Merge pull request #22 from TARGENE/argparse

Argparse

.github/workflows/CI.yml

@@ -15,40 +15,31 @@ jobs:
  fail-fast: false
  matrix:
  version:
- - '1.9'
+ - '1'
  os:
  - ubuntu-latest
+ - macOS-latest
  arch:
- - x64
+ - 'x64'
  steps:
  - uses: actions/checkout@v2
- - name: Install curl
- run: sudo apt-get update && sudo apt-get install -y libcurl4-openssl-dev libharfbuzz-dev libfribidi-dev
- - name: Setup R
- uses: r-lib/actions/setup-r@v2
- with:
- r-version: 4.2.3
- - name: Install R dependencies
- run: |
- install.packages("devtools", repos="http://cran.us.r-project.org", dependecies=TRUE)
- 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 }}
  arch: ${{ matrix.arch }}
  - uses: julia-actions/cache@v1
  - uses: julia-actions/julia-buildpkg@v1
  - uses: julia-actions/julia-runtest@v1
- - uses: julia-actions/julia-processcoverage@v1
  - uses: codecov/codecov-action@v2
  with:
  files: lcov.info
+ - uses: julia-actions/julia-processcoverage@v1
+ # - name: Build App
+ # run: julia --project --startup-file=no deps/build_app.jl
+ # - uses: actions/upload-artifact@v4
+ # with:
+ # name: tmle-${{ matrix.os }}-${{ matrix.arch }}
+ # path: tmle
  docs:
  name: Documentation
  runs-on: ubuntu-latest

.gitignore

@@ -12,12 +12,14 @@ deps/build.log
 deps/downloads/
 deps/usr/
 deps/src/
+tmle/
 
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
+docs/Manifest.toml
 
 test/Manifest.toml
-sysimage/Manifest.toml
-
 Manifest.toml
+
+build/

Project.toml

@@ -1,19 +1,21 @@
 name = "TargetedEstimation"
 uuid = "2573d147-4098-46ba-9db2-8608d210ccac"
 authors = ["Olivier Labayle"]
-version = "0.7.4"
+version = "0.8.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
+Configurations = "5218b696-f38b-4ac9-8b61-a12ec717816d"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 EvoTrees = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5"
 GLMNet = "8d5ece8b-de18-5317-b113-243142960cc6"
-HighlyAdaptiveLasso = "c5dac772-1445-43c4-b698-9440de7877f6"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
 MLJ = "add582a8-e3ab-11e8-2d5e-e98b27df1bc7"
 MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
@@ -24,31 +26,36 @@ MLJXGBoostInterface = "54119dfa-1dab-4055-a167-80440f4f7a91"
 Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
 MultipleTesting = "f8716d33-7c4a-5097-896f-ce0ecbd3ef6b"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 TMLE = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
+PackageCompiler = "2.1.16"
 ArgParse = "1.1.4"
 Arrow = "2.5.2"
 CSV = "0.10"
 CategoricalArrays = "0.10"
 Combinatorics = "1.0.2"
+Configurations = "0.17.6"
 DataFrames = "1.3.4"
-EvoTrees = "0.16"
+EvoTrees = "0.16.5"
 GLMNet = "0.7"
-HighlyAdaptiveLasso = "0.2.0"
 JLD2 = "0.4.22"
+JSON = "0.21.4"
 MKL = "0.6"
-MLJ = "0.19"
-MLJBase = "0.21"
-MLJLinearModels = "0.9"
+MLJ = "0.20.0"
+MLJBase = "1.0.1"
+MLJLinearModels = "0.10.0"
 MLJModelInterface = "1.8.0"
 MLJModels = "0.16"
 MLJXGBoostInterface = "0.3.4"
-MultipleTesting = "0.5.1"
+MultipleTesting = "0.6.0"
 Optim = "1.7"
-TMLE = "0.11.4"
+TMLE = "0.14.0"
 Tables = "1.10.1"
+YAML = "0.4.9"
 julia = "1.7, 1"

