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Develop #346

Merged
merged 180 commits into from
Sep 25, 2024
Merged

Develop #346

merged 180 commits into from
Sep 25, 2024

Commits on Feb 5, 2024

  1. updating documentation on the html help files for all modules

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Commits on Feb 12, 2024

  1. Update cohort-method.html 

    temp fix for CohortMethod module automatically opening help link - disabling link
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Commits on Feb 16, 2024

  1. protocol generator fix 

    - added message when generating
- added trycatch when target cohort json has issues (subset?)
- added chunk names for debugging
    @jreps
    jreps committed Feb 16, 2024
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  2. Merge pull request #256 from OHDSI/issue_111 

    protocol generator fix
    @jreps
    jreps authored Feb 16, 2024
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Commits on Feb 22, 2024

  1. Fixed for orphan concepts not displaying in cd reports

    @azimov
    azimov committed Feb 22, 2024
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Commits on Feb 23, 2024

  1. fixing plot color palette to work for a higher number of dbs in stand… 

    …ard plots and to be colorblind-friendly
    @nhall6
    nhall6 committed Feb 23, 2024
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  2. fixing bugs in some standard plots

    @nhall6
    nhall6 committed Feb 23, 2024
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  3. home module 

    - adding home module
    @jreps
    jreps committed Feb 23, 2024
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  4. Dynamic module load

    @azimov
    azimov committed Feb 23, 2024
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  5. Fixes for query and module load

    @azimov
    azimov committed Feb 23, 2024
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  6. splitting up column definition for evidence synth cohort method and sccs 

    splitting up column definition for evidence synth cohort method and sccs
    @jreps
    jreps committed Feb 23, 2024
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  7. Merge pull request #260 from OHDSI/es_sccs_cm_dynamic_load 

    Fixes for query and module load
    @jreps
    jreps authored Feb 23, 2024
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  8. Update evidence-synth-main.R 

    adding distinct to sccs column name pull
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  9. Merge branch 'es_split_cm_sccs' of https://github.com/OHDSI/OhdsiShin… 

    …yModules into es_split_cm_sccs
    @jreps
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  10. Merge pull request #259 from OHDSI/es_sccs_cm_dynamic_load 

    Dynamic module load
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    azimov authored Feb 23, 2024
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Commits on Feb 26, 2024

  1. Merge pull request #258 from OHDSI/incidence_plot_fixes 

    Incidence plot fixes
    @jreps
    jreps authored Feb 26, 2024
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  2. Merge pull request #255 from OHDSI/issue_173 

    updating documentation on the html help files for all modules
    @jreps
    jreps authored Feb 26, 2024
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Commits on Mar 1, 2024

  1. Update characterization-main.R 

    fixing wrong position of selectVal = F causing tab to not show in characterization if 'Target Viewer' is not run.
    @jreps
    jreps committed Mar 1, 2024
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Commits on Mar 14, 2024

  1. updating about module

    @nhall6
    nhall6 committed Mar 14, 2024
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  2. Update about-main.R

    @nhall6
    nhall6 committed Mar 14, 2024
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Commits on Mar 15, 2024

  1. Updating new about module

    @nhall6
    nhall6 committed Mar 15, 2024
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  2. Update about.html

    @nhall6
    nhall6 committed Mar 15, 2024
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  3. further updating the about module

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    nhall6 committed Mar 15, 2024
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Commits on Mar 22, 2024

  1. updating about module further, fixing link issues

    @nhall6
    nhall6 committed Mar 22, 2024
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Commits on Mar 26, 2024

  1. updating about-main further and oxygenising

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Commits on Mar 28, 2024

  1. adding some of the new Rmd files for the modules

    @nhall6
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  2. style tweaks

    @fdefalco
    fdefalco committed Mar 28, 2024
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  3. Delete about-dataSources.html

    @nhall6
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Commits on Apr 1, 2024

  1. Adding sample app.R file into extras folder

    @nhall6
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  2. updating some Rmds for vignettes

    @nhall6
    nhall6 committed Apr 1, 2024
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  3. Delete app.R

