Cvtmle (#188)

* update from_param_files

* rename parameters estimands

* fix tests

* drop unused files

* remove deprecated info from readme

* add serialization into test deps

* up TMLE and remove Manifest

* add joint allele indep mode

* faster genotype calling and estimands generation

* add more general interaction generation

* update syntax for interaction

* update deps

* add negative control files

* update BGEN deps

* add permutation_test cli

* add random variants cli

* reorg tl_inputs script

* add plot generation

* add sysimage build

* fix script

* remove deprecated option

* add compiler

* add generate_dataset cli

* add test

* fix limit problem

* add verbosity to script

* update script arg table

* add script for plotting

* fix pvalue bug and deal with nans

* up TMLE dep

* add filter SAMPLE_IDS from estimators

* up Targeted Estimation dep

* up version to match github

---------

Co-authored-by: Olivier Labayle <s2042526>

Author: olivierlabayle

.gitignore

@@ -25,7 +25,6 @@ docs/site/
 # Manifest.toml
 test/Manifest.toml
 
-
 # Develop dependencies
 dev/