Publish all current staging branch changes #442
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* Update github actions to reflect staging branch
* Add libglpk40 to Dockerfile
* Make it gh-pages-stages!
* Remove dockerfile change that should have been on its own all along
* Does this work?
* Declare a uses
* Switch how env is declared
* Force it to run so we can test it
* try no curly brackets
* What's up with the branch
* Move to bash if instead
* Need quotes?
* forgot a `then`
* Try dollar signs
* Doesn't like the `.`?
* Use curly brackets
* Try ${GITHUB_REF}
* Try ${BRANCH_NAME}
* try ${GITHUB_REF#refs/*/}
* use jashapiro suggestion
* Change to base ref
* Change back to `github.ref`
* Get rid of PR `on:`
* Try another test
* Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316)
* Add lib package 40 thing that clusterprofiler needs
* Try adding options(warn = 2)
* Test if options(warn =2) means it breaks like it should
* Revert "Test if options(warn =2) means it breaks like it should"
This reverts commit d9f688f.
* Revert "Try another test"
This reverts commit 845cf1a.
* Try adding google analytics * Add to header using includes * temporary file snuck in there * Restore master version so they aren't in the review * Let's call an html file and html file * Docker dep fix: Add lib package 40 thing that clusterprofiler needs (#316) * Add lib package 40 thing that clusterprofiler needs * Try adding options(warn = 2) * Test if options(warn =2) means it breaks like it should * Revert "Test if options(warn =2) means it breaks like it should" This reverts commit d9f688f.
For simplicity, we will now run this even if the dockerfile hasn't changed.
This reverts commit 6a38574.
Okay, so the branch name is now inaccurate, but that is fine...
Made changes to css/navbar.html Tried to add the logo but it but it cuts out and not sure how to make it decent.
…g-docker Stop staging from pushing to dockerhub
* Scrapbooking together an analysis * switch back to kcdf = "Gaussian" * Rearrange based on chat with Jackie * Fix the two things from jaclyn-taroni partial review * Few wording edits * Make the dup checks more relevant * Make PNG a bit bigger * incorporate most of jaclyn-taroni review comments * Try out the msigdbr list thing * Re-render * Update based on part 1 review * Add bit that shows overlaps * Make wording changes based on jaclyn-taroni review * Do some wording/explanation edits
* Introduce SRP123625 * Updating wording and some other items * Re-render it * Spell error fixes * jashapiro review suggestions * one more change and re-render
* Add principal component background Also shortened code lines and results tables * Add some more context and explanation of results * Updates to rnaseq PCA * Format and rerender * update screenshots * Apply suggestions from code review Co-authored-by: Candace Savonen <[email protected]> * Don't call it a matrix it's been here for years * rerender Co-authored-by: Candace Savonen <[email protected]>
* Change download steps to download file * re-render * Spell error fixes * Use jashapiro wording
* Bring over the GSEA changes * Add download.file() to the other three places * Found a typo * Fix two things cbethell mentioned in review
* add part 2 of RNA-seq GSEA example notebook (take 2) * rerun snakefile * incorporate jaclyn-taroni's review suggestions
* UMAP polish edits * rendering * Apply suggestions from code review Co-authored-by: Candace Savonen <[email protected]> * rerender
* re-render it * Further fix merge conflicts and re-render * Address jashapiro comments
* Polishing edits to heatmap pages * Style and render * OSPL fix Co-authored-by: Candace Savonen <[email protected]> * rownames -> row names * rerender all the things and delete a stray space
* Changes to differential exp microarray notebook * Spelling updates * Add comments and releveling, as suggested by @cansavvy * code formatting updates embrace the pipe * remove apeglm * Add some eBayes info! * polishing microarray multiple groups * Rerender everything * Split off multiple testing * Rerender
* Minor polishing to RNAseq Diff Expr * render changes * Apply suggestions from code review Co-authored-by: Candace Savonen <[email protected]> * render Co-authored-by: Candace Savonen <[email protected]>
* Update MSigDB section + rerender Also fixes long comments and rownames.print=FALSE * A few more edits to comments
* Add print.rownames = FALSE where its helpful * Apparently it doesn't affect design matrices * Push the htmls so that people can actually see them!!!