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Commits on Apr 2, 2024

  1. report module 

    adding initial code to generate reports
    @jreps
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  2. adding explicit pkg calls to pass test

    @nhall6
    nhall6 committed Apr 2, 2024
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  3. Merge pull request #269 from OHDSI/about-updates 

    About module updates to content and UI
    @jreps
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  4. Merge pull request #270 from OHDSI/report-module 

    report module
    @jreps
    jreps authored Apr 2, 2024
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  5. Update DESCRIPTION

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Commits on Apr 3, 2024

  1. Merge branch 'develop' of https://github.com/OHDSI/OhdsiShinyModules … 

    …into develop
    @nhall6
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  2. adding vignette Rmds for all modules

    @nhall6
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Commits on Apr 4, 2024

  1. adding vignette Rmds for all modules

    @nhall6
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Commits on Apr 5, 2024

  1. Update _pkgdown.yml 

    -updating the pkgdown yml
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  2. Merge branch 'develop' of https://github.com/OHDSI/OhdsiShinyModules … 

    …into develop
    @nhall6
    nhall6 committed Apr 5, 2024
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  3. updating pkgdown

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Commits on Apr 9, 2024

  1. updating pkgdown yml

    @nhall6
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Commits on Apr 10, 2024

  1. Merge pull request #271 from OHDSI/vignette-updates 

    Vignette updates
    @jreps
    jreps authored Apr 10, 2024
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  2. fixing yml with proper formatting for website

    @nhall6
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Commits on Apr 11, 2024

  1. Merge branch 'develop' of https://github.com/OHDSI/OhdsiShinyModules … 

    …into develop
    @nhall6
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  2. update pkgdown_yml

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  3. changing doctype in OhdsiShinyModules.R 

    #'
@doctype _PACKAGE
to be:
#' @doctype
package
    @nhall6
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  4. oxygenizing

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  5. Merge pull request #273 from OHDSI/website-updates 

    Website updates
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    jreps authored Apr 11, 2024
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Commits on Apr 12, 2024

  1. starting updates on adding hrefs to value boxes

    @nhall6
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  2. adding links to each valueBox for each module

    @nhall6
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  3. Merge pull request #274 from OHDSI/website-updates 

    Website updates
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Commits on Apr 19, 2024

  1. Fixes and optimisations for cd load up on postgres servers causing ha… 

    …ngs when using DBI functions
    @azimov
    azimov committed Apr 19, 2024
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  2. Fixed missing reports error

    @azimov
    azimov committed Apr 19, 2024
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  3. Fix for sqlite

    @azimov
    azimov committed Apr 19, 2024
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  4. Actual fix for sqlite...

    @azimov
    azimov committed Apr 19, 2024
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Commits on Apr 23, 2024

  1. Merge pull request #276 from OHDSI/postgres-dbi-issues 

    DBI issues fix
    @jreps
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  2. adding covariate balance table functionality and custom colDefs for t… 

    …he table
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  3. Merge branch 'hotfix-3.1.3' into develop 

    # Conflicts:
#	DESCRIPTION
#	NEWS.md
#	docs/404.html
#	docs/authors.html
#	docs/index.html
#	docs/pkgdown.yml
#	man/OhdsiShinyModules.Rd
    @azimov
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Commits on Apr 25, 2024

  1. Fixed missing library call

    @azimov
    azimov committed Apr 25, 2024
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Commits on Apr 26, 2024

  1. Merge branch 'hotfix-2.1.14' into develop 

    # Conflicts:
#	DESCRIPTION
#	NEWS.md
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Commits on May 2, 2024

  1. example app added 

    adding example app in extra folder and example Eunomia result data
    @jreps
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  2. Update report-main.R 

    bug fixes to report-main.R
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    jreps committed May 2, 2024
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Commits on May 3, 2024

  1. Update covariate balance table after primary key generation

    @nhall6
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Commits on May 6, 2024

  1. Adding database filter to results selection to address issue #265

    @nhall6
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  2. Merge pull request #281 from OHDSI/issue-265 

    Adding database filter to results selection to address issue #265
    @jreps
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  3. Merge pull request #280 from OHDSI/cm-covariate-balance-table 

