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Topic/repetitive measurements2#5233

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lukasmueller wants to merge 129 commits intomastersolgenomics/sgn:masterfrom topic/repetitive_measurements2solgenomics/sgn:topic/repetitive_measurements2Copy head branch name to clipboard

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Commits on Feb 27, 2024

• retrieve more term props; refactor into get_term_props function.

  lukasmueller

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Commits on Feb 28, 2024

• add some comments how the system should work with multiple phenotypico observations.

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Commits on Mar 1, 2024

• add trait_repeat_type to the load_trait_props.pl script and its backend.

  lukasmueller

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• adjust storing logic to trait_repeat_type parameter.

  lukasmueller

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  a8d6236

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• fix some issues with variable declarations.

  lukasmueller

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Commits on Mar 3, 2024

• fix issue with query parameters.

  lukasmueller

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Commits on Mar 5, 2024

• fix typo in variable name

  lukasmueller

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  a03f71f

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• add support for multiple measurements.

  lukasmueller

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  21c7f4d

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• add support for multiple observations.

  lukasmueller

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• fix typo in variable name.

  lukasmueller

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Commits on Mar 8, 2024

• implement multiple values features.

  lukasmueller

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Commits on Mar 13, 2024

• add support for multiple measurements for native search in phenotype matrix.

  lukasmueller

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• comment out debug info.

  lukasmueller

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• add missing Perl module CXGN::Trial.

  lukasmueller

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Commits on Mar 15, 2024

• remove debug messages.

  lukasmueller

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Commits on Mar 25, 2024

• Merge branch 'master' into topic/repetitive_measurements

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Commits on Mar 29, 2024

• add phenotype matrix test.

  lukasmueller

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Commits on Mar 31, 2024

• add trait_repeat_type to trait properties add function.

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• Merge branch 'master' into topic/repetitive_measurements

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Commits on Apr 1, 2024

• add repetitive_measurements key and tweak pod.

  lukasmueller

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• prevent errors when there are no observations.

  lukasmueller

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  30260e0

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• fix typo in assignment.

  lukasmueller

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  ceb1fc7

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• add new accessor for repetitive measurements.

  lukasmueller

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• rename multiple_observations_treatment to repetitive_measurements; add UI elements for downloads; adapt code to changes.

  lukasmueller

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Commits on Apr 2, 2024

• add trait repeat prop cvterm and transfer timestamps to correct field.

  lukasmueller

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Commits on May 23, 2024

• add time based queries to phenotype download in the wizard

  lukasmueller

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Commits on May 24, 2024

• add date related queries to downloads.

  lukasmueller

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Commits on Nov 1, 2024

• resolve conflicts.

  lukasmueller

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  e5d96fc

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• add separate section for repetitve measurements in trial detail page

  Sri-2023

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• fix the ID names; and fix indentation in repetitive_measurement options

  Sri-2023

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• add value attributes to reptitive values in search page

  Sri-2023

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• Fix ID names for repetitive options in download phenotypes dialog

  Sri-2023

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• swap 'phenotype_raw_data' and 'phenotype_summary_statistics' sections on the trial detail page

  Sri-2023

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Commits on Nov 2, 2024

• add date range option and slider to phenotype summary stats section to filter trait values accordingly

  Sri-2023

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• add start_date, and end_date params to the trait_pheno and pheno_summary methods

  Sri-2023

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Commits on Nov 3, 2024

• add trial_collect_date_range endpoint to retrieve trial start and end date

  Sri-2023

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• add start_date and end_date to search query

  Sri-2023

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• refactor to use the consistent trial_id

  Sri-2023

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Commits on Nov 4, 2024

• add small line graph to see trend, and zoomable large graph to view

  Sri-2023

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  0dc88f9

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• fix typo

  Sri-2023

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  57b9872

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• add title to line_graph

  Sri-2023

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  1eaf2e0

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• correct repetitive_params in download_phenotypes_action

  Sri-2023

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• add seperate section to show # of phenotypes recorded in a trial; and also, filter the trait values based on the obs_level

  Sri-2023

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• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

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  fbcff9c

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• add 'sum' option to the repetitive_values

  Sri-2023

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• handle sum values

  Sri-2023

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Commits on Nov 5, 2024

• comment out alter messages

  Sri-2023

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• two options to retrieve all values: single line and multi line

  Sri-2023

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  5ebe930

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• fix BrApi phenotyping test

  Sri-2023

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• parse the time-series repetitive values

  Sri-2023

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• handle collect_date in Native search

  Sri-2023

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  4a7ffd9

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• add package for storing phenotype additional info and references

  Sri-2023

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  5da8d4b

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• add accessors to max, min, duplicates, value_count

  Sri-2023

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Commits on Nov 7, 2024

• modify POD

  Sri-2023

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• missing true value

  Sri-2023

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Commits on Nov 8, 2024

• add date params get_phennotypes_for_trait function

  Sri-2023

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  42e1f9b

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• refactor phenotypes in-progress

  Sri-2023

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Commits on Nov 11, 2024

• add the sum_observations method repetitive_values; fix indent

  Sri-2023

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  15771e4

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• fix phenotype_multi_categories test

  Sri-2023

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  07f0303

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• update PhenotypeMatrix test with all_values_single_line and sum params

