New strategies (#172)

* remove code that was migrated to targetedEstimation

* add sample_ids filtering on prepare confounders

* include snp filtering

* remove R from CI deps

* add workflow dispatch to branch

* convert sample_ids to strings for BGEN/BED compat

* remove compulsory option

* remove geneatlas phenotypes based preparation

* add tmle_inputs

* update to account for both binary and continuous phenotypes

* rename package and start to work on extra treatments

* update project

* more tests

* maybe asb mode

* need to test asb mode

* add some test

* add some tests for asb trans mode

* more tests and cleanup dir

* add more tests

* add YAML deps

* cleanup repo

* fix targets section

* update badge

* update badges

* update argument syntax of script

* add new parameter filename

* add no influence curve support to summary (#170)

* SAMPLE_IDS as strings

* Project.toml only (no Manifest.toml)

* add work in progress

* work in progress

* add work in progress

* add validated_params method

* rewrite of strategies

* start to work on ate param for actors

* update sample_ids to traits

* update script

* add ATE generation

* update project

* update project

* update script

* update dockerfile

* update manifest

* update dockerfile julai version

* fix Manifest

* update docker root dir name

* add load package to docker image

* temporarily remove sieve tests

* fix script arg table

* try update JULIA_DEPOT_PATH

* add verbosity and deal with missing estimates

* add restore slash method

* add push_sieveless methof for missing result

* fix types of output

Author: olivierlabayle

.github/workflows/CI.yml

@@ -10,29 +10,13 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.7'
+          - '1.8'
         os:
           - ubuntu-latest
         arch:
           - x64
     steps:
       - uses: actions/checkout@v2
-      - name: Install bunch of things
-        run: sudo apt-get install -y libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev build-essential libxml2-dev libssl-dev
-      - name: Setup R
-        uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.R }}
-      - name: Install R dependencies
-        run: |
-          install.packages("devtools", repos="http://cran.us.r-project.org")
-          require(devtools)
-          install_version("hal9001", version = "0.4.1", repos = "http://cran.us.r-project.org")
-        shell: Rscript {0}
-      - name: Set R_HOME
-        run: echo "R_HOME=$(R RHOME)" >> $GITHUB_ENV
-      - name: Set LD_LIBRARY
-        run: echo "LD_LIBRARY_PATH=$R_HOME/lib" >> $GITHUB_ENV
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}

.gitignore

@@ -22,8 +22,10 @@ docs/site/
 # It records a fixed state of all packages used by the project. As such, it should not be
 # committed for packages, but should be committed for applications that require a static
 # environment.
+Manifest.toml
 test/Manifest.toml
 
+
 # Develop dependencies
 dev/