    CM covariate balance table addition after primary key generation
    @jreps
    jreps authored May 6, 2024
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Commits on May 8, 2024

  1. remove help & information sections in most modules due to About modul… 

    …e update
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Commits on May 9, 2024

  1. estimation module 

    - adding estimation module that includes CM/SCCS/Evidence synthesis
    @jreps
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  2. estimation module updates 

    - adding evidence synth into SCCS
- adding plots for SCCS and CM
    @jreps
    jreps committed May 9, 2024
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  3. estimation edits 

    - optimizing sccs negative control plot
- removing prints
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Commits on May 17, 2024

  1. - updating characterization 

    - updating characterization
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Commits on May 20, 2024

  1. added targeting of value box hrefs

    @fdefalco
    fdefalco committed May 20, 2024
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  2. Merge pull request #283 from OHDSI/removing-help-sections 

    remove help & information sections in most modules due to About modul...
    @nhall6
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  3. adding links to valueBoxes even if modules are not included

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Commits on May 21, 2024

  1. improving characterization

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    jreps committed May 21, 2024
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  2. Update characterization-incidence.R 

    - adding code to use CI TAR lookup if available
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    jreps committed May 21, 2024
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  3. Merge branch 'develop' into estimation-updated

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Commits on May 22, 2024

  1. minor exclude fixes 

    minor exclude fixes
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  2. Update characterization-riskFactors.R

    @jreps
    jreps committed May 22, 2024
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  3. fixes 

    fixes
    @jreps
    jreps committed May 22, 2024
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  4. Update characterization-caseSeries.R 

    adding two extra columns
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  5. Update characterization-caseSeries.R 

    restricting case series to during covariates
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  6. Update characterization-main.R 

    adding CI outcomes to char options
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Commits on May 23, 2024

  1. Update characterization-riskFactors.R 

    fixing multiple washout and min obs bug in risk factors
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Commits on May 28, 2024

  1. Update cohort-diagnostics-main.R 

    Get table names faile when schema specified
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  2. Update cohort-diagnostics-main.R 

    Get table names faile when schema specified
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Commits on Jun 1, 2024

  1. updating for new char tables 

    updating for new char tables
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Commits on Jun 3, 2024

  1. Update characterization-riskFactors.R

    @jreps
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  2. updating bug fixes and column cleanliness

    @nhall6
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  3. Merge branch 'estimation-updated' of https://github.com/OHDSI/OhdsiSh… 

    …inyModules into estimation-updated
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Commits on Jun 4, 2024

  1. Update characterization-timeToEvent.R 

    changing selection for tte
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Commits on Jun 6, 2024

  1. cleaning characterization tables 

    cleaning characterization tables
    @jreps
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  2. minor update 

    adding box to show selected tar/database for RF and case series.
    @jreps
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  3. Update characterization-dechallengeRechallenge.R 

    updating warning for dechal-rechal
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  4. Update characterization-dechallengeRechallenge.R 

    - only display warning when there are warnings
    @jreps
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  5. fixing column alignment and incidence error messages

    @nhall6
    nhall6 committed Jun 6, 2024
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  6. Merge branch 'estimation-updated' of https://github.com/OHDSI/OhdsiSh… 

    …inyModules into estimation-updated
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Commits on Jun 7, 2024

  1. adding drop down and slide filters

    @jreps
    jreps committed Jun 7, 2024
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  2. fixing scrolls 

    fixing scrolls
    @jreps
    jreps committed Jun 7, 2024
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Commits on Jun 11, 2024

  1. Update characterization-cohorts.R 

    fixing SMD calculation in cohorts
    @jreps
    jreps committed Jun 11, 2024
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  2. minor bug fixes 

    - fixing tar changing before generate in case series
- fixing columns showing in selection that should be hidden
    @jreps
    jreps committed Jun 11, 2024
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  3. updating table download 

    - updating csv export to excel export with a details sheet
    @jreps
    jreps committed Jun 11, 2024
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  4. Update components-data-viewer.R 

    changing saving file type
    @jreps
    jreps committed Jun 11, 2024
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  5. adding details to exported results 

    adding details to exported results for characterization cohorts and databases
    @jreps
    jreps committed Jun 11, 2024
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Commits on Jun 12, 2024