  Sri-2023

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  23cfc93

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• refactor phenotypes to store the multiple measurement values

  Sri-2023

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Commits on Nov 12, 2024

• fix the BrAPI phenotying test

  Sri-2023

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• refactor phenotypes

  Sri-2023

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• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

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• fix ValidateNIRS test.

  lukasmueller

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Commits on Nov 13, 2024

• exlude notes from trait check.

  lukasmueller

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• update the default end date to the current date

  Sri-2023

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  2b5da46

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• fix indent

  Sri-2023

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  4571f3c

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• exclude notes from normal phenotype storage.

  lukasmueller

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• make test labels distinct.

  lukasmueller

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Commits on Nov 14, 2024

• fix a test, one more to go.

  lukasmueller

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• fix typo (oops) and fix last test.

  lukasmueller

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Commits on Nov 15, 2024

• remove duplicated repeat_type

  Sri-2023

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  83c8c59

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• filter the values based on the timestamp

  Sri-2023

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Commits on Nov 19, 2024

• make the values of end_date inclusive, when they select the last date; sort the values as per the date

  Sri-2023

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• comment the sorting values by date from line_graph package

  Sri-2023

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Commits on Nov 21, 2024

• sort observations by date; and use latest(last) date as timestamp for avg and sum values

  Sri-2023

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  a169caf

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• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

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Commits on Nov 22, 2024

• add timestamp check for the avg and sum options

  Sri-2023

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  da35fb7

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• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

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  ac38f76

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Commits on Dec 3, 2024

• modify the phenotype_matrix function to retrieve reptitive values in multi-line

  Sri-2023

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  23f68c2

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• modify note field to store multiple entries for repetitive_measurements

  Sri-2023

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  3809678

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• typo

  Sri-2023

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• use clean_up_db to clean up some tests; in SGN::Test::Fixture, also clean cvtermprop in clean_up_db function.

  lukasmueller

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Commits on Dec 4, 2024

• clean up db after some tests and also re-run matviews so they are correct for the following tests.

  lukasmueller

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  4efa217

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• try to fix tests.

  lukasmueller

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Commits on Dec 6, 2024

• hmmm... changing the order of the values may not help in the long run...

  lukasmueller

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• more sustainable approach is to sort the returned data before checking.

  lukasmueller

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• more attempts to make tests pass...

  lukasmueller

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• Merge branch 'master' into topic/repetitive_measurements2

  lukasmueller

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Commits on Dec 12, 2024

• fix upload_phenotype tests to handle potential delays

  Sri-2023

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• add strict and warnings options

  Sri-2023

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• add ability to load multiple phenotypic values by pushing on an array in generic simple upload.

  

  Production User

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• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

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• Merge remote-tracking branch 'origin/topic/repetitive_measurements2' into topic/repetitive_measurements2

  Sri-2023

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  2a6aea6

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• fix lint issues

  Sri-2023

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• make Phenotype_with_multi_categories.t test pass more reliably by checking substring of returned error.

  lukasmueller

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Commits on Dec 13, 2024

• fix all linting issues

  Sri-2023

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• update branch

  Sri-2023

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• fix this last lint issue

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Commits on Dec 16, 2024

• update the manual with repetitive_measurements

  Sri-2023

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• update bookdown docs

  

  github-actions

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Commits on Dec 17, 2024

• make trait values dynamic as trait option changes

  Sri-2023

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• update bookdown docs

  

  github-actions

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• requested to make a defualt option - as Average on UI under repetitive_measurements option

  Sri-2023

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• typo in passing the type param

  Sri-2023

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• update bookdown docs

  

  github-actions

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Commits on Dec 22, 2024

• add a conversion file for ncsu excel format.

  lukasmueller

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• update bookdown docs

  

  github-actions

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Commits on Jan 9, 2025

• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

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• Merge remote-tracking branch 'origin/topic/repetitive_measurements2' into topic/repetitive_measurements2

  Sri-2023

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  539f65f

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• update bookdown docs

  

  github-actions

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Commits on Jan 16, 2025

• Merge remote-tracking branch 'origin/master' into topic/repetitive_measurements2

  Sri-2023

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  bd78e5a

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• update bookdown docs

  

  github-actions

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• parse date without timezone

  Sri-2023

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• fix mousover on zoomed-in graph

  Sri-2023

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• Merge remote-tracking branch 'origin/topic/repetitive_measurements2' into topic/repetitive_measurements2

  Sri-2023

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  4b13376

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• update bookdown docs

  

  github-actions

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Commits on Jan 17, 2025

• fix margin to display labees for zoomed-in grpah

  Sri-2023

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• update bookdown docs

  

  github-actions

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• make lint ignore docs dir

  Sri-2023

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• update bookdown docs

  

  github-actions

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Commits on Jan 20, 2025

• add spinning wheel for repetitive section

  Sri-2023

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• update bookdown docs

  

  github-actions

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Commits on Jan 21, 2025

• add spinning wheel to phenotype raw data section

  Sri-2023

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• update bookdown docs

  

  github-actions

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Commits on Jan 23, 2025

• Update linter.yml

  ClayBirkett

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• Create .htmlhintrc

  ClayBirkett

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• update bookdown docs

  

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