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Update to 3.4.0 #59

Merged
merged 117 commits into from
Jun 13, 2024
Merged

Update to 3.4.0 #59

merged 117 commits into from
Jun 13, 2024

Commits on Apr 29, 2024

  1. Fixed variable inversion error

    @llegregam
    llegregam committed Apr 29, 2024
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  2. Bump to 3.3.7

    @llegregam
    llegregam committed Apr 29, 2024
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  3. removed obelete TODO

    @llegregam
    llegregam committed Apr 29, 2024
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  4. Added docstring to Configparser

    @llegregam
    llegregam committed Apr 29, 2024
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  5. Bugfix by coercing experiment name to string

    @llegregam
    llegregam committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. Sent logs to stream

    @llegregam
    llegregam committed Apr 30, 2024
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  2. Added test for monod model

    @llegregam
    llegregam committed Apr 30, 2024
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  3. PEP8 cleanup

    @llegregam
    llegregam committed Apr 30, 2024
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  4. added logger

    @llegregam
    llegregam committed Apr 30, 2024
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  5. Added np functions instead of python operators

    @llegregam
    llegregam committed Apr 30, 2024
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  6. added monod model test

    @llegregam
    llegregam committed Apr 30, 2024
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  7. Updated lock file

    @llegregam
    llegregam committed Apr 30, 2024
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  8. Changed python minimum version to 3.8.1 to handle flake8 version

    @llegregam
    llegregam committed Apr 30, 2024
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  9. Added flake8 testing on the 3.11 python env.

    @llegregam
    llegregam committed Apr 30, 2024
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Commits on May 6, 2024

  1. Refactoring

    @llegregam
    llegregam committed May 6, 2024
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  2. Refactoring

    @llegregam
    llegregam committed May 6, 2024
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Commits on May 7, 2024

  1. IMPORTANT: Changed names "parameters_to_estimate" to "parameters" 

    Changed "fixed_parameters" to "args"
    @llegregam
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  2. IMPORTANT: Changed names "parameters_to_estimate" to "parameters" 

    Changed "fixed_parameters" to "args"
    @llegregam
    llegregam committed May 7, 2024
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  3. refactoring

    @llegregam
    llegregam committed May 7, 2024
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  4. changed "params_opti" to "parameters" & "params_not_opti" to "args"

    @llegregam
    llegregam committed May 7, 2024
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Commits on May 14, 2024

  1. changed "model_name" attr to "name"

    @llegregam
    llegregam committed May 14, 2024
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  2. Added data for model tests

    @llegregam
    llegregam committed May 14, 2024
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  3. changed "model_name" to "name"

    @llegregam
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  4. changed "model_name" to "name"

    @llegregam
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  5. Fixed bug where t_lag wasn't actually being used in simulation. Made … 

    …code clearer. Added clip on values beneath zero.
    @llegregam
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  6. Fixed bug where t_lag wasn't actually being used in simulation. Made … 

    …code clearer. Added clip on values beneath zero.
    @llegregam
    llegregam committed May 14, 2024
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  7. Added clip on values beneath zero.

    @llegregam
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  8. "model_name" to "name"

    @llegregam
    llegregam committed May 14, 2024
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  9. Updated max version to 4.0.0

    @llegregam
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  10. Modified test data. Put all sds to 0.2 as default for tests.

    @llegregam
    llegregam committed May 14, 2024
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  11. Added unit tests for all models

    @llegregam
    llegregam committed May 14, 2024
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Commits on May 15, 2024

  1. refactoring

    @llegregam
    llegregam committed May 15, 2024
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  2. removed clipping of simulated dataframe. 