  1. Update components-data-viewer.R 

    fixing actions not being includes as it is an extra column that is added outside the coldDef
    @jreps
    jreps committed Jun 12, 2024
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  2. Update characterization-caseSeries.R 

    - adding details to case-series download
    @jreps
    jreps committed Jun 12, 2024
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  3. Merge pull request #287 from OHDSI/pooled_connection_tablenames 

    Fix issue with pooled connection
    @azimov
    azimov authored Jun 12, 2024
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Commits on Jun 13, 2024

  1. fixing issue with SCCS not showing 

    fixing issue with SCCS not showing
    @jreps
    jreps committed Jun 13, 2024
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  2. fixing characterization 

    updating data downloads for char tables, fixing cohort names in CI, adding caption to custom CI plot
    @nhall6
    nhall6 committed Jun 13, 2024
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  3. Update characterization-main.R 

    sorting outcomes in char
    @jreps
    jreps committed Jun 13, 2024
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Commits on Jun 14, 2024

  1. fixing estimation 

    - adding missing shiny::
- updating code to get T and Os for SCCS so it removed negative controls
    @jreps
    jreps committed Jun 14, 2024
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  2. adding fix for ci_lookup 

    adding fix for ci_lookup
    @jreps
    jreps committed Jun 14, 2024
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Commits on Jun 20, 2024

  1. Update estimation-sccs-results-full.R

    @jreps
    jreps committed Jun 20, 2024
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  2. Update DESCRIPTION 

    adding Nathan Hall and Jamie Gilbert as co-authors
    @nhall6
    nhall6 authored Jun 20, 2024
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Commits on Jun 28, 2024

  1. minor updates 

    - fixed bug with control estimates plot not showing all results
- added ease value to control estimate plot
- added validation checks to print informative reason for missing plots
    @jreps
    jreps committed Jun 28, 2024
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  2. error handling for estimation plots 

    replacing estimation plot error message with useful notification
    @jreps
    jreps committed Jun 28, 2024
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  3. minor updates to estimation 

    - removing old sccs and cohort method files
- making estimation options be ordered by cohort name
- adding indication column into sccs diagnostics
- updating estimation outcome input to have the search options
    @jreps
    jreps committed Jun 28, 2024
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Commits on Jul 2, 2024

  1. characterization test updates 

    - updating characterization tests and fixing issues identified by tests
    @jreps
    jreps committed Jul 2, 2024
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Commits on Jul 9, 2024

  1. Update characterization-main.R 

    removing odd code
    @jreps
    jreps committed Jul 9, 2024
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Commits on Jul 10, 2024

  1. passing R check 

    - passing tests 78% coverage
- cleaning checks but still some notes
    @jreps
    jreps committed Jul 10, 2024
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Commits on Jul 15, 2024

  1. Merge pull request #286 from OHDSI/shiny-pool-issue 

    Update cohort-diagnostics-main.R
    @azimov
    azimov authored Jul 15, 2024
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  2. Merge branch 'develop' into hotfix-2.1.5-develop-merge 

    # Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/OhdsiShinyModules.R
#	_pkgdown.yml
#	docs/articles/AddingShinyModules.html
#	docs/articles/index.html
#	docs/news/index.html
#	docs/reference/LargeDataTable.html
#	docs/reference/OhdsiShinyModules.html
#	docs/reference/aboutHelperFile.html
#	docs/reference/aboutServer.html
#	docs/reference/aboutViewer.html
#	docs/reference/characterizationAggregateFeaturesServer.html
#	docs/reference/characterizationAggregateFeaturesViewer.html
#	docs/reference/characterizationDechallengeRechallengeServer.html
#	docs/reference/characterizationDechallengeRechallengeViewer.html
#	docs/reference/characterizationHelperFile.html
#	docs/reference/characterizationIncidenceServer.html
#	docs/reference/characterizationIncidenceViewer.html
#	docs/reference/characterizationServer.html
#	docs/reference/characterizationTableServer.html
#	docs/reference/characterizationTableViewer.html
#	docs/reference/characterizationTimeToEventServer.html
#	docs/reference/characterizationTimeToEventViewer.html
#	docs/reference/characterizationViewer.html
#	docs/reference/cohortCountsModule.html
#	docs/reference/cohortCountsView.html
#	docs/reference/cohortDefinitionsModule.html
#	docs/reference/cohortDefinitionsView.html
#	docs/reference/cohortDiagCharacterizationView.html
#	docs/reference/cohortDiagnosticsHelperFile.html
#	docs/reference/cohortDiagnosticsServer.html
#	docs/reference/cohortDiagnosticsView.html
#	docs/reference/cohortGeneratorHelperFile.html
#	docs/reference/cohortGeneratorServer.html
#	docs/reference/cohortGeneratorViewer.html
#	docs/reference/cohortMethodAttritionServer.html
#	docs/reference/cohortMethodAttritionViewer.html
#	docs/reference/cohortMethodCovariateBalanceServer.html
#	docs/reference/cohortMethodCovariateBalanceViewer.html
#	docs/reference/cohortMethodDiagnosticsSummaryServer.html
#	docs/reference/cohortMethodDiagnosticsSummaryViewer.html
#	docs/reference/cohortMethodHelperFile.html
#	docs/reference/cohortMethodKaplanMeierServer.html
#	docs/reference/cohortMethodKaplanMeierViewer.html
#	docs/reference/cohortMethodPopulationCharacteristicsServer.html
#	docs/reference/cohortMethodPopulationCharacteristicsViewer.html
#	docs/reference/cohortMethodPowerServer.html
#	docs/reference/cohortMethodPowerViewer.html
#	docs/reference/cohortMethodPropensityModelServer.html
#	docs/reference/cohortMethodPropensityModelViewer.html
#	docs/reference/cohortMethodPropensityScoreDistServer.html
#	docs/reference/cohortMethodPropensityScoreDistViewer.html
#	docs/reference/cohortMethodResultSummaryServer.html
#	docs/reference/cohortMethodResultSummaryViewer.html
#	docs/reference/cohortMethodServer.html
#	docs/reference/cohortMethodSystematicErrorServer.html
#	docs/reference/cohortMethodSystematicErrorViewer.html
#	docs/reference/cohortMethodViewer.html
#	docs/reference/cohortOverlapView.html
#	docs/reference/compareCohortCharacterizationView.html
#	docs/reference/conceptsInDataSourceView.html
#	docs/reference/createCdDatabaseDataSource.html
#	docs/reference/createCustomColDefList.html
#	docs/reference/createLargeSqlQueryDt.html
#	docs/reference/dataDiagnosticDrillServer.html
#	docs/reference/dataDiagnosticDrillViewer.html
#	docs/reference/dataDiagnosticHelperFile.html
#	docs/reference/dataDiagnosticServer.html
#	docs/reference/dataDiagnosticSummaryServer.html
#	docs/reference/dataDiagnosticSummaryViewer.html
#	docs/reference/dataDiagnosticViewer.html
#	docs/reference/databaseInformationView.html
#	docs/reference/datasourcesHelperFile.html
#	docs/reference/datasourcesServer.html
#	docs/reference/datasourcesViewer.html
#	docs/reference/evidenceSynthesisHelperFile.html
#	docs/reference/evidenceSynthesisServer.html
#	docs/reference/evidenceSynthesisViewer.html
#	docs/reference/getCirceRenderedExpression.html
#	docs/reference/getEnabledCdReports.html
#	docs/reference/getLogoImage.html
#	docs/reference/incidenceRatesView.html
#	docs/reference/inclusionRulesView.html
#	docs/reference/index.html
#	docs/reference/indexEventBreakdownView.html
#	docs/reference/largeTableServer.html
#	docs/reference/largeTableView.html
#	docs/reference/makeButtonLabel.html
#	docs/reference/orpahanConceptsView.html
#	docs/reference/patientLevelPredictionCalibrationServer.html
#	docs/reference/patientLevelPredictionCalibrationViewer.html
#	docs/reference/patientLevelPredictionCovariateSummaryServer.html
#	docs/reference/patientLevelPredictionCovariateSummaryViewer.html
#	docs/reference/patientLevelPredictionCutoffServer.html
#	docs/reference/patientLevelPredictionCutoffViewer.html
#	docs/reference/patientLevelPredictionDesignSummaryServer.html
#	docs/reference/patientLevelPredictionDesignSummaryViewer.html
#	docs/reference/patientLevelPredictionDiagnosticsServer.html
#	docs/reference/patientLevelPredictionDiagnosticsViewer.html
#	docs/reference/patientLevelPredictionDiscriminationServer.html
#	docs/reference/patientLevelPredictionDiscriminationViewer.html
#	docs/reference/patientLevelPredictionHelperFile.html
#	docs/reference/patientLevelPredictionModelSummaryServer.html
#	docs/reference/patientLevelPredictionModelSummaryViewer.html
#	docs/reference/patientLevelPredictionNbServer.html
#	docs/reference/patientLevelPredictionNbViewer.html
#	docs/reference/patientLevelPredictionServer.html
#	docs/reference/patientLevelPredictionSettingsServer.html
#	docs/reference/patientLevelPredictionSettingsViewer.html
#	docs/reference/patientLevelPredictionValidationServer.html
#	docs/reference/patientLevelPredictionValidationViewer.html
#	docs/reference/patientLevelPredictionViewer.html
#	docs/reference/phevaluatorHelperFile.html
#	docs/reference/phevaluatorServer.html
#	docs/reference/phevaluatorViewer.html
#	docs/reference/resultTableServer.html
#	docs/reference/resultTableViewer.html
#	docs/reference/sccsHelperFile.html
#	docs/reference/sccsServer.html
#	docs/reference/sccsView.html
#	docs/reference/timeDistributionsView.html
#	docs/reference/visitContextView.html
#	docs/sitemap.xml
    @azimov
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  3. Merge pull request #305 from OHDSI/hotfix-2.1.5-develop-merge 

