspielman
fix up some of the ewings files with diffs
e249172
@sjspielman
Clean up notebooks in a few more places, directly grabbing from main …
b1df31c 
…to avoid whitespace diffs
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sjspielman commented Jul 17, 2024 •
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I'm betting the links action failed because GitHub is having some problems right now (although those problems aren't with Actions specifically). Locally when I serve, all the links are fine (and spelling is ok too!).

Edit: yup!

@allyhawkins
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Let me know if we prefer that I first file sjspielman/reproducibility-docs -> AlexsLemonade/reproducibility-docs to make sure this repo's branch is its final version, before this PR heading into main. I didn't think it mattered too much to do that, but I definitely can!

Are we planning on deleting that branch once this goes in? If so then I don't think it matters. But if it's going to stay for any reason then I don't think we want it to be out of date. I can't think of why it would stay though...

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Are we planning on deleting that branch once this goes in? If so then I don't think it matters

As far as I know we're deleting it, or at least I planned to

allyhawkins
allyhawkins approved these changes Jul 17, 2024
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LGTM unless others have opinions on the branch situation, I'm good with this.

jashapiro
jashapiro approved these changes Jul 18, 2024
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LGTM

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😢

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@sjspielman sjspielman Jul 18, 2024 •
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sorry, @allyhawkins.... ❤️

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But I'm noting that GH shows the branch as out of date, so it won't allow a merge right now. We should check again after merging in main.

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Still looks good to me after cbf22f3.
The only non-docs changes are still analyses/cell-type-ewings/.gitignore, some template yml files, and the dictionary.

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Woops meant to tag @allyhawkins @jashapiro in case you wanted to look again now that we're up-to-date with main! Feel free to give me a thumbs up here.

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👍

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Oop, another main merge needed! Didn't change anything relevant 👍

@sjspielman sjspielman merged commit 8dc2490 into AlexsLemonade:main Jul 18, 2024
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@sjspielman sjspielman deleted the reproducibility-docs branch July 18, 2024 17:09
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@allyhawkins allyhawkins allyhawkins approved these changes

@jashapiro jashapiro jashapiro approved these changes

@dvenprasad dvenprasad Awaiting requested review from dvenprasad dvenprasad is a code owner

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Release the reproducibility docs
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@sjspielman @allyhawkins @jashapiro @jaclyn-taroni