data/sample_dataset.csv

@@ -0,0 +1,101 @@
+T,W_1,W_2,Y
+false,0.18102554215580358,0.5450806703063027,2.9940372099784027
+false,0.3674899461902501,0.6384329204193084,3.6556468914971756
+false,0.6690584311411027,0.43792082835867485,3.6566892558262984
+false,0.04273056581197765,0.7757285573916282,3.4160794440612667
+false,0.4379909608992427,0.3047310991183463,2.789125420976082
+true,0.4832901297478609,0.7451730217771686,1.5859557539740305
+false,0.7639737291557767,0.8904601966212045,5.188296343573969
+true,0.9244830959536434,0.13974660123511873,0.4982270316308855
+false,0.5150451217580685,0.6374757520926937,3.935855162247756
+false,0.49504171746863457,0.8565155620522915,4.561765097844799
+false,0.7013399928855184,0.8136974906450547,4.829305702798148
+false,0.6935693200259092,0.7770630474285287,4.708377370910661
+false,0.8762727975157072,0.6985801341473621,4.853277788606795
+true,0.9442193089864095,0.152194194900529,4.037983372295075
+false,0.7392125921999604,0.15113069121626244,2.928937148645259
+false,0.5595446681103335,0.32420235015472953,3.0840500870314176
+true,0.5068756305502102,0.7933086736255439,4.003336818622111
+true,0.6460238520948196,0.09241238685905295,1.8598644023282838
+false,0.26637285700482627,0.32928469720586406,2.5254756391406956
+true,0.25314126112406954,0.005639780239579784,2.0525644282124227
+false,0.3516179276178317,0.562947511861783,3.3891190015292962
+true,0.5273890936851706,0.5791653992166597,2.236487556841665
+true,0.7210925534616786,0.0815702398426259,3.0907289031725105
+false,0.18851150251759496,0.4507062485489093,2.7103706395089318
+false,0.637996251650204,0.2796408144910678,3.1179620782873023
+false,0.42784339776115243,0.05608349255807643,2.021998670506748
+false,0.36344680674044993,0.8176529855849277,4.187058502288485
+false,0.5776470899697952,0.5038402847145775,3.664411058533266
+false,0.4552051132605446,0.80168727438732,4.324422128772599
+true,0.16582015869838074,0.6517102569667845,3.4493844928436257
+true,0.3485177133589714,0.6950429952352082,3.6465473336626584
+false,0.7370786697973803,0.38967172496607816,3.634455876824883
+false,0.8097943410644535,0.30785356657086305,3.5631085002530503
+true,0.17116662327378251,0.38189260775289746,1.4561452308524758
+true,0.2239059463776638,0.37754440958420843,2.9358196480011927
+false,0.8482049921559374,0.7931999164105743,5.073800536916948
+false,0.6129496106778634,0.5582656110841486,3.9006286335176275
+false,0.9525421237374148,0.7075371298070849,5.027958774493786
+false,0.329471340006501,0.8244276908646733,4.133141608706676
+true,0.9183731870724761,0.5155924027190455,2.1766450039509775
+true,0.5406318800132754,0.7964424508760488,4.684487622068989
+false,0.820474440393214,0.3278374872665033,3.6201478925383053
+false,0.22304578643880224,0.15454141257308707,1.9141989300490125
+true,0.5987759444612732,0.8176931599179378,4.883829492724324
+true,0.5391280234619427,0.0800996880924989,-0.15332305595018275
+true,0.6195348270893413,0.04758713076380294,1.5044413418755769
+false,0.4197760589260566,0.6919387484370496,3.913552132910235
+false,0.45325909384306007,0.8196586617380355,4.361479188698554
+false,0.458012070794656,0.16787410906435518,2.3890361585879396
+false,0.8360692316060747,0.12572716005598905,3.0494749469842053
+false,0.68704221750134,0.9336977783694771,5.162792856806991
+false,0.3539590866764071,0.4938068514848526,3.201878898498728
+false,0.15146985093210463,0.9318499781184257,4.0825781392628055
+true,0.7036713552821277,0.3110022402796051,4.247461621524256
+false,0.7858058549340399,0.7913869099880062,4.9487597218140555
+false,0.5516353577049822,0.7651183843708445,4.394357280603648
+false,0.33689370624999193,0.8200595760169511,4.122787054444181
+false,0.7103550345192344,0.5218538906399544,3.9851980589961844
+false,0.3437537135972244,0.7082383555963896,3.8223674411348094
+true,0.40543796744015514,0.07340489667656125,-0.44867162036508734
+false,0.418787685820859,0.9537197956213714,4.671368501348916
+false,0.3461876693258523,0.17116028512837467,2.196479242014222
+false,0.256693308150987,0.7535261803886308,3.7658816939059676
+false,0.15717578481324845,0.9086295629550201,4.041940493212971
+false,0.06397027012871725,0.748570362698747,3.3694111418545805
+true,0.5960710257852946,0.6663504027833114,3.367016019904959
+true,0.3313524247810329,0.6591751071404244,1.591879202485502
+true,0.09653466861970061,0.6363397790684187,2.9197943852934563
+false,0.2444274100956212,0.2098958139673206,2.1388072276125003
+true,0.128071302925437,0.2212452403166849,0.2377448923043096
+true,0.42570257768498054,0.19674477205988938,1.387006507647053
+true,0.9265378351770237,0.2414821377114318,3.7979295737435383
+false,0.49186280724413045,0.12746729440853555,2.384783686379066
+false,0.13454928219280093,0.4781845302027954,2.710629287272798
+true,0.7767793160877585,0.524392439209832,2.5943698653629785
+false,0.5975255336244989,0.390410633670742,3.3711308436058625
+true,0.36037123968128437,0.08296139972284933,-0.759956439158037
+false,0.0346420282305675,0.0617778348993705,1.2471920828108296
+false,0.002639461613289207,0.7009785602029246,3.0993420302705896
+false,0.6043418433725678,0.6486688636856162,4.156769560508067
+false,0.34013328112005636,0.1345850741469954,2.08159579861953
+false,0.08884383382645145,0.3088038486943412,2.1056178972765487
+false,0.27042373335313585,0.006888583580566321,1.556777817484051
+false,0.2906905645217257,0.541835309258762,3.2236471704885887
+false,0.1159966466957052,0.5135297293779133,2.783128796238891
+true,0.8470732321945746,0.42816797170836707,2.0301351712154556
+true,0.8139519778944555,0.24560986612792113,1.7245624951948406
+false,0.060180250784984235,0.49673727324525174,2.622413005826214
+true,0.42137186429269047,0.16330846948665134,0.8216594084825344
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+false,0.7229464588051613,0.43577650941532386,3.7550371808310166
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+true,0.4312330027658198,0.24848292057152732,2.172648627086597