    Hotfix 2.1.5 develop merge
    @azimov
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Commits on Jul 23, 2024

  1. Update characterization-incidence.R to use lookup tables.

    @chrisknoll
    chrisknoll committed Jul 23, 2024
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Commits on Jul 30, 2024

  1. Switch coldef json to CSV.

    @chrisknoll
    chrisknoll committed Jul 30, 2024
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  2. Removed dead code.

    @chrisknoll
    chrisknoll committed Jul 30, 2024
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  3. Fixes estimation bug when target has no comparator for CM

    @anthonysena
    anthonysena committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. fixing tests 

    - fixing tests
- updates for Characterization v1.1.0
- updating example app
    @jreps
    jreps committed Jul 31, 2024
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  2. fixing example sqlite database_ids 

    fixing example sqlite database_ids
    @jreps
    jreps committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Merge branch 'prerelease' into estimation-updated-cohortIncidence

    @jreps
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  2. Merge pull request #310 from OHDSI/estimation-updated-cohortIncidence 

    Estimation updated cohort incidence
    @jreps
    jreps authored Aug 1, 2024
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  3. CohortIncidence updates 

    - updating test database for new CohortIncidence
- fixing tests for new CohortIncidence
    @jreps
    jreps committed Aug 1, 2024
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  4. fixing check issues due to cohort incidence 

    fixing check issues due to cohort incidence
    @jreps
    jreps committed Aug 1, 2024
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  5. adding hot fixes from main 

    - adding hot fixes from main
- adding incidence results into example app
    @jreps
    jreps committed Aug 1, 2024
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  6. updating example app for CI 

    updating example app for CI
    @jreps
    jreps committed Aug 1, 2024
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  7. updating docs 

    - website update
- manual update
    @jreps
    jreps committed Aug 1, 2024
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Commits on Aug 6, 2024

  1. Update characterization-riskFactors.R 

    fixing minor bug in risk factor that happens when there is multiple outcomeWashoutdays
    @jreps
    jreps committed Aug 6, 2024
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Commits on Aug 9, 2024

  1. Fixing issue #315 , diagonal line along x = y

    @nhall6
    nhall6 committed Aug 9, 2024
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  2. Fixing issue #314 - adding T, C, and O IDs to the table to allow bett… 

