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Optimization develop read npx to main #377

Merged
merged 587 commits into from
May 31, 2024
Merged

Optimization develop read npx to main #377

merged 587 commits into from
May 31, 2024

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klevdiamanti
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Title: Write a very short summary here

Problem: Write a description of your problem here.

Solution: Write a short summary of your solution.

Key Features:

  • Key feature 1
  • Key feature 2
  • ...

Checklist

  • Make sure you are requesting to pull a feature/bugfix branch (right side). This should not be main or develop.
  • Make sure you are make a pull request against either main or develop (left side). (Requesting to main should be reserved for bugfixes and new releases)
  • Add or update unit tests (if applicable)
  • Check your code with any unit tests (Run devtools::check() locally)
  • Add neccessary documentation (if applicable)

Type of changes

What type of changes does your code introduce?
Put an x in the boxes that apply

  • Bugfix (non-breaking change which fixes an issue) (link the issue on the right)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • Code style update (formatting, renaming)
  • Documentation Update
  • Other (explain)

Further comments

If this is a relatively large or complex change, kick off the discussion by explaining why you chose the solution you did and what alternatives you considered, any questions you have, etc...

Consider linking any issues (#issue-number ) or adding @mentions to ensure specific people see it.

@klevdiamanti
Remove the check of expect_no_condition when reading the dummy file. …
f9278cd 
…Aiming at not having Windows CI fail
@klevdiamanti
Check if test using with_mocked_bindings works
6c60055
@klevdiamanti
Print messages to debug
6de6ba6
@klevdiamanti
Remove tests checking that temp direcotry was removed. on.exit is epx…
2b9713e 
…ected to solve this.
@klevdiamanti
Compute Panel_Version
242cc39
@klevdiamanti
Extract df_head from wide files
1db4448
@klevdiamanti
Function extracting NPXS version from Olink wide file
e556af2
@klevdiamanti
Rename read_npx_wide output column names according to NPXS
68c5b62
@klevdiamanti
Minor fixes
96b0fed
@klevdiamanti
Remove requirement of 45 assays for T48
06c5b74
@klevdiamanti
read_npx_wide accepts df as input to allow for csv wide format files
6fbb5f7
@klevdiamanti
read_npx_parquet accepts Explore3072 data
aaca813
@klevdiamanti
read_npx can handle csv files in wide format
3367a44
@klevdiamanti
remove 'sep' from read_npx_excel
6512646
@klevdiamanti
Update documentation for read_npx_delim and read_npx_excel
e39dcea
@klevdiamanti
Update documentation of read_npx_parquet
70d37a9
@klevdiamanti
Update seealso in documentation
79b61c9
@klevdiamanti
Update docuemntation for read_npx_zip
134a007
@klevdiamanti
Remove check_is_data_frame and add check_is_arrow_or_tibble
78f7c35
@klevdiamanti
Update remove_all_na_cols to handle arrow
446b2a9
@klevdiamanti
Update convert_read_npx_output to handle tibble and arrow input only
c27a614
@klevdiamanti
Update check_columns to support tibble and arrow only
363132a
@klevdiamanti
Minor typos fixed in read_npx_delim tests
b4fe671
@klevdiamanti
Bugfix in read_npx_delim_wide
d3ccaca
@klevdiamanti
Update read_npx_format to handle only tibble and arrow
d1efddd
@klevdiamanti
Minor lint fixes in tests for check_npx_format
286100d
@klevdiamanti
Remove discontinued functions from df checks.
dab90c5
@klevdiamanti
Update documentation for check_out_df_arg
01d9261
@klevdiamanti
Update documentation for check_olink_vars
a8d477b
@klevdiamanti
Update documentation for read_npx_wide
62d329e
klevdiamanti added 28 commits May 28, 2024 22:08
@klevdiamanti
Needs R >= 4.1.0
b8d75bd
@klevdiamanti
Do not install arrow from r-universe for OSX
dcba9c8
@klevdiamanti
Continue installing arrow from r-universe for OSX
d059602
@klevdiamanti
Run one of the tests with tibble instead of arrow_table
548cac3
@klevdiamanti
Merge pull request #370 from Olink-Proteomics/optimization_develop_ro…
ea8e7f1 
…llback_ci