    Fixed bug in model name attribute
    @llegregam
    llegregam committed May 15, 2024
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  3. split model tests into different files

    @llegregam
    llegregam committed May 15, 2024
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  4. split model tests into different files

    @llegregam
    llegregam committed May 15, 2024
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  5. Removed fold test_models file

    @llegregam
    llegregam committed May 15, 2024
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  6. Changed some methods to static 

    refactoring
    @llegregam
    llegregam committed May 15, 2024
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  7. shifted datasets to test individual test files

    @llegregam
    llegregam committed May 15, 2024
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  8. type-hint

    @llegregam
    llegregam committed May 15, 2024
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  9. finished tests

    @llegregam
    llegregam committed May 15, 2024
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  10. Added more data points to simulated matrixes for plotting

    @llegregam
    llegregam committed May 15, 2024
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  11. Added args (fixed parameters)

    @llegregam
    llegregam committed May 15, 2024
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  12. Added args (fixed parameters)

    @llegregam
    llegregam committed May 15, 2024
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  13. fix model 1

    @pierremillard
    pierremillard committed May 15, 2024
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Commits on May 16, 2024

  1. Refactoring

    @llegregam
    llegregam committed May 16, 2024
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  2. Made large matrix be created with shape defined by length of the time… 

    … vector

Fixed bug where log level was not being taken into account
    @llegregam
    llegregam committed May 16, 2024
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  3. Fixed test data

    @llegregam
    llegregam committed May 16, 2024
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  4. refactored

    @llegregam
    llegregam committed May 16, 2024
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  5. updated gitignore

    @llegregam
    llegregam committed May 16, 2024
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  6. Improved logging and added log file export

    @llegregam
    llegregam committed May 16, 2024
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Commits on May 17, 2024

  1. Improved logging and added log file export

    @llegregam
    llegregam committed May 17, 2024
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  2. Removed logs from __init__

    @llegregam
    llegregam committed May 17, 2024
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  3. Fixed tests

    @llegregam
    llegregam committed May 17, 2024
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  4. Changed "Degradation" to "Degradation constants" & made t-lag default… 

    … lower bound 1e-6
    @llegregam
    llegregam committed May 17, 2024
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  5. Fixed tests

    @llegregam
    llegregam committed May 17, 2024
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  6. Added check_data_path method

    @llegregam
    llegregam committed May 17, 2024
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  7. Started work on data_path_select from config

    @llegregam
    llegregam committed May 17, 2024
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Commits on May 21, 2024

  1. Added methods to handle wrong data path in config file

    @llegregam
    llegregam committed May 21, 2024
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  2. Spacing

    @llegregam
    llegregam committed May 21, 2024
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  3. PEP8

    @llegregam
    llegregam committed May 21, 2024
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  4. Merge pull request #58 from MetaSys-LISBP/dev_config_data_selector 

    Dev config data selector
    @llegregam
    llegregam committed May 21, 2024
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Commits on May 22, 2024

  1. Fixed config parser path input prompting. 

    changed results folder to use the name of data file
    @llegregam
    llegregam committed May 22, 2024
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  2. changed python minimum version to 3.9 for scipy

    @llegregam
    llegregam committed May 22, 2024
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  3. Made function for generating logger 

    made new dataframe for printing results in GUI and put into expanders the printed dfs
    @llegregam
    llegregam committed May 22, 2024
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  4. Removed actions for 3.8 (not supported anymore)

    @llegregam
    llegregam committed May 22, 2024
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  5. Update to 3.4.0

    @llegregam
    llegregam committed May 22, 2024
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  6. shutdown logger at the end of execution

    @llegregam
    llegregam committed May 22, 2024
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  7. Added khi2 test results to output expanders

    @llegregam
    llegregam committed May 22, 2024
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Commits on May 23, 2024

  1. Updated some logs

    @llegregam
    llegregam committed May 23, 2024
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  2. Added Akaike's information criterion (AIC)

    @llegregam
    llegregam committed May 23, 2024
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  3. Added Akaike's information criterion (AIC) and model selection in FAQ

    @llegregam
    llegregam committed May 23, 2024
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  4. Adding aic_c 