    …er filtering to users
    @nhall6
    nhall6 committed Aug 9, 2024
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Commits on Aug 15, 2024

  1. addressing issue #307 

    adding global fuzzy string matching to table search
    @nhall6
    nhall6 committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. Characterization updates 

    - updating Characterization for new censoring
- adding counts to risk factor view
    @jreps
    jreps committed Aug 16, 2024
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  2. Merge pull request #316 from OHDSI/prerelease-issue#315 

    Fixing issue #315 , diagonal line along x = y
    @jreps
    jreps authored Aug 16, 2024
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  3. Merge pull request #317 from OHDSI/prerelease-issue#314 

    Fixing issue #314 - adding T, C, and O IDs to the table to allow better filtering capabilities for users in large studies
    @jreps
    jreps authored Aug 16, 2024
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Commits on Aug 19, 2024

  1. Update components-data-viewer.R 

    removing new dep on htmlwidgets
    @jreps
    jreps committed Aug 19, 2024
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  2. document updates 

    - updating version ready for release
- updating docs
- updating readme
    @jreps
    jreps committed Aug 19, 2024
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  3. Merge pull request #321 from OHDSI/prerelease-issue#307 

    addressing issue #307
    @jreps
    jreps authored Aug 19, 2024
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Commits on Aug 20, 2024

  1. Merge branch 'prerelease' into nhall6-author-updates

    @jreps
    jreps authored Aug 20, 2024
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  2. Merge branch 'develop' into prerelease

    @jreps
    jreps committed Aug 20, 2024
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  3. merging in develop 

    - merging in develop
- recreating docs after merge
    @jreps
    jreps committed Aug 20, 2024
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  4. fixing formatting of authors 

    fixing formatting of authors
    @jreps
    jreps committed Aug 20, 2024
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  5. Merge pull request #297 from OHDSI/nhall6-author-updates 

    Update DESCRIPTION
    @jreps
    jreps authored Aug 20, 2024
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  6. Merge pull request #312 from OHDSI/prerelease 

    Prerelease
    @jreps
    jreps authored Aug 20, 2024
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Commits on Aug 21, 2024

  1. Update characterization-main.R 

    fixing missing schema
    @jreps
    jreps committed Aug 21, 2024
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  2. Update characterization-riskFactors.R 

    updating as setting id is now a character
    @jreps
    jreps committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. updating website

    @jreps
    jreps committed Aug 22, 2024
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Commits on Sep 12, 2024

  1. Fixing #301 (#326) 

    Adding alphabetical sort to DB input options
    @nhall6
    nhall6 authored Sep 12, 2024
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  2. Fixing #296 (#327) 

    Standardizing pickerInput type for database selection where multiple options are possible to improve UX. Also fixed some colDefs in Exposed Cases
    @nhall6
    nhall6 authored Sep 12, 2024
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  3. Fixing #302 and Filtered Data Downloads (#332) 

    * Fixing #302 and Filtered Data Downloads

All filtered data downloads across all modules should work now, with a button styled the same as the full download. It needs to be a CSV handler though due to the reactable statte

* Updating the fix

Also fixed download buttons in Cohorts module, addressing #298
    @nhall6
    nhall6 authored Sep 12, 2024
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  4. Update R_CMD_check_Hades.yaml

    @jreps
    jreps committed Sep 12, 2024
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  5. Update R_CMD_check_Hades.yaml

    @jreps
    jreps committed Sep 12, 2024
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  6. Update R_CMD_check_Hades.yaml

    @jreps
    jreps committed Sep 12, 2024
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  7. fixing R checks 

    fixing R checks
    @jreps
    jreps committed Sep 12, 2024
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Commits on Sep 13, 2024

  1. Update cohort-diagnostics-databaseInformation.R (#333) 

    Fixing the issue reported in #162
    @jreps
    jreps authored Sep 13, 2024
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  2. fixing issue issue_330 (#334) 

    fixing time plot x-axis
    @jreps
    jreps authored Sep 13, 2024
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  3. fixing issue 167 (#335) 

    added code to get long database names on multiple lines
    @jreps
    jreps authored Sep 13, 2024
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  4. Update cohort-diagnostics-timeDistributions.R (#336) 

    adding fix for issue 168
    @jreps
    jreps authored Sep 13, 2024
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  5. Update patient-level-prediction-modelSummary.R (#337)