deps/build_app.jl

@@ -0,0 +1,6 @@
+using PackageCompiler
+PackageCompiler.create_app(".", "tmle",
+ executables = ["tmle" => "julia_main"],
+ precompile_execution_file="deps/execute.jl", 
+ include_lazy_artifacts=true
+)

deps/build_sysimage.jl

@@ -0,0 +1,7 @@
+using PackageCompiler
+PackageCompiler.create_sysimage(
+ ["TargetedEstimation"], 
+ cpu_target="generic",
+ sysimage_path="TMLESysimage.so", 
+ precompile_execution_file="deps/execute.jl", 
+)

sysimage/precompile_exec_file.jl → deps/execute.jl

@@ -1,6 +1,7 @@
-import TargetedEstimation
+using TargetedEstimation
 
+@info "Running precompilation script."
+# Run workload
 TEST_DIR = joinpath(pkgdir(TargetedEstimation), "test")
 push!(LOAD_PATH, TEST_DIR)
-cd(TEST_DIR)
 include(joinpath(TEST_DIR, "runtests.jl"))

docker/Dockerfile

@@ -1,47 +1,28 @@
-FROM julia:1.9.0-bullseye
+FROM julia:1.10-bullseye
 
 ARG DEBIAN_FRONTEND=noninteractive
 
 ENV TZ=Europe/Amsterdam
 
 ENV JULIA_DEPOT_PATH=/opt
 
-RUN apt-get update && apt-get install -y wget unzip procps
+RUN apt-get update && \
+ apt-get -y install gcc mono-mcs vim procps wget lsb-release software-properties-common gnupg && \
+ rm -rf /var/lib/apt/lists/*
 
