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Two-step hybrid refactoring #34

Merged
merged 87 commits into from
May 10, 2022
Merged

Two-step hybrid refactoring #34

merged 87 commits into from
May 10, 2022

Commits on Feb 9, 2022

  1. init two-step hybrid test

    @maximskorik
    maximskorik committed Feb 9, 2022
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  2. update library calls to rcx aplcms

    @maximskorik
    maximskorik committed Feb 9, 2022
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  3. complete two-step-hybrid test

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    maximskorik committed Feb 9, 2022
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Commits on Feb 11, 2022

  1. reformat two.step.hybrid.R

    @maximskorik
    maximskorik committed Feb 11, 2022
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  2. add all test data to two-step-hybrid test

    @maximskorik
    maximskorik committed Feb 11, 2022
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  3. reformat inputs and comments

    @maximskorik
    maximskorik committed Feb 11, 2022
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Commits on Feb 15, 2022

  1. refactor semi.sup arg list

    @maximskorik
    maximskorik committed Feb 15, 2022
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Commits on Feb 18, 2022

  1. add colnames to metadata table

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    maximskorik committed Feb 18, 2022
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Commits on Mar 16, 2022

  1. add first step

    @maximskorik
    maximskorik committed Mar 16, 2022
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  2. add get_sample_names to NAMESPACE

    @maximskorik
    maximskorik committed Mar 16, 2022
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  3. add vim

    @maximskorik
    maximskorik committed Mar 16, 2022
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  4. add cmd-line tools

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    maximskorik committed Mar 16, 2022
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  5. capitalize dockerfile name

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    maximskorik committed Mar 16, 2022
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  6. reformat indentation

    @maximskorik
    maximskorik committed Mar 16, 2022
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  7. add batch-splitting; add dplyr to dependencies

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    maximskorik committed Mar 16, 2022
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  8. extract intensity-median computation

    @maximskorik
    maximskorik committed Mar 16, 2022
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  9. reformat function calls

    @maximskorik
    maximskorik committed Mar 16, 2022
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  10. fit function for tibble dataframes

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    maximskorik committed Mar 16, 2022
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  11. refactor mz, rt, and batch label binding

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    maximskorik committed Mar 16, 2022
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  12. remove feature indicies from tables

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    maximskorik committed Mar 16, 2022
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  13. adjust for varying rt colname

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    maximskorik committed Mar 16, 2022
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  14. add common colname to cbind to ensure proper rbind

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    maximskorik committed Mar 16, 2022
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  15. extract repeating method

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    maximskorik committed Mar 16, 2022
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  16. rename function

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    maximskorik committed Mar 16, 2022
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  17. put feature.align in wrapper

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    maximskorik committed Mar 16, 2022
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  18. omit warnings

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    maximskorik committed Mar 16, 2022
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Commits on Mar 23, 2022

  1. move median-intensity computation inside loop

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    maximskorik committed Mar 23, 2022
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  2. reformat table

    @maximskorik
    maximskorik committed Mar 23, 2022
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  3. edit stdout message

    @maximskorik
    maximskorik committed Mar 23, 2022
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  4. change variable names for iteration

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    maximskorik committed Mar 23, 2022
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Commits on Mar 24, 2022

  1. add comments with context

    @maximskorik
    maximskorik committed Mar 24, 2022
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  2. extract rt readjusting

    @maximskorik
    maximskorik committed Mar 24, 2022
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  3. add long to wide conversion

    @maximskorik
    maximskorik committed Mar 24, 2022
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  4. fit function to wide dataframes

    @maximskorik
    maximskorik committed Mar 24, 2022
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  5. remove unused variables

    @maximskorik
    maximskorik committed Mar 24, 2022
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  6. correct indentation

    @maximskorik
    maximskorik committed Mar 24, 2022
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  7. reformat aligned table

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    maximskorik committed Mar 24, 2022
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Commits on Apr 4, 2022

  1. refactor multiple-peak matching

    @maximskorik
    maximskorik committed Apr 4, 2022
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  2. reformat individual-feature matching

    @maximskorik
    maximskorik committed Apr 4, 2022
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  3. finish time feature-adjustment loop

    @maximskorik
    maximskorik committed Apr 4, 2022
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  4. correct mz-range colnames

    @maximskorik
    maximskorik committed Apr 4, 2022
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  5. make slicing work