    Fixed small bug in build_logger
    @llegregam
    llegregam committed May 23, 2024
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Commits on May 24, 2024

  1. Added AIC & AICc 

    Added debug logs for MC & changed var name in for loop
    @llegregam
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  2. Added AIC & AICc

    @llegregam
    llegregam committed May 24, 2024
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  3. Added AIC & AICc

    @llegregam
    llegregam committed May 24, 2024
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  4. Updated docs for 3.4.0

    @llegregam
    llegregam committed May 24, 2024
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  5. Temporary fix of data_path_config_context retrieving

    @llegregam
    llegregam committed May 24, 2024
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  6. Added repr ConfigParser

    @llegregam
    llegregam committed May 24, 2024
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Commits on May 28, 2024

  1. update doc

    @pierremillard
    pierremillard committed May 28, 2024
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  2. update doc

    @pierremillard
    pierremillard committed May 28, 2024
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  3. update doc

    @pierremillard
    pierremillard committed May 28, 2024
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  4. update doc

    @pierremillard
    pierremillard committed May 28, 2024
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  5. update doc

    @pierremillard
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  6. update doc

    @pierremillard
    pierremillard committed May 28, 2024
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  7. update doc

    @pierremillard
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  8. update readme

    @pierremillard
    pierremillard committed May 28, 2024
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  9. update doc typo

    @pierremillard
    pierremillard committed May 28, 2024
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Commits on May 29, 2024

  1. update tests

    @pierremillard
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  2. Added AIC to overview

    @llegregam
    llegregam committed May 29, 2024
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  3. Fixed chi2 test p value explanation

    @llegregam
    llegregam committed May 29, 2024
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  4. Updated image with new name for degradation constants

    @llegregam
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  5. Added "simulate data from parameters" section

    @llegregam
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  6. Clean up FAQ

    @llegregam
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  7. PEP8

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  8. Rearranged the model testing section

    @llegregam
    llegregam committed May 29, 2024
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  9. Set rtol back to 1e-3

    @llegregam
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  10. minor changes to text for clarity

    @llegregam
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Commits on May 30, 2024

  1. update validation data

    @pierremillard
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  2. update validation data

    @pierremillard
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  3. Merge branch 'dev' of https://github.com/MetaSys-LISBP/PhysioFit into… 

    … dev
    @pierremillard
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  4. Fixed bug with data paths pointing to config file instead of data

    @llegregam
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  5. update validation doc

    @pierremillard
    pierremillard committed May 30, 2024
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Commits on Jun 4, 2024

  1. change test name

    @pierremillard
    pierremillard committed Jun 4, 2024
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Commits on Jun 13, 2024

  1. Updated CLI

    @llegregam
    llegregam committed Jun 13, 2024
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  2. removed useless f-string literal

    @llegregam
    llegregam committed Jun 13, 2024
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  3. Added some debug logs

    @llegregam
    llegregam committed Jun 13, 2024
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  4. Added flake8 to tox

    @llegregam
    llegregam committed Jun 13, 2024
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  5. PEP8

    @llegregam
    llegregam committed Jun 13, 2024
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  6. Merge remote-tracking branch 'origin/dev' into dev

    @llegregam
    llegregam committed Jun 13, 2024
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  7. Fixed bug when reading config_file in degradation model

    @llegregam
    llegregam committed Jun 13, 2024
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  8. added check that chosen data path in config parser is tsvv or txt

    @llegregam
    llegregam committed Jun 13, 2024
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  9. bugfix

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    llegregam committed Jun 13, 2024
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  10. added import

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    llegregam committed Jun 13, 2024
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  11. removed CI on python 3.8

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    llegregam committed Jun 13, 2024
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  12. Changed checkout in CI/CD to v4

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    llegregam committed Jun 13, 2024
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  13. Removed macos tests

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    llegregam committed Jun 13, 2024
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  14. flake8 linting

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    llegregam committed Jun 13, 2024
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