Optimization develop rollback ci
@klevdiamanti
Merge pull request #358 from Olink-Proteomics/optimization_develop_di…
62b1c49 
…ct_resolve

Optimization develop dict to optimization to optimization develop
@klevdiamanti
Run lint, test-coverage and R-CMD-check_no-suggests only on PRs to ma…
9df2089 
…in, develop and optimization_develop
@klevdiamanti
Drop R < 4.4 from R-CMD-check matrix
58d2890
@klevdiamanti
Add docker file
35de3ca
@klevdiamanti
Add docker yaml file to workflows
5ba4442
@klevdiamanti
Imports arrow>=14.0.0 and cli>=3.6.1
ee3d96d
@klevdiamanti
Merge pull request #372 from Olink-Proteomics/optimization_develop_do…
ad5beab 
…cker

Optimization develop docker
@klevdiamanti
Include Ubuntu 22.04 in CI
6b1bff4
@klevdiamanti
Upgrade to actions/checkout@v4
a13783f
@klevdiamanti
Upgrade to actions/upload-artifact@v4
c515e10
@klevdiamanti
Remove Ubuntu 24.04
4c5388c
@klevdiamanti
Run render-and-document always
3af8f2d
@klevdiamanti
Merge pull request #375 from Olink-Proteomics/optimization_develop_ub…
d8b301b 
…untu_24.04

Optimization develop ubuntu 24.04
@klevdiamanti
Include 'optimization_main' to CI to mirror 'main'
f7bfb1e
@klevdiamanti
Merge pull request #376 from Olink-Proteomics/optimization_develop
ad06a0a 
Include 'optimization_main' to CI to mirror 'main'
@klevdiamanti
Disable CI
ec1be1f
@klevdiamanti
OA version 4.0.0
7c31853
@klevdiamanti
Check branch on push
182ccbf
@klevdiamanti
No CRAN check on optimization_main
860f906
@klevdiamanti
Remove check_npx-related functions
8c77b11
@klevdiamanti
Bring back R-CMD-check and render-and-document
3a61a94
@klevdiamanti
Remove .DS_Store
87970f0 
Merge branch 'optimization_main' of https://github.com/Olink-Proteomics/OlinkRPackage into optimization_develop_read_npx_to_main

# Conflicts:
#	.github/workflows/R-CMD-check.yaml
#	OlinkAnalyze/DESCRIPTION
#	OlinkAnalyze/NEWS.md
#	OlinkAnalyze/R/Olink_bridgeselector.R
#	OlinkAnalyze/R/Olink_normalization.R
#	OlinkAnalyze/R/Read_NPX_data.R
#	OlinkAnalyze/R/globals.R
#	OlinkAnalyze/R/npxProcessing.R
#	OlinkAnalyze/R/pca_plot.R
#	OlinkAnalyze/R/read_npx_csv.R
#	OlinkAnalyze/R/read_npx_parquet.R
#	OlinkAnalyze/inst/extdata/npx_data_ext.parquet
#	OlinkAnalyze/tests/testthat/_snaps/Read_NPX_data.md
#	OlinkAnalyze/tests/testthat/test-Olink_normalization.R
#	OlinkAnalyze/tests/testthat/test-npxProcessing.R
#	OlinkAnalyze/tests/testthat/test-olink_normalization_n.R
#	OlinkAnalyze/tests/testthat/test-pca_plot.R
#	OlinkAnalyze/vignettes/OutlierExclusion.Rmd
#	OlinkAnalyze/vignettes/Vignett.Rmd
#	OlinkAnalyze/vignettes/bridging_introduction.Rmd
#	OlinkAnalyze/vignettes/plate_randomizer.Rmd
@klevdiamanti
Minor updates from optimization_main
da9c1b8
@klevdiamanti klevdiamanti merged commit 05a9e50 into optimization_main May 31, 2024
15 checks passed
@klevdiamanti klevdiamanti deleted the optimization_develop_read_npx_to_main branch May 31, 2024 11:48
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@klevdiamanti