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    maximskorik committed Apr 4, 2022
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Commits on Apr 5, 2022

  1. refactor intensity & rt tables construction

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    maximskorik committed Apr 5, 2022
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  2. adapt to refactored weaker-signal recovery

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    maximskorik committed Apr 5, 2022
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  3. extract filtering by presence into a function

    @maximskorik
    maximskorik committed Apr 5, 2022
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  4. rename output variables

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    maximskorik committed Apr 5, 2022
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  5. replace on with by to omit redundant stdout

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    maximskorik committed Apr 5, 2022
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Commits on Apr 7, 2022

  1. harmonize variable names with their content

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    maximskorik committed Apr 7, 2022
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  2. update dependencies

    @maximskorik
    maximskorik committed Apr 7, 2022
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  3. harmonize output-variable names

    @maximskorik
    maximskorik committed Apr 7, 2022
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  4. sort features by mz & rt

    @maximskorik
    maximskorik committed Apr 7, 2022
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  5. add data comparer

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    maximskorik committed Apr 7, 2022
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  6. add num_workers to arguments

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    maximskorik committed Apr 7, 2022
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Commits on Apr 20, 2022

  1. return semi.sup as first step

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    maximskorik committed Apr 20, 2022
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  2. upd mismatched feature

    @maximskorik
    maximskorik committed Apr 20, 2022
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  3. make test run in tempdir

    @maximskorik
    maximskorik committed Apr 20, 2022
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  4. remove redundant variables and comments from test

    @maximskorik
    maximskorik committed Apr 20, 2022
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  5. extract feature recovery into method

    @maximskorik
    maximskorik committed Apr 20, 2022
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  6. reformat with styler pkg

    @maximskorik
    maximskorik committed Apr 20, 2022
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  7. clean up stdout

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    maximskorik committed Apr 20, 2022
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  8. rename variable

    @maximskorik
    maximskorik committed Apr 20, 2022
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  9. update dependencies

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    maximskorik committed Apr 20, 2022
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Commits on Apr 21, 2022

  1. update meta.yaml

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    maximskorik committed Apr 21, 2022
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  2. save feature table in long format

    @maximskorik
    maximskorik committed Apr 21, 2022
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Commits on Apr 23, 2022

  1. bump pkg version

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    maximskorik committed Apr 23, 2022
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  2. add function to namespace

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    maximskorik committed Apr 23, 2022
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Commits on May 2, 2022

  1. remove redundant parallelization

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    maximskorik committed May 2, 2022
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  2. make tibble tables for proper naming

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    maximskorik committed May 2, 2022
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  3. move metadata csv-reader out

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    maximskorik committed May 2, 2022
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Commits on May 4, 2022

  1. move table reformatting to utils

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    maximskorik committed May 4, 2022
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  2. remove utility methods from NAMESPACE

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    maximskorik committed May 4, 2022
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  3. expose a function for testthat

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    maximskorik committed May 4, 2022
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  4. remove deprecated test

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    maximskorik committed May 4, 2022
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  5. clear cache after test

    @maximskorik
    maximskorik committed May 4, 2022
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  6. rename median intensity column

    @maximskorik
    maximskorik committed May 4, 2022
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  7. replace indicies with column names

    @maximskorik
    maximskorik committed May 4, 2022
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  8. add descriptive method name

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    maximskorik committed May 4, 2022
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  9. iterate through batch indicies

    @maximskorik
    maximskorik committed May 4, 2022
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  10. add sorting back to NAMESPACE

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    maximskorik committed May 4, 2022
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Commits on May 7, 2022

  1. add corrected features to the output

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    maximskorik committed May 7, 2022
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  2. add aligned table to the output

    @maximskorik
    maximskorik committed May 7, 2022
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  3. make robust extention stripping

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    maximskorik committed May 7, 2022
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  4. reformat aligned_features output

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    maximskorik committed May 7, 2022
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  5. reformat adjust.time input and revert 7d0656d

    @maximskorik
    maximskorik committed May 7, 2022
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Commits on May 9, 2022

  1. add known table to the output

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    maximskorik committed May 9, 2022
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  2. complete identifiers list

    @maximskorik
    maximskorik committed May 9, 2022
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  3. bump correct version

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    maximskorik committed May 9, 2022
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