-# Install R and hal9001
+RUN bash -c "$(wget -O - https://apt.llvm.org/llvm.sh)"
 
-RUN apt-get install -y r-base \
- r-base-core \
- r-recommended \
- r-base-dev
-
-RUN apt-get install -y libssl-dev \
- libxml2-dev \
- libcurl4-openssl-dev \
- libgit2-dev \
- libharfbuzz-dev \
- libfribidi-dev \
- libfontconfig1-dev \
- libfreetype6-dev \
- libpng-dev \
- libtiff5-dev \
- libjpeg-dev
-
-RUN R -e "install.packages('devtools', repos='http://cran.us.r-project.org', dependecies=TRUE); \
- require(devtools);\
- install_version('hal9001', version = '0.4.1', repos = 'http://cran.us.r-project.org')"
-
-# Import project, build and precompile
+# Import the project
 
 COPY . /TargetedEstimation.jl 
 
 WORKDIR /TargetedEstimation.jl
 
-# Precompile project
-RUN julia -q --project -e'using Pkg; Pkg.instantiate(); Pkg.resolve(); Pkg.precompile()'
+# Precompile the project
+RUN julia --project -e'using Pkg; Pkg.instantiate(); Pkg.resolve(); Pkg.precompile()'
 
-# Precompile Sysimage project
-RUN julia -q --project=/TargetedEstimation.jl/sysimage -e'using Pkg;Pkg.instantiate(); Pkg.resolve(); Pkg.precompile()'
+# Build CLI
+RUN julia --project --startup-file=no deps/build_sysimage.jl
 
-# Build Sysimage
-RUN julia --project -t auto --startup-file=no sysimage/create_sysimage.jl
+# Test the CLI runs
+RUN julia --startup-file=no --project -JTMLESysimage.so tmle.jl tmle data/sample_dataset.csv

docs/Project.toml

@@ -2,4 +2,4 @@
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 
 [compat]
-Documenter = "1.1.2"
+Documenter = "1.2.1"

docs/make.jl

@@ -15,7 +15,7 @@ makedocs(
  modules = [TargetedEstimation],
  pages=[
  "Home" => "index.md",
- "Command Line Interfaces" => ["environment.md", "tmle_estimation.md", "sieve_variance.md", "merge.md"],
+ "Command Line Interface" => ["cli.md", "tmle_estimation.md", "sieve_variance.md", "make_summary.md"],
  "MLJ Extensions" => ["models.md", "resampling.md"],
  ],
  pagesonly=true,

docs/src/cli.md

@@ -0,0 +1,30 @@
+# The Command Line Interface (CLI)
+
+## CLI Installation
+
+### Via Docker (requires Docker)
+
+While we are getting close to providing a standalone application, the most reliable way to use the app is still via the provided [Docker container](https://hub.docker.com/r/olivierlabayle/targeted-estimation/tags). In this container, the command line interface is accessible and can be used directly. For example via:
+
+```bash
+docker run -it --rm -v HOST_DIR:CONTAINER_DIR olivierlabayle/targeted-estimation:TAG tmle --help
+```
+
+where `HOST_DIR:CONTAINER_DIR` will map the host directory `HOST_DIR` to the container's `CONTAINER_DIR` and `TAG` is the currently released version of the project.
+
+### Build (requires Julia)
+
+Alternatively, provided you have Julia installed, you can build the app via:
+
+```bash
+julia --project deps/build_app.jl app
+```
+
+Bellow is a description of the functionalities offered by the CLI.
+
+## CLI Description
+
+```@contents
+Pages = ["tmle_estimation.md", "sieve_variance.md", "make_summary.md"]
+Depth = 5
+```