From 12ba044d605f7f8c6863d65c25f9aace6996a548 Mon Sep 17 00:00:00 2001
From: Olivier Labayle <olabayle@gmail.com>
Date: Thu, 21 Dec 2023 14:59:42 +0100
Subject: [PATCH] try build in CI

---
 .github/workflows/CI.yml |  2 +-
 .gitignore               |  1 +
 Comonicon.toml           | 20 --------------------
 Project.toml             |  2 ++
 deps/build_app.jl        |  3 ++-
 deps/execute.jl          |  7 -------
 docker/Dockerfile        |  5 +----
 7 files changed, 7 insertions(+), 33 deletions(-)
 delete mode 100644 Comonicon.toml

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 19683a3..29551c4 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -30,7 +30,7 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - name: Build App
-        run: julia --project -t auto deps/build_app.jl app tarball
+        run: julia --project --startup-file=no deps/build_app.jl
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v2
         with:
diff --git a/.gitignore b/.gitignore
index 63898a4..eb170c5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@ deps/build.log
 deps/downloads/
 deps/usr/
 deps/src/
+tmle/
 
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
diff --git a/Comonicon.toml b/Comonicon.toml
deleted file mode 100644
index 4acd652..0000000
--- a/Comonicon.toml
+++ /dev/null
@@ -1,20 +0,0 @@
-name = "tmle"
-
-[install]
-completion = true
-quiet = false
-optimize = 2
-
-# [sysimg]
-# incremental=true
-# filter_stdlibs=false
-
-# [sysimg.precompile]
-# execution_file = ["deps/execute.jl"]
-
-# [application]
-# incremental=true
-# filter_stdlibs=false
-
-# [application.precompile]
-# execution_file = ["deps/execute.jl"]
\ No newline at end of file
diff --git a/Project.toml b/Project.toml
index 7575ae0..f5df5c6 100644
--- a/Project.toml
+++ b/Project.toml
@@ -26,6 +26,7 @@ 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"
@@ -33,6 +34,7 @@ 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"
diff --git a/deps/build_app.jl b/deps/build_app.jl
index e0a9f11..cb0b99c 100644
--- a/deps/build_app.jl
+++ b/deps/build_app.jl
@@ -1 +1,2 @@
-using TargetedEstimation; TargetedEstimation.comonicon_install()
\ No newline at end of file
+using PackageCompiler
+PackageCompiler.create_app(".", "tmle", precompile_execution_file="execute.jl")
diff --git a/deps/execute.jl b/deps/execute.jl
index bde1b1b..70f58fe 100644
--- a/deps/execute.jl
+++ b/deps/execute.jl
@@ -1,13 +1,6 @@
 using TargetedEstimation
 
 @info "Running precompilation script."
-
-# Run help messages
-TargetedEstimation.command_main(["-h"])
-TargetedEstimation.command_main(["tmle", "-h"])
-TargetedEstimation.command_main(["make-summary", "-h"])
-TargetedEstimation.command_main(["sieve-variance-plateau", "-h"])
-
 # Run workload
 TEST_DIR = joinpath(pkgdir(TargetedEstimation), "test")
 push!(LOAD_PATH, TEST_DIR)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 547da61..741a9ba 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -22,8 +22,5 @@ RUN julia --project -e'using Pkg; Pkg.instantiate(); Pkg.resolve(); Pkg.precompi
 # Build CLI
 RUN julia --project --startup-file=no deps/build_app.jl
 
-# Add CLI to PATH
-ENV PATH="${PATH}:/opt/bin/"
-
 # Test the CLI runs
-RUN tmle tmle data/sample_dataset.csv
\ No newline at end of file
+RUN tmle/bin/tmle tmle data/sample_dataset.csv
\ No newline at end of file