Co-authored-by: jashapiro <[email protected]>
* Polish wording and add introductory paragraphs * A bit more polishing * Apply suggestions from code review Co-authored-by: jashapiro <[email protected]> * Response to code review * Apply suggestions from code review Co-authored-by: jashapiro <[email protected]> * Propagate citation suggestion to multiple pathway notebooks * Missed these quotes * A few mapIds() items Co-authored-by: jashapiro <[email protected]>
* Polish wording and add introductory paragraphs * A bit more polishing * Apply suggestions from code review Co-authored-by: jashapiro <[email protected]> * Response to code review * Apply suggestions from code review Co-authored-by: jashapiro <[email protected]> * Propagate citation suggestion to multiple pathway notebooks * Missed these quotes * A few mapIds() items * Polish RNA-seq GSEA example * Missed a long comment * Update components/references.bib Co-authored-by: jashapiro <[email protected]> * Let the algorithm handle it Co-authored-by: jashapiro <[email protected]>
* Add Slack notification to docker-build-push.yml * Add Slack notification to docker-build.yml * Add branch for testing * Add library load of package not installed * Revert "Add library load of package not installed" This reverts commit 4e83ed1. * Revert "Add branch for testing" This reverts commit 0607350.
* Polish wording and add introductory paragraphs * A bit more polishing * Reference updates * ensembl gene id polish * Get out of here capital Refine.bio * No more bare dfs * Transfer changes to RNAseq (and some back) * Apply suggestions from code review Co-authored-by: jashapiro <[email protected]> * Response to code review * Some numeric updates * Add rendered files * render update * Citation update * Render updates * add comment & rerender Co-authored-by: Jaclyn Taroni <[email protected]>
* Ignore the gene_sets directory * Polish the microarray GSVA example * Missed a couple mentions of GSEA * Borrow some polishing from #427 * Apply suggestions from code review Co-authored-by: Candace Savonen <[email protected]> * Newline in intro paragraph everywhere * Add note about model organisms with GSVA Link to RNA-seq GSVA example * Rerender notebooks Co-authored-by: Candace Savonen <[email protected]>
* Polish wording and add introductory paragraphs * A bit more polishing * Reference updates * ensembl gene id polish * Get out of here capital Refine.bio * No more bare dfs * Transfer changes to RNAseq (and some back) * Apply suggestions from code review Co-authored-by: jashapiro <[email protected]> * Response to code review * Some numeric updates * Add rendered files * render update * Citation update * Add polishing for ortholog examples * Transfer intro sentence updates to related notebooks * more polish - remove duplicates from counts * Transfer changes to rnaseq * Rendering updates * other rendering updates * Render updates * Change ftp -> http for ftp.ebi As noted here: #439 (comment) Confirmed that this does work as expected by rendering. * Add branch to docker-build-push.yml for render test * Apply suggestions from code review Co-authored-by: Candace Savonen <[email protected]> * Clarify real genes * add some spelling words * Revert "Add branch to docker-build-push.yml for render test" This reverts commit 8e7b6ec. * rendering * Caught an igor Co-authored-by: Jaclyn Taroni <[email protected]> Co-authored-by: Candace Savonen <[email protected]>
jaclyn-taroni
approved these changes
Dec 21, 2020
Makes sense to me. |
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Changes Being Published
We're publishing everything that's in staging. This is mostly polishing PRs #289 and #290, but also includes adding the RNA-seq pathway analyses.
This will close #390 and #391
List of Commits/PR's Included
Highlights are that the RNA-seq pathway analyses have been added:
And the rest are a lot of polishing PRs as well as "make github louder" PR.
Link to html Preview
For reviewing purposes, you can take a browse through htmlpreview: http://htmlpreview.github.io/?https://github.com/AlexsLemonade/refinebio-examples/gh-pages-stages/01-getting-started/getting-started.html
Effectively every html has had some changes at this point.
Publishing Checklist:
Does everything look good using html preview -- having taken a particularly close look at any new html files?
Have any new examples been added to the refinebio-examples feedback survey? Ideally, don't click publish until this PR is merged (changes are autosaved).
Survey is updated but not published yet.