    @jreps
    jreps authored Sep 13, 2024
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Commits on Sep 19, 2024

  1. Fixing #300 (#329) 

    * Fixing #300

Syntax error in code was causing an issue in the rule sequencing, leading to incorrect attrition values. thanks to @chrisknoll for all the help

* fixing R check

fixing R check and removing a pointless file

---------

Co-authored-by: jreps <[email protected]>
    @nhall6 @jreps
    nhall6 and jreps authored Sep 19, 2024
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Commits on Sep 20, 2024

  1. Issue114 (#339) 

    * Fixing Power tables re: #114

Standardizing power table outputs to adhere to OSM standard theme (reactable via resultTableViewer and resultTableServer). Also split the tables into 2 sub-tabs for easier readability

* Updating propensity score table

Adding conditional formatting of colors to values to aid in interpretation, and also adding an absolute value of beta column.

* Updates to propensity score plot

Overlaying equipoise statistic onto the plot, and truncating cohort names in legend

* Updating covariate balance plot

Adding maxSDM to covariate balance plot

* Updating  captions and systematic error

Adding to caption descriptions in figures and overlaying EASE statistic on systematic error plot

* Updating systematic error

Adding more descriptive filenames for plot downloads

* Develop (#340)

* Fixing #301 (#326)

Adding alphabetical sort to DB input options

* Fixing #296 (#327)

Standardizing pickerInput type for database selection where multiple options are possible to improve UX. Also fixed some colDefs in Exposed Cases

* Fixing #302 and Filtered Data Downloads (#332)

* Fixing #302 and Filtered Data Downloads

All filtered data downloads across all modules should work now, with a button styled the same as the full download. It needs to be a CSV handler though due to the reactable statte

* Updating the fix

Also fixed download buttons in Cohorts module, addressing #298

* Update R_CMD_check_Hades.yaml

* Update R_CMD_check_Hades.yaml

* Update R_CMD_check_Hades.yaml

* fixing R checks

fixing R checks

* Update cohort-diagnostics-databaseInformation.R (#333)

Fixing the issue reported in #162

* fixing issue issue_330 (#334)

fixing time plot x-axis

* fixing issue 167 (#335)

added code to get long database names on multiple lines

* Update cohort-diagnostics-timeDistributions.R (#336)

adding fix for issue 168

* Update patient-level-prediction-modelSummary.R (#337)

---------

Co-authored-by: Nathan Hall <[email protected]>

* fixing testing errors

---------

Co-authored-by: jreps <[email protected]>
    @nhall6 @jreps
    nhall6 and jreps authored Sep 20, 2024
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  2. fixing #342 (#343) 

    * fixing #342

cohort count and cohort generation tables are now fixed and will render

* fixing tests for Cohorts

* Delete Rplots.pdf

---------

Co-authored-by: jreps <[email protected]>
    @nhall6 @jreps
    nhall6 and jreps authored Sep 20, 2024
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  3. removing prints 

    removing prints
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  4. Update R_CMD_check_Hades.yaml (#344) 

    - adding testing on linux back (after setting java options)
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  5. fixing issue 211 (#345) 

    fixing issue 211
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    jreps authored Sep 20, 2024
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Commits on Sep 23, 2024

  1. Update characterization-cohorts.R 

    missing values in database comparison was causing an error.  This is fixed by imputing 0 when values are NA.
    @jreps
    jreps committed Sep 23, 2024
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  2. Update DESCRIPTION

    @jreps
    jreps committed Sep 23, 2024
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Commits on Sep 25, 2024

  1. Merge branch 'main' into develop

    @jreps
    jreps committed Sep 25, 2024
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  2. fixing dup download 

    removing download button since it is repeated
    @jreps
    jreps committed Sep 25, 2024
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  3. preparing for 3.0.1 release 

    preparing for 3.0.1 release
    @jreps
    jreps committed Sep 25, 2024
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