Merge pull request #133 from TARGENE/argparse

Argparse
TARGENE · Feb 5, 2024 · 467f562 · 467f562
2 parents 3f96860 + e262c2f
commit 467f562
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -16,8 +16,10 @@ jobs:
       matrix:
         testrun:
           - "ukb_from_actors.jl"
-          - "ukb_from_param_file.jl"
+          - "ukb_custom.jl"
+          - "ukb_allele_independent.jl"
           - "custom_from_actors.jl"
+          - "make_dataset.jl"
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -38,7 +40,7 @@ jobs:
       - name: Instantiate test environment
         run: julia --project=test --startup-file=no -e'using Pkg;Pkg.instantiate()'
       - name: Run tests
-        run: julia --project=test --startup-file=no test/${{ matrix.testrun }} -profile ci
+        run: julia --project=test --startup-file=no test/${{ matrix.testrun }} -profile ci -resume
   docs:
     name: Documentation
     runs-on: ubuntu-latest

diff --git a/.gitignore b/.gitignore
@@ -13,5 +13,4 @@ test/sandbox.jl
 docs/Manifest.toml
 *.DS_Store
 trace.txt*
-test/Manifest.toml
 trace.txt
diff --git a/.vscode/ltex.dictionary.en-US.txt b/.vscode/ltex.dictionary.en-US.txt
@@ -0,0 +1,2 @@
+TarGene
+estimands
diff --git a/assets/NO_EXTRA_CONFOUNDER b/assets/NO_EXTRA_CONFOUNDER
diff --git a/assets/NO_EXTRA_COVARIATE b/assets/NO_EXTRA_COVARIATE
diff --git a/assets/NO_EXTRA_TREATMENT b/assets/NO_EXTRA_TREATMENT
diff --git a/assets/NO_LD_BLOCKS b/assets/NO_LD_BLOCKS
diff --git a/assets/NO_QC_FILE b/assets/NO_QC_FILE
diff --git a/assets/NO_WITHDRAWAL_LIST b/assets/NO_WITHDRAWAL_LIST
diff --git a/data/exclusion_regions_hg19.txt → assets/exclusion_regions_hg19.txt b/data/exclusion_regions_hg19.txt → assets/exclusion_regions_hg19.txt
diff --git a/data/exclusion_regions_hg38.txt → assets/exclusion_regions_hg38.txt b/data/exclusion_regions_hg38.txt → assets/exclusion_regions_hg38.txt