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Merged
ALuesink merged 104 commits into from
Jun 10, 2025
Merged

DIMS Refactor GenerateExcel #70

ALuesink merged 104 commits into from
Jun 10, 2025

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@ALuesink
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@ALuesink ALuesink commented Apr 17, 2025

Refactor GenerateExcel:

  • Combining sum adducts files moved to CollectSumAdducts
  • Moved all QC functions to new CheckQC step
  • Restructure code into functions
  • Added unit tests

rernst and others added 30 commits January 9, 2025 10:15
@rernst
Merge pull request #56 from UMCUGenetics/hotfix/v2.4.1
673473c 
v2.4.1
@ALuesink
Fix for positive control error
9cd6b15
@ALuesink
Merge pull request #59 from UMCUGenetics/hotfix/v2.4.2
45ec6ca 
v2.4.2
@ALuesink
Merge pull request #60 from UMCUGenetics/hotfix/v2.4.2
4c806ef 
v2.4.2 to develop
@ALuesink
Refactor: moved functions to seperate file, moved combining intensiti…
83f13f4 
…es scanmodes from GenerateExcel
@ALuesink
Added preprocessing_scripts_dir
9620d72
@ALuesink
Changed modi to modes
f4e999f
@ALuesink
Added new GenerateQC step
e2495f9
@ALuesink
Input and output changes for refactor
21761cb
@ALuesink
Code moved to CollectSumAdducts and GenerateQC, moved functions to se…
3788e5a 
…parate file
@ALuesink
Typos fixed
093c9de
@ALuesink
Fixed issue's with adding plots to an Excel file
3eb176f
@ALuesink
Fixed test issues
12b700b
@ALuesink
Changes due to testing
518b5b5
@ALuesink
Fixed column name error
efbf18b
@ALuesink
Changed output to tuple
a439e72
@ALuesink
Fixed parentheses error
6f0b52c
@ALuesink
Fixed output error missing files with optional
a3768bc
@ALuesink
Removed unnecessary directory making
723ab9d
@ALuesink
Output to tuple output of all files to publish dir
63153a0
@ALuesink
Fixed typo
88a83ba
@ALuesink
Renamed GenerateQC to CheckQC
33cd021
@ALuesink
Changes positive control QC
96d06a9
@ALuesink
Changed layout Excel output and added Excel with only Helix metabs
9999da5
@ALuesink
Changed missing mz to highest_mz instead of hardcoded 599
bc673d4
@ALuesink
Fixed issue test variable
6edc2aa
@mraves2
bug fix DIMS/Utils/estimate_area to avoid increasing intensity at hig…
253fd41 
…her m/z
@mraves2
Merge pull request #62 from UMCUGenetics/hotfix/v2.4.3
f2eaa85 
Hotfix 2.4.3 to main
@mraves2
Merge pull request #63 from UMCUGenetics/hotfix/v2.4.3
8ec0566 
Hotfix v2.4.3 to develop
@ALuesink
Fixed plot insert in Excel
9f81a6f
ALuesink added 24 commits May 22, 2025 16:29
@ALuesink
Fixed source location function files
8cea9e9
@ALuesink
Fixed issue missing variable unit test
ab7bc0e
@ALuesink
Added package to install and snapshot barplot
fbcf05b
@ALuesink
Fixes QC unit testing
97d0a69
@ALuesink
Fix exit status unit tests
5dd60f1
@ALuesink
Fixed path test plot
008ae1b
@ALuesink
Fixed vapply error
78d05bd
@ALuesink
Fixed issue CRAN error
2556bf5
@ALuesink
Fixed snapshotting issue
245f30f
@ALuesink
Removed old snapshot
4004d9c
@ALuesink
Removed listing files and added new snapshot
99a7088
@ALuesink
Testing why snapshot doesn't work on GitHub
dce64b9
@ALuesink
Correct snapshot for docker container
8572d48
@ALuesink
Removed snapshot_review
464e7ee
@ALuesink
Added .lintr file to change linter settings for linting workflow
6f6832c
@ALuesink
Linting changes
8e520a2
@ALuesink
Added new line at end of file
050a85a
@ALuesink
Fixed linter error
b69dcb1
@ALuesink
Fixed forgotten comma
69b61ed
@ALuesink
Changed CheckQC to GenerateQCOutput
4be85da
@ALuesink
Linting changes
f154f06
@ALuesink
Changed source location to new and correct location
c7f688c
@ALuesink
Changed dir name for snapshot
69a097e
@ALuesink
Added dplyr package
1363e65
BasMonkey
BasMonkey requested changes Jun 5, 2025
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Love to see all the resolved comments from last time and the working GitHub actions with unittesting! Some minor remarks / questions.

BasMonkey
BasMonkey approved these changes Jun 10, 2025
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All OK now!

@ALuesink ALuesink merged commit 97b769a into feature/refactor_DIMS Jun 10, 2025
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@ALuesink ALuesink mentioned this pull request Jun 10, 2025
Merged
@mraves2 mraves2 deleted the feature/refactor_DIMS_GenerateExcel branch July 15, 2025 09:21
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@ALuesink @BasMonkey @rernst @mraves2