Loco gwas (#193)

* changes from retired branch

* testing for loco_gwas complete

* loco-gwas specific bed, bim, fam files

* Updated Manifest

* Changed Float64 SnpArrays to UInt8

* up TMLE

* remove too stringent test

* add nothing threshold that always aclls max prob

* update dep TMLE

* add prefix to JointEstimate

* fix random variants tests

* loco-gwas respects verbosity

* fix allele eindependent estimands

* remove unused bed files

* include gwas mode in allele independent

* integrate gwas mode into allele independent

* fix estimands_from_group

* fix tests loco GWAS

* removal of loco-gwas command in argparse and merge functionality with allele-independent-estimands

* fix corrupt manifest

* revert to working commit

* revert to stable commit

* Revert "revert to stable commit"

This reverts commit 5c30fc3.

* Revert "fix corrupt manifest"

This reverts commit 782525c.

* Revert "Merge branch 'main' into loco-gwas"

This reverts commit c1c303f, reversing
changes made to 0832103.

* up CairoMakie compat

* more efficient memory usage in read_bed_chromosome()

* ignore test results file

* up TMLE and TargetedEstimation

* merge loco gwas into simulation

* add missing changes

* refuse some changes from loco gwas that delete some tests

* integrate loco gwas without losing changes from main

* update variable accessors

* enable multithreading in generating GWAS estimands

* removing the biallelic filter; multithreading speedup

* added append estimates for serial processes

* start to clean repo

* add a standalone CLI interface

* more refactorization of the code

* remove more unused functions

* remove parameter in favor of estimand

* more syntax fixes

* export estimands accessor

* add more cleaning

* add another change

* fix docker image build

* up TargetedEstimation dep

* gracefully catch nans

* up manifest

* NamedTuple to Dictionary changes for overhead alleviation

* add and export pvalue_or_nan

* fix test

* updated manifest for TMLE.jl#frequency_table dictionary issue

* internals OrderedDict implementation

* updated tests and functions for TMLE.jl#treatment_values and TargetedEstimation.jl#treatment_values

* remove bin directory

* update deps and fix tests

* some renamings

* remove unused files

* add some comments

* add some compats

* change pcs read to get read of intermediate process

* update get_treatments

* up TMLECLI name

* up deps

---------

Co-authored-by: Olivier Labayle <[email protected]>

Author: joshua-slaughter

.github/workflows/CI.yml

@@ -11,6 +11,7 @@ jobs:
       matrix:
         version:
           - '1'
+          - '1.10'
         os:
           - ubuntu-latest
         arch:

.github/workflows/TagBot.yml

@@ -1,10 +1,25 @@
-
 name: TagBot
 on:
   issue_comment:
     types:
       - created
   workflow_dispatch:
+    inputs:
+      lookback:
+        default: "3"
+permissions:
+  actions: read
+  checks: read
+  contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
@@ -13,4 +28,4 @@ jobs:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.gitignore

@@ -33,3 +33,6 @@ sandbox.jl
 
 # Jupyter
 *checkpoints
+src/generate_results.jl
+test_grid.csv
+test/tl_inputs/real_data.jl